PROTEIN COMPLEXES AND METHODS FOR THEIR USE

COMPLEXES DE PROTEINES ET LEURS PROCEDES D'UTILISATION

English Abstract

The present invention relates to multiprotein complexes from eukaryotes. The
complexes are obtainable by using a protein as a bait and isolating the set of
proteins which is attached thereto from cells. Such protein complexes may
comprise up to 30 distinct proteins.

French Abstract

La présente invention concerne des complexes multiprotéiques tirés d'eukaryotes. Les complexes peuvent être obtenus par utilisation d'une protéine en tant qu'appât et par isolement de l'ensemble de protéines qui lui est attaché à partir de cellules. Ces complexes protéiques peuvent contenir jusqu'à trente protéines distinctes.

Claims

1061
CLAIMS
1. ~A protein complex selected from complex (I) and comprising
(a) at least one first protein, which first protein is selected from the group
of
proteins in table 1, sixth column of a given complex, or a functionally active
derivative thereof, or a functionally active fragment thereof, or a homologue
thereof, or a variant of said protein, the variant being, the variant being
encoded by a nucleic acid that hybridizes to the nucleic acid encoding said
protein under low stringency conditions; and
(b) at least one second protein, which second protein is selected from the
group of proteins in table 1, seventh column of said given complex, or a
functionally active derivative thereof, or a functionally active fragment
thereof,
or a homologue thereof, or a variant of said second protein, said variant
being
encoded by a nucleic acid that hybridizes to the nucleic acid encoding said
protein under low stringency conditions;
and a complex (II) comprising at least two of said second proteins,
wherein said low stringency conditions comprise hybridization in a buffer
comprising 35% formamide, 5X SSC, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA,
0.02% PVP, 0.02% BSA, 100 µg/ml denatured salmon sperm DNA, and 10%
(wt/vol) dextran sulfate for 18-20 hours at 40°C, washing in a buffer
consisting
of 2X SSC, 25 mM Tris-HCI (pH 7.4), 5 mM EDTA, and 0.1% SDS for 1-5
hours at 55°C, and washing in a buffer consisting of 2X SSC, 25 mM Tris-
HCl
(pH 7.4) 5 mM EDTA, and 0.1 % SDS for 1.5 hours at 60°C.
2. A protein complex comprising a first protein selected from the proteins
listed
in table 1, second column of a given complex or a homologue or variant
thereof, or a functionally active fragment or functionally active derivative
of
said first protein, the variant being encoded by a nucleic acid that
hybridizes
to the nucleic acid of said first protein under low stringency conditions, and
at
least one second protein selected from the group of proteins in table 1,
seventh column of a given complex, or a variant or homologue thereof, or a
functionally active fragment or a functionally active derivative of said
second
protein, the variant of said second protein being encoded by a nucleic acid
that hybridizes to the nucleic acid of said second protein under low-
stringency
conditions, and wherein said low stringency conditions comprise hybridization

1062~
in a buffer comprising 35% formamide, 5X SSC, 50 mM Tris-HCl (pH 7.5),5
mM EDTA, 0.02% PVP, 0.02% BSA, 100 ug/ml denatured salmon sperm
DNA, and 10% (wt/vol) dextran sulfate for 18-20 hours at 40.degree,C, washing
in a
buffer consisting of 2X SSC, 25 mM Tris-HCl (pH 7.4), 5 mM EDTA, and 0.1 %
SDS for 1-5 hours at 55.degree,C, and washing in a buffer consisting of 2X
SSC, 25
mM Tris-HCl (pH 7.4) 5 mM EDTA, and 0.1 % SDS for 1.5 hours at 60.degree,C.
3. A protein complex comprising all proteins selected from the proteins in
table
1, third column of a given complex or at least one protein being a homologue
thereof, or a variant thereof or functionally active fragment or functionally
active derivative of said protein, said variant being encoded by a nucleic
acid
that hybridizes to the nucleic acid of said protein under low stringency
conditions;
wherein said low stringency conditions comprise hybridization in a buffer
comprising 35% formamide, 5X SSC, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA,
0.02% PVP, 0.02% Ficoll, 0.2% BSA, 100 ug/ml denatured salmon sperm
DNA, and 10% (wt/vol) dextran sulfate for 18-20 hours at 40.degree,C, washing
in a
buffer consisting of 2X SSC, 25 mM Tris-HCl (pH 7.4), 5 mM EDTA, and 0.1%
SDS for 1-5 hours at 55.degree,C, and washing in a buffer consisting of 2X
SSC, 25
mM Tris-HCl (pH 7.4), 5 mM EDTA, and 0.1 % SDS for 1.5 hours at 60.degree,C.
4. A protein complex that comprises all proteins as listed in table 1, third
column
for a given complex or at least one protein being a homologue or a variant
thereof, or a functionally active fragment or a functionally active derivative
thereof, the variant being encoded by a nucleic acid that hybridizes to the
nucleic acid of any of said proteins under low stringency conditions, except
at
least one protein of the proteins listed in table 1, third column, wherein
said
low stringency conditions comprise hybridization in a buffer comprising 35%
formamide, 5X SSC, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.02% PVP,
0.02% Ficoll, 0.2% BSA, 100 ug/ml denatured salmon sperm DNA, and 10%
(wt/vol) dextran sulfate for 18-20 hours at 40.degree,C, washing in a buffer
consisting
of 2X SSC, 25 mM Tris-HCl (pH 7.4), 5 mM EDTA, and 0.1% SDS for 1-5
hours at 55.degree,C, and washing in a buffer consisting of 2X SSC, 25 mM Tris-
HCI
(pH 7.4), 5 mM EDTA, and 0.1 % SDS for 1.5 hours at 60.degree,C, with the
provisio

1063
that the complex comprises at least one protein selected from table 1,
seventh column of a given complex.
5. ~The complex of any of claims 1 - 4 comprising at least one functionally
active
derivative of said first protein and/or a functionally active derivative of
said
second protein, wherein the functionally active derivative is a fusion protein
comprising said first protein or said second protein fused to an amino acid
sequence different from the first protein or second protein.
6. ~The complex of claim 5 wherein the functionally active derivative is a
fusion
protein comprising said first protein or said second protein fused to an
affinity
tag or label.
7. ~The complex of any of claims 1 - 4 comprising a fragment of said first
protein
and/or a fragment of said second protein, which fragment binds to another
protein component of said complex.
8. ~The complex of any of claims 1 - 7 that is involved in at least one
biochemical
activity as stated in table 2, column 8 for a given complex.
9. ~A process for preparing a complex of any of claims 1 - 8 and optionally
the
components thereof comprising the following steps:
expressing a protein of the complex, preferably a tagged protein, in a target
cell, or a tissue or an organ, isolating the protein complex which is attached
to
the protein, preferably the tagged protein, and optionally disassociating the
protein complex and isolating the individual complex members.
10. ~The process according to claim 9 wherein the tagged protein comprises two
different tags which allow two separate affinity purification steps.
11. ~The process according to any of claims 9 - 10 wherein the two tags are
separated by a cleavage site for a protease.
12. ~Component of a protein complex obtainable by a process according to any
of
claims 9 - 11.

1064
13. Protein selected from the group of proteins in table 1, ninth column of a
given
complex or a homologue or a variant of thereof, or a functionally active
fragment or a functionally active derivative of said protein, the variant
being
encoded by a nucleic acid that hybridizes to the nucleic acid encoding said
protein under low stringency conditions, wherein said low stringency
conditions comprise hybridization in a buffer comprising 35% formamide, 5X
SSC, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.2%
BSA, 100 ug/ml denatured salmon sperm DNA, and 10% (wt/vol) dextran
sulfate for 18-20 hours at 40°C, washing in a buffer consisting of 2X
SSC, 25
mM Tris-HCl (pH 7.4), 5 mM EDTA, and 0.1 % SDS for 1.5 hours at 55°C,
and
washing in a buffer consisting of 2X SSC, 25 mM Tris-HCl (pH 7.4), 5 mM
EDTA, and 0.1 % SDS for 1.5 hours at 60°C.
14. Nucleic acid encoding a protein according to claim 13.
15. Construct, preferably a vector construct, comprising
(a) ~a nucleic acid according to claim 14 and at least one further nucleic
acid
which is normally not associated with said nucleic acid, or
(b) ~at least two separate nucleic acid sequences each encoding a different
protein, or a functionally active fragment or a functionally active
derivative~
thereof, or a homologue or a variant thereof, at least one of said proteins
being selected from the first group of proteins according to claim 1 (a) and
at least one of said proteins, being selected from the second group of
proteins according to claim 1 (b) or
(c) ~at least two separate nucleic acid sequences each encoding a different
protein, or a functionally active fragment or a functionally active derivative
thereof, or a homologue or a variant thereof, said proteins being selected
from the proteins of complex (II) according to claim 1.
16. Host cell, containing a vector comprising at least one nucleic acid of
claim 14
and for a construct of claim 15 or containing several vectors each comprising
at least one nucleic acid encoding at least one protein selected from the
first
group of proteins according to claim 1 (a) and at least one nucleic acid

1065
encoding at least one protein selected from the second group of proteins
according to claim 1(b).
17. ~An antibody or a fragment of said antibody containing the binding domain
thereof, selected from an antibody or fragment thereof, which binds the
complex of any of claims 1 - 8 and which does not bind any of the proteins of
said complex when uncomplexed and an antibody or a fragment of said
antibody containing the binding domain thereof which binds to any of the
proteins of the group of proteins according to claim 13.
18. ~A kit comprising in one or more containers:
(a) the complex of any of claims 1 - 8 and/or the proteins of claim 13 and/or
(b) an antibody according to claim 17 and/or
(c) a nucleic acid encoding a protein of the complex of any of claims 1 - 8
and/or a protein of claim 13 and/or
(d) cells expressing the complex of any of claims 1 - 8 and/or a protein of
claim 13 and, optionally,
(e) further components such as reagents, buffers and working instructions.
19. ~The kit according to claim 18 for processing a substrate of a complex of
any
one of claims 1 - 8.
20. ~The kit according to claim 18 for the diagnosis or prognosis of a disease
or a
disease risk, preferentially for a disease or disorder as stated in table 4,
third
column for a given complex.
21. ~Array, preferably a microarray, in which at least a complex according to
any of
claims 1 - 8 and/or at least one protein according to claim 13 and/or at least
one antibody according to claim 17 is attached to a solid carrier.
22. ~A process for modifying a substrate of a complex of any one of claims 1 -
8
comprising the step of bringing into contact a complex of any of claims 1 - 8
with said substrate, such that said substrate is modified.

1066
23. A pharmaceutical composition comprising the protein complex of any of
claims 1 - 8 and/or a protein according to claim 13.
24. A pharmaceutical composition according to claim 23 for the treatment of
diseases and disorders, preferentially for diseases or disorders as stated in
table 4, third column of said complex.
25. A method for screening for a molecule that binds to a complex of any one
of
claims 1 - 8 and/or a protein of claim 13, comprising the following steps:
(a) exposing said complex or protein, or a cell or organism containing said
complex or said protein, to one or more candidate molecules; and
(b) determining whether said candidate molecule is bound to the complex or
protein.
26. A method for screening for a molecule that modulates directly or
indirectly the
function, activity, composition or formation of a complex of any one of claims
1 - 8 comprising the steps of:
(a) exposing said complex, or a cell or organism containing said complex to
one or more candidate molecules; and
(b) determining the amount of, activity of, protein components of, and/or
intracellular localization of, said complex and/or the transcription level of
a gene regulated by the complex and/or the abundance and/or activity of
a protein or protein complex dependent upon the function of the complex
and/or product of a gene dependent on the complex in the presence of
the one or more candidate molecules, wherein a change in said amount,
activity, protein components or intracellular localization relative to said
amount, activity, protein components and/or intracellular localization
and/or a change in the transcription level of a gene regulated by the
complex and/or the abundance and/or activity of a protein or protein
complex dependent on the function of the complex and/or product of a
gene dependent on the complex in the absence of said candidate
molecules indicates that the molecule modulates function, activity, or
composition of said complex.
27. The method of claim 26, wherein the amount of said complex is determined.

1067
28. The method of claim 26, wherein the activity of said complex is
determined.
29. The method of claim 28, wherein said determining step comprises isolating
from the cell or organism said complex to produce said isolated complex and
contacting said isolated complex in the presence or absence of a candidate
molecule with a substrate of said complex and determining whether said
substrate is processed in the absence of the candidate molecule and whether
the processing of said substrate is modified in the presence of said candidate
molecule.
30. The method of claim 26, wherein the amount of the individual protein
components of said complex is determined.
31. The method of claim 30, wherein said determining step comprises
determining whether any of the proteins listed in table 1, third column of
said
complex, or a functionally active fragment or a functionally active derivative
thereof, or a variant or a homologue thereof, the variant being encoded by a
nucleic acid that hybridizes to the nucleic acid of said protein under low-
stringency conditions, is present in the complex.
32. The method of any of claims 26 - 31, wherein said method is a method of
screening for a drug for treatment or prevention of a disease or disorder,
preferentially of a disease or disorder selected from the diseases or
disorders
as listed in table 4, third column.
33. Use of a molecule that modulates the amount of, activity of, or the
protein
components of the complex of any one of claims 1 - 8 for the manufacture of
a medicament for the treatment or prevention of a disease or disorder,
preferentially of a disease or disorder as listed in table 4, third column.
34. A method for the production of a pharmaceutical composition comprising
carrying out the method of claims 26 - 31 to identify a molecule that
modulates the function, activity, composition or formation of said complex,

1068
and further comprising mixing the identified molecule with a pharmaceutically
acceptable carrier.
35. A method for diagnosing or screening for the presence of a disease or
disorder or a predisposition for developing a disease or disorder in a
subject,
which disease or disorder is characterized by an aberrant amount of,
component disposition of, or intracellular localization of the complex of any
one of the claims 1 - 8, comprising determining the amount of, activity of,
protein components of, and/or intracellular localization of, said complex
and/or
the transcription level of a gene regulated by the complex and/or the
abundance and/or activity of a protein or protein complex dependent on the
function of the complex and/or product of a gene dependent on the complex
in a comparative sample derived from a subject, wherein a difference in said
amount, activity, or protein components of, said complex in a corresponding
sample from a subject not having the disease or disorder or predisposition
indicated the presence in the subject of the disease or disorder or
predisposition in the subject.
36. The method of claim 35, wherein the amount of said complex is determined.
37. The method of claim 35, wherein the activity of said complex is
determined.
38. The method of claim 37, wherein said determining step comprises isolating
from the cell or organism said complex to produce said isolated complex and
contacting said isolated complex in the presence or absence of a candidate
molecule with a substrate of said complex and determining whether said
substrate is processed in the absence of the candidate molecule and whether
the processing of said substrate is modified in the presence of said candidate
molecule.
39. The method of claim 35, wherein the amount of the individual protein
components of said complex is determined.

1069
40. The method of claim 39, wherein said determining step comprises
determining whether any of the proteins according to claim 13 is present in
the complex.
41. The complex of any one of claims 1 - 8, or a protein of claim 13 or an
antibody
or fragment thereof of claim 17, for use in a method of diagnosing a disease
or disorder, preferentially of a disease or disorder as listed in table 4,
third
column of said complex.
42. A method for treating or preventing a disease or disorder characterized by
an
aberrant amount of, activity of, component composition of or intracellular
localization of, the complex of any one of claims 1 - 8, comprising
administering to a subject in need of such treatment or prevention a
therapeutically effective amount of one or more molecules that modulate the
amount of, activity of, or protein composition of, said complex.
43. The method according to claim 42, wherein said disease or disorder
involves
decreased levels of the amount or activity of said complex.
44. The method according to claim 42, wherein said disease or disorder
involves
increased levels of the amount or activity of said complex.
45. Complex of claims 1 - 8 and/or a protein as listed in table 1, seventh
column of said complex as a target for an active agent of a pharmaceutical,
preferably a drug target, in the treatment or prevention of a disease or
disorder,
preferentially of a disease or disorder as listed in table 4, third column of
said
complex.

Description

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PROTEIN COMPLEXES AND METHODS FOR THEIR USE
1. FIELD OF THE INVENTION
The present invention relates to protein complexes, component proteins of the
complexes, fragments and derivatives of the component proteins, and antibodies
specific
to the complexes. The present invention also relates to methods for use of the
complexes in, inter alia, screening, diagnosis, and therapy, as well as to
methods of
preparing the complexes.
2. BACKGROUND OF THE INVENTION
A formidable challenge of postgenomic biology is to understand how genetic
information results in the concerted action of gene products in time and space
to
generate function. In medicine, this is perhaps best reflected in the numerous
disorders
based on polygenic traits and the notion that the number of human diseases
exceeds the
number of genes in the genome. Roses, 2000, Pharmacogenetics and the practice
of
medicine, Nature 405:857-65. Moreover, the total number of human genes does
not
differ substantially from that~of the worm C. elegans, suggesting that
complexity may
partly rely on the contextual combination of the gene products. Lander et al.,
2001, Initial
sequencing and analysis of the human genome, Nature 409:860-921. Dissecting
the
genetic and biochemical circuitry of a cell is a fundamental problem in
biology. At the
biochemical level, proteins rarely act alone; rather they interact with other
proteins to
perform particular cellular tasks. Alberts, 1998, The cell as a collection of
protein
machines: preparing the next generation of molecular biologists, Cell 92:291-
294. These
assemblies represent more than the sum of their parts by having a new
function. Jacob,
1993, The Logic of Life. Princeton University Press. Such "integrons", may
then come
together to build, in turn, "integrons" of higher order and function, such as
a cell, a tissue,
an organism.
Our knowledge regarding the identity of the building elements of specific
complexes is very limited and is based on selected biochemical approaches and
genetic
analyses. The only comprehensive protein interaction studies to date are based
on ex
vivo systems and need to be integrated with more physiological approaches.
Whenever
it has been possible to retrieve and analyze particular cellular protein
complexes under

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2
physiological conditions, the insight gained from the analysis has been
fundamental for
the biological understanding of their function and has often taken the
analysis well
beyond the limits of genetic analysis. Blackstock & Weir, 1999, Proteomics:
quantitative
and physical mapping of cellular proteins, Trends Biotechnol. 17:121-127;
Pandey &
Mann, 2000, Proteomics to study genes and genomes, Nature 405:837-846.
Prominent
examples are the spliceosome, the cyclosome (Anaphase-Promoting-Complex), the
proteasome and the synaptosome. Neubauer et a1.,1998, Mass spectrometry and
EST-
database searching allows characterization of the multi-protein spliceosome
complex,
Nat. Genet. 20:46-50; Zachariae et al., 1996, Identification of subunits of
the anaphase-
promoting complex of Saccharomyces cerevisiae, Science 274:1201-1204; Varga-
Weisz
et al., 1997, Chromatin-remodelling factor CHRAC contains the ATPases ISWI and
topoisomerase II, Nature 388:598-602; Verma et al., 2000, Proteasomal
proteomics:
identification of nucleotide-sensitive proteasome-interacting proteins by mass
spectrometric analysis of affinity-purified proteasomes, Mol. Biol. Cell
11:3425-3439;
Neubauer et al., 1997, Identification of the proteins of the yeast U1 small
nuclear
ribonucleoprotein complex by mass spectrometry, Proc. Natl. Acad. Sci. USA
94:385-
390; Husi et al., 2000, Proteomic analysis of NMDA receptor-adhesion protein
signaling
complexes. Nat. Neurosci. 3:661-669. No systematic analysis of protein
complexes from
the same cell type using the same technique has yet been reported.
Citation of a reference in this or any section of the specification shall not
be construed as an admission that such reference is prior art to the present
invention.
3. SUMMARY OF THE INVENTION
The invention relates to:
1. A protein complex selected from complex (I) and comprising
(a) at least one first protein, which first protein is selected from the group
of proteins
in table 1, sixth column of a given complex, or a functionally active
derivative thereof,
or a functionally active fragment thereof, or a homologue thereof, or a
variant of said
protein, the variant being, the variant being encoded by a nucleic acid that
hybridizes
to the nucleic acid encoding said protein under low stringency conditions; and
(b) at least one second protein, which second protein is selected from the
group of
proteins in table 1, seventh column of said given complex, or a functionally
active

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3
derivative thereof, or a functionally active fragment thereof, or a homologue
thereof,
or a variant of said second protein, said variant being encoded by a nucleic
acid that
hybridizes to the nucleic acid encoding said protein under low stringency
conditions;
and a complex (II) comprising at least two of said second proteins,
wherein said low stringency conditions comprise hybridization in a buffer
comprising
35% formamide, 5X SSC, 50 mM Tris-HCI (pH 7.5), 5 mM EDTA, 0.02% PVP, 0.02%
BSA, 100 ug/ml denatured salmon sperm DNA, and 10% (wt/vol) dextran sulfate
for
18-20 hours at 40°C, washing in a buffer consisting of 2X SSC, 25 mM
Tris-HCI (pH
7.4), 5 mM EDTA, and 0.1 % SDS for 1-5 hours at 55°C, and washing in a
buffer
consisting of 2X SSC, 25 mM Tris-HCI (pH 7.4) 5 mM EDTA, and 0.1 % SDS for 1.5
hours at 60°C.
2. A protein complex comprising a first protein selected from the proteins
listed in table
1, second column of a given complex or a homologue or variant thereof, or a
functionally active fragment or functionally active derivative of said first
protein, the
variant being encoded by a nucleic acid that hybridizes to the nucleic acid of
said first
protein under low stringency conditions, and at least one second protein
selected
from the group of proteins in table 1, seventh column of a given complex, or a
variant
or homologue thereof, or a functionally active fragment or a functionally
active
derivative of said second protein, the variant of said second protein being
encoded by
a nucleic acid that hybridizes to the nucleic acid of said second protein
under low-
stringency conditions, and wherein said low stringency conditions comprise
hybridization in a buffer comprising 35% formamide, 5X SSC, 50 mM Tris-HCI (pH
7.5), 5 mM EDTA, 0.02% PVP, 0.02% BSA, 100 ug/ml denatured salmon sperm
DNA, and 10% (wt/vol) dextran sulfate for 18-20 hours at 40°C, washing
in a buffer
consisting of 2X SSC, 25 mM Tris-HCI (pH 7.4), 5 mM EDTA, and 0.1 % SDS for 1-
5
hours at 55°C, and washing in a buffer consisting of 2X SSC, 25 mM Tris-
HCI (pH
7.4) 5 mM EDTA, and 0.1 % SDS for 1.5 hours at 60°C.
3. A protein complex comprising all proteins selected from the proteins in
table 1, third
column of a given complex or at least one protein being a homologue thereof,
or a
variant thereof or functionally active fragment or functionally active
derivative of said
protein, said variant being encoded by a nucleic acid that hybridizes to the
nucleic
acid of said protein under low stringency conditions;

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4
wherein said low stringency conditions comprise hybridization in a buffer
comprising
35% formamide, 5X SSC, 50 mM Tris-HCI (pH 7.5), 5 mM EDTA, 0.02% PVP, 0.02%
Ficoll, 0.2% BSA, 100 ug/ml denatured salmon sperm DNA, and 10% (wt/vol)
dextran
sulfate for 18-20 hours at 40°C, washing in a buffer consisting of 2X
SSC, 25 mM
Tris-HCI (pH 7.4), 5 mM EDTA, and 0.1 % SDS for 1-5 hours at 55°C, and
washing in
a buffer consisting of 2X SSC, 25 mM Tris-HCI (pH 7.4), 5 mM EDTA, and 0.1 %
SDS
for 1.5 hours at 60°C.
4. A protein complex that comprises all proteins as listed in table 1, third
column for a
given complex or at least one protein being a homologue or a variant thereof,
or a
functionally active fragment or a functionally active derivative thereof, the
variant
being encoded by a nucleic acid that hybridizes to the nucleic acid of any of
said
proteins under low stringency conditions, except at least one protein of the
proteins
listed in table 1, third column, wherein said low stringency conditions
comprise
hybridization in a buffer comprising 35% formamide, 5X SSC, 50 mM Tris-HCI (pH
7.5), 5 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.2% BSA, 100 ug/ml denatured salmon
sperm DNA, and 10% (wt/vol) dextran sulfate for 18-20 hours at 40°C,
washing in a
buffer consisting of 2X SSC, 25 mM Tris-HCI (pH 7.4), 5 mM EDTA, and 0.1 % SDS
for 1-5 hours at 55°C, and washing in a buffer consisting of 2X SSC, 25
mM Tris-HCI
(pH 7.4), 5 mM EDTA, and 0.1 % SDS for 1.5 hours at 60°C, with the
provisio that the
complex comprises at least one protein selected from table 1, seventh column
of a
given complex.
5. The complex of any of No. 1 - 4 comprising at least one functionally active
derivative
of said first protein and/or a functionally active derivative of said second
protein,
wherein the functionally active derivative is a fusion protein comprising said
first
protein or said second protein fused to an amino acid sequence different from
the first
protein or second protein.
6. The complex of No. 5 wherein the functionally active derivative is a fusion
protein
comprising said first protein or said second protein fused to an affinity tag
or label.

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7. The complex of any of No. 1 - 4 comprising a fragment of said first protein
and/or a
fragment of said second protein, which fragment binds to another protein
component
of said complex.
8. The complex of any of No. 1 - 7 that is involved in at least one
biochemical activity as
stated in table 2, column 8 for a given complex.
9. A process for preparing a complex of any of No. 1 - 8 and optionally the
components
thereof comprising the following steps:
expressing a protein of the complex, preferably a tagged protein, in a target
cell, or a
tissue or an organ, isolating the protein complex which is attached to the
protein,
preferably the tagged protein, and optionally disassociating the protein
complex and
isolating the individual complex members.
10. The process according to No. 9 wherein the tagged protein comprises two
different
tags which allow two separate affinity purification steps.
11. The process according to any of No. 9 - 10 wherein the two tags are
separated by a
cleavage site for a protease.
12. Component of a protein complex obtainable by a process according to any of
No. 9 -
11.
13. Protein selected from the group of proteins in table 1, ninth column of a
given
complex or a homologue or a variant of thereof, or a functionally active
fragment or a
functionally active derivative of said protein, the variant being encoded by a
nucleic
acid that hybridizes to the nucleic acid encoding said protein under low
stringency
conditions, wherein said low stringency conditions comprise hybridization in a
buffer
comprising 35% formamide, 5X SSC, 50 mM Tris-HCI (pH 7.5), 5 mM EDTA, 0.02%
PVP, 0.02% Ficoll, 0.2% BSA, 100 ug/ml denatured salmon sperm DNA, and 10%
(wt/vol) dextran sulfate for 18-20 hours at 40°C, washing in a buffer
consisting of 2X
SSC, 25 mM Tris-HCI (pH 7.4), 5 mM EDTA, and 0.1 % SDS for 1.5 hours at
55°C,
and washing in a buffer consisting of 2?C SSC, 25 mM Tris-HCI (pH 7.4), 5 mM
EDTA,
and 0.1 % SDS for 1.5 hours at 60°C.

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14. Nucleic acid encoding a protein according to No. 13.
15. Construct, preferably a vector construct, comprising
(a) a nucleic acid according to No. 14 and at least one further nucleic acid
which is
normally not associated with said nucleic acid, or
(b) at least two separate nucleic acid sequences each encoding a different
protein, or
a functionally active fragment or a functionally active derivative thereof, or
a
homologue or a variant thereof, at least one of said proteins being selected
from
the first group of proteins according to No. 1 (a) and at least one of said
proteins,
being selected from the second group of proteins according to No. 1 (b) or
(c) at least two separate nucleic acid sequences each encoding a different
protein, or
a functionally active fragment or a functionally active derivative thereof, or
a
homologue or a variant thereof, said proteins being selected from the proteins
of
complex (II) according to No. 1.
16. Host cell, containing a vector comprising at least one nucleic acid of No.
14 and /or a
construct of No. 15 or containing several vectors each comprising at least one
nucleic
acid encoding at least one protein selected from the first group of proteins
according
to No. 1 (a) and at least one nucleic acid encoding at least one protein
selected from
the second group of proteins according to No. 1 (b).
17. An antibody or a fragment of said antibody containing the binding domain
thereof,
selected from an antibody or fragment thereof, which binds the complex of any
of No.
1 - 8 and which does not bind any of the proteins of said complex when
uncomplexed
and an antibody or a fragment of said antibody containing the binding domain
thereof
which binds to any of the proteins of the group of proteins according to No.
13.
18. A kit comprising in one or more containers:
(a) the complex of any of No. 1 - 8 and/or the proteins of No. 13 and/or
(b) an antibody according to No. 17 and/or
(c) a nucleic acid encoding a protein of the complex of any of No. 1 - 8
and/or a
protein of No. 13 and/or

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(d) cells expressing the complex of any of No. 1 - 8 and/or a protein of No.
13 and,
optionally,
(e) further components such as reagents, buffers and working instructions.
19. The kit according to No. 18 for processing a substrate of a complex of any
one of No.
1-8.
20. The kit according to No. 18 for the diagnosis or prognosis of a disease or
a disease
risk, preferentially for a disease or disorder as stated in table 4, third
column for a
given complex..
21. Array, preferably a microarray, in which at least a complex according to
any of No. 1 -
8 and/or at least one protein according to No. 13 and/or at least one antibody
according to No. 17 is attached to a solid carrier.
22. A process for modifying a substrate of a complex of any one of No. 1 - 8
comprising
the step of bringing into contact a complex of any of No. 1 - 8 with said
substrate,
such that said substrate is modified.
23. A pharmaceutical composition comprising the protein complex of any of No.
1 - 8
and/or a protein according to No. 13.
24. A pharmaceutical composition according to No. 23 for the treatment of
diseases and
disorders, preferentially for diseases or disorders as stated in table 4,
third column of
said complex.
25. A method for screening for a molecule that binds to a complex of any one
of No. 1 - 8
and/or a protein of No. 13, comprising the following steps:
(a) exposing said complex or protein, or a cell or organism containing said
complex
or said protein, to one or more candidate molecules; and
(b) determining whether said candidate molecule is bound to the complex or
protein.

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26. A method for screening for a molecule that modulates directly or
indirectly the
function, activity, composition or formation of a complex of any one of No. 1 -
8
comprising the steps of:
(a) exposing said complex, or a cell or organism containing said complex to
one or
more candidate molecules; and
(b) determining the amount of, activity of, protein components of, and/or
intracellular
localization of, said complex and/or the transcription level of a gene
regulated by
the complex and/or the abundance and/or activity of a protein or protein
complex dependent upon the function of the complex and/or product of a gene
dependent on the complex in the presence of the one or more candidate
molecules, wherein a change in said amount, activity, protein components or
intracellular localization relative to said amount, activity, protein
components
and/or intracellular localization and/or a change in the transcription level
of a
gene regulated by the complex and/or the abundance and/or activity of a
protein
or protein complex dependent on the function of the complex and/or product of
a gene dependent on the complex in the absence of said candidate molecules
indicates that the molecule modulates function, activity, or composition of
said
complex.
27. The method of No. 26, wherein the amount of said complex is determined.
28. The method of No. 26, wherein the activity of said complex is determined.
29. The method of No. 28, wherein said determining step comprises isolating
from the
cell or organism said complex to produce said isolated complex and contacting
said
isolated complex in the presence or absence of a candidate molecule with a
substrate of said complex and determining whether said substrate is processed
in the
absence of the candidate molecule and whether the processing of said substrate
is
modified in the presence of said candidate molecule.
30. The method of No. 26, wherein the amount of the individual protein
components of
said complex is determined.

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31. The method of No. 30, wherein said determining step comprises determining
whether
any of the proteins listed in table 1, third column of said complex, or a
functionally
active fragment or a functionally active derivative thereof, or a variant or a
homologue
thereof, the variant being encoded by a nucleic acid that hybridizes to the
nucleic acid
of said protein under low-stringency conditions, is present in the complex.
32. The method of any of No. 26 - 31, wherein said method is a method of
screening for
a drug for treatment or prevention of a disease or disorder, preferentially of
a disease
or disorder selected from the diseases or disorders as listed in table 4,
third column.
33. Use of a molecule that modulates the amount of, activity of, or the
protein
components of the complex of any one of No. 1 - 8 for the manufacture of a
medicament for the treatment or prevention of a disease or disorder,
preferentially of
a disease or disorder as Nsted in table 4, third column.
34. A method for the production of a pharmaceutical composition comprising
carrying out
the method of No. 26 - 31 to identify a molecule that modulates the function,
activity,
composition or formation of said complex, and further comprising mixing the
identified
molecule with a pharmaceutically acceptable carrier.
35. A method for diagnosing or screening for the presence of a disease or
disorder or a
predisposition for developing a disease or disorder in a subject, which
disease or
disorder is characterized by an aberrant amount of, component disposition of,
or
intracellular localization of the complex of any one of the No. 1 - 8,
comprising
determining the amount of, activity of, protein components of, and/or
intracellular
localization of, said complex and/or the transcription level of a gene
regulated by the
complex and/or the abundance and/or activity of a protein or protein complex
dependent on the function of the complex and/or product of a gene dependent on
the
complex in a comparative sample derived from a subject, wherein a difference
in said
amount, activity, or protein components of, said complex in a corresponding
sample
from a subject not having the disease or disorder or predisposition indicated
the
presence in the subject of the disease or disorder or predisposition in the
subject.
36. The method of No. 35, wherein the amount of said complex is determined.

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37. The method of No. 35, wherein the activity of said complex is determined.
38. The method of No. 37, wherein said determining step comprises isolating
from the
cell or organism said complex to produce said isolated complex and contacting
said
isolated complex in the presence or absence of a candidate molecule with a
substrate of said complex and determining whether said substrate is processed
in the
absence of the candidate molecule and whether the processing of said substrate
is
modified in the presence of said candidate molecule.
39. The method of No. 35, wherein the amount of the individual protein
components of
said complex is determined.
40. The method of No. 39, wherein said determining step comprises determining
whether
any of the proteins according to No. 13 is present in the complex.
41. The complex of any one of No. 1 - 8, or a protein of No. 13 or an antibody
or fragment
thereof of No. 17, for use in a method of diagnosing a disease or disorder,
preferentially of a disease or disorder as listed in table 4, third column of
said
complex.
42. A method for treating or preventing a disease or disorder characterized by
an
aberrant amount of, activity of, component composition of or intracellular
localization
of, the complex of any one of No. 1 - 8, comprising administering to a subject
in need
of such treatment or prevention a therapeutically effective amount of one or
more
molecules that modulate the amount of, activity of, or protein composition of,
said
complex.
43. The method according to No. 42, wherein said disease or disorder involves
decreased levels of the amount or activity of said complex.
44. The method according to No. 42, wherein said disease or disorder involves
increased
levels of the amount or activity of said complex.

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45. Complex of No. 1 - 8 and/or a protein as listed in table 1, seventh column
of said
complex as a target for an active agent of a pharmaceutical, preferably a drug
target, in
the treatment or prevention of a disease or disorder, preferentially of a
disease or
disorder as listed in table 4, third column of said complex.
In a preferred embodiment of the present invention, the protein
components of the complex are vertebrate homologs of the yeast proteins, or a
mixture
of yeast and vertebrate homolog proteins. In a more preferred embodiment, the
protein
components of the complex are mammalian homologs of the yeast proteins, or a
mixture
of yeast and mammalian homolog proteins. In particular aspects,n the native
component
proteins, or derivatives or fragments of the complex are obtained from a
mammal such
as mouse, rat, pig, cow, dog, monkey, human, sheep or horse. In another
preferred
embodiment, the protein components of the complex are human homologs of the
yeast
proteins, or a mixture of yeast and human homolog proteins. In yet another
preferred
embodiment, the protein components of the complex are a mixture of yeast,
vertebrate,
mammalian and/or human proteins.
The present invention is also directed to methods for production of a
protein complex of the present invention, and derivatives of the complex
and/or
fragments and/or derivatives of individual component proteins or the complex,
e.g., by
isolation from a cell expressing the complex or by recombinantly expressing
the
component proteins of the complex and combining the component proteins in
vitro.
Pharmaceutical compositions are also provided.
The present invention is further directed to complexes comprising a fusion
protein which comprises a component of the complex or a fragment thereof
linked via a
covalent bond to an amino acid sequence different from said component protein,
as well
as nucleic acids encoding the protein, fusions and fragments thereof. For
example, the
non-component protein portion of the fusion protein, which can be added to the
N-
terminal, the C-terminal or inserted into the amino acid sequence of the
complex
component can comprise a few amino acids, which provide an epitope that is
used as a
target for affinity purification of the fusion protein and/or complex.
The invention is further directed to methods for modulating (i.e., inhibiting
or enhancing) the amount of, activity of, or the identity of the protein
components of, a
complex of the present invention. The protein components of a complex of the
present
invention have been implicated in many physiological processes. The present
invention

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is also directed to methods for screening a complex, as well as a derivative
of the
complex, for the ability to alter a cell function, particularly a cell
function in which the
complex and/or a component protein of the complex has been implicated.
Moreover, the present invention provides a process for the identification
and/or preparation of an effector of a composition according to the invention
which
process comprises the steps of bringing into contact the composition of the
invention or
of a component thereof with a compound, a mixture of compounds or a library of
compounds and determining whether the compounds or certain compounds of the
mixture or library bind to the composition of the invention and/or a component
thereof
and/or affects the biological activity of such a composition or component and
then
optionally further purifying the compound positively tested as effector by
such a process.
A major application of the composition according to the invention results in
the identification of an active agent capable of binding thereto. Hence, the
compositions
of the invention are useful tools in screening for new pharmaceutical drugs.
The present invention is also directed to a method for isolating the a
complex of the invention and the component proteins comprising tagging a
protein of the
complex with a sequence that allows affinity purification of the tagged
protein, expressing
such protein in a target cell, isolating the protein complex which is attached
to the tagged
protein, and optionally disassociating the protein complex and isolating the
individual
complex members.
The present invention further relates to a composition, preferably a protein
complex, which is obtainable by the method comprising the following steps:
tagging a
protein as defined above, i.e. a protein which forms part of a protein
complex, with a
moiety, preferably an amino acid sequence, that allows affinity purification
of the tagged
protein and expressing such protein in a target cell and isolating the protein
complex
which is attached to the tagged protein. The details of such purification are
described in
WO 00/09716 and in Rigaut, G. et al. (1999), Nature Biotechnology, Vol. 17
(10): 1030-
1032 and further herein below. The tagging can essentially be performed with
any
moiety which is capable of providing a specific interaction with a further
moiety, e.g. in
the sense of a ligand receptor interaction, antigen antibody interaction or
the like. The
tagged protein can also be expressed in an amount in the target cell which
comes close
to the physiological concentration in order to avoid a complex formation
merely due to
high concentration of the expressed protein but not reflecting the natural
occurring
complex.

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In a further preferred embodiment, the composition is obtained by using a
tagged protein which comprises two different tags which allow two different
affinity
purification steps. This measure allows a higher degree of purification of the
composition
in question. In a further preferred embodiment the tagged protein comprises
two tags
that are separated by a cleavage site for a protease. This allows a step-by-
step
purification on affinity columns.
The present invention is also directed to therapeutic and prophylactic, as
well as diagnostic, prognostic, and screening methods and compositions based
upon the
a complex of the present invention (and the nucleic acids encoding the
individual
proteins that participate in the complex). Therapeutic compounds of the
invention
include, but are not limited to, a complex of the invention, and a complex
where one or
more members of the complex is a derivative or fragment thereof. The present
invention
is also directed to complex specific antibodies to and nucleic acids encoding
the
foregoing; and antisense nucleic acids to the nucleotide sequences encoding
the
complex components. Diagnostic, prognostic and screening kits are also
provided.
The present invention further relates to a kit comprising a composition as
described above, optionally together with further reagents and working
instructions. The
further reagents may be, for example, buffers, substrates for enzymes but also
carrier
material such as beads, filters, microarrays and other solid carries. The
working
instructions may indicate how to use the ingredients of the kit in order to
perform a
desired assay.
The present invention further relates to a nucleic acid encoding a component
of a composition as defined above. Such a nucleic acid may be used for example
to
express a desired tagged protein in a given cell for the isolation of a
complex or
component according to the invention. Such a nucleic acid may also be used for
the
identification and isolation of genes from other organisms by cross species
hybridization.
The present invention further relates to a construct, preferably a vector
construct, which comprises a nucleic acid as described above. Such constructs
may
comprise expression controlling elements such as promoters, enhancers and
terminators
in order to express the nucleic acids in a given host cell, preferably under
conditions
which resemble the physiological concentrations.
The present invention further relates to a host cell containing a construct as
defined above. Such a host cell can be, e.g., any eukaryotic cell such as
yeast, plant or

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mammalian, whereas human cells are preferred. Such host cells may form the
starting
material for isolation of a complex according to the present invention.
Animal models and methods of screening for modulators (i.e., agonists,
and antagonists) of the amount of, activity of, or protein component
composition of, a
complex of the present invention are also provided.
3.1 DEFINITIONS
The term "activity" as used herein, refers to the function of a molecule in
its
broadest sense. It generally includes, but is not limited to, biological,
biochemical,
physical or chemical functions of the molecule. It includes for example the
enzymatic
activity, the ability to interact with other molecules and ability to
activate, facilitate,
stabilize, inhibit, suppress or destabilize the function of other molecules,
stability, ability
to localize to certain subcellular locations. Where applicable, said term also
relates to the
function of a protein complex in its broadest sense.
The term "agonist" as used herein, means a molecule which modulates the
formation of a protein complex or which, when bound to a complex or protein of
the
invention or a molecule in the protein complex, increases the amount of, or
prolongs the
duration of, the activity of the complex. The stimulation may be direct or
indirect,
including effects on the expression of a gene encoding a member of the protein
complex,
or by a competitive or non-competitive mechanism. Agonists may include
proteins,
nucleic acids, carbohydrates or any other organic or anorganic molecule or
metals.
Agonists also include a functional peptide or peptide fragment derived from a
protein
member of the complexes of the invention or a protein member itself of the
complexes of
the invention. Preferred activators are those which, when added to the complex
and/or
the protein of the invention under physiological conditions and/or in vitro
assays,
including diagnostic or prognostic assays, result in a change of the level of
any of the
activities of the protein complex and/or the proteins of the invention as
exemplary
illustrated above by at least 10%, at least 25%, at least 50%, at least 100%,
at least,
200%, at least 500% or at least 1000% at a concentration of the activator 1 pg
m I-~, 1 Opg
ml-~, 100pg ml-~, 500pg ml-~, 1mg ml-~, 10mg ml-~ or 100mg ml-~. Any
combination of the
above mentioned degrees of percentages and concentration may be used to define
an
agonist of the invention, with greater effect at lower concentrations being
preferred.

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The term "amount" as used herein and as applicable to the embodiment
described relates to the amount of the particular protein or protein complex
described,
including the value of null, i.e. where no protein or protein complex
described in that
particular embodiment is present under the or any of the conditions which
might be
specified in that particular embodiment.
The term "animal" as used herein includes, but is not limited to mammals,
preferably mammals such as cows, pigs, horses, mice, rats, cats, dogs, sheep,
goats
and most preferably humans. Other animals used in agriculture, such as
chickens, ducks
etc. are also included in the definition as used herein.
The term "animal" as used herein does not include humans if being used in the
context of
genetic alterations to the germline.
The term "antagonist" as used herein, means a molecule which modulates the
formation of a protein complex or which, when bound to a complex or protein of
the
invention or a molecule in the protein complex, decreases the amount of, or
the duration
or level of activity of the complex. The effect may be direct or indirect,
including effects
on the expression of a gene encoding a member of the protein complex, or by a
competitive or non-competitive mechanism. Antagonists may include proteins,
including
antibodies, nucleic acids, carbohydrates or any other organic or anorganic
molecule or
metals. Antagonists also include a functional peptide or peptide fragment
derived from a
protein member of the complexes of the invention or a protein member itself of
the
complexes of the invention. Preferred antagonists are those which, when added
to the
complex and/or the protein of the invention under physiological conditions
and/or in vitro
assays, including diagnostic or prognostic assays, result in a change of the
level of any
of the activities of the protein complex and/or the proteins of the invention
as exemplary
illustrated above by at least 10%, at least 20%, at least 30%, at least 40% at
least 50%,
at least 60%, at least 70%, at least 80%, at least 90%, at least 95% or at
least 99% at a
concentration of the inhibitor of 1pg ml-~, 10pg mfg, 100pg ml-~, 500pg ml-~,
1mg ml-~,
10mg ml-~ or 100mg ml-~.
Any combination of the above mentioned degrees of percentages and
concentration may
be used to define antagonist of the invention, with greater effect at lower
concentrations
being preferred.
The term "antibodies" as used herein, include include, but are not limited to,
polyclonal, monoclonal, chimeric, single chain, Fab fragments, and an Fab
expression
library.

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The term "binding" as used herein means a stable or transient association
between two molecules, including electrostatic, hydrophobic, ionic and/or
hydrogen-bond
interaction under physiological conditions and/or conditions being used in
diagnostic or
prognostic method or process or procedure.
The term "carrier" as used herein refers to a diluent, adjuvant, excipient, or
vehicle with which the therapeutic is administered. Such pharmaceutical
carriers can be
sterile liquids, such as water and oils, including those of petroleum, animal,
vegetable or
synthetic origin, including but not limited to peanut oil, soybean oil,
mineral oil, sesame
oil and the like. Water is a preferred carrier when the pharmaceutical
composition is
administered orally. Saline and aqueous dextrose are preferred carriers when
the
pharmaceutical composition is administered intravenously. Saline solutions and
aqueous
dextrose and glycerol solutions are preferably employed as liquid carriers for
injectable
solutions. Suitable pharmaceutical excipients include starch, glucose,
lactose, sucrose,
gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol
monostearate, talc,
sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol
and the like.
The composition, if desired, can also contain minor amounts of wetting or
emulsifying
agents, or pH buffering agents. These compositions can take the form of
solutions,
suspensions, emulsions, tablets, pills, capsules, powders, sustained-release
formulations
and the like. The composition can be formulated as a suppository, with
traditional
binders and carriers such as triglycerides. Oral formulation can include
standard carriers
such as pharmaceutical grades of mannitol, lactose, starch, magnesium
stearate, sodium
saccharine, cellulose, magnesium carbonate, etc. Examples of suitable
pharmaceutical
carriers are described in "Remington's Pharmaceutical Sciences" by E.W.
Martin. Such
compositions will contain a therapeutically effective amount of the
therapeutic, preferably
in purified form, together with a suitable amount of carrier so as to provide
the form for
proper administration to the patient. The formulation should suit the mode of
administration.
If not stated otherwise, the terms "complex" aid "protein complex" are used
interchangeably herein and refer to a complex of proteins that is able to
perform one or
more functions of the wild type protein complex. The protein complex may or
may not
include and/or be associated with other molecules such as nucleic acid, such
as RNA or
DNA, or lipids or further cofactors or moieties selected from a metal ions,
hormones,
second messengers, phosphate, sugars.

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A "complex" of the invention may also be part of or a unit of a larger
physiological
protein assembly.
If not stated otherwise, the term "compound" as used herein are include but
are
not limited to peptides, nucleic acids, carbohydrates, natural product extract
librariesorganic molecules, preferentially small organic molecules, anorganic
molecules,
including but not limited to chemicals, metals and organometallic molecules.
The terms "derivatives" or "analogs of component proteins" or "variants" as
used
herein include, but are not limited, to molecules comprising regions that are
substantially
homologous to the component proteins, in various embodiments, by at least 30%,
40%,
50%, 60%, 70%, 80%, 90%, 95% or 99% identity over an amino acid sequence of
identical size or when compared to an aligned sequence in which the alignment
is done
by a computer homology program known in the art, or whose encoding nucleic
acid is
capable of hybridizing to a sequence encoding the component protein under
stringent,
moderately stringent, or nonstringent conditions. It means a protein which is
the outcome
of a modification of the naturally occurring protein, by amino acid
substitutions, deletions
and additios, respectively, which derivatives still exhibit the biological
function of the
naturally occurring protein although not necessarily to the same degree. The
biological
function of such proteins can e.g. be examined by suitable available in vitro
assays as
provided in the invention.
The term "functionally active" as used herein refers to a polypeptide, namely
a
fragment or derivative, having structural, regulatory, or biochemical
functions of the
protein according to the embodiment of which this polypeptide, namely fragment
or
derivative is related to.
The term "fragment" as used herein refers to a polypeptide of at least 10, 20,
30,
40 or 50 amino acids of the component protein according to the embodiment. In
specific
embodiments, such fragments are not larger than 35, 100 or 200 amino acids.
The term "gene" as used herein refers to a nucleic acid comprising an open
reading frame encoding a polypeptide of, if not stated otherwise, the present
invention,
including both exon and optionally intron sequences.
The terms " homologue" or "homologous gene products" as used herein mean a
protein in another species, preferably mammals, which performs the same
biological
function as the a protein component of the complex further described herein.
Such
homologues are also termed "orthologous gene products". The algorithm for the
detection of orthologue gene pairs from humans and mammalians or other species
uses

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the whole genome of these organisms. First, pairwise best hits are retrieved,
using a full
Smith-Waterman alignment of predicted proteins. To further improve
reliability, these
pairs are clustered with pairwise best hits involving Drosophila melanogaster
and C.
elegans proteins. Such analysis is given, e.g., in Nature, 2001, 409:860-921.
The
homologues of the proteins according to the invention can either be isolated
based on
the sequence homology of the genes encoding the proteins provided herein to
the genes
of other species by cloning the respective gene applying conventional
technology and
expressing the protein from such gene, or by isolating proteins of the other
species by
isolating the analogous complex according to the methods provided herein or to
other
suitable methods commonly known in the art.
The term "host cells" or, were applicable, "cells" or "hosts" as used herein
is
intended to be understood in a broadest sense and include, but are not limited
to
mammalian cell systems infected with virus (e.g., vaccinia virus, adenovirus,
etc.); insect
cell systems infected with virus (e.g., baculovirus); microorganisms such as
yeast
containing yeast vectors; or bacteria transformed with bacteriophage, DNA,
plasmid
DNA, or cosmid DNA. The expression elements of vectors vary in their strengths
and
specificities. Depending on the host vector system utilized, any one of a
number of
suitable transcription and translation elements may be used. It is understood
that this
term not only refers to the particular subject cell but to the progeny or
potential progeny
of such a cell. Because certain modifications may occur in succeeding
generations due
to either mutation of environmental influences, such progeny may not, in fact,
be identical
to the parent cell, but are still included within the scope of the term as
used herein.
The term "modification" as used herein refers to all modifications of a
protein or
protein complex of the invention including cleavage and addition or removal of
a group.
The term "nuleic acid" as used herein refers to polynucleotides such as
deoxyribonucleic acid (DNA), and, where appropriate, ribonucleic acid (RNA).
They may
also be polynucleotides which include within them synthetic or modified
nucleotides. A
number of different types of modification to polynucleotides are known in the
art. These
include methylphosphonate and phosphorothioate backbones, addition of acridine
or
polylysine chains at the 3' and/or 5' 'ends of the molecule. For the purposes
of the
present invention, it is to be understood that the polynucleotides described
herein may
be modified by any method available in the art. Such modifications may be
carried out in
order to enhance the in vivo activity or lifespan of polynucleotides of the
invention.
Polynucleotides according to the invention may be produced recombinantly,

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synthetically, or by any means available to those of skill in the art. They
may also be
cloned by standard techniques. The polynucleotides are typically provided in
isolated
and/or purified form. As applicable to the embodiment being described, they
include both
single stranded and double-stranded polynucleotides.
The term "percent identity", as used herein, means the number of identical
residues as defined by an optimal alignment using the Smith-Waterman algorithm
divided by the length of the overlap multiplied by 100. The alignment is
performed by the
search program (Pearson, 1991, Genomics 11:635-650) with the constraint to
align the
maximum of both sequences.
The terms "polypeptides" and "proteins" are, where applicable, used
interchangeably herein. They may be chemically modified, e.g. post-
translationally
modified. For example, they may be glycosylated or comprise modified amino
acid
residues. They may also be modified by the addition of a signal sequence to
promote
their secretion from a cell where the polypeptide does not naturally contain
such a
sequence. They may be tagged with a tag. They may be tagged with different
labels
which may assists in identification of the proteins in a protein complex.
Polypeptides/proteins for use in the invention may be in a substantially
isolated form. It
will be understood that the polypeptid/protein may be mixed with carriers or
diluents
which will not interfere with the intended purpose of the polypeptide and
still be regarded
as substantially isolated. A polypeptide/protein for use in the invention may
also be in a
substantially purified form, in which case it will generally comprise the
polypeptide in a
preparation in which more than 50%, e.g. more than 80%, 90%, 95% or 99%, by
weig ht
of the polypeptide in the preparation is a polypeptide of the invention.
"Target for therapeutic drug" means that the respective protein (target) can
bind
the active ingredient of a pharmaceutical composition and thereby changes its
biological
activity in response to the drug binding.
The term "tag" as used herein is meant to be understood in its broadest sense
and to include, but is not limited to any suitable enzymatic, fluorescent, or
radioactive
labels and suitable epitopes, incuding but not limited to HA tag, Myc-tag, T7,
His-tag,
FLAG-tag, Calmodulin binding proteins, glutathione-S-transferase, strep-tag,
KT3-
epitope, EEF-epitpopes, green-fluorescent protein and variants thereof.
The term "therapeutics" as used herein, includes, but is not limited to, a
protein
complex of the present invention, the individual component proteins, and
analogs and
derivatives (including fragments); antibodies thereto; nucleic acids encoding
the

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component protein, and analogs or derivatives thereof; component protein
antisense
nucleic acids, and agents that modulate complex formation and/or activity
(i.e., agonists
and antagonists).
The term "vector" as used herein means a nucleic acid molecule capable of
transporting another nucleic acid sequence to which it has been linked.
Preferred vectors
are those capable of autonomous replication and/or expression of nueclic acids
to which
they linked. The terms "plasmid" and "vector" are used interchangeably herein
when
applicable to the embodiment. However, vectors other than plasmids are also
included
herein. The expression elements of vectors vary in their strengths and
specificities.
Depending on the host vector system utilized, any one of a number of suitable
transcription and translation elements may be used.
4. BRIEF DESCRIPTION OF THE DRAWINGS
Fig. 1 shows a synopsis of the screen. Left is a schematic representation of
the
sequential steps used for the purification and identification of TAP-
complexes. Right:
Number of experiments and success rate at each step of the procedure.
Fig. 2 shows a schematic representation of the gene targeting procedure. The
TAP
cassette is inserted at the C-terminus of a given yeast ORF by homologous
recombination, generating the TAP-tagged fusion protein.
Fig. 3 shows the protein pattern obtained for the human Arp2/3-complex using
ARPC2
as a bait usint TAP. The proteins identified as members of the complex (ARP3,
ARP2,
ARPC1A, ARPC2, ARPC3, ARPC4, ARPCS) as well as the yeast orthologs thereof
(Arp3, Arp2, Arc40, Arc35, Arc19, Arc18, Arc16), which constitute the
orthologueos yeast
complex, are indicated.
Fig. 4 shows elements of mammalian and yeast mRNA, respectively, which are
involved
in polyadenylation/cleavage of precursor mRNA.
Fig. 5. showns the protein pattern obtained by separation of the members of
the
polyadenylation-complex of yeast using Pta1 as a bait using TAP. Protein bands
for Cft1,
Cft2, Ysh1, Rna14, Pab1, Pcf11, Ref2, Pap1, CIp1, YKL059c, Pfs2, YGR156w,
Fip1,
Rnal5, YKL018w, GIc7, Ythl, Ssu72, YOR179c and Pta1 (in bold) are labeled.
(Further
proteins identified as components of the yeast complex as described in the
EXAMPLES-
section (infra) are not stated in the figure)

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Fig. 6 shows the protein pattern obtained by the separation of the members of
the
polyadenylation-complex in some of the reverse tagging-experiments and re-
purification
of a selection of the novel interactors. The baits using TAP used for the
different
experiments are given on top of each gel picture. The band constituing the
protein used
as the bait in the res pective experiments is indicated by an arrow.
Previously known
members of the complex are listed in bold letters. (Note: only experiments
using Cft1,
Cft2, Pap1, Ref2, YKL059c, Pfs2, YOR179c and Pta1 as a bait are shown and only
the
proteins bands of Cft1, Cft2, Ysh1, Rnal4, Pab1, Ref2, CLp1, Ygr156w, Fip1,
GIc7,
Yht1, Yor179c, Pta1, Pcf11, Pab1, YIe1059c, Pfs2, Rna15, Yk1018w and Ssu72 are
labelled).
Fig 7 shows the protein pattern obtained for the human Ccr4/Not-complex
using NOT2 as a bait using TAP. The proteins identified as members of the
complex are
labeled (KIAA1007,AAH02928, KIAA1194, Rqcd1, CALIF, CAF1). Furthermore, the
respective orthologues in yeast are indicated to the left (Not1, Ccr4, Caf40,
Caf1). (The
complete yeast complex is described in detail in the EXAMPLES section
(infra)).
Fig. 8 shows the protein pattern obtained for the human TRAPP-(Bet3)-
complex using BET3 as a bait using TAP. Identified human proteins are
indicated
(FASN, CAD, KIAA1012, EHOC-1, AL136752.1, CGI-87, alpha/f3-tubulin, FLJ13611,
Glucorticoid Receptor specific elongation factor, hBet3, PTD009, MUM2, 832611
2
(MGC2650), Sedlin. Proteins identified as members of the human TRAPP-complex
are
KIAA1012, EHOC-1, hBet3, PTD009, MUM2, 832611 2 (MGC2650) and Sedlin. The
corresponding yeast orthologues are given on the left. (The complete yeast
complex is
described in detail in the EXAMPLES-section (infra)).
5. DETAILED DESCRIPTION OF THE INVENTION
Our analysis allowed us to group cellular proteins into approximately 380
complexes. These are connected to each other by sharing components. The
network
that results is a functional description of the eukaryotic proteome at an
unprecedented
level of organization. Such higher order maps will bring increasing quality to
our
appreciation of biological systems. It is anticipated that this may provide
drug discovery
programs with a molecular context for the choice and evaluation of drug
targets.

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The invention thus relates to the following embodiments:
1. A protein complex selected from complex (I) and comprising
(a) at least one first protein, which first protein is selected from the group
of proteins
in table 1, sixth column of a given complex, or a functionally active
derivative thereof,
or a functionally active fragment thereof, or a homologue thereof, or a
variant of said
protein, the variant being, the variant being encoded by a nucleic acid that
hybridizes
to the nucleic acid encoding said protein under low stringency conditions; and
(b) at least one second protein, which second protein is selected from the
group of
proteins in table 1, seventh column of said given complex, or a functionally
active
derivative thereof, or a functionally active fragment thereof, or a homologue
thereof,
or a variant of said second protein, said variant being encoded by a nucleic
acid that
hybridizes to the nucleic acid encoding said protein under low stringency
conditions;
and a complex (II) comprising at least two of said second proteins,
wherein said low stringency conditions comprise hybridization in a buffer
comprising
35% formamide, 5X SSC, 50 mM Tris-HCI (pH 7.5), 5 mM EDTA, 0.02% PVP, 0.02%
BSA, 100 ug/ml denatured salmon sperm DNA, and 10% (wtlvol) dextran sulfate
for
18-20 hours at 40°C, washing in a buffer consisting of 2X SSC, 25 mM
Tris-HCI (pH
7.4), 5 mM EDTA, and 0.1 % SDS for 1-5 hours at 55°C, and washing in a
buffer
consisting of 2X SSC, 25 mM Tris-HCI (pH 7.4) 5 mM EDTA, and 0.1 % SDS for 1.5
hours at 60°C.
2. A protein complex comprising a first protein selected from the proteins
listed in table
1, second column of a given complex or a homologue or variant thereof, or a
functionally active fragment or functionally active derivative of said first
protein, the
variant being encoded by a nucleic acid that hybridizes to the nucleic acid of
said first
protein under low stringency conditions, and at least one second protein
selected
from the group of proteins in table 1, seventh column of a given complex, or a
variant
or homologue thereof, or a functionally active fragment or a functionally
active
derivative of said second protein, the variant of said second protein being
encoded by
a nucleic acid that hybridizes to the nucleic acid of said second protein
under low-
stringency conditions, and wherein said low stringency conditions comprise
hybridization in a buffer comprising 35% formamide, 5X SSC, 50 mM Tris-HCI (pH

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7.5), 5 mM EDTA, 0.02% PVP, 0.02% BSA, 100 ug/ml denatured salmon sperm
DNA, and 10% (wt/vol) dextran sulfate for 18-20 hours at 40°C, washing
in a buffer
consisting of 2X SSC, 25 mM Tris-HCI (pH 7.4), 5 mM EDTA, and 0.1 % SDS for 1-
5
hours at 55°C, and washing in a buffer consisting of 2X SSC, 25 mM Tris-
HCI (pH
7.4) 5 mM EDTA, and 0.1 % SDS for 1.5 hours at 60°C.
3. A protein complex comprising all proteins selected from the proteins in
table 1, third
column of a given complex or at least one protein being a homologue thereof,
or a
variant thereof or functionally active fragment or functionally active
derivative of said
protein, said variant being encoded by a nucleic acid that hybridizes to the
nucleic
acid of said protein under low stringency conditions;
wherein said low stringency conditions comprise hybridization in a bufFer
comprising
35% formamide, 5X SSC, 50 mM Tris-HCI (pH 7.5), 5 mM EDTA, 0.02% PVP, 0.02%
Ficoll, 0.2% BSA, 100 ug/ml denatured salmon sperm DNA, and 10% (wtlvol)
dextran
sulfate for 18-20 hours at 40°C, washing in a buffer consisting of 2X
SSC, 25 mM
Tris-HCI (pH 7.4), 5 mM EDTA, and 0.1 % SDS for 1-5 hours at 55°C, and
washing in
a buffer consisting of 2X SSC, 25 m M Tris-HCI (pH 7.4), 5 mM EDTA, and 0.1 %
SDS
for 1.5 hours at 60°C.
4. A protein complex that comprises all proteins as listed in table 1, third
column for a
given complex or at least one protein being a homologue or a variant thereof,
or a
functionally active fragment or a functionally active derivative thereof, the
variant
being encoded by a nucleic acid that hybridizes to the nucleic acid of any of
said
proteins under low stringency conditions, except at least one protein of the
proteins
listed in table 1, third column, wherein said low stringency conditions
comprise
hybridization in a buffer comprising 35% formamide, 5X SSC, 50 mM Tris-HCI (pH
7.5), 5 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.2% BSA, 100 ug/ml denatured salmon
sperm DNA, and 10% (wt/vol) dextran sulfate for 18-20 hours at 40°C,
washing in a
buffer consisting of 2X SSC, 25 mM Tris-HCI (pH 7.4), 5 mM EDTA, and 0.1 % SDS
for 1-5 hours at 55°C, and washing in a buffer consisting of 2X SSC, 25
mM Tris-HCI
(pH 7.4), 5 mM EDTA, and 0.1 % SDS for 1.5 hours at 60°C, with the
provisio that the
complex comprises at least one protein selected from table 1, seventh column
of a
given complex.

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5. The complex of any of No. 1 - 4 comprising at least one functionally active
derivative
of said first protein and/or a functionally active derivative of said second
protein,
wherein the functionally active derivative is a fusion protein comprising said
first
protein or said second protein fused to an amino acid sequence different from
the first
protein or second protein.
6. The complex of No. 5 wherein the functionally active derivative is a fusion
protein
comprising said first protein or said second protein fused to an affinity tag
or label.
7. The complex of any of No. 1 - 4 comprising a fragment of said first protein
and/or a
fragment of said second protein, which fragment binds to another protein
component
of said complex.
8. The complex of any of No. 1 - 7 that is involved in at least one
biochemical activity as
stated in table 2, column 8 for a given complex.
9. A process for preparing a complex of any of No. 1 - 8 and optionally the
components
thereof comprising the following steps:
expressing a protein of the complex, preferably a tagged protein, in a target
cell, or a
tissue or an organ, isolating the protein complex which is attached to the
protein,
preferably the tagged protein, and optionally disassociating the protein
complex and
isolating the individual complex members.
10. The process according to No. 9 wherein the tagged protein comprises two
different
tags which allow two separate affinity purification steps.
11. The process according to any of No. 9 - 10 wherein the two tags are
separated by a
cleavage site for a protease.
12. Component of a protein complex obtainable by a process according to any of
No. 9 -
11.
13. Protein selected from the group of proteins in table 1, ninth column of a
given
complex or a homologue or a variant of thereof, or a functionally active
fragment or a

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functionally active derivative of said protein, the variant being encoded by a
nucleic
acid that hybridizes to the nucleic acid encoding said protein under low
stringency
conditions, wherein said low stringency conditions comprise hybridization in a
buffer
comprising 35% formamide, 5X SSC, 50 mM Tris-HCI (pH 7.5), 5 mM EDTA, 0.02%
PVP, 0.02% Ficoll, 0.2% BSA, 100 ug/ml denatured salmon sperm DNA, and 10%
(wt/vol) dextran sulfate for 18-20 hours at 40°C, washing in a buffer
consisting of 2X
SSC, 25 mM Tris-HCI (pH 7.4), 5 mM EDTA, and 0.1 % SDS for 1.5 hours at
55°C,
and washing in a buffer consisting of 2X SSC, 25 mM Tris-HCI (pH 7.4), 5 mM
EDTA,
and 0.1 % SDS for 1.5 hours at 60°C.
14. Nucleic acid encoding a protein according to No. 13.
15. Construct, preferably a vector construct, comprising
(a) a nucleic acid according to No. 14 and at least one further nucleic acid
which is
normally not associated with said nucleic acid, or
(b) at least two separate nucleic acid sequences each encoding a different
protein, or
a functionally active fragment or a functionally active derivative thereof, or
a
homologue or a variant thereof, at least one of said proteins being selected
from
the first group of proteins according to No. 1 (a) and at least one of said
proteins,
being selected from the second group of proteins according to No. 1 (b) or
(c) at least two separate nucleic acid sequences each encoding a different
protein, or
a functionally active fragment or a functionally active derivative thereof, or
a
homologue or a variant thereof, said proteins being selected from the proteins
of
complex (II) according to No. 1.
16. Host cell, containing a vector comprising at least one nucleic acid of No.
14 and /or a
construct of No. 15 or containing several vectors each comprising at least one
nucleic
acid encoding at least one protein selected from the first group of proteins
according
to No. 1 (a) and at least one nucleic acid encoding at least one protein
selected from
the second group of proteins according to No. 1 (b).
17. An antibody or a fragment of said antibody containing the binding domain
thereof,
selected from an antibody or fragment thereof, which binds the complex of any
of No.
1 - 8 and which does not bind any of the proteins of said complex when
uncomplexed

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26
and an antibody or a fragment of said antibody containing the binding domain
thereof
which binds to any of the proteins of the group of proteins according to No.
13.
18. A kit comprising in one or more containers:
(a) the complex of any of No. 1 - 8 and/or the proteins of No. 13 andlor
(b) an antibody according to No. 17 and/or
(c) a nucleic acid encoding a protein of the complex of any of No. 1 - 8
and/or a
protein of No. 13 and/or
(d) cells expressing the complex of any of No. 1 - 8 and/or a protein of No.
13 and,
optionally,
(e) further components such as reagents, buffers and working instructions.
19. The kit according to No. 18 for processing a substrate of a complex of any
one of No.
1-8.
20. The kit according to No. 18 for the diagnosis or prognosis of a disease or
a disease
risk, preferentially for a disease or disorder as stated in table 4, third
column for a
given complex..
21. Array, preferably a microarray, in which at least a complex according to
any of No. 1 -
8 and/or at least one protein according to No. 13 and/or at least one antibody
according to No. 17 is attached to a solid carrier.
22. A process for modifying a substrate of a complex of any one of No. 1 - 8
comprising
the step of bringing into contact a complex of any of No. 1 - 8 with said
substrate,
such that said substrate is modified.
23. A pharmaceutical composition comprising the protein complex of any of No.
1 - 8
and/or a protein according to No. 13.
24. A pharmaceutical composition according to No. 23 for the treatment of
diseases and
disorders, preferentially for diseases or disorders as stated in table 4,
third column of
said complex.

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25. A method for screening for a molecule that binds to a complex of any one
of No. 1 - 8
and/or a protein of No. 13, comprising the following steps:
(a) exposing said complex or protein, or a cell or organism containing said
complex
or said protein, to one or more candidate molecules; and
(b) determining whether said candidate molecule is bound to the complex or
protein.
26. A method for screening for a molecule that modulates directly or
indirectly the
function, activity, composition or formation of a complex of any one of No. 1 -
8
comprising the steps of:
(a) exposing said complex, or a cell or organism containing said complex to
one or
more candidate molecules; and
(b) determining the amount of, activity of, protein components of, and/or
intracellular
localization of, said complex and/or the transcription level of a gene
regulated by
the complex and/or the abundance and/or activity of a protein or protein
complex dependent upon the function of the complex and/or product of a gene
dependent on the complex in the presence of the one or more candidate
molecules, wherein a change in said amount, activity, protein components or
intracellular localization relative to said amount, activity, protein
components
and/or intracellular localization and/or a change in the transcription level
of a
gene regulated by the complex and/or the abundance and/or activity of a
protein
or protein complex dependent on the function of the complex and/or product of
a gene dependent on the complex in the absence of said candidate molecules
indicates that the molecule modulates function, activity, or composition of
said
complex.
27. The method of No. 26, wherein the amount of said complex is determined.
28. The method of No. 26, wherein the activity of said complex is determined.
29. The method of No. 28, wherein said determining step comprises isolating
from the
cell or organism said complex to produce said isolated complex and contacting
said
isolated complex in the presence or absence of a candidate molecule with a
substrate of said complex and determining whether said substrate is processed
in the

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absence of the candidate molecule and whether the processing of said substrate
is
modified in the presence of said candidate molecule.
30. The method of No. 26, wherein the amount of the individual protein
components of
said complex is determined.
31. The method of No. 30, wherein said determining step comprises determining
whether
any of the proteins listed in table 1, third column of said complex, or a
functionally
active fragment or a functionally active derivative thereof, or a variant or a
homologue
thereof, the variant being encoded by a nucleic acid that hybridizes to the
nucleic acid
of said protein under low-stringency conditions, is present in the complex.
32. The method of any of No. 26 - 31, wherein said method is a method of
screening for
a drug for treatment or prevention of a disease or disorder, preferentially of
a disease
or disorder selected from the diseases or disorders as listed in table 4,
third column.
33. Use of a molecule that modulates the amount of, activity of, or the
protein
components of the complex of any one of No. 1 - 8 for the manufacture of a
medicament for the treatment or prevention of a disease or disorder,
preferentially of
a disease or disorder as listed in table 4, third column.
34. A method for the production of a pharmaceutical composition comprising
carrying out
the method of No. 26 - 31 to identify a molecule that modulates the function,
activity,
composition or formation of said complex, and further comprising mixing the
identified
molecule with a pharmaceutically acceptable carrier.
35. A method for diagnosing or screening for the presence of a disease or
disorder or a
predisposition for developing a disease or disorder in a subject, which
disease or
disorder is characterized by an aberrant amount of, component disposition of,
or
intracellular localization of the complex of any one of the No. 1 - 8,
comprising
determining the amount of, activity of, protein components of, and/or
intracellular
localization of, said complex and/or the transcription level of a gene
regulated by the
complex and/or the abundance and/or activity of a protein or protein complex
dependent on the function of the complex and/or product of a gene dependent on
the

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complex in a comparative sample derived from a subject, wherein a difference
in said
amount, activity, or protein components of, said complex in a corresponding
sample
from a subject not having the disease or disorder or predisposition indicated
the
presence in the subject of the disease or disorder or predisposition in the
subject.
36. The method of No. 35, wherein the amount of said complex is determined.
37. The method of No. 35, wherein the activity of said complex is determined.
38. The method of No. 37, wherein said determining step comprises isolating
from the
cell or organism said complex to produce said isolated complex and contacting
said
isolated complex in the presence or absence of a candidate molecule with a
substrate of said complex and determining whether said substrate is processed
in the
absence of the candidate molecule and whether the processing of said substrate
is
modified in the presence of said candidate molecule.
39. The method of No. 35, wherein the amount of the individual protein
components of
said complex is determined.
40. The method of No. 39, wherein said determining step comprises determining
whether
any of the proteins according to No. 13 is present in the complex.
41. The complex of any one of No. 1 - 8, or a protein of No. 13 or an antibody
or fragment
thereof of No. 17, for use in a method of diagnosing a disease or disorder,
preferentially of a disease or disorder as listed in table 4, third column of
said
complex.
42. A method for treating or preventing a disease or disorder characterized by
an
aberrant amount of, activity of, component composition of or intracellular
localization
of, the complex of any one of No. 1 - 8, comprising administering to a subject
in need
of such treatment or prevention a therapeutically effective amount of one or
more
molecules that modulate the amount of, activity of, or protein composition of,
said
complex.

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43. The method according to No. 42, wherein said disease or disorder involves
decreased levels of the amount or activity of said complex.
44. The method according to No. 42, wherein said disease or disorder involves
increased
levels of the amount or activity of said complex.
45. Complex of No. 1 - 8 and/or a protein as listed in table 1, seventh column
of said
complex as a target for an active agent of a pharmaceutical, preferably a drug
target, in
the treatment or prevention of a disease or disorder, preferentially of a
disease or
disorder as listed in table 4, third column of said complex.
In a preferred embodiment of the present invention, the protein
components of the complex are vertebrate homologs of the yeast proteins, or a
mixture
of yeast and vertebrate homolog proteins. In a more preferred embodiment, the
protein
components of the complex are mammalian homologs of the yeast proteins, or a
mixture
of yeast and mammalian homolog proteins. In particular aspects,n the native
component
proteins, or derivatives or fragments of the complex are obtained from a
mammal such
as mouse, rat, pig, cow, dog, monkey, human, sheep or horse. In another
preferred
embodiment, the protein components of the complex are human homologs of the
yeast
proteins, or a mixture of yeast and human homolog proteins. In yet another
preferred
embodiment, the protein components of the complex are a mixture of yeast,
vertebrate,
mammalian and/or human proteins.
The present invention is also directed to methods for production of a
protein complex of the present invention, and derivatives of the complex
and/or
fragments and/or derivatives of individual component proteins or the complex,
e.g., by
isolation from a cell expressing the complex or by recombinantly expressing
the
component proteins of the complex and combining the component proteins in
vitro.
Pharmaceutical compositions are also provided.
The present invention is further directed to complexes comprising a fusion
protein which comprises a component of the complex or a fragment thereof
linked via a
covalent bond to an amino acid sequence different from said component protein,
as well
as nucleic acids encoding the protein, fusions and fragments thereof. For
example, the
non-component protein portion of the fusion protein, which can be added to the
N-
terminal, the C-terminal or inserted into the amino acid sequence of the
complex

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31
component can comprise a few amino acids, which provide an epitope that is
used as a
target for affinity purification of the fusion protein and/or complex.
The invention is further directed to methods for modulating (i.e., inhibiting
or enhancing) the amount of, activity of, or the identity of the protein
components of, a
complex of the present invention. The protein components of a complex of the
present
invention have been implicated in many physiological processes. The present
invention
is also directed to methods for screening a complex, as well as a derivative
of the
complex, for the ability to alter a cell function, particularly a cell
function in which the
complex and/or a component protein of the complex has been implicated.
Moreover, the present invention provides a process for the identification
and/or preparation of an effector of a composition according to the invention
which
process comprises the steps of bringing into contact the composition of the
invention or
of a component thereof with a compound, a mixture of compounds or a library of
compounds and determining whether the compounds or certain compounds of the
mixture or library bind to the composition of the invention and/or a component
thereof
and/or affects the biological activity of such a composition or component and
then
optionally further purifying the compound positively tested as effector by
such a process.
A major application of the composition according to the invention results in
the identification of an active agent capable of binding thereto. Hence, the
compositions
of the invention are useful tools in screening for new pharmaceutical drugs.
The present invention is also directed to a method for isolating the a
complex of the invention and the component proteins comprising tagging a
protein of the
complex with a sequence that allows affinity purification of the tagged
protein, expressing
such protein in a target cell, isolating the protein complex which is attached
to the tagged
protein, and optionally disassociating the protein complex and isolating the
individual
complex members.
The present invention further relates to a composition, preferably a protein
complex, which is obtainable by the method comprising the following steps:
tagging a
protein as defined above, i.e. a protein which forms part of a protein
complex, with a
moiety, preferably an amino acid sequence, that allows affinity purification
of the tagged
protein and expressing such protein in a target cell and isolating the protein
complex
which is attached to the tagged protein. The details of such purification are
described in
WO 00/09716 and in Rigaut, G. et al. (1999), Nature Biotechnology, Vol. 17
(10): 1030-
1032 and further herein below. The tagging can essentially be performed with
any

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32
moiety which is capable of providing a specific interaction with a further
moiety, e.g. in
the sense of a ligand receptor interaction, antigen antibody interaction or
the like. The
tagged protein can also be expressed in an amount in the target cell which
comes close
to the physiological concentration in order to avoid a complex formation
merely due to
high concentration of the expressed protein but not reflecting the natural
occurring
complex.
In a further preferred embodiment, the composition is obtained by using a
tagged protein which comprises two difFerent tags which allow two different
affinity
purification steps. This measure allows a higher degree of purification of the
composition
in question. In a further preferred embodiment the tagged protein comprises
two tags
that are separated by a cleavage site for a protease. This allows a step-by-
step
purification on affinity columns.
The present invention is also directed to therapeutic and prophylactic, as
well as diagnostic, prognostic, and screening methods and compositions based
upon the
a complex of the present invention (and the nucleic acids encoding the
individual
proteins that participate in the complex). Therapeutic compounds of the
invention
include, but are not limited to, a complex of the invention, and a complex
where one or
more members of the complex is a derivative or fragment thereof. The present
invention
is also directed to complex-specific antibodies to and nucleic acids encoding
the
foregoing; and antisense nucleic acids to the nucleotide sequences encoding
the
complex components. Diagnostic, prognostic and screening kits are also
provided.
The present invention further relates to a kit comprising a composition as
described above, optionally together with further reagents and working
instructions. The
further reagents may be, for example, buffers, substrates for enzymes but also
carrier
material such as beads, filters, microarrays and other solid carries. The
working
instructions may indicate how to use the ingredients of the kit in order to
perform a
desired assay.
The present invention further relates to a nucleic acid encoding a component
of a composition as defined above. Such a nucleic acid may be used for example
to
express a desired tagged protein in a given cell for the isolation of a
complex or
component according to the invention. Such a nucleic acid may also be used for
the
identification and isolation of genes from other organisms by cross species
hybridization.
The present invention further relates to a construct, preferably a vector
construct, which comprises a nucleic acid as described above. Such constructs
may

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comprise expression controlling elements such as promoters, enhancers and
terminators
in order to express the nucleic acids in a given host cell, preferably under
conditions
which resemble the physiological concentrations.
The present invention further relates to a host cell containing a construct as
defined above. Such a host cell can be, e.g., any eukaryotic cell such as
yeast, plant or
mammalian, whereas human cells are preferred. Such host cells may form the
starting
material for isolation of a complex according to the present invention.
Animal models and methods of screening for modulators (i.e., agonists,
and antagonists) of the amount of, activity of, or protein component
composition of, a
complex of the present invention are also provided.
TABLES:
Table 1: Composition of Complexes: Table A shows the compositions of the yeast
complexes, table B shows the composition of the human complexes.
First column ('No. of complex') lists the number of the complexes used herein.
Second column ('Entry point') lists the bait proteins (TAP-tag fusion
proteins) that have
been chosen for the isolation of the given complex. Note: in several cases,
different baits
have been used for validation in reverse tagging experiments.
Third column ("Components") lists the proteins of the complex of the invention
Fourth column ( °Known complex') lists any known complexes which have
been shown
herein to be parts of the complexes as provided herein and their components.
Complexes are separated by semicolon.
Fifth column ('Known Interactions°) briefly lists any known
interactions between different
members of the complex (Abbrevations: '2-hybrid': interaction as identified in
yeast 2-
hybrid screens; 'far-western': interaction as identified in far-western
experiments;
'coipp': interaction as identified by co-immunoprecipitation experiments;
'high-throughput
2 hybrid': interaction as identified by high-throughput yeast 2-hybrid
screens;
'copurification°: interaction as identified by copurification
experiments; 'immuno-affinity-
columns': interaction as identified in experiments using immuno-afFinity
columns; °in vitro
binding': interaction as identified in in-vitro-binding experiments. If a core
complex has
been known previously containing several of the identified proteins, the name
of the
complex is stated.

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Sixth column (°Known components of the complex°) lists the
components of the complex
of the invention, which have been known to interact with other members of the
complex
as identified herein..
Seventh column ( 'Novel interactors of the complex') lists the novel members
of the
complex as provided in the invention.
Seventh column ( 'Activity of the complex'): List the biochemical activities
of the newly
identified complex.
Eighth column ( 'Proteins of unknown function°): Separately lists again
the members of
the newly identified complex whose function has previously been unknown..
Table 2: Individual Yeast Proteins of the Complexes
A) Table lists in alphabetical order all yeast proteins which have been
identified as
members of the complex presented herein (first column). Furthermore, the SEQ
ID of the
proteins are listed as used herein (second column). Also the systematic name
of the
individual proteins are listed (third column). The fourth column lists the
number of the
complex/complexes of the invention in which the protein has been identified.
Further
columns lists the Accession-Number of the respective sequences in Genbank,
MIPS,
SWISS-PROT, SGD . In addition, where applicable, the GenBank accession numbers
of
the respective orthologues in humans is listed listed.
B) Table lists again the proteins and SEQ ID as in part A. In addition, the
table contains
an overview about what has been previously reported on the protein, the
biochemical
function thereof and the cellular function thereof as stated in YPD
(Constanzo, M.C. et
al., 2001, Nucl. Acid Res, 29: 75-9; Hodges, P.E. et al., 1999, Nucl. Acids
Res 27: 69-
73).
Table 3: Medical Application of the complexes:
First column ('Number of complex°) lists the number of the complex as
used herein.
Second column ('Name of complex') lists a descriptive name of the complex as
used
herein.
Third column ('Cellular role') lists keyword'on the cellular role of the
complex
Forth column ('Medical applications') lists disorder, diseases, disease areas
etc. which
are treatable and/or preventable and/or diagnosable etc. by therapeutics and
methods
interacting with/acting via the complex.

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Table 4: Characterization of previously undescribed individual proteins of the
complexes:
The table provides data on proteins which have not been annotated previously
but which
have now been linked to a functional complex as described in table 1. Names
are listed
on the left. In addition the table contains a list of motifs found by sequence
analysis
which has been part of the invention provided herein. Futhermore, the
predicted known
human orthologues are listed on the right (By SWISS-PROT Accession numbers).
Used
Abbrevations are listed at the end of the table. The function of the
individual proteins as
deduced from the association with the complex, the sequence analysis and the
analysis
of the predicted ortholgues is listed in the second column ('Putative
function').
Table 5: Overview on Experimental Steps: The tables illustrates the
construction of a
yeast strain expressing a TAP-tagged bait in a high-throuphput fashion.
Table 6: Known and Novel Components of the yeast mRNA 3'-end processing
machinery: Top part of the table states the different known subcomponents of
the
polyadenylation complex, the function thereof, the proteins constituting the
different
subcomplexes as known so far (including their molecular weight and sequence
motifs
contained in the protein). Bottom part lists the novel components of the
complex as
provided herein
5.1. PROTEIN COMPLEXES/PROTEINS OF THE INVENTION
The protein complexes of the present invention and their component
proteins are described in different aspectsin the Tables 1,2,3,4,5 (whereas
Table 5 gives
an overview on the construction of the yeast strains). The protein complexes
and
component proteins can be obtained by methods well known in the art for
protein
purification and recombinant protein expression. For example, the protein
complexes of
the present invention can be isolated using the TAP method described in
Section 6, infra,
and in WO 00/09716 and Rigaut et al., 1999, Nature Biotechnology 17:1030-1032,
which
are each incorporated by reference in their entirety. Additionally, the
protein complexes
can be isolated by immunoprecipitation of the component proteins and combining
the
immunoprecipitated proteins. The protein complexes can also be produced by
recombinantly expressing the component proteins and combining the expressed
proteins.

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The nucleic and amino acid sequences of the component proteins of the
protein complexes of the present invention are provided herein (SEQ ID NOS:1-
3282),
and can be obtained by any method known in the art, e.g., by PCR amplification
using
synthetic primers hybridizable to the 3' and 5' ends of each sequence, and/or
by cloning
from a cDNA or genomic library using an oligonucleotide specific for each
nucleotide
sequence.
Homologs (e.g., nucleic acids encoding component proteins from other
species) or other related sequences (e.g., variants, paralogs) which are
members of a
native cellular protein complex can be obtained by low, moderate or high
stringency
hybridization with all or a portion of the particular nucleic acid sequence as
a probe,
using methods well known in the art for nucleic acid hybridization and
cloning.
Exemplary moderately stringent hybridization conditions are as follows:
prehybridization of filters containing DNA is carried out for 8 hours to
overnight at 65?C
in buffer composed of 6X SSC, 50 mM Tris-HCI (pH 7.5), 1 mM EDTA, 0.02% PVP,
0.02% Ficoll, 0.02% BSA, and 500 pg/ml denatured salmon sperm DNA. Filters are
hybridized for 48 hours at 65 °C in prehybridization mixture containing
100 pg/ml
denatured salmon sperm DNA and 5-20 X 106 cpm of 32P-labeled probe. Washing of
filters is done at 37 °C for 1 hour in a solution containing 2X SSC,
0.01 % PVP, 0.01
Ficoll, and 0.01 % BSA. This is followed by a wash in 0.1X SSC at 50 °C
for 45 min
before autoradiography. Alternatively, exemplary conditions of high stringency
are as
follows: e.g., hybridization to filter-bound DNA in 0.5 M NaHP04, 7% sodium
dodecyl
sulfate (SDS), 1 mM EDTA at 65 °C, and washing in 0.1xSSC/0.1 % SDS at
68 °C
(Ausubel F.M. et al., eds., 1989, Current Protocols in Molecular Biology, Vol.
I, Green
Publishing Associates, Inc., and John Wiley & sons, Inc., New York, at p.
2.10.3). Other
conditions of high stringency which may be used are well known in the art.
Exemplary
low stringency hybridization conditions comprise hybridization in a buffer
comprising 35%
formamide, 5X SSC, 50 mM Tris-HCI (pH 7.5), 5 mM EDTA, 0.02% PVP, 0.02%
Ficoll,
0.2% BSA, 100 pg/ml denatured salmon sperm DNA, and 10% (wt/vol) dextran
sulfate
for 18-20 hours at 40°C, washing in a buffer consisting of 2X SSC, 25
mM Tris-HCI (pH
7.4), 5 mM EDTA, and 0.1 % SDS for 1.5 hours at 55°C, and washing in a
buffer
consisting of 2X SSC, 25 mM Tris-HCI (pH 7.4), 5 mM EDTA, and 0.1% SDS for 1.5
hours at 60°C.
For recombinant expression of one or more of the proteins, the nucleic
acid containing all or a portion of the nucleotide sequence encoding the
protein can be

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inserted into an appropriate expression vector, i.e., a vector that contains
the necessary
elements for the transcription and translation of the inserted protein coding
sequence.
The necessary transcriptional and translational signals can also be supplied
by the native
promoter of the component protein gene, and/or flanking regions.
A variety of host-vector systems may be utilized to express the protein
coding sequence. These include but are not limited to mammalian cell systems
infected
with virus (e.g., vaccinia virus, adenovirus, etc.); insect cell systems
infected with virus
(e.g., baculovirus); microorganisms such as yeast containing yeast vectors; or
bacteria
transformed with bacteriophage, DNA, plasmid DNA, or cosmid DNA. The
expression
elements of vectors vary in their strengths and specificities. Depending on
the host-
vector system utilized, any one of a number of suitable transcription and
translation
elements may be used.
In a preferred embodiment, a complex of the present invention is obtained
by expressing the entire coding sequences of the component proteins in the
same cell,
either under the control of the same promoter or separate promoters. In yet
another
embodiment, a derivative, fragment or homolog of a component protein is
recombinantly
expressed. Preferably the derivative, fragment or homolog of the protein forms
a
complex with the other components of the complex, and more preferably forms a
complex that binds to an anti-complex antibody.
Any method available in the art can be used for the insertion of DNA
fragments into a vector to construct expression vectors containing a chimeric
gene
consisting of appropriate transcriptional/translational control signals and
protein coding
sequences. These methods may include in vitro recombinant DNA and synthetic
techniques and in vivo recombinant techniques (genetic recombination).
Expression of
nucleic acid sequences encoding a component protein, or a derivative, fragment
or
homolog thereof, may be regulated by a second nucleic acid sequence so that
the gene
or fragment thereof is expressed in a host transformed with the recombinant
DNA
molecule(s). For example, expression of the proteins may be controlled by any
promoter/enhancer known in the art. In a specific embodiment, the promoter is
not
native to the gene for the component protein. Promoters that may be used can
be
selected from among the many known in the art, and are chosen so as to be
operative in
the selected host cell.
In a specific embodiment, a vector is used that comprises a promoter
operably linked to nucleic acid sequences encoding a component protein, or a
fragment,

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derivative or homolog thereof, one or more origins of replication, and
optionally, one or
more selectable markers (e.g., an antibiotic resistance gene).
In another specific embodiment, an expression vector containing the
coding sequence, or a portion thereof, of a component protein, either
togefiher or
separately, is made by subcloning the gene sequences into the EcoRl
restriction site of
each of the three pGEX vectors (glutathione S-transferase expression vectors;
Smith and
Johnson, 1988, Gene 7:31-40). This allows for the expression of products in
the correct
reading frame.
Expression vectors containing the sequences of interest can be identified
by three general approaches: (a) nucleic acid hybridization, (b) presence or
absence of
"marker" gene function, and (c) expression of the inserted sequences. In the
first
approach, coding sequences can be detected by nucleic acid hybridization to
probes
comprising sequences homologous and complementary to the inserted sequences.
In
the second approach, the recombinant vector/host system can be identified and
selected
based upon the presence or absence of certain "marker" functions (e.g.,
resistance to
antibiotics, occlusion body formation in baculovirus, etc.) caused by
insertion of the
sequences of interest in the vector. For example, if a component protein gene,
or portion
thereof, is inserted within the marker gene sequence of the vector,
recombinants
containing the encoded protein or portion will be identified by the absence of
the marker
gene function (e.g., loss of beta-galactosidase activity). In the third
approach,
recombinant expression vectors can be identified by assaying for the component
protein
expressed by the recombinant vector. Such assays can be based, for example, on
the
physical or functional properties of the interacting species in in vitro assay
systems, e.g.,
formation of a complex comprising the protein or binding to an anti-complex
antibody.
Once recombinant component protein molecules are identified and the
complexes or individual proteins isolated, several methods known in the art
can be used
to propagate them. Using a suitable host system and growth conditions,
recombinant
expression vectors can be propagated and amplified in quantity. As previously
described, the expression vectors or derivatives which can be used include,
but are not
limited to, human or animal viruses such as vaccinia virus or adenovirus;
insect viruses
such as baculovirus, yeast vectors; bacteriophage vectors such as lambda
phage; and
plasmid and cosmid vectors.
In addition, a host cell strain may be chosen that modulates the expression
of the inserted sequences, or modifies or processes the expressed proteins in
the

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specific fashion desired. Expression from certain promoters can be elevated in
the
presence of certain inducers; thus expression of the genetically-engineered
component
proteins may be controlled. Furthermore, different host cells have
characteristic and
specific mechanisms for the translational and post translational processing
and
modification (e.g., glycosylation, phosphorylation, etc.) of proteins.
Appropriate cell lines
or host systems can be chosen to ensure that the desired modification and
processing of
the foreign protein is achieved. For example, expression in a bacterial system
can be
used to produce an unglycosylated core protein, while expression in mammalian
cells
ensures "native" glycosylation of a heterologous protein. Furthermore,
different
vector/host expression systems may effect processing reactions to different
extents.
In other specific embodiments, a component protein or a fragment,
homolog or derivative thereof, may be expressed as fusion or chimeric protein
product
comprising the protein, fragment, homolog, or derivative joined via a peptide
bond to a
heterologous protein sequence of a different protein. Such chimeric products
can be
made by ligating the appropriate nucleic acid sequences encoding the desired
amino
acids to each other by methods known in the art, in the proper coding frame,
and
expressing the chimeric products in a suitable host by methods commonly known
in the
art. Alternatively, such a chimeric product can be made by protein synthetic
techniques,
e.g., by use of a peptide synthesizer. Chimeric genes comprising a portion of
a
component protein fused to any heterologous protein-encoding sequences may be
constructed.
In particular, protein component derivatives can be made by altering their
sequences by substitutions, additions or deletions that provide for
functionally equivalent
molecules. Due to the degeneracy of nucleotide coding sequences, other DNA
sequences that encode substantially the same amino acid sequence as a
component
gene or cDNA can be used in the practice of the present invention. These
include but
are not limited to nucleotide sequences comprising all or portions of the
component
protein gene that are altered by the substitution of different codons that
encode a
functionally equivalent amino acid residue within the sequence, thus producing
a silent
change. Likewise, the derivatives of the invention include, but are not
limited to, those
containing, as a primary amino acid sequence, all or part of the amino acid
sequence of
a component protein, including altered sequences in which functionally
equivalent amino
acid residues are substituted for residues within the sequence resulting in a
silent
change. For example, one or more amino acid residues within the sequence can
be

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substituted by another amino acid of a similar polarity that acts as a
functional
equivalent, resulting in a silent alteration. Substitutes for an amino acid
within the
sequence may be selected from other members of the class to which the amino
acid
belongs. For example, the nonpolar (hydrophobic) amino acids include alanine,
leucine,
isoleucine, valine, proline, phenylalanine, tryptophan and methionine. The
polar neutral
amino acids include glycine, serine, threonine, cysteine, tyrosine,
asparagine, and
glutamine. The positively charged (basic) amino acids include arginine, lysine
and
histidine. The negatively charged (acidic) amino acids include aspartic acid
and glutamic
acid.
In a specific embodiment, up to 1 %, 2%, 5%, 10%, 15% or 20% of the total
number of amino acids in the wild type protein are substituted or deleted; or
1, 2, 3, 4, 5,
or 6 amino acids are inserted, substituted or deleted relative to the wild
type protein.
In a specific embodiment of the invention, the nucleic acids encoding a
protein component and protein components consisting of or comprising a
fragment of or
consisting of at least 6 (continuous) amino acids of the protein are provided.
In other
embodiments, the fragment consists of at least 10, 20, 30, 40, or 50 amino
acids of the
component protein. In specific embodiments, such fragments are not larger than
35, 100
or 200 amino acids. Derivatives or analogs of component proteins include, but
are not
limited, to molecules comprising regions that are substantially homologous to
the
component proteins, in various embodiments, by at least 30%, 40%, 50%, 60%,
70%,
80%, 90% or 95% identity over an amino acid sequence of identical size or when
compared to an aligned sequence in which the alignment is done by a computer
homology program known in the art, or whose encoding nucleic acid is capable
of
hybridizing to a sequence encoding the component protein under stringent,
moderately
stringent, or nonstringent conditions.
The protein component derivatives and analogs of the invention can be
produced by various methods known in the art. The manipulations which result
in their
production can occur at the gene or protein level. For example, the cloned
gene
sequences can be modified by any of numerous strategies known in the art
(Sambrook
et al., 1989, Molecular Cloning, A Laboratory Manual, 2d' Ed., Cold Spring
Harbor
Laboratory Press, Cold Spring Harbor, New York). The sequences can be cleaved
at
appropriate sites with restriction endonuclease(s), followed by further
enzymatic
modification if desired, isolated, and ligated in vitro. In the production of
the gene
encoding a derivative, homolog or analog of a component protein, care should
be taken

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to ensure that the modified gene retains the original translational reading
frame,
uninterrupted by translational stop signals, in the gene region where the
desired activity
is encoded.
Additionally, the encoding nucleic acid sequence can be mutated in vitro or
in vivo, to create and/or destroy translation, initiation, and/or termination
sequences, or to
create variations in coding regions and/or form new restriction endonuclease
sites or
destroy pre-existing ones, to facilitate further in vitro modification. Any
technique for
mutagenesis known in the art can be used, including but not limited to,
chemical
mutagenesis and in vitro site-directed mutagenesis (Hutchinson et al., 1978,
J. Biol.
Chem 253:6551-6558), amplification with PCR primers containing a mutation,
etc.
Once a recombinant cell expressing a component protein, or fragment or
derivative thereof, is identified, the individual gene product or complex can
be isolated
and analyzed. This is achieved by assays based on the physical and/or
functional
properties of the protein or complex, including, but not limited to,
radioactive labeling of
the product followed by analysis by gel electrophoresis, immunoassay, cross-
linking to
marker-labeled product, etc.
The component proteins and complexes may be isolated and purified by
standard methods known in the art (either from natural sources or recombinant
host cells
expressing the complexes or proteins), including but not restricted to column
chromatography (e.g., ion exchange, affinity, gel exclusion, reversed-phase
high
pressure, fast protein liquid, etc.), differential centrifugation,
differential solubility, or by
any other standard technique used for the purification of proteins. Functional
properties
may be evaluated using any suitable assay known in the art.
Alternatively, once a component protein or its derivative, is identified, the
amino acid sequence of the protein can be deduced from the nucleic acid
sequence of
the chimeric gene from which it was encoded. As a result, the protein or its
derivative
can be synthesized by standard chemical methods known in the art (e.g.,
Hunkapiller et
al., 1984, Nature 310: 105-111).
Manipulations of component protein sequences may be made at the
protein level. Included within the scope of the invention is a complex in
which the
component proteins or derivatives and analogs that are differentially modified
during or
after translation, e.g., by glycosylation, acetylation, phosphorylation,
amidation,
derivatization by known protecting/blocking groups, proteolytic cleavage,
linkage to an
antibody molecule or other cellular ligand, etc. Any of numerous chemical
modifications

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may be carried out by known techniques, including but not limited to specific
chemical
cleavage by cyanogen bromide, trypsin, chymotrypsin, papain, V8 protease, NaBI-
I~,
acetylation, formylation, oxidation, reduction, metabolic synthesis in the
presence of
tunicamycin, etc.
In specific embodiments, the amino acid sequences are modified to
include a fluorescent label. In another specific embodiment, the protein
sequences are
modified to have a heterofunctional reagent; such heterofunctional reagents
can be used
to crosslink the members of the complex.
In addition, complexes of analogs and derivatives of component proteins
can be chemically synthesized. For example, a peptide corresponding to a
portion of a
component protein, which comprises the desired domain or mediates the desired
activity
in vitro (e.g., complex formation) can be synthesized by use of a peptide
synthesizer.
Furthermore, if desired, non-classical amino acids or chemical amino acid
analogs can
be introduced as a substitution or addition into the protein sequence.
In cases where natural products are suspected of being mutant or are
isolated from new species, the amino acid sequence of a component protein
isolated
from the natural source, as well as those expressed in vitro, or from
synthesized
expression vectors in vivoor in vitro, can be determined from analysis of the
DNA
sequence, or alternatively, by direct sequencing of the isolated protein. Such
analysis
can be performed by manual sequencing or through use of an automated amino
acid
sequenator.
The complexes can also be analyzed by hydrophilicity analysis (Hopp and
Woods, 1981, Proc. Natl. Acad. Sci. USA 78:3824-3828). A hydrophilicity
profile can be
used to identify the hydrophobic and hydrophilic regions of the proteins, and
help predict
their orientation in designing substrates for experimental manipulation, such
as in binding
experiments, antibody synthesis, etc. Secondary structural analysis can also
be done to
identify regions of the component proteins, or their derivatives, that assume
specific
structures (Chou and Fasman, 1974, Biochemistry 13:222-23). Manipulation,
translation,
secondary structure prediction, hydrophilicity and hydrophobicity profile
predictions, open
reading frame prediction and plotting, and determination of sequence
homologies, etc.;
can be accomplished using computer software programs available in the art.
Other methods of structural analysis including but not limited to X ray
crystallography (Engstrom, 1974 Biochem. Exp. Biol. 11:7-13), mass
spectroscopy and
gas chromatography (Methods in Protein Science, J. Wiley and Sons, New York,
1997),

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and computer modeling (Fletterick and Zoller, eds., 1986, Computer Graphics
and
Molecular Modeling, In: Current Communications in Molecular Biology, Cold
Spring
Harbor Laboratory, Cold Spring Harbor Press, New York) can also be employed.
5.2. ANTIBODIES TO PROTEIN COMPLEXES
According to the present invention, a protein complex of the present
invention comprising a first protein, or a functionally active fragment or
functionally active
derivative thereof, selected from the group consisting of proteins listed in
table 1, third
column of a given complex, or a functionally active fragment or functionally
active
derivative thereof, or a homologue thereof or a variant encoded by a nucleic
acid of any
of said proteins, can be used as an immunogen to generate antibodies which
immunospecifically bind such immunogen.
Such antibodies include, but are not limited to, polyclonal, monoclonal,
chimeric, single chain, Fab fragments, and an Fab expression library. In a
specific
embodiment, antibodies to a complex comprising human protein components are
produced. In another embodiment, a complex formed from a fragment of said
first
protein and a fragment of said second protein, which fragments contain the
protein
domain that interacts with the other member of the complex, are used as an
immunogen
for antibody production. In a preferred embodiment, the antibody specific for
the
complex in that the antibody does not bind the individual protein components
of the
complex.
Polyclonal antibodies can be prepared as described above by immunizing
a suitable subject with a polypeptide of the invention as an immunogen.
Preferred
polyclonal antibody compositions are ones that have been selected for
antibodies
directed against a polypeptide or polypeptides of the invention. Particularly
preferred
polyclonal antibody preparations are ones that contain only antibodies
directed against a
polypeptide or polypeptides of the invention. Particularly preferred immunogen
compositions are those that contain no other human proteins such as, for
example,
immunogen compositions made using a non-human host cell for recombinant
expression
of a polypeptide of the invention. In such a manner, the only human epitope or
epitopes
recognized by the resulting antibody compositions raised against this
immunogen will be
present as part of a polypeptide or polypeptides of the invention.
The antibody titer in the immunized subject can be monitored over time by
standard techniques, such as with an enzyme linked immunosorbent assay (ELISA)

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44
using immobilized polypeptide. If desired, the antibody molecules can be
isolated from
the mammal (e,g., from the blood) and further purified by well-known
techniques, such as
protein A chromatography to obtain the IgG fraction. Alternatively, antibodies
specific for
a protein or polypeptide of the invention can be selected for (e.g., partially
purified) or
purified by, e.g., affinity chromatography. For example, a recombinantly
expressed and
purified (or partially purified) protein of the invention is produced as
described herein,
and covalently or non-covalently coupled to a solid support such as, for
example, a
chromatography column. The column can then be used to affinity purify
antibodies
specific for the proteins of the invention from a sample containing antibodies
directed
against a large number of different epitopes, thereby generating a
substantially purified
antibody composition, i.e., one that is substantially free of contaminating
antibodies. By
a substantially purified antibody composition is meant, in this context, that
the antibody
sample contains at most only 30% (by dry weight) of contaminating antibodies
directed
against epitopes other than those on the desired protein or polypeptide of the
invention,
and preferably at most 20%, yet more preferably at most 10%, and most
preferably at
most 5% (by dry weight) of the sample is contaminating antibodies. A purified
antibody
composition means that at least 99% of the antibodies in the composition are
directed
against the desired protein or polypeptide of the invention.
At an appropriate time after immunization, e.g., when the specific antibody
titers are highest, antibody-producing cells can be obtained from the subject
and used to
prepare monoclonal antibodies by standard techniques, such as the hybridoma
technique originally described by Kohler and Milstein, 1975, Nature 256:495-
497, the
human B cell hybridoma technique (Kozbor et al., 1983, Immunol. Today 4:72),
the
EBV hybridoma technique (Cole et al., 1985, Monoclonal Antibodies and Cancer
Therapy, Alan R. Liss, Inc., pp. 77-96) or trioma techniques. The technology
for
producing hybridomas is well known (see generally Current Protocols in
Immunology
(1994) Coligan et al. (eds.) John Wiley & Sons, Inc., New York, NY). Hybridoma
cells
producing a monoclonal antibody of the invention are detected by screening the
hybridoma culture supernatants for antibodies that bind the polypeptide of
interest, e.g.,
using a standard ELISA assay.
Alternative to preparing monoclonal antibody-secreting hybridomas, a
monoclonal antibody directed against a polypeptide of the invention can be
identified and
isolated by screening a recombinant combinatorial immunoglobulin library
(e.g., an
antibody phage display library) with the polypeptide of interest. Kits for
generating and

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screening phage display libraries are commercially available (e.g,, the
Pharmacia
Recombinant Phage Antibody System, Catalog No. 27-9400-01; and the Stratagene
SurfZAP Phage Display Kit, Catalog No. 240612). Additionally, examples of
methods
and reagents particularly amenable for use in generating and screening
antibody display
library can be found in, for example, U.S. Patent No. 5,223,409; PCT
Publication No. WO
92/18619; PCT Publication No. WO 91/17271; PCT Publication No. WO 92/20791;
PCT
Publication No. WO 92/15679; PCT Publication No. WO 93/01288; PCT Publication
No.
WO 92/01047; PCT Publication No. WO 92/09690; PCT Publication No. WO 90/02809;
Fuchs et al., 1991, Bio/Technology 9:1370-1372; Hay et al., 1992, Hum.
Antibod.
Hybridomas 3:81-85; Huse et al., 1989, Science 246:1275-1281; Griffiths et
al., 1993,
EMBO J. 12:725-734.
Additionally, recombinant antibodies, such as chimeric and humanized
monoclonal antibodies, comprising both human and non-human portions, which can
be
made using standard recombinant DNA techniques, are within the scope of the
invention.
A chimeric antibody is a molecule in which different portions are derived from
different
animal species, such as those having a variable region derived from a murine
mAb and a
human immunoglobulin constant region. (See, e.g., Cabilly et al., U.S. Patent
No.
4,816,567; and Boss et al., U.S. Patent No. 4,816,397, which are incorporated
herein by
reference in their entirety.) Humanized antibodies are antibody molecules from
non-
human species having one or more complementarily determining regions (CDRs)
from
the non-human species and a framework region from a human immunoglobulin
molecule. (See, e.g., Queen, U.S. Patent No. 5,585,089, which is incorporated
herein by
reference in its entirety.) Such chimeric and humanized monoclonal antibodies
can be
produced by recombinant DNA techniques known in the art, for example using
methods
described in PCT Publication No. WO 87/02671; European Patent Application
184,187;
European Patent Application 171,496; European Patent Application 173,494; PCT
Publication No. WO 86/01533; U.S. Patent No. 4,816,567; European Patent
Application
125,023; Better et al., 1988, Science 240:1041-1043; Liu et al., 1987, Proc.
Natl. Acad.
Sci. USA 84:3439-3443; Liu et al., 1987, J. Immunol. 139:3521-3526; Sun et
al., 1987,
Proc. Natl. Acad. Sci. USA 84:214-218; Nishimura et al., 1987, Canc. Res.
47:999-1005;
Wood et al., 1985, Nature 314:446-449; and Shaw et al., 1988, J. Natl. Cancer
Inst.
80:1553-1559); Morrison, 1985, Science 229:1202-1207; Oi et al., 1986,
Bio/Techniques
4:214; U.S. Patent 5,225,539; Jones et al., 1986, Nature 321:552-525;
Verhoeyan et al.,
1988, Science 239:1534; and Beidler et al., 1988, J. Immunol. 141:4053-4060.

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46
Completely human antibodies are particularly desirable for therapeutic
treatment of human patients. Such antibodies can be produced, for example,
using
transgenic mice which are incapable of expressing endogenous immunoglobulin
heavy
and light chains genes, but which can express human heavy and light chain
genes. The
transgenic mice are immunized in the normal fashion with a selected antigen,
e.g., all or
a portion of a polypeptide of the invention. Monoclonal antibodies directed
against the
antigen can be obtained using conventional hybridoma technology. The human
immunoglobulin transgenes harbored by the transgenic mice rearrange during B
cell
differentiation, and subsequently undergo class switching and somatic
mutation. Thus,
using such a technique, it is possible to produce therapeutically useful IgG,
IgA and IgE
antibodies. For an overview of this technology for producing human antibodies,
see
Lonberg and Huszar, 1995, Int. Rev. Immunol. 13:65-93). For a detailed
discussion of
this technology for producing human antibodies and human monoclonal antibodies
and
protocols for producing such antibodies, see, e.g., U.S. Patent 5,625,126;
U.S. Patent
5,633,425; U.S. Patent 5,569,825; U.S. Patent 5,661,016; and U.S. Patent
5,545,806. In
addition, companies such as Abgenix, Inc. (Freemont, CA), can be engaged to
provide
human antibodies directed against a selected antigen using technology similar
to that
described above.
Completely human antibodies which recognize a selected epitope can be
generated using a technique referred to as "guided selection." In this
approach a
selected non-human monoclonal antibody, e.g., a murine antibody, is used to
guide the
selection of a completely human antibody recognizing the same epitope.
(Jespers et al.,
1994, Biotechnology 12:899-903).
Antibody fragments that contain the idiotypes of the complex can be
generated by techniques known in the art. For example, such fragments include,
but are
not limited to, the F(ab')2 fragment which can be produced by pepsin digestion
of the
antibody molecule; the Fab' fragment that can be generated by reducing the
disulfide
bridges of the F(ab')2 fragment; the Fab fragment that can be generated by
treating the
antibody molecular with papain and a reducing agent; and Fv fragments.
In the production of antibodies, screening for the desired antibody can be
accomplished by techniques known in the art, e.g., ELISA (enzyme-linked
immunosorbent assay). To select antibodies specific to a particular domain of
the
complex, or a derivative thereof, one may assay generated hybridomas for a
product that
binds to the fragment of the complex, or a derivative thereof, that contains
such a

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47
domain. For selection of an antibody that specifically binds a complex of the
present, or
a derivative; or homolog thereof, but which does not specifically bind to the
individual
proteins of the complex, or a derivative, or homolog thereof, one can select
on the basis
of positive binding to the complex and a lack of binding to the individual
protein
components.
Antibodies specific to a domain of the complex, or a derivative, or homolog
thereof, are also provided.
The foregoing antibodies can be used in methods known in the art relating
to the localization and/or quantification of the complexes of the invention,
e.g., for
imaging these proteins, measuring levels thereof in appropriate physiological
samples
(by immunoassay), in diagnostic methods, etc. This hold true also for a
derivative, or
homolog thereof of a complex.
In another embodiment of the invention (see infra), an antibody to a
complex or a fragment of such antibodies containing the antibody binding
domain, is a
Therapeutic.
5.3. DIAGNOSTIC, PROGNOSTIC. AND SCREENING USES OF PROTEIN
COMPLEXES
The particular protein complexes of the present invention may be markers
of normal physiological processes, and thus have diagnostic utility. Further,
definition of
particular groups of patients with elevations or deficiencies of a protein
complex of the
present invention, or wherein the protein complex has a change in protein
component
composition, can lead to new nosological classifications of diseases,
furthering
diagnostic ability.
(see: diseases or disorders in which the complexes provided herein are
involved in
and/or associated with are listed in table 3)
Detecting levels of protein complexes, or individual component proteins
that form the complexes, or detecting levels of the mRNAs encoding the
components of
the complex, may be used in diagnosis, prognosis, and/or staging to follow the
course of
a disease state, to follow a therapeutic response, etc.
A protein complex of the present invention and the individual components
of the complex and a derivative, analog or subsequence thereof, encoding
nucleic acids
(and sequences complementary thereto), and anti-complex antibodies and
antibodies
directed against individual components that can form the complex, are useful
in

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diagnostics. The foregoing molecules can be used in assays, such as
immunoassays, to
detect, prognose, diagnose, or monitor various conditions, diseases, and
disorders
characterized by aberrant levels of a complex or aberrant component
composition of a
complex, or monitor the treatment of such various conditions, diseases, and
disorders.
In particular, such an immunoassay is carried out by a method comprising
contacting a sample derived from a patient with an anti-complex antibody under
conditions such that immunospecific binding can occur, and detecting or
measuring the
amount of any immunospecific binding by the antibody. In a specific aspect,
such
binding of antibody, in tissue sections, can be used to detect aberrant
complex
localization, or aberrant (e.g., high, low or absent) levels of a protein
complex or
complexes. In a specific embodiment, an antibody to the complex can be used to
assay
a patient tissue or serum sample for the presence of the complex, where an
aberrant
level of the complex is an indication of a diseased condition. By "aberrant
levels" is
meant increased or decreased levels relative to that present, or a standard
level
representing that present, in an analogous sample from a portion or fluid of
the body, or
from a subject not having the disorder.
The immunoassays which can be used include but are not limited to
competitive and non-competitive assay systems using techniques such as Western
blots,
radioimmunoassays, ELISA (enzyme linked immunosorbent assay), "sandwich"
immunoassays, immunoprecipitation assays, precipitin reactions, gel diffusion
precipitin
reactions, immunodiffusion assays, agglutination assays, complement-fixation
assays,
immunoradiometric assays, fluorescent immunoassays, protein A immunoassays, to
name but a few known in the art.
Nucleic acids encoding the components of the protein complex and related
nucleic acid sequences and subsequences, including complementary sequences,
can be
used in hybridization assays. The nucleic acid sequences, or subsequences
thereof,
comprising about at least 8 nucleotides, can be used as hybridization probes.
Hybridization assays can be used to detect, prognose, diagnose, or monitor
conditions,
disorders, or disease states associated with aberrant levels of the mRNAs
encoding the
components of a complex as described, supra. In particular, such a
hybridization assay
is carried out by a method comprising contacting a sample containing nucleic
acid with a
nucleic acid probe capable of hybridizing to component protein coding DNA or
RNA,
under conditions such that hybridization can occur, and detecting or measuring
any
resulting hybridization.

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In specific embodiments, diseases and disorders involving or
characterized by aberrant levels of a protein complex or aberrant complex
composition
can be diagnosed, or its suspected presence can be screened for, or a
predisposition to
develop such disorders can be detected, by determining the component protein
composition of the complex, or detecting aberrant levels of a member of the
complex or
un-complexed component proteins or encoding nucleic acids, or functional
activity
including, but not restricted to, binding to an interacting partner, or by
detecting mutations
in component protein RNA, DNA or protein (e.g., mutations such as
translocations,
truncations, changes in nucleotide or amino acid sequence relative to wild-
type that
cause increased or decreased expression or activity of a complex, and/or
component
protein. Such diseases and disorders include, but are not limited to, those
described in
Section 5.4 and its subsections.
By way of example, levels of a protein complex and the individual
components of a complex can be detected by immunoassay, levels of component
protein
RNA or DNA can be detected by hybridization assays (e.g., Northern blots, dot
blots,
RNase protection assays), and binding of component proteins to each other
(e.g.,
complex formation) can be measured by binding assays commonly known in the
art.
Translocations and point mutations in component protein genes can be detected
by
Southern blotting, RFLP analysis, PCR using primers that preferably generate a
fragment spanning at least most of the gene by sequencing of genomic DNA or
cDNA
obtained from the patient, etc.
Assays well known in the art (e.g., assays described above such as
immunoassays, nucleic acid hybridization assays, activity assays, etc.) can be
used to
determine whether one or more particular protein complexes are present at
either
increased or decreased levels, or are absent, in samples from patients
suffering from a
particular disease or disorder, or having a predisposition to develop such a
disease or
disorder, as compared to the levels in samples from subjects not having such a
disease
or disorder, or having a predisposition to develop such a disease or disorder.
Additionally, these assays can be used to determine whether the ratio of the
complex to
the un-complexed components of the complex, is increased or decreased in
samples
from patients suffering from a particular disease or disorder, or having a
predisposition to
develop such a disease or disorder, as compared to the ratio in samples from
subjects
not having such a disease or disorder. In the event that levels of one or more
particular
protein complexes (i.e., complexes formed from component protein derivatives,

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homologs, fragments, or analogs) are determined to be increased in patients
suffering
from a particular disease or disorder, or having a predisposition to develop
such a
disease or disorder, then the particular disease or disorder, or
predisposition for a
disease or disorder, can be diagnosed, have prognosis defined for, be screened
for, or
be monitored by detecting increased levels of the one or more protein
complexes,
increased levels of the mRNA that encodes one or more members of the one or
more
particular protein complexes, or by detecting increased complex functional
activity.
Accordingly, in a specific embodiment of the present invention, diseases
and disorders involving increased levels of one or more protein complexes can
be
diagnosed, or their suspected presence can be screened for, or a
predisposition to
develop such disorders can be detected, by detecting increased levels of the
one or
more protein complexes, the mRNA encoding both members of the complex, or
complex
functional activity, or by detecting mutations in the component proteins that
stabilize or
enhance complex formation, e.g., mutations such as translocations in nucleic
acids,
truncations in the gene or protein, changes in nucleotide or amino acid
sequence relative
to wild-type, that stabilize or enhance complex formation.
In the event that levels of one or more particular protein complexes are
determined to be decreas ed in patients suffering from a particular disease or
disorder, or
having a predisposition to develop such a disease or disorder, then the
particular disease
or disorder or predisposition for a disease or disorder can be diagnosed, have
its
prognosis determined, be screened for, or be monitored by detecting decreased
levels of
the one or more protein complexes, the mRNA that encodes one or more members
of
the particular one or more protein complexes, or by detecting decreased
protein complex
functional activity.
Accordingly, in a specific embodiment of the invention, diseases and
disorders involving decreased levels of one or more protein complexes can be
diagnosed, or their suspected presence can be screened for, or a
predisposition to
develop such disorders can be detected, by detecting decreased levels of the
one or
more protein complexes, the mRNA encoding one or more members of the one or
more
complexes, or complex functional activity, or by detecting mutations in the
component
proteins that decrease complex formation, e.g., mutations such as
translocations in
nucleic acids, truncations in the gene or protein, changes in nucleotide or
amino acid
sequence relative to wild-type, that decrease complex formation.

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51
Accordingly, in a specific embodiment of the invention, diseases and
disorders involving aberrant compositions of the complexes can be diagnosed,
or their
suspected presence can be screened for, or a predisposition to develop such
disorders
can be detected, by detecting the component proteins of one or more complexes,
or the
mRNA encoding the members of the one or more complexes.
The use of detection techniques, especially those involving antibodies
against a protein complex, provides a method of detecting specific cells that
express the
complex or component proteins. Using such assays, specific cell types can be
defined in
which one or more particular protein complexes are expressed, and the presence
of the
complex or component proteins can be correlated with cell viability, state,
health, etc.
Also embodied are methods to detect a protein complex of the present
invention in cell culture models that express particular protein complexes or
derivatives
thereof, for the purpose of characterizing or preparing the complexes for
harvest. This
embodiment includes cell sorting of prokaryotes such as but not restricted to
bacteria
(Davey and Kell, 1996, Microbiol. Rev. 60:641-696), primary cultures and
tissue
specimens from eukaryotes, including mammalian species such as human (Steele
et al.,
1996, Clin. Obstet. Gynecol 39:801-813), and continuous cell cultures (Orfao
and Ruiz-
Arguelles, 1996, Clin. Biochem. 29:5-9). Such isolations can be used as
methods of
diagnosis, described, supra.
5.4. THERAPEUTIC USES OF PROTEIN COMPLEXES
The present invention is directed to a method for treatment or prevention
of various diseases and disorders by administration of a therapeutic compound
(termed
herein "Therapeutic"). Such "Therapeutics" include, but are not limited to, a
protein
complex of the present invention, the individual component proteins, and
analogs and
derivatives (including fragments) of the foregoing (e.g., as described
hereinabove);
antibodies thereto (as described hereinabove); nucleic acids encoding the
component
protein, and analogs or derivatives, thereof (e.g., as described hereinabove);
component
protein antisense nucleic acids, and agents that modulate complex formation
and/or
activity (i.e., agonists and antagonists).
The protein complexes, as identified herein, are implicated significantly in
normal physiological processes. For example, see the processes listed in table
3.
Furthermore, the protein complexes as identified herein are implicated in
processes which are implicated in or associated with pathological conditions.

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Diseases and disorders which can be treated andlor prevented and/or
diagnosed by Therapeutics interacting with any of the complexes provided
herein are
listed in table 3.
These disorders are treated or prevented by administration of a
Therapeutic that modulates (i.e. inhibits or promotes) protein complex
activity or
formation. Diseases or disorders associated with aberrant levels of complex
activity or
formation, or aberrant levels or activity of the component proteins, or
aberrant complex
composition, may be treated by administration of a Therapeutic that modulates
complex
formation or activity or by the administration of a protein complex.
Therapeutic may also be administered to modulate complex formation or
activity or level thereof in a microbial organism such as yeast, fungi such as
candida
albicans causing an infectious disease in animals or humans.
Diseases and disorders characterized by increased (relative to a subject
not suffering from the disease or disorder) complex levels or activity can be
treated with
Therapeutics that antagonize (i.e., reduce or inhibit) complex formation or
activity.
Therapeutics that can be used include, but are not limited to, the component
proteins or
an analog, derivative or fragment of the component protein; anti-complex
antibodies
(e.g., antibodies specific for the protein complex, or a fragment or
derivative of the
antibody containing the binding region thereof; nucleic acids encoding the
component
proteins; antisense nucleic acids complementary to nucleic acids encoding the
component proteins; and nucleic acids encoding the component protein that are
dysfunctional due to, e.g., a heterologous insertion within the protein coding
sequence,
that are used to "knockout" endogenous protein function by homologous
recombination,
see, e.g., Capecchi, 1989, Science 244:1288-1292. In one embodiment, a
Therapeutic
is 1, 2 or more antisense nucleic acids which are complementary to 1, 2, or
more nucleic
acids, respectfully, that encode component proteins of a complex.
In a specific embodiment of the present invention, a nucleic acid
containing a portion of a component protein gene in which gene sequences flank
(are
both 5' and 3' to) a different gene sequence, is used as a component protein
antagonist,
or to promote component protein inactivation by homologous recombination (see
also,
Koller and Smithies, 1989, Proc. Natl. Acad. Sci. USA 86:8932-8935; Zijlstra
et al., 1989,
Nature 342: 435-438). Additionally, mutants or derivatives of a component
protein that
has greater affinity for another component protein or the complex than wild
type may be
administered to compete with wild type protein for binding, thereby reducing
the levels of

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53
complexes containing the wild type protein. Other Therapeutics that inhibit
complex
function can be identified by use of known convenient in vitro assays, e.g.,
based on their
ability to inhibit complex formation, or as described in Section 5.5, infra.
In specific embodiments, Therapeutics that antagonize complex formation
or activity are administered therapeutically, including prophylactical.ly, (1)
in diseases or
disorders involving an increased (relative to normal or desired) level of a
complex, for
example, in patients where complexes are overactive or overexpressed; or (2)
iri
diseases or disorders where an in vitro (or in vivo) assay (see infra)
indicates the utility of
antagonist administration. Increased levels of a complex can be readily
detected, e.g.,
by quantifying protein and/or RNA, by obtaining a patient tissue sample (e.g.,
from
biopsy tissue) and assaying it in vitro for RNA or protein levels, or
structure and/or
activity of the expressed complex (or the encoding mRNA). Many methods
standard in
the art can be thus employed including, but not limited to, immunoassays to
detect
complexes and/or visualize complexes (e.g., Western blot analysis,
immunoprecipitation
followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis [SDS-
PAGE],
immunocytochemistry, etc.), and/or hybridization assays to detect concurrent
expression
of component protein mRNA (e.g., Northern assays, dot blot analysis, in situ
hybridization, etc.).
A more specific embodiment of the present invention is directed to a
method of reducing complex expression (i.e., expression of the protein
components of
the complex and/or formation of the complex) by targeting mRNAs that express
the
protein moieties. RNA therapeutics currently fall within three classes,
antisense species,
ribozymes, or RNA aptamers (Good et al., 1997, Gene Therapy 4:45-54).
Antisense oligonucleotides have been the most widely used. By way of
example, but not limitation, antisense oligonucleotide methodology to reduce
complex
formation is presented below, infra. Ribozyme therapy involves the
administration,
induced expression, etc. of small RNA molecules with enzymatic ability to
cleave, bind,
or otherwise inactivate specific RNAs, to reduce or eliminate expression of
particular
proteins (Grassi and Marini, 1996, Annals of Medicine 28:499-510; Gibson,
1996, Cancer
and Metastasis Reviews 15:287-299). RNA aptamers are specific RNA ligand
proteins,
such as for Tat and Rev RNA (Good et al., 1997, Gene Therapy 4:45-54) that can
specifically inhibit their translation. Aptamers specific for component
proteins can be
identified by many methods well known in the art, for example, by affecting
the formation
of a complex in the protein-protein interaction assay described, infra.

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In another embodiment, the activity or levels of a component protein are
reduced by administration of another component protein, or the encoding
nucleic acid, or
an antibody that immunospecifically binds to the component protein, or a
fragment or a
derivative of the antibody containing the binding domain thereof.
In another aspect of the invention, diseases or disorders associated with
increased levels of an component protein of the complex may be treated or
prevented by
administration of a Therapeutic that increases complex formation if the
complex
formation acts to reduce or inactivate the component protein through complex
formation.
Such diseases or disorders can be treated or prevented by administration of
one
component member of the complex, administration of antibodies or other
molecules that
stabilize the complex, etc.
Diseases and disorders associated with underexpression of a com plea, or
a component protein, are treated or prevented by administration of a
Therapeutic that
promotes (i.e., increases or supplies) complex levels and/or function, or
individual
component protein function. Examples of such a Therapeutic include but are not
limited
to a complex or a derivative, analog or fragment of the complex that are
functionally
active (e.g., able to form a complex), un-complexed component proteins and
derivatives,
analogs, and fragments of un-complexed component proteins, and nucleic acids
encoding the members of a complex or functionally active derivatives or
fragments of the
members of the complex, e.g., for use in gene therapy. In a specific
embodiment, a
Therapeutic includes derivatives, homologs or fragments of a component protein
that
increase and/or stabilize complex formation. Examples of other agonists can be
identified using in vitro assays or animal models, examples of which are
described, infra.
In yet other specific embodiments of the present invention, Therapeutics
that promote complex function are administered therapeutically, including
prophylactically, (1) in diseases or disorders involving an absence or
decreased (relative
to normal or desired) level of a complex, for example, in patients where a
complex, or the
individual components necessary to form the complex, is lacking, genetically
defective,
biologically inactive or underactive, or under-expressed; or (2)~ in diseases
or disorders
wherein an in vitro or in vivo assay (see, infra) indicates the utility of
complex agonist
administration. The absence or decreased level of a complex, component protein
or
function can be readily detected, e.g., by obtaining a patient tissue sample
(e.g., from
biopsy tissue) and assaying it in vitro for RNA or protein levels, structure
and/or activity
of the expressed complex and/or the concurrent expression of mRNA encoding the
two

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components of the complex. Many methods standard in the art can be thus
employed,
including but not limited to immunoassays to detect and/or visualize a
complex, or the
individual components of a complex (e.g., Western blot analysis,
immunoprecipitation
followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis [SDS-
PAGE],
immunocytochemistry, etc.) and/or hybridization assays to detect expression of
mRNAs
encoding the individual protein components of a complex by detecting and/or
visualizing
component mRNA concurrently or separately using, e.g., Northern assays, dot
blot
analysis, in situ hybridization, etc.
In specific embodiments, the activity or levels of a component protein are
increased by administration of another component protein of the same complex,
or a
derivative, homolog or analog thereof, a nucleic acid encoding the other
component, or
an agent that stabilizes or enhances the other component, or a fragment or
derivative of
such an agent.
Generally, administration of products of species origin or species reactivity
(in the case of antibodies) that is the same species as that of the patient is
preferred.
Thus, in a preferred embodiment, a human complex, or derivative, homolog or
analog
thereof; nucleic acids encoding the members of the human complex or a
derivative,
homolog or analog thereof; an antibody to a human complex, or a derivative
thereof; or
other human agents that affect component proteins or the complex, are
therapeutically or
prophylactically administered to a human patient.
Preferably, suitable in vitro or in vivo assays are utilized to determine the
effect of a specific Therapeutic and whether its administration is indicated
for treatment
of the affected tissue or individual.
In various specific embodiments, in vitro assays can be carried out with
representative cells of cell types involved in a patient's disorder, to
determine if a
Therapeutic has a desired effect upon such cell types.
Compounds for use in therapy can be tested in suitable animal model
systems prior to testing in humans, including, but not limited to, rats, mice,
chicken,
cows, monkeys, rabbits, etc. For in vivo testing, prior to administration to
humans, any
animal model system known in the art may be used. Additional descriptions and
sources
of Therapeutics that can be used according to the invention are found in
Sections 5.1 to
5.3 and 5.7 herein.
5.4.1. GENE THERAPY

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In a specific embodiment of the present invention, nucleic acids comprising
a sequence encoding the component proteins, or a functional derivative
thereof, are
administered to modulate complex activity or formation by way of gene therapy.
Gene
therapy refers to therapy performed by the administration of a nucleic acid to
a subject.
In this embodiment of the present invention, the nucleic acid expresses its
encoded
proteins) that mediates a therapeutic effect by modulating complex activity or
formation.
Any of the methods for gene therapy available in the art can be used according
to the
present invention. Exemplary methods are described below.
For general reviews of the methods of gene therapy, see Goldspiel et al.,
1993, Clinical Pharmacy 12:488-505; Wu and Wu, 1991, Biotherapy 3:87-95;
Tolstoshev,
1993, Ann. Rev. Pharmacol. Toxicol. 32:573-596; Mulligan, 1993, Science
260:926-932;
Morgan and Anderson, 1993, Ann. Rev. Biochem. 62:191-217; and May, 1993,
TIBTECH
11:155-215. Methods commonly known in the art of recombinant DNA technology
which
can be used are described in Ausubel et al., eds., 1993, Current Protocols in
Molecular
Biology, John Wiley & Sons, NY; and Kriegler, 1990, Gene Transfer and
Expression, A
Laboratory Manual, Stockton Press, NY.
In a preferred aspect, the Therapeutic comprises a nucleic acid that is part
of an expression vector that expresses one or more of the component proteins,
or
fragments or chimeric proteins thereof, in a suitable host. In particular,
such a nucleic
acid has a promoter operably linked to the protein coding regions) (or, less
preferably
separate promoters linked to the separate coding regions separately), said
promoter
being inducible or constitutive, and optionally, tissue-specific. In another
particular
embodiment, a nucleic acid molecule is used in which the coding sequences, and
any
other desired sequences, are flanked by regions that promote homologous
recombination at a desired site in the genome, thus providing for intra-
chromosomal
expression of the component protein nucleic acids (Koller and Smithies, 1989,
Proc. Natl.
Acad. Sci. USA 86:8932-8935; Zijlstra et al., 1989, Nature 342:435-438).
Delivery of the nucleic acid into a patient may be either direct, in which
case the patient is directly exposed to the nucleic acid or nucleic acid-
carrying vector, or
indirect, in which case, cells are first transformed with the nucleic acid in
vitro, then
transplanted into the patient. These two approaches are known, respectively,
as in vivo
or ex vivo gene therapy.
In a specific embodiment, the nucleic acid is directly administered in vivo,
where it is expressed to produce the encoded product. This can be accomplished
by any

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of numerous methods known in the art, e.g., by constructing it as part of an
appropriate
nucleic acid expression vector and administering it so that it becomes
intracellular, e.g.,
by infection using a defective or attenuated retroviral or other viral vector
(U.S. Patent
No. 4,980,286), or by direct injection of naked DNA, or by use of
microparticle
bombardment (e.g., a gene gun; Biolistic, Dupont), or coating with lipids or
cell-surface
receptors, or through use of transfecting agents, by encapsulation in
liposomes,
microparticles, or microcapsules, or by administering it in linkage to a
peptide that is
known to enter the nucleus, or by administering it in linkage to a ligand
subject to
receptor-mediated endocytosis that can be used to target cell types
specifically
expressing the receptors (e.g., Wu and Wu, 1987, J. Biol. Chem. 262:4429-
4432), etc.
In another embodiment, a nucleic acid-ligand complex can be formed in which
the ligand
comprises a fusogenic viral peptide that disrupts endosomes, allowing the
nucleic acid to
avoid lysosomal degradation. In yet another embodiment, the nucleic acid can
be
targeted in vivo for cell specific uptake and expression, by targeting a
specific receptor
(see, e.g., International Patent Publications WO 92/06180; WO 92/22635; WO
92/20316;
WO 93/14188; and WO 93/20221. Alternatively, the nucleic acid can be
introduced
intracellularly and incorporated within host cell DNA for expression, by
homologous
recombination (Koller and Smithies, 1989, Proc. Natl. Acad. Sci. USA 86:8932-
8935;
Zijlstra et al., 1989, Nature 342:435-438).
In a specific embodiment, a viral vector that contains the component
protein encoding nucleic acids is used. For example, a retroviral vector can
be used
(Miller et al., 1993, Meth. Enzymol. 217:581-599). These retroviral vectors
have been
modified to delete retroviral sequences that are not necessary for packaging
of the viral
genome and integration into host cell DNA. The encoding nucleic acids to be
used in
gene therapy is/are cloned into the vector, which facilitates delivery of the
gene into a
patient. More detail about retroviral vectors can be found in Boesen et al.,
1994,
Biotherapy 6:291-302, which describes the use of a retroviral vector to
deliver the mdr1
gene to hematopoetic stem cells in order to make the stem cells more resistant
to
chemotherapy. Other references illustrating the use of retroviral vectors in
gene therapy
are Clowes et al., 1994, J. Clin. Invest. 93:644-651; Kiem et al., 1994, Blood
83:1467-
1473; Salmons and Gunzberg, 1993, Human Gene Therapy 4:129-141; and Grossman
and Wilson, 1993, Curr. Opin. in Genetics and Devel. 3:110-114.
Adenoviruses are other viral vectors that can be used in gene therapy.
Adenoviruses are especially attractive vehicles for delivering genes to
respiratory

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epithelia. Adenoviruses naturally infect respiratory epithelia where they
cause a mild
disease. Other targets for adenovirus-based delivery systems are the liver,
the central
nervous system, endothelial cells and muscle. Adenoviruses have the advantage
of
being capable of infecting non-dividing cells. Kozarsky and Wilson, 1993,
Current
Opinion in Genetics and Development 3:499-503, discuss adenovirus-based gene
therapy. The use of adenovirus vectors to transfer genes to the respiratory
epithelia of
rhesus monkeys has been demonstrated by Bout et al., 1994, Human Gene Therapy
5:3-
10. Other instances of the use of adenoviruses in gene therapy can be found in
Rosenfeld et al., 1991, Science 252:431-434; Rosenfeld et al., 1992, Cell
68:143-155;
and Mastrangeli et al., 1993, J. Clin. Invest. 91:225-234.
Adeno-associated virus (AAV) has also been proposed for use in gene
therapy (Walsh et al., 1993, Proc. Soc. Exp. Biol. Med. 204:289-300.
Another approach to gene therapy involves transferring a gene into cells in
tissue culture by methods such as electroporation, lipofection, calcium
phosphate-
mediated transfection, or viral infection. Usually, the method of transfer
includes the
transfer of a selectable marker to the cells. The cells are then placed under
selection to
isolate those cells that have taken up and are expressing the transferred gene
from
these that have not. Those cells are then delivered to a patient.
In this embodiment, the nucleic acid is introduced into a cell prior to
administration in vivo of the resulting recombinant cell. Such introduction
can be carried
out by any method known in the art including, but not limited to, transfection
by
electroporation, microinjection, infection with a viral or bacteriophage
vector containing
the nucleic acid sequences, cell fusion, chromosome-mediated gene transfer,
microcell-
mediated gene transfer, spheroplast fusion, etc. Numerous techniques are known
in the
art for the introduction of foreign genes into cells (see, e.g., Loeffler and
Behr, 1993,
Meth. Enzymol. 217:599-618; Cohen et al., 1993, Meth. Enzymol. 217:618-644;
Cline,
1985, Pharmac. Ther. 29:69-92) and may be used in accordance with the present
invention, provided that the necessary developmental and physiological
functions of the
recipient cells are not disrupted. The technique should provide for the stable
transfer of
the nucleic acid to the cell, so that the nucleic acid is expressible by the
cell and
preferably, is heritable and expressible by its cell progeny.
The resulting recombinant cells can be delivered to a patient by various
methods known in the art. In a preferred embodiment, epithelial cells are
injected, e.g.,
subcutaneously. In another embodiment, recombinant skin cells may be applied
as a

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skin graft onto the patient. Recombinant blood cells (e.g., hematopoetic stem
or
progenitor cells) are preferably adm inistered intravenously. The amount of
cells
envisioned for use depends on the desired effect, patient state, etc., and can
be
determined by one skilled in the art.
Cells into which a nucleic acid can be introduced for purposes of gene
therapy encompass any desired, available cell type, and include but are not
limited to
epithelial cells, endothelial cells, keratinocytes, fibroblasts, muscle cells,
hepatocytes,
blood cells such as T lymphocytes, B lymphocytes, monocytes, macrophages,
neutrophils, eosinophils, megakaryocytes, and granulocytes, various stem or
progenitor
cells, in particular hematopoetic stem or progenitor cells, e.g., as obtained
from bone
marrow, umbilical cord blood, peripheral blood, fetal liver, etc.
In a preferred embodiment, the cell used for gene therapy is autologous to
the patient.
In an embodiment in which recombinant cells are used in gene therapy, a
component protein encoding nucleic acid is/are introduced into the cells such
that the
gene or genes are expressible by the cel Is or their progeny, and the
recombinant cells
are then administered in vivo for therapeutic effect. In a specific
embodiment, stem or
progenitor cells are used. Any stem and/or progenitor cells which can be
isolated and
maintained in vitro can potentially be used in accordance with this embodiment
of the
present invention. Such stem cells include but are not limited to hematopoetic
stem cells
(HSCs), stem cells of epithelial tissues such as the skin and the lining of
the gut,
embryonic heart muscle cells, liver stem cells (International Patent
Publication WO
94/08598), and neural stem cells (Stemple and Anderson, 1992, Cell 71:973-
985).
Epithelial stem cells (ESCs), or keratinocytes, can be obtained from
tissues such as the skin and the lining of the gut by known procedures
(Rheinwald, 1980,
Meth. Cell Biol. 2A:229). In stratified epithelial tissue such as the skin,
renewal occurs by
mitosis of stem cells within the germinal layer, the layer closest to the
basal lamina.
Similarly, stem cells within the lining of the gut provide for a rapid renewal
rate of this
tissue. ESCs or keratinocytes obtained from the skin or lining of the gut of a
patient or
donor can be grown in tissue culture (Rheinwald, 1980, Meth. Cell Bio. 2A:229;
Pittelkow
and Scott, 1986, Mayo Clinic Proc. 61:771). If the ESCs are provided by a
donor, a
method for suppression of host versus graft reactivity (e.g., irradiation, or
drug or
antibody administration to promote moderate immunosuppression) can also be
used.

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With respect to hematopoetic stem cells (HSCs), any technique that
provides for the isolation, propagation, and maintenance in vitro of HSCs can
be used in
this embodiment of the invention. Techniques by which this may be accomplished
include (a) the isolation and establishment of HSC cultures from bone marrow
cells
isolated from the future host, or a donor, or (b) the use of previously
established long-
term HSC cultures, which may be allogeneic or xenogeneic. Non-autologous HSCs
are
used preferably in conjunction with a m ethod of suppressing transplantation
immune
reactions between the future host and patient. In a particular embodiment of
the present
invention, human bone marrow cells can be obtained from the posterior iliac
crest by
needle aspiration (see, e.g., Kodo et al., 1984, J. Clin. Invest. 73: 1377-
1384). In a
preferred embodiment of the present invention, the HSCs can be made highly
enriched
or in substantially pure form. This enrichment can be accomplished before,
during, or
after long-term culturing, and can be done by any technique known in the art.
Long-term
cultures of bone marrow cells can be established and maintained by using, for
example,
modified Dexter cell culture techniques (Dexter et al., 1977, J. Cell Physiol.
91:335) or
Witlock-Witte culture techniques (Witlock and Witte, 1982, Proc. Natl. Acad.
Sci. USA
79:3608-3612).
In a specific embodiment, the nucleic acid to be introduced for purposes of
gene therapy comprises an inducible promoter operably linked to the coding
region, such
that expression of the nucleic acid is controllable by controlling the
presence or absence
of the appropriate inducer of transcription.
Additional methods can be adapted for use to deliver a nucleic acid
encoding the component proteins, or functional derivatives thereof, e.g., as
described in
Section 5.1, supra.
5.4.2. USE OF ANTISENSE OLIGONUCLEOTIDES FOR SUPPRESSION OF
PROTEIN COMPLEX ACTIVITY OR FORMATION
In a specific embodiment of the present invention, protein complex activity
and formation is inhibited by use of antisense nucleic acids for the component
proteins of
the complex, that inhibit transcription and/or translation of their
complementary
sequence. The present invention provides the therapeutic or prophylactic use
of nucleic
acids of at least six nucleotides that are antisense to a gene or cDNA
encoding a
component protein, or a portion thereof. An "antisense" nucleic acid as used
herein
refers to a nucleic acid capable of hybridizing to a sequence-specific portion
of a

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component protein RNA (preferably mRNA) by virtue of some sequence
complementarity. The antisense nucleic acid may be complementary to a coding
and/or
noncoding region of a component protein mRNA. Such antisense nucleic acids
that
inhibit complex formation or activity have utility as Therapeutics, and can be
used in the
treatment or prevention of disorders as described supra.
The antisense nucleic acids of the invention can be oligonucleotides that
are double-stranded or single-stranded, RNA or DNA, or a modification or
derivative
thereof, which can be directly administered to a cell, or which can be
produced
intracellularly by transcription of exogenous, introduced sequences.
In another embodiment, the present invention is directed to a method for
inhibiting the expression of component protein nucleic acid sequences, in a
prokaryotic
or eukaryotic cell, comprising providing the cell with an effective amount of
a composition
comprising an antisense nucleic acid of the component protein, or a derivative
thereof, of
the invention.
The antisense nucleic acids are of at least six nucleotides and are
preferably oligonucleotides, ranging from 6 to about 200 nucleotides. In
specific aspects,
the oligonucleotide is at least 10 nucleotides, at least 15 nucleotides, at
least 100
nucleotides, or at least 200 nucleotides. The oligonucleotides can be DNA or
RNA or
chimeric mixtures, or derivatives or modified versions thereof, and either
single-stranded
or double-stranded. The oligonucleotide can be modified at the base moiety,
sugar
moiety, or phosphate backbone. The oligonucleotide may include other appending
groups such as peptides, agents facilitating transport across the cell
membrane (see,
e.g., Letsinger et al., 1989, Proc. Natl. Acad. Sci. U.S.A. 86:6553-6556;
Lemaitre et al.,
1987, Proc. Natl. Acad. Sci. 84:648-652; International Patent Publication No.
WO 88/09810) or blood-brain barrier (see, e.g., International Patent
Publication No.
WO 89/10134), hybridization-triggered cleavage agents (see, e.g., Krol et al.,
1988,
BioTechniques 6:958-976), or intercalating agents (see, e.g., Zon, 1988,
Pharm. Res.
5:539-549).
In a preferred aspect of the invention, an antisense oligonucleotide is
provided, preferably as single-stranded DNA. The oligonucleotide may be
modified at
any position in its structure with constituents generally known in the art.
The antisense oligonucleotides may comprise at least one modified base
moiety which is selected from the group including but not limited to 5-
fluorouracil,
5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4-
acetylcytosine,

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5-(carboxyhydroxylmethyl)uracil, 5-carboxymethylaminomethyl-2-thin-uridine,
5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine,
inosine,
N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine,
2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-
adenine,
7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil,
beta-D-mannosylqueosine, 5N-methoxycarboxymethyluracil, 5-methoxyuracil, 2-
methyl-
thio-N6-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine,
pseudouracil,
queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-
methyluracil,
uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid (v), 5-methyl-2-
thiouracil,
3-(3-amino-3-N-2-carboxypropyl) uracil, (acp3)w, and 2,6-diaminopurine.
In another embodiment, the oligonucleotide comprises at least one
modified sugar moiety selected from the group including, but not limited to,
arabinose,
2-fluoroarabinose, xylulose, and hexose.
In yet another embodiment, the oligonucleotide comprises at least one
modified phosphate backbone selected from the group consisting of a
phosphorothioate,
a phosphorodithioate, a phosphoramidothioate, a phosphoramidate, a
phosphordiamidate, a methylphosphonate, an alkyl phosphotriester, and a
formacetal, or
an analog of the foregoing.
In yet another embodiment, the oligonucleotide is a 2-a-anomeric
oligonucleotide. An a-anomeric oligonucleotide forms specific double-stranded
hybrids
with complementary RNA in which, contrary to the usual (3-units, the strands
run parallel
to each other (Gautier et al., 1987, Nucl. Acids Res. 15:6625-6641).
The oligonucleotide may be conjugated to another molecule, e.g., a
peptide, hybridization-triggered cross-linking agent, transport agent,
hybridization-
triggered cleavage agent, etc.
Oligonucleotides of the invention may be synthesized by standard
methods known in the art, e.g., by use of an automated DNA synthesizer (such
as are
commercially avail-able from Biosearch, Applied Biosystems, etc.). As
examples,
phosphorothioate oligo-nucleotides may be synthesized by the method of Stein
et al.
(1988, Nucl. Acids Res. 16:3209), methylphosphonate oligohucleotides can be
prepared
by use of controlled pore glass polymer supports (Sarin et al., 1988, Proc.
Natl. Acad.
Sci. U.S.A. 85:7448-7451), etc.
In a specific embodiment, the antisense oligonucleotides comprise
catalytic RNAs, or ribozymes (see, e.g., International Patent Publication No.

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WO 90/11364; Sarver et al., 1990, Science 247:1222-1225). In another
embodiment, the
oligonucleotide is a 2'-0-methylribonucleotide (Inoue et al., 1987, Nucl.
Acids Res.
15:6131-6148), or a chimeric RNA-DNA analog (Inoue et al., 1987, FEBS Lett.
215:327-
330).
In an alternative embodiment, the antisense nucleic acids of the invention
are produced intracellularly by transcription from an exogenous sequence. For
example,
a vector can be introduced in vivo such that it is taken up by a cell, within
which cell the
vector or a portion thereof is transcribed, producing an antisense nucleic
acid (RNA) of
the invention. Such a vector would contain a sequence encoding the component
protein.
Such a vector can remain episomal or become chromosomally integrated, as long
as it
can be transcribed to produce the desired antisense RNA. Such vectors can be
constructed by recombinant DNA technology methods standard in the art. Vectors
can
be plasmid, viral, or others known in the art to be capable of replication and
expression in
mammalian cells. Expression of the sequences encoding the antisense RNAs can
be by
any promoter known in the art to act in mammalian, preferably human, cells.
Such
promoters can be inducible or constitutive. Such promoters include, but are
not limited
to, the SV40 early promoter region (Bernoist and Chambon, 1981, Nature 290:304-
310),
the promoter contained in the 3' long terminal repeat of Rous sarcoma virus
(Yamamoto
et al., 1980, Cell 22:787-797), the herpes thymidine kinase promoter (Wagner
et al.,
1981, Proc. Natl. Acad. Sci. U.S.A. 78:1441-1445), the regulatory sequences of
the
metallothionein gene (Brinster et al., 1982, Nature 296:39-42), etc.
The antisense nucleic acids of the invention comprise a sequence
complementary to at least a portion of an RNA transcript of a component
protein gene,
preferably a human gene. However, absolute complementarity, although
preferred, is
not required. A sequence "complementary to at least a portion of an RNA," as
referred
to herein, means a sequence having sufficient complementarity to be able to
hybridize
with the RNA, forming a stable duplex; in the case of double-stranded
antisense nucleic
acids, a single strand of the duplex DNA may thus be tested, or triplex
formation may be
assayed. The ability to hybridize will depend on both the degree of
complementarity and
the length of the antisense nucleic acid. Generally, the longer the
hybridizing nucleic
acid, the more base mismatches with a component protein RNA it may contain and
still
form a stable duplex (or triplex, as the case may be). One skilled in the art
can ascertain
a tolerable degree of mismatch by use of standard procedures to determine the
melting
point of the hybridized complex.

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The component protein antisense nucleic acids can be used to treat (or
prevent) disorders of a cell type that expresses, or preferably overexpresses,
a protein
complex.
Cell types that express or overexpress component protein RNA can be
identified by various methods known in the art. Such methods include, but are
not
limited to, hybridization with component protein-specific nucleic acids (e.g.,
by Northern
blot hybridization, dot blot hybridization, or in situ hybridization), or by
observing the
ability of RNA from the cell type to be translated in vifro into the component
protein by
immunohistochemistry, Western blot analysis, ELISA, etc. In a preferred
aspect, primary
tissue from a patient can be assayed for protein expression prior to
treatment, e.g., by
immunocytochemistry, in situ hybridization, or any number of methods to detect
protein
or mRNA expression.
Pharmaceutical compositions of the invention (see Section 5.7, infra),
comprising an effective amount of a protein component antisense nucleic acid
in a
pharmaceutically acceptable carrier can be administered to a patient having a
disease or
disorder that is of a type that expresses or overexpresses a protein complex
of the
present invention.
The amount of antisense nucleic acid that will be effective in the treatment
of a particular disorder or condition will depend on the nature of the
disorder or condition,
and can be determined by standard clinical techniques. Where possible, it is
desirable to
determine the antisense cytotoxicity in vitro, and then in useful animal model
systems,
prior to testing and use in humans.
In a specific embodiment, pharmaceutical compositions comprising
antisense nucleic acids are administered via liposomes, microparticles, or
microcapsules. In various embodiments of the invention, it may be useful to
use such
compositions to achieve sustained release of the antisense nucleic acids. In a
specific
embodiment, it may be desirable to utilize liposomes targeted via antibodies
to specific
identifiable central nervous system cell types (Leonetti et al., 1990, Proc.
Natl. Acad. Sci.
U.S.A. 87:2448-2451; Renneisen et al., 1990, J. Eiol. Chem. 265:16337-16342).
5.5. ASSAYS OF PROTEIN COMPLEXES AND DERIVATIVES AND ANALOGS
THEREOF
The functional activity of a protein complex of the present invention, or a
derivative, fragment or analog thereof, can be assayed by various methods.
Potential

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modulators (e.g., agonists and antagonists) of complex activity or formation,
e.g., anti-
complex antibodies and antisense nucleic acids, can be assayed for the ability
to
modulate complex activity or formation.
In one embodiment of the present invention, where one is assaying for the
ability to bind or compete with a wild-type complex for binding to an anti-
complex
antibody, various immunoassays known in the art can be used, including but not
limited
to competitive and non-competitive assay systems using techniques such as
radioimmunoassay, ELISA (enzyme linked immunosorbent assay), "sandwich"
immunoassays, immunoradiometric assays, gel diffusion precipitin reactions,
immunodiffusion assays, in situ immunoassays (using colloidal gold, enzyme or
radioisotope labels), western blot analysis, precipitation reactions,
agglutination assays
(e.g., gel agglutination assays, hemagglutination assays), complement fixation
assays,
immunofluorescence assays, protein A assays, immunoelectrophoresis assays,
etc. In
one embodiment, antibody binding is detected by detecting a label on the
primary
antibody. In another embodiment, the primary antibody is detected by detecting
binding
of a secondary antibody or reagent to the primary antibody. In a further
embodiment, the
secondary antibody is labeled. Many means are known in the art for detecting
binding in
an immunoassay and are within the scope of the present invention.
The expression of the component protein genes (both endogenous and
those expressed from cloned DNA containing the genes) can be detected using
techniques known in the art, including but not limited to Southern
hybridization
(Southern, 1975, J. Mol. Biol. 98:503-517), northern hybridization (see, e.g.,
Freeman et
al., 1983, Proc. Natl. Acid. Sci. USA 80:4094-4098), restriction endonuclease
mapping
(Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, 2"d Ed. Cold
Spring
Harbor Laboratory Press, New York), RNase protection assays (Current Protocols
in
Molecular Biology, John Wiley and Sons, New York, 1997), DNA sequence
analysis, and
polymerise chain reaction amplification (PCR; U.S. Patent Nos. 4,683,202,
4,683,195,
and 4,889,818; Gyllenstein et al., 1988, Proc. Natl. Acid. Sci. USA 85:7652-
7657;
Ochman et al., 1988, Genetics 120:621-623; Loh et al., 1989, Science 243:217-
220)
followed by Southern hybridization with probes specific for the component
protein genes,
in various cell types. Methods of amplification other than PCR commonly known
in the
art can be employed. In one embodiment, Southern hybridization can be used to
detect
genetic linkage of component protein gene mutations to physiological or
pathological
states. Various cell types, at various stages of development, can be
characterized for

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their expression of component proteins at the same time and in the same cells.
The
stringency of the hybridization conditions for northern or Southern blot
analysis can be
manipulated to ensure detection of nucleic acids with the desired degree of
relatedness
to the specific probes used. Modifications to these methods and other methods
commonly known in the art can be used.
Derivatives (e.g., fragments), homologs and analogs of one component
protein can be assayed for binding to another component protein in the same
complex by
any method known in the art, for example the modified yeast matrix mating test
described in Section 5.6.1 infra, immunoprecipitation with an antibody that
binds to the
component protein complexed with other component proteins in the same complex,
followed by size fractionation of the immunoprecipitated proteins (e.g., by
denaturing or
nondenaturing polyacrylamide gel electrophoresis), Western blot analysis, etc.
One embodiment of the invention provides a method for screening a
derivative, homolog or analog of a component protein for biological activity
comprising
contacting said derivative, homolog or analog of the component protein with
the other
component proteins in the same complex; and detecting the formation of a
complex
between said derivative, homolog or analog of the component protein and the
other
component proteins; wherein detecting formation of said complex indicates that
said
derivative, homolog or analog of has biological (e.g., binding) activity.
The invention also provides methods of modulating the activity of a
component protein that can participate in a protein complex by administration
of a
binding partner of that protein or derivative, homolog or analog thereof.
In a specific embodiment of the present invention, a protein complex of the
present invention is administered to treat or prevent a disease or disorder,
since the
complex and/or component proteins have been implicated in the disease and
disorder.
Accordingly, a protein complex or a derivative, homolog, analog or fragment
thereof,
nucleic acids encoding the component proteins, anti-complex antibodies, and
other
modulators of protein complex activity, can be tested for activity in treating
or preventing
a disease or disorder in in vitro and in vivo assays.
In one embodiment, a Therapeutic of the invention can be assayed for
activity in treating or preventing a disease by contacting cultured cells that
exhibit an
indicator of the disease in vitro, with the Therapeutic, and comparing the
level of said
indicator in the cells contacted with the Therapeutic, with said level of said
indicator in

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cells not so contacted, wherein a lower level in said contacted cells
indicates that the
Therapeutic has activity in treating or preventing the disease.
In another embodiment of the invention, a Therapeutic of the invention can
be assayed for activity in treating or preventing a disease by administering
the
Therapeutic to a test animal that is predisposed to develop symptoms of a
diseas e, and
measuring the change in said symptoms of the disease after administration of
said
Therapeutic, wherein a reduction in the severity of the symptoms of the
disease or
prevention of the symptoms of the disease indicates that the Therapeutic has
activity in
treating or preventing the disease. Such a test animal can be any one of a
number of
animal models known in the art for disease. These animal models are well known
in the
art. These animal models include, but are not limited to those which are
listed in the
section 5.6 (supra) as exemplary animald models to study any of the complexes
provided
in the invention.
5.6 SCREENING FOR MODULATORS OF THE PROTEIN COMPLEXES
A complex of the present invention, the component proteins of the complex
and nucleic acids encoding the component proteins, as well as derivatives and
fragments
of the amino and nucleic acids, can be used to screen for compounds that bind
to, or
modulate the amount of, activity of, or protein component composition of, said
complex,
and thus, have potential use as modulators, i.e., agonists or antagonists, of
complex
activity, and/or complex formation, i.e., the amount of complex formed, and/or
protein
component composition of the complex.
Thus, the present invention is also directed to methods for screening for
molecules that bind to, or modulate the function of, amount of, activity of,
formation of or
protein component composition of, a complex of the present invention. In one
embodiment of the invention, the method for screening for a molecule that
modulates
directly or indirectly the function, activity or formation of a complex of the
present
invention comprises exposing said complex, or a cell or organism containing
the complex
machinery, to one or more candidate molecules under conditions conducive to
modulation; and determining the amount of, the biochemical activity of,
protein
components of, and/or intracellular localization of, said complex and/or the
transcription
level of a gene dependend on the complex and/or the abundance and/or activity
of a

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protein or protein complex dependend on the function of the complex and/or
product of a
gene dependent on the complex in the presence of the one or more candidate
molecules, wherein a change in said amount, activity, protein components or
intracellular
localization relative to said amount, activity, protein components and/or
intracellular ,
localization and/or a change in the transcription level of a gene dependend on
the
complex and/or the abundance and/or activity of a protein or protein complex
dependent
on the function of the complex and/or product of a gene dependent on the
complex in the
absence of said candidate molecules indicates that the molecule modulates
function,
activity or composition of said complex.
In a further specific embodiment, a modulation of the formation process of a
complex can be determined.
Such a modulation can either be a change in the typical time course of its
formation or a change in the typical steps leading to the formation of the
complete
complex.
Such changes can for example be detected by analysing and comparing the
process of
complex formation in untreated wild type cells of a particular type and/or
cells showing or
having the predisposition to develop a certain disease phenotype and/or cells
which have
been treated with particular conditions and/or particular agents in a
particular situation.
Methods to study such changes in time course are well known in the art and
include for
example Western-blot analysis of the proteins in the complex isolated at
different steps
of its formation.
Furthermore an aberrant intracellular localization of the protein complex
and/or an
abberant transcription level of a gene dependent on the complex and/or the
abundance
and/or activity of a protein or protein complex dependent on the function of
the complex
and/or a gene dependent on the complex can serve as a marker for a disease and
thus
have diagnostic utility for any disease which is caused by an aberrant
activity, function,
composition or formation of the complex of the invention.
Methods to study the intracellular localization are well known in the art and
include, but
are not limited to immunofluorescence analysis using antibodies specific for
components
of the protein. Preferentially, double-stainirigs including staining of other
cellular
structures are being used to facilitate the detection of the intracellular
localization.
Methods to analyse the transcription levels of a gene dependent on the complex
are also
well known in the art and include Northern blot analysis, quantitative PCR
etc. The
abundance of proteins dependent on the protein can be analyzed as described
supra.

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Methods to study changes in the activity of proteins dependent on complex
depend on
the protein. The choice of such methods will be apparent to any person skilled
in the art.
In another embodiment, the present invention is directed to a method for
screening for a
molecule that binds a protein complex of the present invention comprising
exposing said
complex, or a cell or organism containing the complex mac hinery, to one or
more
candidate molecules; and determining whether said complex is bound by any of
said
candidate molecules. Such screening assays can be carried out using cell-free
and cell-
based methods that are commonly known in the art in vitro, in vivo or ex vivo.
For
example, an isolated complex can be employed, or a cell can be contacted with
the
candidate molecule and the complex can be isolated from such contacted cells
and the
isolated complex can be assayed for activity or component composition. In
another
example, a cell containing the complex can be contacted with the candidate
molecule
and the levels of the complex in the contacted cell can be measured.
Additionally, such
assays can be carried out in cells recombinantly expressing a component
protein from
table 1, third column of a given complex, or a functionally active fragment or
functionally
active derivative thereof, or a homologue thereof or a variant encoded by a
nucleic acid
of any of said proteins.
For example, assays can be carried out using recombinant cells
expressing the protein components of a complex, to screen for molecules that
bind to, or
interfere with, or promote complex activity or formation. In preferred
embodiments,
polypeptide derivatives that have superior stabilities but retain the ability
to form a
complex (e.g., one or more component proteins modified to be resistant to
proteolytic
degradation in the binding assay buffers, or to be resistant to oxidative
degradation), are
used to screen for modulators of complex activity or formation. Such resistant
molecules
can be generated, e.g., by substitution of amino acids at proteolytic cleavage
sites, the
use of chemically derivatized amino acids at proteolytic susceptible sites,
and the
replacement of amino acid residues subject to oxidation, i.e. methionine and
cysteine.
A particular aspect of the present invention relates to identifying molecules
that inhibit or promote formation or degradation of a complex of the present
invention,
e.g., using the method described for isolating the complex and identifying
members of
the complex using the TAP assay described in Section 6, infra, and in WO
00/09716 and
Rigaut et al., 1999, Nature Biotechnology 17:1030-1032, which are each
incorporated by
reference in their entirety.

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In another embodiment of the invention, a modulator is identified by
administering a candidate molecule to a transgenic non-human animal expressing
the
complex component proteins from promoters that are not the native promoters of
the
respective proteins, more preferably where the candidate molecule is also
recombinantly
expressed in the transgenic non-human animal. Alternatively, the method for
identifying
such a modulator can be carried out in vitro, preferably with a purified
complex, and a
purified candidate molecule.
Agents/molecules (candidate molecules) to be screened can be provided
as mixtures of a limited number of specified compounds, or as compound
libraries,
peptide libraries and the like. Agents/molecules to be screened may also
include all
forms of antisera, antisense nucleic acids, etc., that can modulate complex
activity or
formation. Exemplary candidate molecules and libraries for screening are set
forth in
Section 5.6.1, infra.
Screening the libraries can be accomplished by any of a variety of
commonly known methods. See, e.g., the following references, which disclose
screening
of peptide libraries: Parmley and Smith, 1989, Adv. Exp. Med. Biol. 251:215-
218; Scott
and Smith, 1990, Science 249:386-390; Fowlkes et al., 1992, BioTechniques
13:422-
427; Oldenburg et al., 1992, Proc. Natl. Acad. Sci. USA 89:5393-5397; Yu et
al., 1994,
Cell 76:933-945; Staudt et al., 1988, Science 241:577-580; Bock et al., 1992,
Nature
355:564-566; Tuerk et al., 1992, Proc. Natl. Acad. Sci. USA 89:6988-6992;
Ellington et
al., 1992, Nature 355:850-852; U.S. Patent No. 5,096,815, U.S. Patent No.
5,223,409,
and U.S. Patent No. 5,198,346, all to Ladner et al.; Rebar and Pabo, 1993,
Science
263:671-673; and International Patent Publication No. WO 94/18318.
In a specific embodiment, screening can be carried out by contacting the
library members with a complex immobilized on a solid phase, and harvesting
those
library members that bind to the protein (or encoding nucleic acid or
derivative).
Examples of such screening methods, termed "panning" techniques, are described
by
way of example in Parmley and Smith, 1988, Gene 73:305-318; Fowlkes et al.,
1992,
BioTechniques 13:422-427; International Patent Publication No. WO 94/18318;
and in
references cited hereinabove.
In a specific embodiment, fragments and/or analogs of protein components
of a complex, especially peptidomimetics, are screened for activity as
competitive or non-
competitive inhibitors of complex formation (amount of complex or composition
of

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complex) or activity in the cell, which thereby inhibit complex activity or
formation in the
cell.
In one embodiment, agents that modulate (i.e., antagonize or agonize)
complex activity or formation can be screened for using a binding inhibition
assay,
wherein agents are screened for their ability to modulate formation of a
complex under
aqueous, or physiological, binding conditions in which complex formation
occurs in the
absence of the agent to be tested. Agents that interfere with the formation of
complexes
of the invention are identified as antagonists of complex formation. Agents
that promote
the formation of complexes are identified as agonists of complex formation.
Agents that
completely block the formation of complexes are identified as inhibitors of
complex
formation.
Methods for screening may involve labeling the component proteins of the
complex with radioligands (e.g., ~25I or 3H), magnetic ligands (e.g.,
paramagnetic beads
covalently attached to photobiotin acetate), fluorescent ligands (e.g.,
fluorescein or
rhodamine), or enzyme ligands (e.g., luciferase or beta-galactosidase). The
reactants
that bind in solution can then be isolated by one of many techniques known in
the art,
including but not restricted to, co-immunoprecipitation of the labeled complex
moiety
using antisera against the unlabeled binding partner (or labeled binding
partner with a
distinguishable marker from that used on the second labeled complex moiety),
immunoaffinity chromatography, size exclusion chromatography, and gradient
density
centrifugation. In a preferred embodiment, the labeled binding partner is a
small
fragment or peptidomimetic that is not retained by a commercially available
filter. Upon
binding, the labeled species is then unable to pass through the filter,
providing for a
simple assay of complex formation.
Methods commonly known in the art are used to label at least one of the
component members of the complex. Suitable labeling methods include, but are
not
limited to, radiolabeling by incorporation of radiolabeled amino acids, e.g.,
3H-leucine or
ssS-methionine, radiolabeling by post translational iodination with X251 or
~3~ I using the
chloramine T method, Solton-Hunter reagents, etc., or labeling with 32P using
phosphorylase and inorganic radiolabeled phosphorous, biotin labeling with
photobiotin-
acetate and sunlamp exposure, etc. In cases where one of the members of the
complex
is immobilized, e.g., as described infra, the free species is labeled. Where
neither of the
interacting species is immobilized, each can be labeled with a distinguishable
marker
such that isolation of both moieties can be followed to provide for more
accurate

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quantification, and to distinguish the formation of homomeric from heteromeric
complexes. Methods that utilize accessory proteins that bind to one of the
modified
interactants to improve the sensitivity of detection, increase the stability
of the complex,
etc., are provided.
Typical binding conditions are, for example, but not by way of limitation, in
an aqueous salt solution of 10-250 mM NaCI, 5-50 mM Tris-HCI, pH 5-8, and 0.5%
Triton
X 100 or other detergent that improves specificity of interaction. Metal
chelators and/or
divalent cations may be added to improve binding and/or reduce proteolysis.
Reaction
temperatures may include 4, 10, 15, 22, 25, 35, or 42 degrees Celsius, and
time of
incubation is typically at least 15 seconds, but longer times are preferred to
allow binding
equilibrium to occur. Particular complexes can be assayed using routine
protein binding
assays to determine optimal binding conditions for reproducible binding.
The physical parameters of complex formation can be analyzed by
quantification of complex formation using assay methods specific for the label
used, e.g.,
liquid scintillation counting for radioactivity detection, enzyme activity for
enzyme-labeled
moieties, etc. The reaction results are then analyzed utilizing Scatchard
analysis, Hill
analysis, and other methods commonly known in the arts (see, e.g., Proteins,
Structures,
and Molecular Principles, 2nd Edition (1993) Creighton, Ed., W.H. Freeman and
Company, New York).
In a second common approach to binding assays, one of the binding
species is immobilized on a filter, in a microtiter plate well, in a test
tube, to a
chromatography matrix, etc., either covalently or non-covalently. Proteins can
be
covalently immobilized using any method well known in the art, for example,
but not
limited to the method of ICadonaga and Tjian, 1986, Proc. Natl. Acad. Sci. USA
83:5889-
5893, i.e., linkage to a cyanogen-bromide derivatized substrate such as CNBr-
Sepharose 4B (Pharmacia). Where needed, the use of spacers can reduce steric
hindrance by the substrate. Non-covalent attachment of proteins to a substrate
include,
but are not limited to, attachment of a protein to a charged surface, binding
with specific
antibodies, binding to a third unrelated interacting protein, etc.
Assays of agents (including cell extracts or a library pool) for competition
for binding of one member of a complex (or derivatives thereof) with another
member of
the complex labeled by any means (e.g., those means described above) are
provided to
screen for competitors or enhancers of complex formation.

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In specific embodiments, blocking agents to inhibit non-specific binding of
reagents to other protein components, or absorptive losses of reagents to
plastics,
immobilization matrices, etc., are included in the assay mixture. Blocking
agents include,
but are not restricted to bovine serum albumin, beta-casein, nonfat dried
milk, Denhardt's
reagent, Ficoll, polyvinylpyrolidine, nonionic detergents (NP40, Triton X 100,
Tween 20,
Tween 80, etc.), ionic detergents (e.g., SDS, LDS, etc.), polyethylene glycol,
etc.
Appropriate blocking agent concentrations allow complex formation.
After binding is.perFormed, unbound, labeled protein is removed in the
supernatant, and the immobilized protein retaining any bound, labeled protein
is washed
extensively. The amount of bound label is then quantified using standard
methods in the
art to detect the label as described, supra.
In another specific embodiments screening for modulators of the protein
complexes/protein as provided herein can be carried out by attaching those
and/or the
antibodies as provided herein to a solid carrier. In a further specific
embodiment, the
invention relates to an array of said molecules.
The preparation of such an array containing different types of proteins,
including
antibodies) is well known in the art and is apparent to a person skilled in
the art (see e.g.
Ekins et al., 1989, J. Pharm. Biomed. Anal. 7:155-168; Mitchell et al. 2002,
Nature
Biotechnol. 20:225-229; Petricoin et al., 2002, Lancet 359:572-577; Templin et
al., 2001,
Trends Biotechnol. 20:160-166; Wilson and Nock, 2001, Curr. Opin. Chem. Biol.
6:81-85;
Lee et al., 2002 Science 295:1702-1705; MacBeath and Schreiber, 2000, Science
289:1760; Blawas and Reichert, 1998, Biomaterials 19:595; Kane et al., 1999,
Biomaterials 20:2363; Chen et al., 1997, Science 276:1425; Vaugham et al.,
1996,
Nature Biotechnol. 14:309-314; Mahler et al., 1997, Immunotechnology 3:31-43;
Roberts
et al., 1999, Curr. Opin. Chem. Biol. 3:268-273; Nord et al., 1997, Nature
Biotechnol.
15:772-777; Nord et al., 2001, Eur. J. Biochem. 268:4269-4277; Brody and Gold,
2000,
Rev. Mol. Biotechnol. 74:5-13; ICarlstroem and Nygren, 2001, Anal. Biochem.
295:22-30;
Nelson et al., 2000, Electrophoresis 21:1155-1163; Honore et al., 2001, Expert
Rev. Mol.
Diagn. 3:265-274; Albala, 2001, Expert Rev. Mol. Diagn. 2:145-152, Figeys and
Pinto,
2001, Electrophoresis 2:208-216 and references in the publications listed
here).
Complexes can be attached to an array by different means as will be apparent
to
a person skilled in the art. Complexes can for example be added to the array
via a TAP-
tag (as described in WO/0009716 and in Rigaut et al., 1999, Nature Biotechnol.
10:1030-

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74
1032) after the purification step or by another suitable purification scheme
as will be
apparent to a person skilled in the art.
Optionally, the proteins of the complex can be cross-linked to enhance the
stability of the complex. Different methods to cross-link proteins are well
known in the art.
Reactive end-groups of cross-linking agents include but are not limited to -
COOH, -SH, -
NH2 or N-oxy-succinamate.
The spacer of the cross-linking agent should be chosen with respect to the
size of the
complex to be cross-linked. For small protein complexes, comprising only a few
proteins,
relatively short spacers are preferable in order to reduce the likelihood of
cross-linking
separate complexes in the reaction mixture. For larger protein complexes,
additional use
of larger spacers is preferable in order to facilitate cross-linking between
proteins within
the complex.
It is preferable to check the success-rate of cross-linking before linking the
complex to the carrier.
As will be apparent to a person skilled in the art, the optimal rate of cross-
linking
need to be determined on a case by case basis. This can be achieved by methods
well
known in the art, some of which are exemplary described below.
A sufFicient rate of cross-linking can be checked f.e. by analysing the cross-
linked
complex vs. a non-cross-linked complex on a denaturating protein gel.
If cross-linking has been performed successfully, the proteins of the complex
are
expected to be found in the same lane, whereas the proteins of the non-cross-
linked
complex are expected to be separated according to their individual
characteristics.
Optionally the presence of all proteins of the complex can be further checked
by peptide-
sequencing of proteins in the respective bands using methods well known in the
art such
as mass spectrometry and/or Edman degradation.
In addition, a rate of crosslinking which is too high should also be avoided.
If
cross-linking has been carried out too extensively, there will be an
increasing amount of
cross-linking of the individual protein complex, which potentially interferes
with a
screening for potential binding partners and/or modulators etc. using the
arrays.
The presence of such structures can be determined by methods well known in the
art
and include e.g. gel-filtration experiments comparing the gel filtration
profile solutions
containing cross-linked complexes vs. uncross-linked complexes.

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Optionally, functional assays as will be apparent to a person skilled in the
art,
some of which are exemplarily provided herein, can be performed to check the
integrity
of the complex.
Alternatively, members of the protein complex can be expressed as a single
fusion protein and coupled to the matrix as will be apparent to a person
skilled in the art.
Optionally, the attachment of the complex or proteins or antibody as outlined
above can be further monitored by various methods apparent to a person skilled
in the
art. Those include, but are not limited to surface plasmon resonance (see e.g.
McDonnel,
2001, Curr. Opin. Chem. Biol. 5:572-577; Lee, 2001, Trends Biotechnol. 19:217-
222;
Weinberger et al., 2000, 1:395-416; Pearson et al., 2000, Ann. Clin. Biochem.
37:119-
145; Vely et al., 2000, Methods Mol. Biol. 121:313-321; Slepak, 2000, J. Nbl
Recognit.
13:20-26.
Exemplary assays useful for measuring in vitro transcription activity of
complex 1
include but are not limited to those described in Arrebola R et al., 1998, Mol
Cell Biol,
18:1-9.
Exemplary assays useful for measuring UASG-U6 chimeric transcription activity
of cells containing complex 1 include but are not limited to those described
in Martin MP
et al., 2001, Mol Cell Biol, 21:6429-39.
Exemplary assays useful for measuring transcription of U6 RNA in cells
containing complex 1 include but are not limited to those described in
Arrebola R et al.,
1998, Mol Cell Biol, 18:1-9.
Exemplary assays useful for measuring leucine aminotransferase activity of
complex 2 include but are not limited to those described in Taylor RT and
Jenkins WT.,
1966, J Biol Chem, 241:4391-5. and/or Taylor RT and Jenkins WT., 1966, J Biol
Chem,
241:4396-405.
Exemplary assays useful for measuring apoptosis induction in cells
overexpressing Bcat1 belonging to complex 2 include but are not limited to
those
described in Eden A and Benvenisty N., 1999, FEBS Lett, 457:255-61.
Exemplary assays useful for measuring transformation activity of cells
containing
complex 2 include but are not limited to those described in Land H et al.,
Nature,
304:596-602.

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Exemplary assays useful for measuring L-glutamine D-fructose 6-phosphate
amidotransferase activity of complex 3a include but are not limited to those
described in
Huynh QK et ~al., 2000, Arch Biochem Biophys, 379:307-13. and/or Endo A et
al., 1970, J
Bacteriol, 103:588-94.
Exemplary assays useful for measuring ribosomal transporter activity of
complex
3b include but are not limited to those described in Moy TI and Silver PA.,
1999, Genes
Dev, 13:2118-33.
Exemplary assays useful for measuring C1-tetrahydrofolate synthase activity of
complex 4a include but are not limited to those described in Appling DR and
Rabinowitz
JC., 1985, J Biol Chem, 260:1248-56. and/or Paukert JL and Rabinowitz JC.,
1980,
Methods Enzymol, 66:616-26. and/or Schirch V., 1997, Methods Enzymol, 281:146-
61.
Exemplary assays useful for measuring tranlational activity of complex 4b
include
but are not limited to those described in Valasek L et al., 2001, EMBO J,
20:891-904.
Exemplary assays useful for measuring C1-tetrahydrofolate synthase activity of
complex 4b include but are not limited to those described in Appling DR and
Rabinowitz
JC., 1985, J Biol Chem, 260:1248-56, and/or Paukert JL and Rabinowitz JC.,
1980,
Methods Enzymol, 66:616-26. and/or Schirch V., 1997, Methods Enzymol, 281:146-
61.
Exemplary assays useful for measuring ATPase of complex 4b include but are
not limited to those described in Kimura K and Hirano T., 1997, Cell, 90:625-
34.
Exemplary assays useful for measuring protein kinase activity of complex 5a
include but are not limited to those described in Bech-Otschir D et al., 2001,
EMBO J,
20:1630-9. and/or Seeger M et al., 1998, FASEB J, 12:469-78.
Exemplary assays useful for measuring proliferation activity of cells
containing
complex 5a include but are not limited to those described in Tomoda K et al.,
1999,
Nature, 398:160-5.
Exemplary assays useful for measuring protein kinase activity of complex 5b
include but are not limited to those described in Bech-Otschir D et al., 2001,
EMBO J,
20:1630-9.
Exemplary assays useful for measuring deneddylating activity of complex 5b
include but are not limited to those described in Lyapina S et al., 2001;
Science,
292:1382-5.
Exemplary assays useful for measuring protein kinase activity of complex 5b
include but are not limited to those described in .Seeger M et al., 1998,
FASEB J,
12:469-78.

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2000, Am J Hum Genet, 67:1389-99. and/or Achouri Y et al., 1997, Biochem J,
323 ( Pt
2):365-70.
Exemplary assays useful for measuring DNA binding activity of complex 11
include but are not limited to those described in Matangkasombut O et al.,
2000, Genes
Dev, 14:951-62.
Exemplary assays useful for measuring nuclear translocation of RING3 in cells
containing complex 11 include but are not limited to those described in Guo N
et al.,
2000, J Cell Sci, 113 ( Pt 17):3085-91.
Exemplary assays useful for measuring proliferation activity of cells
containing
complex 11 include but are not limited to those described in Denis GV and
Green MR.,
1996, Genes Dev, 10:261-71.
Exemplary assays useful for measuring transcription factor activity of complex
12a include but are not limited to those described in Refines D et al., 1997,
Methods,
12:192-202.
Exemplary assays useful for measuring BDNF (brain-derived neurotrophic factor)
production and secretion in cultured CNS cells containing complex 12a include
but are
not limited to those described in Zuccato C et al., 2001, Science, 293:493-8.
Exemplary animal models useful for assaying compounds interacting with
transgenic
Huntington's disease (HD) mice complex 12b include but are not limited to
those
described in Ishiguro H et al., 2001, J Neurosci Res, 65:289-97.
Exemplary animal models useful for assaying compounds interacting with
transgenic
Huntington's disease (HD) mice complex 12b include but are not limited to
those
described in Hansson O et al., 2001, J Neurochem, 78:694-703.
Exemplary assays useful for measuring transcription factor activity of complex
12b include but are not limited to those described in Refines D et al., 1997,
Methods,
12:192-202.
Exemplary assays useful for measuring BDNF (brain-derived neurotrophic factor)
production and secretion in cultured CNS cells containing complex 12b include
but are
not limited to those described in Zuccato C et al., 2001, Science, 293:493-8.
Exemplary assays useful for measuring poly (A)-binding activity of complex 13a
include but are not limited to those described in Wahle E., 1991, Cell, 66:759-
68.
Exemplary assays useful for measuring poly (A)-binding activity of complex 13a
include but are not limited to those described in Wahle E et al., 1993, J Biol
Chem,
268:2937-45.

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Exemplary assays useful for measuring proliferation activity of cells
containing
complex 13a include but are not limited to those described in Wiristall E et
al., 2000, J
Biol Chem, 275:21817-26.
Exemplary assays useful for measuring subcellular localization/transport of
PABP2 in cells containing complex 13a include but are not limited to those
described in
Calado A et al., 2000, Hum Mol Genet, 9:2321-8.
Exemplary assays useful for measuring neuronal survival/death of cells
containing
complex 13a include but are not limited to those described in Sheline CT and
Choi DW.,
1998, Neurobiol Dis, 5:47-54.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying a dentatorubral-pallidoluysian atrophy (DRPLA)-like phenotype
complex
13b include but are not limited to those described in Marks KH et al., 1977,
Pediatrics,
60:223-6.
Exemplary animal models useful for assaying compounds interacting with
transgenic
Huntington's disease (HD) mice complex 13b include but are not limited to
those
described in Mangiarini L et al., 1996, Cell, 87:493-506.
Exemplary assays useful for measuring poly (A)-binding activity of complex 13b
include but are not limited to those described in Wahle E., 1991, Cell, 66:759-
68.
Exemplary assays useful for measuring poly (A)-binding activity of complex 13b
include but are not limited to those described in Wahle E et al., 1993, J Biol
Chem,
268:2937-45.
Exemplary assays useful for measuring proliferation activity of cells
containing
complex 13b include but are not limited to those described in Winstall E et
al., 2000, J
Biol Chem, 275:21817-26.
Exemplary assays useful for measuring subcellular localization/transport of
PABP2 in cells containing complex 13b include but are not limited to those
described in
Calado A et al., 2000, Hum Mol Genet, 9:2321-8.
Exemplary assays useful for measuring neuronal survival/death of cells
containing
complex 13b include but are not limited to those described in Sheline CT and
Choi DW.,
1998, Neurobiol Dis, 5:47-54.
Exemplary assays useful for measuring serine hydroxymethyltransferase activity
of complex 14a include but are not limited to those described in Elsea SH et
al., 1995,
Am J Hum Genet, 57:1342-50.

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Exemplary assays useful for measuring serine hydroxymethyltransferase activity
of complex 14b include but are not limited to those described in Elsea SH et
al., 1995,
Am J Hum Genet, 57:1342-50.
Exemplary assays useful for measuring guanine nucleotide exchange factor
activity of complex 15 include but are not limited to those described in Hart
MJ et al.,
1996, J Biol Chem, 271:25452-8.
Exemplary assays useful for measuring neuronal outgrowth control by Rho GEF
in cells containing complex 15 include but are not limited to those described
in Gebbink
MF et al., 1997, J Cell Biol, 137:1603-13.
Exemplary assays useful for measuring serine/threonine protein phosphatase
activity of complex 16a include but are not limited to those described in
Mumby MC et
al., 1987, J Biol Chem, 262:6257-65.
Exemplary assays useful for measuring acetyl-coenzyme A carboxylase activity
of
complex 16b include but are not limited to those described in Oizumi J and
Hayakawa
K., 1990, J Chromatogr, 529:55-63.
Exemplary assays useful for measuring GTP exchange activity of complex 16b
include but are not limited to those described in Sasaki T et al., 1990, J
Biol Chem,
265:2333-7.
Exemplary assays useful for measuring serine/threonine protein phosphatase
activity of complex 16b include but are not limited to those described in
Mumby MC et
al., 1987, J Biol Chem, 262:6257-65.
Exem platy assays useful for measuring spermidine synthase activity of complex
17 include but are not limited to those described in Wiest L and Pegg AE.,
1998,
Methods Mol Biol, 79:51-7.
Exemplary assays useful for measuring cell proliferation of mouse leukemia
cells
containing complex 17 include but are not limited to those described in
Bergeron RJ et
al., 2001, J Med Chem, 44:2451-9.
Exemplary assays useful for measuring phosphoglycerate kinase disulfide
reductase activity of complex 18 include but are not limited to those
described in Lay AJ
et al., 2000, Nature, 408:869-73.
Exemplary assays useful for measuring phosphoglycerate kinase secretion by
cultured tumour cells (HT1080) containing complex 18 include but are not
limited to
those described in Lay AJ et al., 2000, Nature, 408:869-73.

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Exemplary assays useful for measuring N-acetyl transferase activity of complex
19 include but are not limited to those described in Bell DA et al., 1995,
Cancer Res,
55:5226-9.
Exemplary assays useful for measuring glucan synthase activity of complex 19
include but are not limited to those described in Thompson JR et al., 1999, J
Bacteriol,
181:444-53.
Exemplary assays useful for measuring casein kinase II activity of complex 20
include but are not limited to those described in Hockman DJ and Schultz MC.,
1996,
Mol Cell Biol, 16:892-8.
Exemplary assays useful for measuring nucleosome assembly activity of
complex 20 include but are not limited to those described in Bortvin A and
Winston F.,
1996, Science, 272:1473-6.
Exemplary assays useful for measuring phosphorylation of the p53 tumor
suppressor protein by protein kinase CKII in cells containing
complex 20 include but are not limited to those described in McKendrick L and
Meek
DW., 1994, Cell Mol Biol Res, 40:555-61.
Exemplary assays useful for measuring translocation into ER activity of
complex
23a include but are not limited to those described in Mason N et al., 2000,
EMBO J,
19:4164-74. and/or Ng DT et al., 1996, J Cell Biol, 134:269-78.
Exemplary assays useful for measuring subcellular localization/transport of a
reporter protein into the ER in cells containing complex 23a include but are
not limited to
those described in Mason N et al., 2000, EMBO J, 19:4164-74. and/or Hann BC et
al.,
1992, Nature, 356:532-3.
Exemplary assays useful for measuring translocation into ER activity of
complex
23b include but are not limited to those described in Mason N et al., 2000,
EMBO J,
19:4164-74. and/or Ng DT et al., 1996, J Cell Biol, 134:269-78.
Exemplary assays useful for measuring subcellular localization/transport of a
reporter protein into the ER in cells containing complex 23b include but are
not limited to
those described in Mason N et al., 2000, EMBO J, 19:4164-74. and/or Hann BC et
al.,
1992, Nature, 356:532-3.
Exemplary assays useful for measuring RNA Pol II activity of complex 24
include
but are not limited to those described in Majello B and Napolitano G., 2001,
Front Biosci,
6:1358-68.

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Exemplary assays useful for measuring protein phosphatase 2A activity of
complex 25 include but are not limited to those described in Chung H et al.,
1999,
Biochemistry, 38:10371-6.
Exemplary assays useful for measuring transporter activity of complex 26a
include but are not limited to those described in Takabatake R et al., 2001, J
Biochem
(Tokyo), 129:827-33.
Exemplary assays useful for measuring nuclear import/export activity of
complex
26a include but are not limited to those described in Lindsay ME et al., 2001,
J Cell Biol,
153:1391-402. and/or Jakel S and Gorlich D., 1998, EMBO J, 17:4491-502.
Exemplary assays useful for measuring gene expression of IFNA/B in cells
containing complex 26a include but are not limited to those described in Juang
YT et
al., 1999, J Biol Chem, 274:18060-6.
Exemplary assays useful for measuring subcellular localization/transport
complex
26a include but are not limited to those described in Kobayashi T et al.,
2001, J Virol,
75:3404-12.
Exemplary assays useful for measuring transporter activity of complex 26b
include but are not limited to those described in Takabatake R et al., 2001, J
Biochem
(Tokyo), 129:827-33.
Exemplary assays useful for measuring nuclear import/export activity of
complex
26b include but are not limited to those described in Lindsay ME et al., 2001,
J Cell Biol,
153:1391-402. and/or Jakel S and Gorlich D., 1998, EMBO J, 17:4491-502.
Exemplary assays useful for measuring gene expression of IFNA/B in cells
containing complex 26b include but are not limited to those described in Juang
YT et
al., 1999, J Biol Chem, 274:18060-6.
Exemplary assays useful for measuring subcellular localization/transport
complex
26b include but are not limited to those described in Kobayashi T et al.,
2001, J Virol,
75:3404-12.
Exemplary assays useful for measuring Cct2 Chaperonin ATP-binding activity of
complex 27 include but are not limited to those described in Charpentier AH et
al., 2000,
Cancer Res, 60:5977-83.
Exemplary assays useful for measuring Cct2 specific antibody uptake and
nuclear
internalization in cells containing complex 27 include but are not limited to
those
described in Tian PY et al., 1989, Yao Xue Xue Bao, 24:16-21.]

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Exemplary assays useful for measuring proliferation activity of cells
containing
complex 5b include but are not limited to those described in Tomoda K et al.,
1999,
Nature, 398:160-5.
Exemplary assays useful for measuring guanine nucleotide exchange factor
activity of complex 6a include but are not limited to those described in
Anthony TG et
al., 2000, Biochim Biophys Acta, 1492:56-62.
Exemplary assays useful for measuring guanine nucleotide exchange factor
activity of complex 6b include but are not limited to those described in
Anthony TG et
al., 2000, Biochim Biophys Acta, 1492:56-62.
Exemplary assays useful for measuring ultrazentirfuagtion of complex 6b
include
but are not limited to those described in Larson DE and Sells BH., 1987, Mol
Cell
Biochem, 74:5-15.
Exemplary assays useful for measuring phosphatidylinositol 4-kinase activity
of
complex 7a include but are not limited to those described in Barylko B et al.,
2001, J Biol
Chem, 276:7705-8. and/or Kato H et al., 1989, J Biol Chem, 264:3116-21. and/or
Yoshida S et al., 1994, J Biol Chem, 269:1166-72.
Exemplary assays useful for measuring protein secretion and endocytosis
activity
of cells containing complex 7a include but are not limited to those described
in Audhya
A et al., 2000, Mol Biol Cell, 11:2673-89.
Exemplary assays useful for measuring phosphatidylinositol 4-kinase activity
of
complex 7b include but are not limited to those described in Barylko B et al.,
2001, J Biol
Chem, 276:7705-8. and/or Kato H et al., 1989, J Biol Chem, 264:3116-21. and/or
Yoshida S et al., 1994, J Biol Chem, 269:1166-72.
Exemplary assays useful for measuring protein secretion and endocytosis
activity
of cells containing complex 7b include but are not limited to those described
in Audhya
A et al., 2000, Mol Biol Cell, 11:2673-89.
Exemplary assays useful for measuring glucose-6-phosphate isomerase activity
of complex 9a include but are not limited to those described in Gracy RW.,
1982,
Methods Enzymol, 89 Pt D:550-8.
Exemplary assays useful for measuring glucose-6-phosphate isomerase activity
of complex 9b include but are not limited to those described in Gracy RW.,
1982,
Methods Enzymol, 89 Pt D:550-8.
Exemplary assays useful for measuring 3- phospoglycerate dehydrogenase
activity of complex 10 include but are not limited to those described in Klomp
LW et al.,

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Exemplary assays useful for measuring transketolase activity of complex 28
include but are not limited to those described in Ali M et al., 1987, Comp
Biochem
Physiol B, 87:833-5, and/or Chamberlain BR et al., 1996, Ann Clin Biochem, 33
( Pt
4):352-4.
Exemplary assays useful for measuring cAMP kinase binding activity of complex
30 include but are not limited to those described in Zakhary DR et al., 2000,
J Biol
Chem, 275:41389-95.
Exemplary assays useful for measuring cAMP kinase activity of complex 30
include but are not limited to those described in Mazon MJ et al., 1993, Eur J
Biochem,
213:501-6. and/or Keryer G et al., 1998, J Biol Chem, 273:34594-602.
Exemplary assays useful for measuring cAM P-dependent aggregation of cells
containing complex 30 include but are not limited to those described in
Faucheux N et
al., 2001, Biomaterials, 22:2993-8.
Exemplary assays useful for measuring cell cycle regulated subcellular
localization of PKA of cells containing complex 30 include but are not limited
to those
described in Keryer G et al., 1998, J Biol Chem, 273:34594-602.
Exemplary assays useful for measuring glutamine synthetase activity of complex
31a include but are not limited to those described in Santoro JC et al., 2001,
Anal
Biochem, 289:18-25.
Exemplary assays useful for measuring glutamine synthetase levels of complex
31a include but are not limited to those described in Gunnersen D and Haley
B., 1992,
Proc Natl Acad Sci U S A, 89:11949-53.
Exemplary assays useful for measuring beta-amyloid induced glutamine
synthetase expression in cultured astrocytes containing complex 31a include
but are not
limited to those described in Pike CJ et al., 1996, Exp Neurol, 139:167-71.
Exemplary assays useful for measuring glutamine synthetase activity of complex
31b include but are not limited to those described in Santoro JC et al., 2001,
Anal
Biochem, 289:18-25.
Exemplary assays useful for measuring glutamine synthetase levels of complex
31 b include but are not limited to those described in Gunnersen D and Haley
B., 1992,
Proc Natl Acad Sci U S A, 89:11949-53.
Exemplary assays useful for measuring trehalose synthase of complex 31 b
include but are not limited to those described in Bell W et al., 1998, J Biol
Chem,
273:33311-9.

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Exemplary assays useful for measuring overexpression of trehalose synthase
complex 31b include but are not limited to those described in Lao G et al.,
2001,
Cryobiology, 43:106-13.
Exemplary assays useful for measuring beta-amyloid induced glutamine
synthetase expression in cultured astrocytes containing complex 31 b include
but are not
limited to those described in Pike CJ et al., 1996, Exp Neurol, 139:167-71.
Exemplary assays useful for measuring phosphatidylinositol 4-kinase activity
of
complex 32a include but are not limited to those described in Barylko B et
al., 2001, J
Biol Chem, 276:7705-8. .
Exemplary assays useful for measuring phosphatidylinositol 4-kinase activity
of
complex 32b include but are not limited to those described in Barylko B et
al., 2001, J
Biol Chem, 276:7705-8.
Exemplary assays useful for measuring Neutral trehalase activity of complex
32b
include but are not limited to those described in App H and Holzer H., 1989, J
Biol
Chem, 264:17583-8.
Exemplary assays useful for measuring methionine adenosyltransferase activity
of complex 33a include but are not limited to those described in Chamberlin ME
et al.,
1996, J Clin Invest, 98:1021-7.
Exemplary animal models useful for assaying compounds interacting with
methionine
adenosyltransferase 1A (MAT1A) knockout mice complex 33b include but are not
limited
to those described in Lu SC et al., 2001, Proc Natl Acad Sci U S A, 98:5560-5.
Exemplary assays useful for measuring methionine adenosyltransferase activity
of complex 33b include but are not limited to those described in Chamberlin ME
et al.,
1996, J Clin Invest, 98:1021-7.
Exemplary assays useful for measuring alcohol dehydrogenase activity of
complex 35a include but are not limited to those described in Chrostek L et
al., 2001,
Hum Exp Toxicol, 20:255-8. and/or Zubarev SF., 1977 Mar-Apr, Zdravookhr Kirg,
:53-5.]
Exemplary assays useful for measuring Ubp14 protease activity of complex 35a
include but are not limited to those described in Wilkinson I<D et al., 1995,
Biochemistry,
34:14535-46.
Exemplary assays useful for measuring isoleucyl tRNA synthetase activity of
complex 35a include but are not limited to those described in Nichols RC et
al., 1995,
Gene, 155:299-304.

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Exemplary assays useful for measuring eIF 3 subunit and 40S ribosomal subunit
binding activity of complex 35a include but are not limited to those described
in
Greenberg JR et al., 1998, J Biol Chem, 273:23485-94.
Exemplary assays useful for measuring Ubp14 differentiation in cells
containing
complex 35a include but are not limited to those described in Lindsey DF et
al., 1998, J
Biol Chem, 273:29178-87.
Exemplary assays useful for measuring Ubp14 protease activity of complex 35b
include but are not limited to those described in Wilkinson KD et al., 1995,
Biochemistry,
34:14535-46.
Exemplary assays useful for measuring isoleucyl tRNA synthetase activity of
complex 35b include but are not limited to those described in Nichols RC et
al., 1995,
Gene, 155:299-304.
Exemplary assays useful for measuring eIF 3 subunit and 40S ribosomal subunit
binding activity of complex 35b include but are not limited to those described
in
Greenberg JR et al., 1998, J Biol Chem, 273:23485-94.
Exemplary assays useful for measuring Ubp14 differentiation in cells
containing
complex 35b include but are not limited to those described in Lindsey DF et
al., 1998, J
Biol Chem, 273:29178-87.
Exemplary assays useful for measuring protein tyrosine phosphatase activity of
complex 36a include but are not limited to those described in Mattison CP et
al., 1999,
Mol Cell Biol, 19:7651-60.
Exemplary assays useful for measuring protein serine/threonine kinase activity
of
complex 36a include but are not limited to those described in Warrior U et
al., 1999, J
Biomol Screen, 4:129-135.
Exemplary assays useful for measuring protein tyrosine phosphatase activity of
complex 36b include but are not limited to those described in Mattison CP et
al., 1999,
Mol Cell Biol, 19:7651-60.
Exemplary assays useful for measuring protein serine/threonine kinase activity
of
complex 36b include but are not limited to those described in Warrior U et
al., 1999, J
Biomol Screen, 4:129-135.
Exemplary assays useful for measuring telomere length in cells containing
complex 38a include but are not limited to those described in Mallory JC and
Petes TD.,
2000, Proc Natl Acad Sci U S A, 97:13749-54.

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Exemplary animal models useful for assaying compounds interacting with ATM
deficient
mice complex 38b include but are not limited to those described in Liao MJ and
Van
Dyke T., 1999, Genes Dev, 13:1246-50.
Exemplary assays useful for measuring telomere length in cells containing
complex 38b include but are not limited to those described in Mallory JC and
Petes TD.,
2000, Proc Natl Acad Sci U S A, 97:13749=54.
Exemplary assays useful for measuring PdrSp drug transport activity of complex
39a include but are not limited to those described in Conseil G et al., 2000,
Biochemistry, 39:6910-7.
Exemplary assays useful for measuring rhodamine transport (drug sensitivity
assay) in cells containing complex 39a include but are not limited to those
described in
Kolaczkowski M et al., 1996, J Biol Chem, 271:31543-8.
Exemplary assays useful for measuring PdrSp drug transport activity of complex
39b include but are not limited to those described in Conseil G et al., 2000,
Biochemistry, 39:6910-7.
Exemplary assays useful for measuring rhodamine transport (drug sensitivity
assay) in cells containing complex 39b include but are not limited to those
described in
Kolaczkowski M et al., 1996, J Biol Chem, 271:31543-8.
Exemplary assays useful for measuring alcohol dehydrogenase activity of
complex 40 include but are not limited to those described in Vaca G et al.,
1982, Hum
Genet, 61:338-41. and/or Freund N et al., 1996, Eur J Biochem, 242:86-9.
Exemplary assays useful for measuring nuclear import/export activity of
complex
40 include but are not limited to those described in Jakel S and Gorlich D.,
1998, EMBO
J, 17:4491-502.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying diabetes type 1-like phenotype d complex 41 include but are
not limited
to those described in Hayashi T and Faustman D., 1999, Mol Cell Biol, 19:8646-
59.
Exemplary assays useful for measuring ATP-dependent DNA helicase activity of
complex 41 include but are not limited to those described in Kanemaki M et
al., 1999, J
Biol Chem, 274:22437-44.
Exemplary assays useful for measuring ATP-dependent RNA helicase activity of
complex 41 include but are not limited to those described in Li Q et al.,
1999, Mol Cell
Biol, 19:7336-46.

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Exemplary assays useful for measuring oncogenic transformation activity of
cells
containing complex 41 include but are not limited to those described in Wood
MA et al.,
2000, Mol Cell, 5:321-30.
Exemplary assays useful for measuring protein degradation activity of complex
42 include but are not limited to those described in Wang CW et al., 2001, J
Biol Chem,
276:30442-51.
Exemplary assays useful for measuring thioredoxin reductase activity of
complex
42 include but are not limited to those described in Noh DY et al., 2001 May-
Jun,
Anticancer Res, 21:2085-90.
Exemplary assays useful for measuring proliferation activity of cells
containing
complex 42 include but are not limited to those described in Ludes-Meyers JH
et al.,
2001, Oncogene, 20:2771-80.
Exemplary animal models us eful for assaying compounds interacting with
rabbits
experimentally infected with immunodeficiency virus complex 43 include but are
not
limited to those described in Walder R et al., 2001, Comp Immunol Microbiol
Infect Dis,
24:1-20.
Exemplary animal models useful for assaying compounds interacting with CD4-
transgenic rabbits complex 43 include but are not limited to those described
in Dunn CS
et al., 1995, J Gen Virol, 76 ( Pt 6):1327-36.
Exemplary assays useful for measuring reconstituted 40S ribosome binding
activity of complex 43 include but are not limited to those described in Li Q
et al., 1999,
Mol Cell Biol, 19:7336-46.
Exemplary assays useful for measuring stress response of cells containing
complex 43 include but are not limited to those described in Pereira MD et
al., 2001,
BMC Microbiol, 1:-.
Exemplary assays useful for measuring ATPase activity of complex 44 include
but are not limited to those described in Rieger CE et al., 1997, Anal
Biochem, 246:86-
95.
Exemplary assays useful for measuring decay of proto-oncogene mRNA, cytokine
mRNA or viral mRNA in HeLa cells containing complex 44 include but are not
limited to
those described in Laroia G et al., 1999, Science, 284:499-502.
Exemplary assays useful for measuring transcription factor activity of complex
45a include but are not limited to those described in Fernandes L et al.,
1997, Mol Cell
Biol, 17:6982-93.

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Exemplary assays useful for measuring the rate of survival/death of cells
containing complex 45a include but are not limited to those described in
Fernandes L et
al., 1997, Mol Cell Biol, 17:6982-93.
Exemplary assays useful for measuring transcription factor activity of complex
45b include but are not limited to those described in Fernandes L et al.,
1997, Mol Cell
Biol, 17:6982-93.
Exemplary assays useful for measuring the rate of survival/death of cells
containing complex 45b include but are not limited to those described in
Fernandes L et
al., 1997, Mol Cell Biol, 17:6982-93.
Exemplary assays useful for measuring guanine nucleotide exchange factor
activity of complex 46a include but are not limited to those described in
Kiyono M et al.,
2000, J Biol Chem, 275:29788-93. and/or Haney SA and Broach JR., 1994, J Biol
Chem,
269:16541-8.
Exemplary assays useful for measuring proliferation activity of cells
containing
complex 46a include but are not limited to those described in Vanoni M et al.,
1999, J
Biol Chem, 274:36656-62.
Exemplary assays useful for measuring guanine nucleotide exchange factor
activity of complex 46b include but are not limited to those described in
Kiyono M et al.,
2000, J Biol Chem, 275:29788-93. and/or Haney SA and Broach JR., 1994, J Biol
Chem,
269:16541-8.
Exemplary assays useful for measuring proliferation activity of cells
containing
complex 46b include but are not limited to those described in Vanoni M et al.,
1999, J
Biol Chem, 274:36656-62.
Exemplary assays useful for measuring arginase activity of complex 47a include
but are not limited to those described in Han S and Viola RE., 2001, Anal
Biochem,
295:117-9.
Exemplary assays useful for measuring antiproliferative and apoptotic actions
on
arginase-expressing human breast cancer cells containing complex 47a include
but are
not limited to those described in Singh R et al., 2000, Cancer Res, 60:3305-
12.
Exemplary animal models useful for assaying compounds interacting with
arginase II
knocfe out mice (as model for hyperargininemia) complex 47b include but are
not limited
to those described in Shi O et al., 2001, Mol Cell Biol, 21:811-3.

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Exemplary assays useful for measuring arginase activity of complex 47b include
but are not limited to those described in Han S and Viola RE., 2001, Anal
Biochem,
295:117-9.
Exemplary assays useful for measuring antiproliferative and apoptotic actions
on
arginase-expressing human breast cancer cells containing complex 47b include
but are
not limited to those described in Singh R et al., 2000, Cancer Res, 60:3305-
12.
Exemplary assays useful for measuring L-glutamine:D-fructose-6-
amidotransferase activity of complex 48a include but are not limited to those
described
in Wu G et al., 2001, Biochem J, 353:245-52. and/or Watzele G and Tanner W.,
1989, J
Biol Chem, 264:8753-8.
Exemplary assays useful for measuring gene expression of glutamine:fructose-6-
phosphate-amidotransferase (GFAT) in cells containing complex 48a include but
are not
limited to those described in Weigert C et al., 2001 Jan 12" FEBS Lett, 488:95-
9.
Exemplary assays useful for measuring morphological changes of cells
containing
complex 48a include but are not limited to those described in Matsui Y et al.,
1996, J
Cell Biol, 133:865-78.
Exemplary assays useful for measuring translational activity of complex 48b
include but are not limited to those described in Valasek L et al., 2001, EMBO
J, 20:891-
904.
Exemplary assays useful for measuring morphological changes of cells
containing
complex 48b include but are not limited to those described in Matsui Y et al.,
1996, J
Cell Biol, 133:865-78.
Exemplary assays useful for measuring DNA helicase activity of complex 50
include but are not limited to those described in ICanemaki M et al., 1999, J
Biol Chem,
274:22437-44.
Exemplary assays useful for measuring transcriptional activity of complex 50
include but are not limited to those described in Lim CR et al., 2000, J Biol
Chem,
275:22409-17.
Exemplary assays useful for measuring transformation activity of cells
containing
complex 50 include but are not limited to those described in Afar DE et al.,
1994,
Science, 264:424-6.
Exemplary assays useful for measuring aminoacyl-tRNA synthase activity of
complex 51 include but are not limited to those described in Targoff IN.,
1990, J

CA 02471307 2004-06-18
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Immunol, 144:1737-43. and/or Harris CL and Kolanko CJ., 1995, Biochem J, 309 (
Pt
1 ):321-4.
Exemplary assays useful for measuring proliferation activity of cells
containing
complex 51 include but are not limited to those described in Cambridge G et
al., Clin
Exp Rheumatol, 7:27-33.
Exemplary assays useful for measuring protein serine/threonine phosphatase
activity of complex 52 include but are not limited to those described in Mumby
MC et al.,
1987, J Biol Chem, 262:6257-65.
Exemplary assays useful for measuring DNA polymerise activity of complex 53a
include but are not limited to those described in Stoeber K et al., 1998, EMBO
J,
17:7219-29.
Exemplary assays useful for measuring cell cycle progression and DNA
replication in cells containing complex 53a include but are not limited to
those described
in Calzada A et al., 2001, Nature, 412:355-8.
Exemplary assays useful for measuring cell cycle progression of cells
containing
complex 53a include but are not limited to those described in Stoeber K et
al., 2001, J
Cell Sci, 114:2027-41.
Exemplary assays useful for measuring DNA polymerise activity of complex 53b
include but are not limited to those described in Stoeber K et al., 1998, EMBO
J,
17:7219-29.
Exemplary assays useful for measuring cell cycle progression and DNA
replication in cells containing complex 53b include but are not limited to
those described
in Calzada A et al., 2001, Nature, 412:355-8.
Exemplary assays useful for measuring cell cycle progression of cells
containing
complex 53b include but are not limited to those described in Stoeber K et
al., 2001, J
Cell Sci, 114:2027-41.
Exemplary assays useful for measuring tRNA pseudouridinylation activity of
complex 54 include but are not limited to those described in Samuelsson T and
Olsson
M., 1990, J Biol Chem, 265:8782-7.
Exemplary assays useful for measuring rRNA pseudouridinylation activity of
complex 54 include but are not limited to those described in Lafontaine DL et
al., 1998,
Genes Dev, 12:527-37.

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Exemplary assays useful for measuring Kcc4 kinase binding activity of complex
55 include but are not limited to those described in Okuzaki D and Nojima H.,
2001,
FEBS Lett, 489:197-201.
Exemplary assays useful for measuring cytokinesis in cells containing complex
55 include but are not limited to those described in Oegema K et al., 2000, J
Cell Biol,
150:539-52.
Exemplary assays useful for measuring bud formation and mitotic arrest of
cells
containing complex 55 include but are not limited to those described in
Krishnan R et
al., 2000, Genetics, 156:489-500.
Exemplary assays useful for measuring DNAse activity of complex 56a include
but are not limited to those described in Dake E et al., 1988, J Biol Chem,
263:7691-
702.
Exemplary assays useful for measuring apoptosis/DNA fragmentation of cells
containing complex 56a include but are not limited to those described in Li LY
et al.,
2001, Nature, 412:95-9.
Exemplary animal models useful for assaying compounds interacting with
DFF45/ICAD
knock out mice complex 56b include but are not limited to those described in
Zhang J et
al., 1998, Proc Natl Acad Sci U S A, 95:12480-5.
Exemplary assays useful for measuring DNAse activity of complex 56b include
but are not limited to those described in Dake E et al., 1988, J Biol Chem,
263:7691-
702.
Exemplary assays useful for measuring apoptosis/DNA fragmentation of cells
containing complex 56b include but are not limited to those described in Li LY
et al.,
2001, Nature, 412:95-9.
Exemplary assays useful for measuring GTPase activity of complex 58 include
but are not limited to those described in Tian G et al., 1999, J Biol Chem,
274:24054-8.
Exemplary assays useful for measuring mRNA deadenylation/stability in cells
containing complex 58 include but are not limited to those described in Olivas
W and
Parker R., 2000, EMBO J, 19:6602-11.
Exemplary assays useful for measuring translational repression in cells
containing
complex 58 include but are not limited to those described in Wharton RP et
al., 1998,
Mol Cell, 1:863-72.

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Exemplary assays useful for measuring esterase activity of complex 59 include
but are not limited to those described in Borhan B et al., 1995, Biochim
Biophys Acta,
1250:171-82.
Exemplary assays useful for measuring inhibition of NTE (neuropathy target
esterase) in cells containing complex 59 include but are not limited to those
described in
Ehrich M et al., 1993, Chem Biol Interact, 87:431-7.
Exemplary assays useful for measuring chromatin assembly activity of complex
60a include but are not limited to those described in Altheim BA and Schultz
MC., 1999,
Proc Natl Acad Sci U S A, 96:1345-50.
Exemplary assays useful for measuring assay for nucleotide binding of NDP
kinase of complex 60b include but are not limited to those described in Prinz
H et al.,
1999, J Biol Chem, 274:35337-42.
Exemplary assays useful for measuring chromatin assembly activity of complex
60b include but are not limited to those described in Altheim BA and Schultz
MC., 1999,
Proc Natl Acad Sci U S A, 96:1345-50.
Exemplary assays useful for measuring mutational analysis of active site of
human inosine 5'-monophosphate DH complex 60b include but are not limited to
those
described in Futer O et al., 2002, Biochim Biophys Acta, 1594:27-39.
Exemplary assays useful for measuring phosphofructokinase activity of complex
61 include but are not limited to those described in Layzer RB et al., 1969, J
Biol Chem,
244:3823-31.
Exemplary assays useful for measuring leukotriene A4 hydrolase activity of
complex 61 include but are not limited to those described in Clamagirand C et
al., 1998,
FEBS Lett, 433:68-72.
Exemplary assays useful for measuring aldolase activity of complex 62a include
but are not limited to those described in Penhoet EE and Rutter WJ., 1975,
Methods
Enzymol, 42:240-9.
Exemplary assays useful for measuring phosphoglycerate mutase activity of
complex 62a include but are not limited to those described in Grisolia S and
Carreras J.,
1975, Methods Enzymol, 42:435-50.
Exemplary assays useful for measuring triosephophate isomerase activity of
complex 62a include but are not limited to those described in Fahey RC and
Fischer
EF., 1974, Anal Biochem, 57:547-54.

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Exemplary assays useful for measuring aldolase activity of complex 62b include
but are not limited to those described in Penhoet EE and Rutter WJ., 1975,
Methods
Enzymol, 42:240-9.
Exemplary assays useful for measuring phosphoglycerate mutase activity of
complex 62b include but are not limited to those described in Grisolia S and
Carreras J.,
1975, Methods Enzymol, 42:435-50.
Exemplary assays useful for measuring triosephophate isomerase activity of
complex 62b include but are not limited to those described in Fahey RC and
Fischer
EF., 1974, Anal Biochem, 57:547-54.
Exemplary assays useful for measuring glutamine:fructose-6-phosphate
amidotransferase activity of complex 63a include but are not limited to those
described
in Traxinger RR and Marshall S., 1991, J Biol Chem, 266:10148-54.
Exemplary assays useful for measuring proteasome activity of complex 63b
include but are not limited to those described in Kuckelkorn U et al., 2000
Sep-Oct, Biol
Chem, 381:1017-23.
Exemplary assays useful for measuring homoisocitrtic acid dehydrogenase of
complex 63b include but are not limited to those described in Gaillardin CM et
al., 1982,
Eur J Biochem, 128:489-94.
Exemplary assays useful for measuring proteasome activity of complex 63b
include but are not limited to those described in Ugai S et al., 1993, J
Biochem (Tokyo),
113:754-68.
Exemplary assays useful for measuring ATPase activity of complex 63b include
but are not limited to those described in Kimura K and Hirano T., 1997, Cell,
90:625-34.
Exemplary assays useful for measuring tRNA nucleotidyltransferase activity of
complex 64 include but are not limited to those described in Chen JY et al.,
1990, J Biol
Chem, 265:16221-4. and/or , 1974, Methods Enzymol, 29:706-16.
Exemplary assays useful for measuring saccharopine dehydrogenase activity of
complex 65a include but are not limited to those described in Papes F et al.,
1999,
Biochem J, 344 Pt 2:555-63.
Exemplary assays useful for measuring saccharopine dehydrogenase activity of
complex 65b include but are not limited to those described in Papes F et al.,
1999,
Biochem J, 344 Pt 2:555-63.

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Exemplary assays useful for measuring saccharopine dehydrogenase activity of
complex 66 include but are not limited to those described in Papes F et al.,
1999,
Biochem J, 344 Pt 2:555-63.
Exemplary assays useful for measuring flavoprotein:ubiquinone oxidoreductase
activity of complex 67 include but are not limited to those described in
Goodman SI et
al., 1994, Eur J Biochem, 219:277-86.
Exemplary assays useful for measuring methionine adenosyl transferase activity
of complex 68a include but are not limited to those described in Cabrero C et
al., 1987,
Eur J Biochem, 170:299-304.
Exemplary assays useful for measuring alpha-ketoglutarate dehydrogenase
activity of complex 68a include but are not limited to those described in
Gohil K and
Jones DA., 1983, Biosci Rep, 3:1-9.
Exemplary assays useful for measuring methionine adenosyl transferase activity
of complex 68b include but are not limited to those described in Cabrero C et
al., 1987,
Eur J Biochem, 170:299-304.
Exemplary assays useful for measuring alpha-ketoglutarate dehydrogenase
activity of complex 68b include but are not limited to those described in
Gohil K and
Jones DA., 1983, Biosci Rep, 3:1-9.
Exemplary assays useful for measuring ubiquitin ligase activity of complex 69a
include but are not limited to those described in King RW et al., 1995, Cell,
81:279-88.
Exemplary assays useful for measuring metaphase arrest of cells containing
complex 69a include but are not limited to those described in Geley S et al.,
2001, J Cell
Biol, 153:137-48. and/or Kramer KM et al., 1998, EMBO J, 17:498-506.
Exemplary assays useful for measuring ubiquitin ligase activity of complex 69b
include but are not limited to those described in King RW et al., 1995, Cell,
81:279-88.
Exemplary assays useful for measuring metaphase arrest of cells containing
complex 69b include but are not limited to those described in Geley S et al.,
2001, J Cell
Biol, 153:137-48. and/or Kramer KM et al., 1998, EMBO J, 17:498-506.
Exemplary assays useful for measuring serine/threonine protein kinase activity
of
complex 70a include but are not limited to those described in Keller DM et
al., 2001, Mol
Cell, 7:283-92.
Exemplary assays useful for measuring expression of a reporter gene in cells
containing complex 70a include but are not limited to those described in
Tabtiang RK
and Herskowitz I., 1998, Mol Cell Biol, 18:4707-18.

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Exemplary animal models useful for assaying compounds interacting with Csnk2a2
(the
human homolog of Cka2) knock-out mice complex 70b include but are not limited
to
those described in Xu X et al., 1999, Nat Genet, 23:118-21.
Exemplary assays useful for measuring serine/threonine protein kinase activity
of
complex 70b include but are not limited to those described in Keller DM et
al., 2001, Mol
Cell, 7:283-92.
Exemplary assays useful for measuring protein phosphatase of complex 70b
include but are not limited to those described in Long X et al., 2002,
Apoptosis, 7:31-9.
Exemplary assays useful for measuring expression of a reporter gene in cells
containing complex 70b include but are not limited to those described in
Tabtiang RK
and Herskowitz I., 1998, Mol Cell Biol, 18:4707-18.
Exemplary assays useful for measuring nitric oxide metabolic activity of
complex
71 a include but are not limited to those described in Liu L et al., 1999,
Proc Natl Acad
Sci U S A, 96:6643-7. and/or Liu L et al., 2000, Proc Natl Acad Sci U S A,
97:4672-6.
Exemplary assays useful for measuring thiol peroxidase activity of complex 71a
include but are not limited to those described in LES Netto et al., 1996, J
Biol Chem,
271:15315-21.
Exemplary assays useful for measuring endocytosis of complex 71 b include but
are not limited to those described in Dulic V et al., 1991, Methods Enzymol,
194:697-
710. and/or Volland C et al., 1994, J Biol Chem, 269:9833-41.
Exemplary assays useful for measuring nucleosome remodeling activity of
complex 72a include but are not limited to those described in Tsukiyama T and
Wu C.,
1995, Cell, 83:1011-20.
Exemplary assays useful for measuring DNA repair in fibroblasts containing
complex 72a include but are not limited to those described in Emmert S et al.,
2000,
Proc Natl Acad Sci U S A, 97:2151-6.
Exemplary assays useful for measuring nucleosome remodeling activity of
complex 72b include but are not limited to those described in Tsukiyama T and
Wu C.,
1995, Cell, 83:1011-20.
Exemplary assays useful for measuring DNA repair in fibroblasts containing
complex 72b include but are not limited to those described in Emmert S et al.,
2000,
Proc Natl Acad Sci U S A, 97:2151-6.
Exemplary animal models useful for assaying compounds interacting with mouse
p23
knock out mice complex 73a include but are not limited to those described in
Denzel A

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et al., 2000, Curr Biol, 10:55-8.(The p24 family member p23 is required for
early
embryonic development.) -
Exemplary assays useful for measuring protein transport /sorting activity of
complex 73a include but are not limited to those described in Schimmoller F et
al., 1995,
EMBO J, 14:1329-39.
Exemplary animal models useful for assaying compounds interacting with mouse
p23
knock out mice complex 73b include but are not limited to those described in
Denzel A
et al., 2000, Curr Biol, 10:55-8.(The p24 family member p23 is required for
early
embryonic development.)
Exemplary assays useful for measuring protein transport /sorting activity of
complex 73b include but are not limited to those described in Schimmoller F et
al., 1995,
EMBO J, 14:1329-39.
Exemplary assays useful for measuring DNA binding activity of complex 74a
include but are not limited to those described in Galarneau L et al., 2000,
Mol Cell,
5:927-37.
Exemplary assays useful for measuring transformation activity of cells
containing
complex 74a include but are not limited to those described in Afar DE et al.,
1994,
Science, 264:424-6.
Exemplary assays useful for measuring DNA-binding activity of complex 74b
include but are not limited to those described in Galarneau L et al., 2000,
Mol Cell,
5:927-37.
Exemplary assays useful for measuring histone acetylation of complex 74b
include but are not limited to those described in Ito K et al., 2001, J Biol
Chem,
276:30208-15.
Exemplary assays useful for measuring transformation activity of cells
containing
complex 74b include but are not limited to those described in Afar DE et al.,
1994,
Science, 264:424-6.
Exemplary assays useful for measuring protein serine/threonine kinase activity
of
complex 75a include but are not limited to those described in McCartney RR and
Schmidt MC., 2001, J Biol Chem, 276:36460-6. and/or Mitchelhill KI et al.,
1994, J Biol
Chem, 269:2361-4.
Exemplary assays useful for measuring invasive growth of cells containing
complex 75a include but are not limited to those described in Cullen PJ and
Sprague
GF., 2000, Proc Natl Acad Sci U S A, 97:13619-24.

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Exemplary assays useful for measuring protein serine/threonine kinase activity
of
complex 75b include but are not limited to those described in McCartney RR and
Schmidt MC., 2001, J Biol Chem, 276:36460-6. and/or Mitchelhill KI et al.,
1994, J Biol
Chem, 269:2361-4.
Exemplary assays useful for measuring invasive growth of cells containing
complex 75b include but are not limited to those described in Cullen PJ and
Sprague
GF., 2000, Proc Natl Acad Sci U S A, 97:13619-24.
Exemplary assays useful for measuring 1,3-beta-D-glucan synthase activity of
complex 76 include but are not limited to those described in Cabib E and Kang
MS.,
1987, Methods Enzymol, 138:637-42. and/or Douglas CM et al., 1994, Proc Natl
Acad
Sci U S A, 91:12907-11.
Exemplary assays useful for measuring beta-1,3-glucan synthase activity in
permeabilized fungal cells containing complex 76 include but are not limited
to those
described in Sestak S and Farkas V., 2001, Anal Biochem, 292:34-9.
Exemplary assays useful for measuring exoribonuclease activity of complex 77
include but are not limited to those described in Brouwer R et al., 2001, J
Biol Chem,
276:6177-84.
Exemplary assays useful for measuring expression of non-poly(A) mRNAs in cells
containing complex 77 include but are not limited to those described in Benard
L et al.,
1999, J Virol, 73:2893-900.
Exemplary assays useful for measuring adenylate cyclase activity of complex
78a include but are not limited to those described in Hatley ME et al., 2000,
J Biol
Chem, 275:38626-32.
Exemplary assays useful for measuring long term potentiation at CA1
hippocampal synapses containing complex 78a include but are not limited to
those
described in Otmakhova NA et al., 2000, J Neurosci, 20:4446-51.
Exemplary assays useful for measuring cyclic AMP-independent growth of cells
containing complex 78a include but are not limited to those described in
Hatley ME et
al., 2000, J Biol Chem, 275:38626-32.
Exemplary assays useful for measuring protein kinase assay of complex 78b
include but are not limited to those described in Wu JJ et al., 2000, J Biomol
Screen,
5:23-30.

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Exemplary assays useful for measuring adenylate cyclase activity of complex
78b include but are not limited to those described in Hatley ME et al., 2000,
J Biol
Chem, 275:38626-32.
Exemplary assays useful for measuring long term potentiation at CA1
hippocampal synapses containing complex 78b include but are not limited to
those
described in Otmalehova NA et al., 2000, J Neurosci, 20:4446-51.
Exemplary assays useful for measuring cyclic AMP-independent growth of cells
containing complex 78b include but are not limited to those described in
Hatley ME et
al., 2000, J Biol Chem, 275:38626-32.
Exemplary assays useful for measuring GTP-binding protein/GTPase activity of
complex 79a include but are not limited to those described in Beites CL et
al., 2001,
Methods Enzymol, 329:499-510. and/or Oegema K et al., 1998, Methods Enzymol,
298:279-95.
Exemplary assays useful for measuring GTP-binding protein/GTPase activity of
complex 79b include but are not limited to those described in Beites CL et
al., 2001,
Methods Enzymol, 329:499-510. and/or Oegema K et al., 1998, Methods Enzymol,
298:279-95.
Exemplary assays useful for measuring protein deacetylase activity of complex
80a include but are not limited to those described in Wu J et al., 2001, Proc
Natl Acad
Sci U S A, 98:4391-6.
Exemplary assays useful for measuring silencing/inhibition of deacetylase
activity
in cells containing complex 80a include but are not limited to those described
in Nielsen
AL et al., 1999, EMBO J, 18:6385-95.
Exemplary assays useful for measuring protein deacetylase activity of complex
80b include but are not limited to those described in Wu J et al., 2001, Proc
Natl Acad
Sci U S A, 98:4391-6.
Exemplary assays useful for measuring silencing/inhibition of deacetylase
activity
in cells containing complex 80b include but are not limited to those described
in Nielsen
AL et al., 1999, EMBO J, 18:6385-95.
Exemplary assays useful for measuring actin polymerization activity of complex
81a include but are not limited to those described in Gieselmann R and Mann
K., 1992,
FEBS Lett, 298:149-53.

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Exemplary assays useful for measuring motility of cells containing complex 81a
include but are not limited to those described in Witke W et al., 2001, J Cell
Biol,
154:775-84.
Exemplary assays useful for measuring actin polymerization activity of complex
81 b include but are not limited to those described in Gieselmann R and Mann
K., 1992,
FEBS Lett, 298:149-53.
Exemplary assays useful for measuring motility of cells containing complex 81
b
include but are not limited to those described in Witke W et al., 2001, J Cell
Biol,
154:775-84.
Exemplary animal models useful for assaying compounds interacting with Vav-1
and
Vav-2 knock out mice complex 82a include but are not limited to those
described in
Tedford K et al., 2001, Nat Immunol, 2:548-55.(Compensation between Vav-1 and
Vav-2
in B cell development and antigen receptor signaling.)
Exemplary assays useful for measuring guanine nucleotide exchange activity of
complex 82a include but are not limited to those described in Zheng Y et al.,
1995, J Biol
Chem, 270:626-30. and/or Han J et al., 1997, Mol Cell Biol, 17:1346-53.
Exemplary assays useful for measuring formation of foci of cells containing
complex 82a include but are not limited to those described in Han J et al.,
1997, Mol Cell
Biol, 17:1346-53.
Exemplary assays useful for measuring regulation of polarized cell growth of
cells
containing complex 82a include but are not limited to those described in Nern
A and
Arkowitz RA., 1998, Nature, 391:195-8.
Exemplary animal models useful for assaying compounds interacting with Vav-1
and
Vav-2 knocfe out mice complex 82b include but are not limited to those
described in
Tedford K et al., 2001, Nat Immunol, 2:548-55.(Compensation between Vav-1 and
Vav-2
in B cell development and antigen receptor signaling.)
Exemplary assays useful for measuring guanine nucleotide exchange activity of
complex 82b include but are not limited to those described in ~heng Y et al.,
1995, J Biol
Chem, 270:626-30. and/or Han J et al., 1997, Mol Cell Biol, 17:1346-53.
Exemplary assays useful for measuring formation of foci of cells containing
complex 82b include but are not limited to those described in Han J et al.,
1997, Mol Cell
Biol, 17:1346-53.

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Exemplary assays useful for measuring regulation of polarized cell growth of
cells
containing complex 82b include but are not limited to those described in Nern
A and
Arkowitz RA., 1998, Nature, 391:195-8.
Exemplary assays useful for measuring protein serine/threonine kinase activity
of
complex 83a include but are not limited to those described in Wu JJ et al.,
2000, J
Biomol Screen, 5:23-30.
Exemplary assays useful for measuring histone H1 kinase activity of complex
83a include but are not limited to those described in Mahalingam S et al.,
1998, Proc
Natl Acad Sci U S A, 95:3419-24.
Exemplary assays useful for measuring cell cycle progression of cells
containing
complex 83a include but are not limited to those described in Mahalingam S et
al., 1998,
Proc Natl Acad Sci U S A, 95:3419-24.
Exemplary animal models useful for assaying compounds interacting with Cdkn1a
(cyclin-dependent kinase inhibitor 1A (P21), also known as Waf1, P21, CIP1,
SD11,
CAP20 and mda6) knock out mice complex 83b include but are not limited to
those
described in Deng C et al., 1995, Cell, 82:675-84.
Exemplary animal models useful for assaying compounds interacting with Kip1
(cyclin-
dependent kinase inhibitor 1 B (p27)) knock out m ice complex 83b include but
are not
limited to those described in Kiyokawa H et al., 1996, Cell, 85:721-32.
Exemplary assays useful for measuring protein serine/threonine kinase activity
of
complex 83b include but are not limited to those described in Wu JJ et al.,
2000, J
Biomol Screen, 5:23-30.
Exemplary assays useful for measuring histone H1 kinase activity of complex
83b include but are not limited to those described in Mahalingam S et al.,
1998, Proc
Natl Acad Sci U S A, 95:3419-24.
Exemplary assays useful for measuring cell cycle progression of cells
containing
complex 83b include but are not limited to those described in Mahalingam S et
al., 1998,
Proc Natl Acad Sci U S A, 95:3419-24.
Exemplary assays useful for measuring phosphoglycerate mutase activity of
complex 84 include but are not limited to those described in Zhang J et al.,
2001, Gene,
264:273-9.
Exemplary assays useful for measuring farnesyltransferase activity of complex
84 include but are not limited to those described in Goodman LE et al., 1990,
Proc Natl
Acad Sci U S A, 87:9665-9.

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Exemplary assays useful for measuring transformation activity of cells
containing
complex 84 include but are not limited to those described in Nagase T et al.,
1999, Int J
Cancer, 80:126-33.
Exemplary assays useful for measuring protein deacetylase activity of complex
85 include but are not limited to those described in Nare B et al., 1999, Anal
Biochem,
267:390-6.
Exemplary assays useful for measuring protease activity of complex 85 include
but are not limited to those described in Susan PP and Dunn WA., 2001, J Cell
Physiol,
187:48-58.
Exemplary assays useful for measuring nuclear import/export activity of
complex
85 include but are not limited to those described in Jakel S and Gorlich D.,
1998, EMBO
J, 17:4491-502.
Exemplary assays useful for measuring autophagy in cells containing complex 85
include but are not limited to those described in Elmore SP et al., 2001,
FASEB J,
15:2286-7.
Exemplary animal models useful for assaying com pounds interacting with
transgenic
mice displaying a human prostate cancer-like phenotype complex 86a include but
are
not limited to those described in Saffran DC et al., 2001, Proc Natl Acad Sci
U S A,
98:2658-63.
Exemplary assays useful for measuring ATPase activity of complex 86a include
but are not limited to those described in Tsukiyama T et al., 1999, Genes Dev,
13:686-
97.
Exemplary assays useful for measuring transcriptional activity of complex 86a
include but are not limited to those described in Kikyo N et al., 2000,
Science, 289:2360-
2.
Exemplary assays useful for measuring the cell cycle regulation activity of
complex 86a include but are not limited to those described in Cao Y et al.,
1997, Mol
Cell Biol, 17:3323-34.
Exemplary assays useful for measuring differentiation of cells containing
complex
86a include but are not limited to those described in de la Serna IL et al.,
2001, Nat
Genet, 27:187-90.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying a human prostate cancer-like phenotype complex 86b include but
are

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not limited to those described in Saffran DC et al., 2001, Proc Natl Acad Sci
U S A,
98:2658-63.
Exemplary assays useful for measuring ATPase activity of complex 86b include
but are not limited to those described in Tsukiyama T et al., 1999, Genes Dev,
13:686-
97.
Exemplary assays useful for measuring transcriptional activity of complex 86b
include but are not limited to those described in Kikyo N et al., 2000,
Science, 289:2360-
2.
Exemplary assays useful for measuring Chromatine remodelling of complex 86b
include but are not limited to those described in Wang W et al., 1996, EMBO J,
15:5370-
82.
Exemplary assays useful for measuring the cell cycle regulation activity of
complex 86b include but are not limited to those described in Cao Y et al.,
1997, Mol
Cell Biol, 17:3323-34.
Exemplary assays useful for measuring differentiation of cells containing
complex
86b include but are not limited to those described in de la Serna IL et al.,
2001, Nat
Genet, 27:187-90.
Exemplary assays useful for measuring N-acetyltransferase activity of complex
87a include but are not limited to those described in ICulkarni MS and Sherman
F., 1994,
J Biol Chem, 269:13141-7.
Exemplary assays useful for measuring transformation activity of cells
containing
complex 87a include but are not limited to those described in Afar DE et al.,
1994,
Science, 264:424-6.
Exemplary assays useful for measuring N-acetyltransferase activity of complex
87b include but are not limited to those described in Kulkarni MS and Sherman
F., 1994,
J Biol Chem, 269:13141-7.
Exemplary assays useful for measuring transformation activity of cells
containing
complex 87b include but are not limited to those described in Afar DE et al.,
1994,
Science, 264:424-6.
Exemplary assays useful for measuring histone deacetylase activity of complex
88a include but are not limited to those described in Nare B et al., 1999,
Anal Biochem,
267:390-6.

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Exemplary assays useful for measuring histone deacetylase activity of complex
88b include but are not limited to those described in Nare B et al., 1999,
Anal Biochem,
267:390-6.
Exemplary assays useful for measuring ATPase stimulation activity of complex
89a include but are not limited to those described in Steel GJ et al., 1999,
Biochemistry,
38:7764-72.
Exemplary assays useful for measuring endocytosis via the uptake of the vital
dye
FM4-64 in cells containing complex 89a include but are not limited to those
described in
Gurunathan S et al., 2000, Mol Biol Cell, 11:3629-43.
Exemplary assays useful for measuring endocytosis of alpha-factor receptor in
cells containing complex 89a include but are not limited to those described in
Stefan CJ
and Blumer KJ., 1999, J Biol Chem, 274:1835-41.
Exemplary assays useful for measuring golgi -endosome fusion of complex 89b
include but are not limited to those described in Brickner JH et al., 2001, J
Cell Biol,
155:969-78.
Exemplary assays useful for measuring endocytosis via the uptake of the vital
dye
FM4-64 in cells containing complex 89b include but are not limited to those
described in
Gurunathan S et al., 2000, Mol Biol Cell, 11:3629-43.
Exemplary assays useful for measuring endocytosis of alpha-factor receptor in
cells containing complex 89b include but are not limited to those described in
Stefan CJ
and Blumer KJ., 1999, J Biol Chem, 274:1835-41.
Exemplary assays useful for measuring acetyl-coenzyme A carboxylase activity
of
complex 90a include but are not limited to those described in Oizumi J and
Hayakawa
K., 1990, J Chromatogr, 529:55-63.
Exemplary assays useful for measuring acetyl-CoA carboxylase activity in
isolated hepatocytes containing complex 90a include but are not limited to
those
described in Bijleveld C and Geelen MJ., 1987, Biochim Biophys Acta, 918:274-
83.
Exemplary assays useful for measuring acetyl-coenzyme A carboxylase activity
of
complex 90b include but are not limited to those described in Oizumi J and
Hayakawa
K., 1990, J Chromatogr, 529:55-63.
Exemplary assays useful for measuring acetyl-CoA carboxylase activity in
isolated hepatocytes containing complex 90b include but are not limited to
those
described in Bijleveld C and Geelen MJ., 1987, Biochim Biophys Acta, 918:274-
83.

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Exemplary assays useful for measuring guanylyl transferase activity of complex
91a include but are not limited to those described in Itoh N et al., 1984, J
Biol Chem,
259:13930-6.
Exemplary assays useful for measuring RNA triphosphatase activity of complex
91 a include but are not limited to those described in Ho CK et al., 1998, J
Biol Chem,
273:34151-6.
Exemplary assays useful for measuring guanylyl transferase activity of complex
91 b include but are not limited to those described in Itoh N et al., 1984, J
Biol Chem,
259:13930-6.
Exemplary assays useful for measuring RNA triphosphatase activity of complex
91 b include but are not limited to those described in Ho CK et al., 1998, J
Biol Chem,
273:34151-6.
Exemplary assays useful for measuring serine palmitoyltransferase activity of
complex 92a include but are not limited to those described in Pinto WJ et al.,
1992, J
Bacteriol, 174:2575-81. and/or Weiss B and Stoffel W., 1997, Eur J Biochem,
249:239-
47.
Exemplary assays useful for measuring differentiation of cells containing
complex
92a include but are not limited to those described in Roberts RL et al., 1997,
Cell,
89:1055-65.
Exemplary assays useful for measuring serine palmitoyltransferase activity of
complex 92b include but are not limited to those described in Pinto WJ et al.,
1992, J
Bacteriol, 174:2575-81. and/or Weiss B and Stoffel W., 1997, Eur J Biochem,
249:239-
47.
Exemplary assays useful for measuring differentiation of cells containing
complex
92b include but are not limited to those described in Roberts RL et al., 1997,
Cell,
89:1055-65.
Exemplary assays useful for measuring nuclear import/export activity of
complex
93a include but are not limited to those described in Singleton DR et al.,
1995, J Cell
Sci, 108 ( Pt 1):265-72.
Exemplary assays useful for measuring receptor/protein translocation activity
of
complex 93a include but are not limited to those described in Shaywitz DA et
al., 1995, J
Cell Biol, 128:769-77. and/or Pryer NK et al., 1993, J Cell Biol, 120:865-75.

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Exemplary assays useful for measuring gene expression of a reporter protein
and
viral replication in cells containing complex 93a include but are not limited
to those
described in Paca RE et al., 2000, J Virol, 74:9507-14.
Exemplary assays useful for measuring nuclear import/export activity of
complex
93b include but are not limited to those described in Singleton DR et al.,
1995, J Cell
Sci, 108 ( Pt 1 ):265-72.
Exemplary assays useful for measuring receptor/protein translocation activity
of
complex 93b include but are not limited to those described in Shaywitz DA et
al., 1995, J
Cell Biol, 128:769-77. and/or Pryer NK et al., 1993, J Cell Biol, 120:865-75.
Exemplary assays useful for measuring gene expression of a reporter protein
and
viral replication in cells containing complex 93b include but are not limited
to those
described in Paca RE et al., 2000, J Virol, 74:9507-14.
Exemplary assays useful for measuring protein translocation activity of
complex
94a include but are not limited to those described in Brodsky JL and Schekman
R.,
1993, J Cell Biol, 123:1355-63.
Exemplary assays useful for measuring 1,3-beta-D-glucan synthase activity of
complex 94a include but are not limited to those described in Mazur P and
Baginsky W.,
1996, J Biol Chem, 271:14604-9.
Exemplary assays useful for measuring in vivo interaction of yeast sec63 using
the split-ubiquitin technique in cells containing complex 94a include but are
not limited to
those described in Wittke S et al., 1999, Mol Biol Cell, 10:2519-30.
Exemplary assays useful for measuring protein translocation activity of
complex
94b include but are not limited to those described in Brodsky JL and Schekman
R.,
1993, J Cell Biol, 123:1355-63.
Exemplary assays useful for measuring in vivo interaction of yeast sec63 using
the split-ubiquitin technique in cells containing complex 94b include but are
not limited to
those described in Wittke S et al., 1999, Mol Biol Cell, 10:2519-30.
Exemplary assays useful for measuring ATP-dependent heteroduplex formation
activity of complex 95 include but are not limited to those described in
Baumann P and
West SC., 1999, J Mol Biol, 291:363-74.
Exemplary assays useful for measuring DNA recombination activity of complex
95 include but are not limited to those described in Song B and Sung P., 2000,
J Biol
Chem, 275:15895-904. and/or Erdile LF et al., 1991, J Biol Chem, 266:12090-8.
and/or
He Z et al., 1996, J Biol Chem, 271:28243-9.

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Exemplary assays useful for measuring DNA repair in chicken B cells containing
complex 95 include but are not limited to those described in Takata M et al.,
2001, Mol
Cell Biol, 21:2858-66.
Exemplary assays useful for measuring Rab recycling activity of complex 96
include but are not limited to those described in Gilbert PM and Burd CG.,
2001, J Biol
Chem, 276:8014-20.
Exemplary assays useful for measuring Rab protein binding activity of complex
96 include but are not limited to those described in D'Adamo P et al., 1998,
Nat Genet,
19:134-9.
Exemplary assays useful for measuring differentiation of neuronal cells
containing
complex 96 include but are not limited to those described in D'Adamo P et al.,
1998, Nat
Genet, 19:134-9.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice used for the study of ovary development complex 97a include but are not
limited to
those described in Freiman RN et al., 2001, Science, 293:2084-7.
Exemplary assays useful for measuring ATPase activity of complex 97a include
but are not limited to those described in Tsukiyama T et al., 1999, Genes Dev,
13:686-
97.
Exemplary assays useful for measuring transcriptional activity of complex 97a
include but are not limited to those described in Kikyo N et al., 2000,
Science, 289:2360-
2.
Exemplary assays useful for measuring cell cycle regulation activity of
complex
97a include but are not limited to those described in Cao Y et al., 1997, Mol
Cell Biol,
17:3323-34.
Exemplary assays useful for measuring differentiation of cells containing
complex
97a include but are not limited to those described in de la Serna IL et al.,
2001, Nat
Genet, 27:187-90.
Exemplary assays useful for measuring ATPase activity of complex 97b include
but are not limited to those described in Tsukiyama T et al., 1999, Genes Dev,
13:686-
97.
Exemplary assays useful for measuring transcriptional activity of complex 97b
include but are not limited to those described in Kikyo N et al., 2000,
Science, 289:2360-
2.

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Exemplary assays useful for measuring cell cycle regulation activity of
complex
97b include but are not limited to those described in Cao Y et al., 1997, Mol
Cell Biol,
17:3323-34.
Exemplary animal models useful for assaying compounds interacting with myosin-
VA or
Rab27a or leaden (In) mutant mice complex 98a include but are not limited to
those
described in Wilson SM et al., 2000, Proc Natl Acad Sci U S A, 97:7933-8.
Exemplary assays useful for measuring Golgi to ER transport activity of
complex
98a include but are not limited to those described in Dogic D et al., 1999,
Eur J Cell Biol,
78:305-10.
Exemplary assays useful for measuring cell free vesicle budding activity of
complex 98a include but are not limited to those described in Ahluwalia JP et
al., 2001, J
Biol Chem, 276:34148-55.
Exemplary assays useful for measuring protein transport /sorting activity of
complex 98a include but are not limited to those described in Schimmoller F et
al., 1995,
EMBO J, 14:1329-39.
Exemplary assays useful for measuring hyperplasticity of Golgi in cells
containing
complex 98a include but are not limited to those described in Carrasco L et
al., 2001, J
Comp Pathol, 125:1-7.
Exemplary assays useful for measuring movements of vaccinia virus
intracellular
enveloped virions in cells containing complex 98a include but are not limited
to those
described in Geada MM et al., 2001, J Gen Virol, 82:2747-60.
Exemplary animal models useful for assaying compounds interacting with myosin-
VA or
Rab27a or leaden (In) mutant mice complex 98b include but are not limited to
those
described in Wilson SM et al., 2000, Proc Natl Acad Sci U S A, 97:7933-8.
Exemplary assays useful for measuring Golgi to ER transport activity of
complex
98b include but are not limited to those described in Dogic D et al., 1999,
Eur J Cell Biol,
78:305-10.
Exemplary assays useful for measuring cell free vesicle budding activity of
complex 98b include but are not limited to those described in Ahluwalia JP et
al., 2001, J
Biol Chem, 276:34148-55.
Exemplary assays useful for measuring protein transport /sorting activity of
complex 98b include but are not limited to those described in Schimmoller F et
al., 1995,
EMBO J, 14:1329-39.

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Exemplary assays useful for measuring hyperplasticity of Golgi in cells
containing
complex 98b include but are not limited to those described in Carrasco L et
al., 2001, J
Comp Pathol, 125:1-7.
Exemplary assays useful for measuring movements of vaccinia virus
intracellular
enveloped virions in cells containing complex 98b include but are not limited
to those
described in Geada MM et al., 2001, J Gen Virol, 82:2747-60.
Exemplary assays useful for measuring carbamylphosphate synthetase activity of
complex 99 include but are not limited to those described in Kaseman DS and
Meister
A., 1985, Methods Enzymol, 113:305-26.
Exemplary assays useful for measuring methionine adenosyl transferase activity
of complex 99 include but are not limited to those described in Cabrero C et
al., 1987,
Eur J Biochem, 170:299-304.
Exemplary assays useful for measuring carbamylphosphate synthetase activity of
complex 99 include but are not limited to those described in Pierson DL and
Brien JM.,
1980, J Biol Chem, 255:7891-5.
Exemplary assays useful for measuring pyruvate dehydrogenase activity of
complex 100a include but are not limited to those described in Pettit FH and
Reed LJ.,
1982, Methods Enzymol, 89 Pt D:376-86. and/or Chretien D et al., 1995, Clin
Chim Acta,
240:129-36.
Exemplary assays useful for measuring pyruvate dehydrogenase activity of
complex 100b include but are not limited to those described in Pettit FH and
Reed LJ.,
1982, Methods Enzymol, 89 Pt D:376-86. and/or Chretien D et al., 1995, Clin
Chim Acta,
240:129-36.
Exemplary animal models useful for assaying compounds interacting with APP
family
members null transgenic mice or combinations of such transgenes complex 101 a
include but are not limited to those described in Heber S et al., 2000, J
Neurosci,
20:7951-63.
Exemplary animal models useful for assaying compounds interacting with ATM
knock
out mice complex 101 a include but are not limited to those described in
Spring K et al.,
2001, Cancer Res, 61:4561-8.
Exemplary assays useful for measuring translational activity of complex 101 a
include but are not limited to those described in Valasek L et al., 2001, EMBO
J, 20:891-
904.

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Exemplary assays useful for measuring protease IC resistance of complex 101a
include but are not limited to those described in Paushkin SV et al., 1997,
Science,
277:381-3.
Exemplary assays useful for measuring guanine nucleotide exchange activity of
complex 101a include but are not limited to those described in Bickle M et
al., 1998,
EMBO J, 17:2235-45.
Exemplary assays useful for measuring apoptosis and radiosensitivity of cells
containing complex 101a include but are not limited to those described in
Shigeta T et
al., 1999, Cancer Res, 59:2602-7.
Exemplary assays useful for measuring suppressor activity and foci formation
of
cells containing complex 101a include but are not limited to those described
in Santoso
A et al., 2000, Cell, 100:277-88.
Exemplary assays useful for measuring amyloid fibrils formation of cells
containing complex 101 a include but are not limited to those described in
Palm M et al.,
1997, APMIS, 105:603-8.
Exemplary animal models useful for assaying compounds interacting with APP
family
members null transgenic mice or combinations of such transgenes complex 101 b
include but are not limited to those described in Heber S et al., 2000, J
Neurosci,
20:7951-63.
Exemplary animal models useful for assaying compounds interacting with ATM
knock-
out mice complex 101b include but are not limited to those described in Spring
K et al.,
2001, Cancer Res, 61:4561-8.
Exemplary assays useful for measuring translational activity of complex 101 b
include but are not limited to those described in Valasek L et al., 2001, EMBO
J, 20:891-
904.
Exemplary assays useful for measuring protein kinase assay of complex 101b
include but are not limited to those described in Chen H et al., 2001,
Biochemistry,
40:11851-9.
Exemplary assays useful for measuring protease IC resistance of complex 101 b
include but are not limited to those described in Paushkin SV et al., 1997,
Science,
277:381-3.
Exemplary assays useful for measuring guanine nucleotide exchange activity of
complex 101 b include but are not limited to those described in Bickle M et
al., 1998,
EMBO J, 17:2235-45.

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Exemplary assays useful for measuring apoptosis and radiosensitivity of cells
containing complex 101 b include but are not limited to those described in
Shigeta T et
al., 1999, Cancer Res, 59:2602-7.
Exemplary assays useful for measuring suppressor activity and foci formation
of
cells containing complex 101b include but are not limited to those described
in Santoso
A et al., 2000, Cell, 100:277-88.
Exemplary assays useful for measuring amyloid fibrils formation of cells
containing complex 101 b include but are not limited to those described in
Palm M et al.,
1997, APMIS, 105:603-8.
Exemplary assays useful for measuring vesicle targeting activity of complex
102a
include but are not limited to those described in Sacher M et al., 2001, Mol
Cell, 7:433-
42.
Exemplary assays useful for measuring ER to Golgi transport activity of
complex
102a include but are not limited to those described in Sacher M et al., 1998,
EMBO J,
17:2494-503.
Exemplary assays useful for measuring vesicle targeting activity of complex
102b
include but are not limited to those described in Sacher M et al., 2001, Mol
Cell, 7:433-
42.
Exemplary assays useful for measuring ER to Golgi transport activity of
complex
102b include but are not limited to those described in Sacher M et al., 1998,
EMBO J,
17:2494-503.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying a fragile X syndrome-like phenotype complex 103 include but
are not
limited to those described in Kooy RF et al., 1996, Am J Med Genet, 64:241-5.
and/or
Oostra BA and Hoogeveen AT., 1997, Ann Med, 29:563-7.
Exemplary assays useful for measuring RNA binding activity of complex 103
include but are not limited to those described in Thisted T et al., 2001, J
Biol Chem,
276:17484-96.
Exemplary assays useful for measuring kinase activity of complex 103 include
but are not limited to those described in Altman R and Kellogg D., 1997, J
Cell Biol,
138:119-30.
Exemplary animal models useful for assaying compounds interacting with snf5
knock out
mice (homozygous or heterozygous ) complex 105a include but are not limited to
those
described in Klochendler-Yeivin A et al., 2000, EMBO Rep, 1:500-6.

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Exemplary assays useful for measuring casein kinase I activity of complex 105a
include but are not limited to those described in DeMaggio AJ et al., 1992,
Proc Natl
Acad Sci U S A, 89:7008-12.
Exemplary assays useful for measuring nucleosomal remodelling activity of
complex 105a include but are not limited to those described in Ostlund
Farrants AK et
al., 1997, Mol Cell Biol, 17:895-905, and/or Logie C and Peterson CL., 1997,
EMBO J,
16:6772-82.
Exemplary assays useful for measuring expression of a reporter gene in cells
containing complex 105a include but are not limited to those described in
Muchardt C
and Yaniv M., 1993, EMBO J, 12:4279-90.
Exemplary animal models useful for assaying compounds interacting with snf5
knoc4e out
mice (homozygous or heterozygous ) complex 105b include but are not limited to
those
described in Klochendler-Yeivin A et al., 2000, EMBO Rep, 1:500-6.
Exemplary assays useful for measuring transcription assay of complex 105b
include but are not limited to those described in Hipskind RA and Nordheim A.,
1991, J
Biol Chem, 266:19572-82.
Exemplary assays useful for measuring nucleosomal remodelling activity of
complex 105b include but are not limited to those described in Ostlund
Farrants AK et
al., 1997, Mol Cell Biol, 17:895-905. and/or Logie C and Peterson CL., 1997,
EMBO J,
16:6772-82.
Exemplary assays useful for measuring expression of a reporter gene in cells
containing complex 105b include but are not limited to those described in
Muchardt C
and Yaniv M., 1993, EMBO J, 12:4279-90.
Exemplary animal models useful for assaying compounds interacting with mice
treated
with alcohol to inhibit proteasome activity complex 106a include but are not
limited to
those described in Bardag-Gorce F et al., 2000, Biochem Biophys Res Commun,
279:23-9.(The effect of ethanol-induced cytochrome p4502E1 on the inhibition
of
proteasome activity by alcohol.)
Exemplary assays useful for measuring the protease activity of complex 106a
include but are not limited to those described in Kuckelkorn U et al:, 2000
Sep-Oct, Biol
Chem, 381:1017-23. and/or Ugai S et al., 1993, J Biochem (Tokyo), 113:754-68.
Exemplary assays useful for measuring chymotryptic and tryptic activities of
the
proteasome in cells containing complex 106a include but are not limited to
those
described in Lightcap ES et al., 2000, Clin Chem, 46:673-83.

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Exemplary assays useful for measuring stability of fluorescent protein markers
in
cells containing complex 106a include but are not limited to those described
in
Andreatta C et al., 2001, Biotechniques, 30:656-60.
Exemplary animal models useful for assaying compounds interacting with mice
treated
with alcohol to inhibit proteasome activity complex 106b include but are not
limited to
those described in Bardag-Gorce F et al., 2000, Biochem Biophys Res Commun,
279:23-9.(The effect of ethanol-induced cytochrome p4502E1 on the inhibition
of
proteasome activity by alcohol.)
Exemplary assays useful for measuring the protease activity of complex 106b
include but are not limited to those described in Kuckelkorn U et al., 2000
Sep-Oct, Biol
Chem, 381:1017-23. and/or Ugai S et al., 1993, J Biochem (Tokyo), 113:754-68.
Exemplary assays useful for measuring chymotryptic and tryptic activities of
the
proteasome in cells containing complex 106b include but are not limited to
those
described in Lightcap ES et al., 2000, Clin Chem, 46:673-83.
Exemplary assays useful for measuring stability of fluorescent protein markers
in
cells containing complex 106b include but are not limited to those described
in
Andreatta C et al., 2001, Biotechniques, 30:656-60.
Exemplary assays useful for measuring actin filament motility regulation
activity of
complex 107a include but are not limited to those described in Evans LL et
al., 1998, J
Cell Sci, 111 ( Pt 14):2055-66.
Exemplary assays useful for measuring motility of cells containing complex
107a
include but are not limited to those described in Williams R and Coluccio LM.,
1994, Cell
Motil Cytoskeleton, 27:41-8.
Exemplary animal models useful for assaying compounds interacting with myosin-
VA or
Rab27a or leaden (In) mutant mice complex 107b include but are not limited to
those
described in Wilson SM et al., 2000, Proc Natl Acad Sci U S A, 97:7933-8.
Exemplary assays useful for measuring RNA 3'-5' exonuclease activity of
complex 107b include but are not limited to those described in Benard L et
al., 1999, J
Virol, 73:2893-900.
Exemplary assays useful for measuring ATPase of complex 107b include but are
not limited to those described in Kimura K and Hirano T., 1997, Cell, 90:625-
34.
Exemplary assays useful for measuring actin filament motility regulation
activity of
complex 107b include but are not limited to those described in Evans LL et
al., 1998, J
Cell Sci, 111 ( Pt 14):2055-66.

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Exemplary assays useful for measuring motility of cells containing complex
107b
include but are not limited to those described in Williams R and Coluccio LM.,
1994, Cell
Motil Cytoskeleton, 27:41-8.
Exemplary assays useful for measuring specific DNA binding activity of complex
108a include but are not limited to those described in Schramke V et al.,
2001, Genes
Dev, 15:1845-58.
Exemplary assays useful for measuring telomere length regulation activity of
complex 108a include but are not limited to those described in Corda Y et al.,
1999, Nat
Genet, 21:204-8.
Exemplary assays useful for measuring telomeric silencing of cll containing
complex 108a include but are not limited to those described in Gottschling DE
et al.,
1990, Cell, 63:751-62.
Exemplary assays useful for measuring telomeric silencing of cells containing
complex 108a include but are not limited to those described in Nislow C et
al., 1997, Mol
Biol Cell, 8:2421-36.
Exemplary assays useful for measuring cell viability after exposure to DNA-
damaging agents of cells containing complex 108a include but are not limited
to those
described in Corda Y et al., 1999, Nat Genet, 21:204-8.
Exemplary assays useful for measuring specific DNA binding activity of complex
108b include but are not limited to those described in Schramke V et al.,
2001, Genes
Dev, 15:1845-58.
Exemplary assays useful for measuring histon methyltransferase of complex
108b include but are not limited to those described in Roguev A et al., 2001,
EMBO J,
20:7137-48.
Exemplary assays useful for measuring histone methylation of complex 108b
include but are not limited to those described in Briggs SD et al., 2001,
Genes Dev,
15:3286-95.
Exemplary assays useful for measuring telomere length regulation activity of
complex 108b include but are not limited to those described in Corda Y et al.,
1999, Nat
Genet, 21:204-8.
Exemplary assays useful for measuring telomeric silencing of cll containing
complex 108b include but are not limited to those described in Gottschling DE
et al.,
1990, Cell, 63:751-62.

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Exemplary assays useful for measuring telomeric silencing of cells containing
complex 108b include but are not limited to those described in Nislow C et
al., 1997, Mol
Biol Cell, 8:2421-36.
Exemplary assays useful for measuring cell viability after exposure to DNA-
damaging agents of cells containing complex 108b include but are not limited
to those
described in Corda Y et al., 1999, Nat Genet, 21:204-8.
Exemplary assays useful for measuring vacuole fusion activity of complex 109a
include but are not limited to those described in Sato TK et al., 2000, Mol
Cell, 6:661-71.
Exemplary assays useful for measuring alanine/arginine aminopeptidase activity
of complex 109a include but are not limited to those described in Caprioglio
DR et al.,
1993, J Biol Chem, 268:14310-5.
Exemplary assays useful for measuring invertase secretion of cells containing
complex 109a include but are not limited to those described in Horazdovsky BF
et al.,
1996, J Biol Chem, 271:33607-15.
Exemplary assays useful for measuring vacuole fusion activity of complex 109b
include but are not limited to those described in Sato TK et al., 2000, Mol
Cell, 6:661-71.
Exemplary assays useful for measuring alanine/arginine aminopeptidase activity
of complex 109b include but are not limited to those described in Caprioglio
DR et al.,
1993, J Biol Chem, 268:14310-5.
Exemplary assays useful for measuring invertase secretion of cells containing
complex 109b include but are not limited to those described in Horazdovsky BF
et al.,
1996, J Biol Chem, 271:33607-15.
Exemplary assays useful for measuring ribonucleotide reductase activity of
complex 110a include but are not limited to those described in Chabes A et
al., 1999, J
Biol Chem, 274:36679-83.
Exemplary assays useful for measuring transcriptional activity of complex 110a
include but are not limited to those described in Paull TT et al., 1996, Genes
Dev,
10:2769-81.
Exemplary assays useful for measuring ATPase activity of complex 110a include
but are not limited to those described in Cairns BR et al., 1996, Cell,
87:1249-60.
Exemplary assays useful for measuring gene expression in cells containing
complex 110a include but are not limited to those described in Liu M et al.,
1999, J Biol
Chem, 274:15433-9.

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Exemplary assays useful for measuring drug resistance of cells expressing
complex 110a include but are not limited to those described in Choy BK et al.,
1988,
Cancer Res, 48:2029-35.
Exemplary assays useful for measuring ribonucleotide reductase activity of
complex 110b include but are not limited to those described in Chabes A et
al., 1999, J
Biol Chem, 274:36679-83.
Exemplary assays useful for measuring transcriptional activity of complex 110b
include but are not limited to those described in Paull TT et al., 1996, Genes
Dev,
10:2769-81.
Exemplary assays useful for measuring ATPase activity of complex 110b include
but are not limited to those described in Cairns BR et al., 1996, Cell,
87:1249-60.
Exemplary assays useful for measuring gene expression in cells containing
complex 110b include but are not limited to those described in Liu M et al.,
1999, J Biol
Chem, 274:15433-9.
Exemplary assays useful for measuring drug resistance of cells expressing
complex 110b include but are not limited to those described in Choy BK et al.,
1988,
Cancer Res, 48:2029-35.
Exemplary assays useful for measuring transporter activity of complex 111
include but are not limited to those described in Moy TI and Silver PA., 1999,
Genes
Dev, 13:2118-33.
Exemplary assays useful for measuring rRNA synthesis activity of complex 111
include but are not limited to those described in Venema J and Tollervey D.,
1996,
EMBO J, 15:5701-14.
Exemplary assays useful for measuring ribosomal assembly regulation activity
of
complex 111 include but are not limited to those described in Kressler D et
al., 1997,
Mol Cell Biol, 17:7283-94.
Exemplary assays useful for measuring cell cycle arrest of cells containing
complex 111 include but are not limited to those described in Pestov DG et
al., 2001,
Mol Cell Biol, 21:4246-55.
Exemplary assays useful for measuring uncoating of viral nucleocapsids in
cells
containing complex 111 include but are not limited to those described in Singh
I and
Helenius A., 1992, J Virol, 66:7049-58.

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Exemplary assays useful for measuring subcellular localization/transport of
ribosomal proteins in cells containing complex 111 include but are not limited
to those
described in Hurt E et al., 1999, J Cell Biol, 144:389-401.
Exemplary assays useful for measuring heatshock protein Hsp90 binding activity
of complex 112a include but are not limited to those described in Marsh JA et
al., 1998,
Mol Cell Biol, 18:7353-9.
Exemplary assays useful for measuring heat-shock induced protein aggregation
in COS cells containing complex 112a include but are not limited to those
described in
Sittler A et al., 2001, Hum Mol Genet, 10:1307-15.
Exemplary assays useful for measuring heatshock protein Hsp90 binding activity
of complex 112b include but are not limited to those described in Marsh JA et
al., 1998,
Mol Cell Biol, 18:7353-9.
Exemplary assays useful for measuring heat-shock induced protein aggregation
in COS cells containing complex 112b include but are not limited to those
described in
Sittler A et al., 2001, Hum Mol Genet, 10:1307-15.
Exemplary assays useful for measuring casein kinase activity of complex 113a
include but are not limited to those described in Park JW and Bae YS., 1999,
Biochem
Biophys Res Commun, 263:475-81.
Exemplary assays useful for measuring transcriptional activity of complex 113a
include but are not limited to those described in Shi X et al., 1997, Mol Cell
Biol,
17:1160-9.
Exemplary assays useful for measuring sensitivity to drugs (6AU or
mycophenolix
acid) of cells containing complex 113a include but are not limited to those
described in
Shaw RJ et al., 2001, J Biol Chem, 276:32905-16.
Exemplary assays useful for measuring casein kinase activity of complex 113b
include but are not limited to those described in Park JW and Bae YS., 1999,
Biochem
Biophys Res Commun, 263:475-81.
Exemplary assays useful for measuring transcriptional activity of complex 113b
include but are not limited to those described in Shi X et al., 1997, Mol Cell
Biol,
17:1160-9.
Exemplary assays useful for measuring sensitivity to drugs (6AU or
mycophenolix
acid) of cells containing complex 113b include but are not limited to those
described in
Shaw RJ et al., 2001, J Biol Chem, 276:32905-16.

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Exemplary assays useful for measuring oligosaccharyltransferase activity of
complex 114a include but are not limited to those described in Kumar V et al.,
1994,
Anal Biochem, 219:305-8.
Exemplary assays useful for measuring oligosaccharyltransferase activity of
complex 114b include but are not limited to those described in Kumar V et al.,
1994,
Anal Biochem, 219:305-8.
Exemplary animal models useful for assaying compounds interacting with ATR
knock-out
mice (chromosomal fragmentation and early embryonic lethality phenotypes)
complex
115 include but are not limited to those described in Brown EJ and Baltimore
D., 2000,
Genes Dev, 14:397-402.
Exemplary assays useful for measuring protein kinase activity of complex 115
include but are not limited to those described in Abe Y et al., 2001, J Biol
Chem,
276:44003-11.
Exemplary assays useful for measuring ATPase activity of complex 115 include
but are not limited to those described in Zhang Y et al., 1998, Cell, 95:279-
89.
Exemplary assays useful for measuring DNA repair in fibroblasts containing
complex 115 include but are not limited to those described in Emmert S et al.,
2000,
Proc Natl Acad Sci U S A, 97:2151-6.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying a human prostate cancer-like phenotype complex 116a include
but are
not limited to those described in Saffran DC et al., 2001, Proc Natl Acad Sci
U S A,
98:2658-63.
Exemplary assays useful for measuring ATPase activity of complex 116a include
but are not limited to those described in Tsukiyama T et al., 1999, Genes Dev,
13:686-
97.
Exemplary assays useful for measuring transcriptional activity of complex 116a
include but are not limited to those described in Kikyo N et al., 2000,
Science, 289:2360-
2.
Exemplary assays useful for measuring differentiation of cells containing
complex
116a include but are not limited to those described in de la Serna IL et al.,
2001, Nat
Genet, 27:187-90.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying a human prostate cancer-like phenotype complex 116b include
but are

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not limited to those described in SafFran DC et al., 2001, Proc Natl Acad Sci
U S A,
98:2658-63.
Exemplary assays useful for measuring ATPase activity of complex 116b include
but are not limited to those described in Tsukiyama T et al., 1999, Genes Dev,
13:686-
97.
Exemplary assays useful for measuring transcriptional activity of complex 116b
include but are not limited to those described in Kikyo N et al., 2000,
Science, 289:2360-
2.
Exemplary assays useful for measuring Chromatin remodeling of complex 116b
include but are not limited to those described in Wang W et al., 1996, EMBO J,
15:5370-
82.
Exemplary assays useful for measuring differentiation of cells containing
complex
116b include but are not limited to those described in de la Serna IL et al.,
2001, Nat
Genet, 27:187-90.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying a breast cancer-like phenotype complex 117 include but are not
limited
to those described in Stewart TA et al., 1984, Cell, 38:627-37.(Spontaneous
mammary
adenocarcinomas in transgenic mice that carry and express MTV/myc fusion
genes.)
Exemplary assays useful for measuring transcriptional activity of complex 117
include but are not limited to those described in Kotova I et al., 2001, Eur J
Biochem,
268:4527-36. and/or Carrozza MJ and DeLuca NA., 1996, Mol Cell Biol, 16:3085-
93.
Exemplary assays useful for measuring gene expression in cells containing
complex 117 include but are not limited to those described in Zhu A and
Kuziora MA.,
1996, J Biol Chem, 271:20993-6.
Exemplary assays useful for measuring gene expression activity of complex 118a
include but are not limited to those described in Lewis ML et al., 2001, FASEB
J,
15:1783-5.
Exemplary assays useful for measuring endocytosis regulation activity of
complex 118a include but are not limited to those described in Dulic V et al.,
1991,
Methods Enzymol, 194:697-710.
Exemplary assays useful for measuring changes in motility of cells containing
complex 118a include but are not limited to those described in Westerberg L et
al.,
2001, Blood, 98:1086-94.

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Exemplary assays useful for measuring cytoskeletal changes of cells containing
complex 118a include but are not limited to those described in Lommel S et
al., 2001,
EMBO Rep, 2:850-7.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying a Wiskott-Aldrich syndrome-like phenotype complex 118b include
but
are not limited to those described in Snapper SB et al., 1998, Immunity, 9:81-
91.
Exemplary assays useful for measuring gene expression activity of complex 118b
include but are not limited to those described in Lewis ML et al., 2001, FASEB
J,
15:1783-5.
Exemplary assays useful for measuring endocytosis regulation activity of
complex 118b include but are not limited to those described in Dulic V et al.,
1991,
Methods Enzymol, 194:697-710.
Exemplary assays useful for measuring changes in motility of cells containing
complex 118b include but are not limited to those described in Westerberg L et
al.,
2001, Blood, 98:1086-94.
Exemplary assays useful for measuring cytoskeletal changes of cells containing
complex 118b include but are not limited to those described in Lommel S et
al., 2001,
EMBO Rep, 2:850-7.
Exemplary assays useful for measuring nuclear import/export activity of
complex
119a include but are not limited to those described in Singleton DR et al.,
1995, J Cell
Sci, 108 ( Pt 1 ):265-72. and/or Shulga N et al., 1996, J Cell Biol, 135:329-
39.
Exemplary assays useful for measuring viral replication activity in cells
containing
complex 119a include but are not limited to those described in Kim AL et al.,
1997,
Virology, 239:340-51.
Exemplary animal models useful for assaying compounds interacting with Nup214
(CAN)
knock out mice complex 119b include but are not limited to those described in
van
Deursen J et al., 1996, EMBO J, 15:5574-83.
Exemplary assays useful for measuring nuclear import/export activity of
complex
119b include but are not limited to those described in Singleton DR et al.,
1995, J Cell
Sci, 108 ( Pt 1):265-72. and/or Shulga N et al., 1996, J Cell Biol, 135:329-
39.
Exemplary assays useful for measuring viral replication activity in cells
containing
complex 119b include but are not limited to those described in Kim AL et al.,
1997,
Virology, 239:340-51.

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Exemplary assays useful for measuring vacuolar membrane H+ ATPase activity
of complex 120a include but are not limited to those described in Uchida E et
al., 1988,
Methods Enzymol, 157:544-62.
Exemplary assays useful for measuring resorption activity in human cells
containing complex 120a include but are not limited to those described in
James IE et
al., 1999, J Bone Miner Res, 14:1562-9.
Exemplary assays useful for measuring modulation of the processing of beta-
amyloid precursor protein (beta-APP) in293 kidney cells containing complex
120a
include but are not limited to those described in Haass C et al., 1995, J Biol
Chem,
270:6186-92.
Exemplary assays useful for measuring vacuolar membrane H+ ATPase activity
of complex 120b include but are not limited to those described in Uchida E et
al., 1988,
Methods Enzymol, 157:544-62.
Exemplary assays useful for measuring resorption activity in human cells
containing complex 120b include but are not limited to those described in
James IE et
al., 1999, J Bone Miner Res, 14:1562-9.
Exemplary assays useful for measuring modulation of the processing of beta-
amyloid precursor protein (beta-APP) in293 kidney cells containing complex
120b
include but are not limited to those described in Haass C et al., 1995, J Biol
Chem,
270:6186-92.
Exemplary assays useful for measuring GASP41 protein binding activity of
complex 121a include but are not limited to those described in Munnia A et
al., 2001,
Oncogene, 20:4853-63.
Exemplary assays useful for measuring GASP41 protein binding activity of
complex 121b include but are not limited to those described in Munnia A et
al., 2001,
Oncogene, 20:4853-63.
Exemplary assays useful for measuring GTP exchange activity of complex 122a
include but are not limited to those described in Sasaki T et al., 1990, J
Biol Chem,
265:2333-7.
Exemplary assays useful for measuring GTP exchange activity of complex 122b
include but are not limited to those described in Sasaki T et al., 1990, J
Biol Chem,
265:2333-7.

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Exemplary assays useful for measuring translational activity of complex 123a
include but are not limited to those described in Pfisterer J and Buetow DE.,
1981, Proc
Natl Acad Sci U S A, 78:4917-21.
Exemplary assays useful for measuring respiration of cells containing complex
123a include but are not limited to those described in Kotter P and Entian
KD., 1995,
Curr Genet, 28:26-31.
Exemplary assays useful for measuring translational activity of complex 123b
include but are not limited to those described in Pfisterer J and Buetow DE.,
1981, Proc
Natl Acad Sci U S A, 78:4917-21.
Exemplary assays useful for measuring respiration of cells containing complex
123b include but are not limited to those described in Kotter P and Entian
KD., 1995,
Curr Genet, 28:26-31.
Exemplary assays useful for measuring protein kinase activity of complex 124a
include but are not limited to those described in Bidwai AP et al., 1993, Arch
Biochem
Biophys, 300:265-70.
Exemplary assays useful for measuring subcellular localization/transport of
lysosomal membrane proteins on the surface of AP-3 deficient fibroblasts
containing
complex 124a include but are not limited to those described in Dell'Angelica
EC et al.,
1999, Mol Cell, 3:11-21.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying a Hermansky Pudlak syndrome-like phenotype complex 124b
include
but are not limited to those described in Swank RT et al., 1998, Pigment Cell
Res,
11:60-80.
Exemplary animal models useful for assaying compounds interacting with the
"pearl"
mouse mutant (alterations in AP-3 beta1 subunit, model for HPS) complex 124b
include
but are not limited to those described in Feng L et al., 1999, Hum Mol Genet,
8:323-30.
Exemplary assays useful for measuring protein kinase activity of complex 124b
include but are not limited to those described in Bidwai AP et al., 1993, Arch
Biochem
Biophys, 300:265-70.
Exemplary assays useful for measuring subcellular localization/transport of
lysosomal membrane proteins on the surface of AP-3 deficient fibroblasts
containing
complex 124b include but are not limited to those described in Dell'Angelica
EC et al.,
1999, Mol Cell, 3:11-21.

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Exemplary animal models useful for assaying compounds interacting with Aurora-
like
kinase knock out mice complex 125a include but are not limited to those
described in
Kaitna S et al., 2000, Curr Biol, 10:1172-81.
Exemplary assays useful for measuring DNA binding activity of complex 125a
include but are not limited to those described in Kimura K et al., 1999, Cell,
98:239-48.
Exemplary assays useful for measuring ATPase activity of complex 125a include
but are not limited to those described in Kimura K and Hirano T., 1997, Cell,
90:625-34.
Exemplary assays useful for measuring chromatid condensation and cohesion in
cells containing complex 125a include but are not limited to those described
in Losada
A et al., 1998, Genes Dev, 12:1986-97.
Exemplary animal models useful for assaying compounds interacting with Aurora-
like
kinase knock out mice complex 125b include but are not limited to those
described in
Kaitna S et al., 2000, Curr Biol, 10:1172-81.
Exemplary assays useful for measuring DNA binding activity of complex 125b
include but are not limited to those described in Kimura K et al., 1999, Cell,
98:239-48.
Exemplary assays useful for measuring ATPase activity of complex 125b include
but are not limited to those described in Kimura K and Hirano T., 1997, Cell,
90:625-34.
Exemplary assays useful for measuring chromatid condensation and cohesion in
cells containing complex 125b include but are not limited to those described
in Losada
A et al., 1998, Genes Dev, 12:1986-97.
Exemplary assays useful for measuring protein deacetylase activity of complex
126a include but are not limited to those described in Nare B et al., 1999,
Anal Biochem,
267:390-6.
Exemplary assays useful for measuring histone acetyltransferase activity of
complex 126a include but are not limited to those described in Ito K et al.,
2001, J Biol
Chem, 276:30208-15.
Exemplary assays useful for measuring PI 3 kinase activity of complex 126a
include but are not limited to those described in Serunian LA et al., 1991,
Methods
Enzymol, 198:78-87.
Exemplary assays useful for measuring cell cycle -progression of cells
containing
complex 126a include but are not limited to those described in Mahalingam S et
al.,
1998, Proc Natl Acad Sci U S A, 95:3419-24.

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Exemplary assays useful for measuring nuclear import/export of ribosomal
proteins of cells containing complex 126a include but are not limited to those
described
in Jakel S and Gorlich D., 1998, EMBO J, 17:4491-502.
Exemplary animal models useful for assaying compounds interacting with Ataxia-
telangiectasia transgenic mice complex 126b include but are not limited to
those
described in Barlow C et al., 1996, Cell, 86:159-71.
Exemplary assays useful for measuring histone acetyltransferase activity of
complex 126b include but are not limited to those described in Ito K et al.,
2001, J Biol
Chem, 276:30208-15.
Exemplary assays useful for measuring cell cycle progression of cells
containing
complex 126b include but are not limited to those described in Mahalingam S et
al.,
1998, Proc Natl Acad Sci U S A, 95:3419-24.
Exemplary assays useful for measuring guanine nucleotide exchange activity of
complex 127a include but are not limited to those described in Nika J et al.,
2000, J Biol
Chem, 275:26011-7.
Exemplary assays useful for measuring proliferation activity of cells complex
127a include but are not limited to those described in Entian KD et al., 1999,
Mol Gen
Genet, 262:683-702.
Exemplary assays useful for measuring guanine nucleotide exchange activity of
complex 127b include but are not limited to those described in Nika J et al.,
2000, J Biol
Chem, 275:26011-7.
Exemplary assays useful for measuring mixed-nucleotide exchange experiments
of complex 127b include but are not limited to those described in Rudoni S et
al., 2001,
Biochim Biophys Acta, 1538:181-9.
Exemplary assays useful for measuring translation factor activity of complex
127b include but are not limited to those described in Choi SK et al., 1998,
Science,
280:1757-60.
Exemplary assays useful for measuring proliferation activity of cells complex
127b include but are not limited to those described in Entian KD et al., 1999,
Mol Gen
Genet, 262:683-702.
Exemplary assays useful for measuring aminoacyl-synthetase activity of complex
128a include but are not limited to those described in Shiba K et al., 1997, J
Biol Chem,
272:22809-16.

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Exemplary assays useful for measuring RNA helicase activity of complex 128a
include but are not limited to those described in Laggerbauer B et al., 1998,
Proc Natl
Acad Sci U S A, 95:4188-92.
Exemplary assays useful for measuring mRNA decay activity of cells containing
complex 128a include but are not limited to those described in Bouveret E et
al., 2000,
EMBO J, 19:1661-71.
Exemplary assays useful for measuring nonsense mediated mRNA decay activity
of cells containing complex 128a include but are not limited to those
described in Sun X
et al., 1998, Proc Natl Acad Sci U S A, 95:10009-14.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying an autoimmune polymyositis-like phenotype complex 128b include
but
are not limited to those described in Kohyama K and Matsumoto Y., 1999, J
Neuroimmunol, 98:130-5.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying an systemic sclerosis-like phenotype complex 128b include but
are not
limited to those described in Nguyen VA et al., 2000, J Autoimmun, 14:143-9.
Exemplary assays useful for measuring aminoacyl-synthetase activity of complex
128b include but are not limited to those described in Shiba K et al., 1997, J
Biol Chem,
272:22809-16.
Exemplary assays useful for measuring RNA helicase activity of complex 128b
include but are not limited to those described in Laggerbauer B et al., 1998,
Proc Natl
Acad Sci U S A, 95:4188-92.
Exemplary assays useful for measuring mRNA decay activity of cells containing
complex 128b include but are not limited to those described in Bouveret E et
al., 2000,
EMBO J, 19:1661-71.
Exemplary assays useful for measuring nonsense mediated mRNA decay activity
of cells containing complex 128b include but are not limited to those
described in Sun X
et al., 1998, Proc Natl Acad Sci U S A, 95:10009-14.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying a fragile X syndrome-like phenotype complex 129a include but
are not
limited to those described in Kooy RF et al., 1996, Am J Med Genet, 64:241-5.
and/or
Oostra BA and Hoogeveen AT., 1997, Ann Med, 29:563-7.

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Exemplary assays useful for measuring dual specificity kinase activity of
complex
129a include but are not limited to those described in Menegay HJ et al.,
2000, J Cell
Sci, 113 ( Pt 18):3241-53.
Exemplary assays useful for measuring RNA helicase activity of complex 129a
include but are not limited to those described in Rogers GW et al., 2001, J
Biol Chem,
276:30914-22.
Exemplary assays useful for measuring serine/threonine protein kinase activity
of
complex 129a include but are not limited to those described in Hartmann AM et
al.,
2001, Mol Cell Neurosci, 18:80-90.
Exemplary assays useful for measuring nuclear transport activity of cells
containing complex 129a include but are not limited to those described in
Stauber RH.,
2001, Curr Top Microbiol Immunol, 259:119-28.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying a fragile X syndrome-like phenotype complex 129b include but
are not
limited to those described in Kooy RF et al., 1996, Am J Med Genet, 64:241-5.
and/or
Oostra BA and Hoogeveen AT., 1997, Ann Med, 29:563-7.
Exemplary assays useful for measuring dual specificity kinase activity of
complex
129b include but are not limited to those described in Menegay HJ et al.,
2000, J Cell
Sci, 113 ( Pt 18):3241-53.
Exemplary assays useful for measuring RNA helicase activity of complex 129b
include but are not limited to those described in Rogers GW et al., 2001, J
Biol Chem,
276:30914-22.
Exemplary assays useful for measuring serine/threonine protein kinase activity
of
complex 129b include but are not limited to those described in Hartmann AM et
al.,
2001, Mol Cell Neurosci, 18:80-90.
Exemplary assays useful for measuring nuclear transport activity of cells
containing complex 129b include but are not limited to those described in
Stauber RH.,
2001, Curr Top Microbiol Immunol, 259:119-28.
Exemplary assays useful for measuring topoisomerase II activity of complex
130a include but are not limited to those described in Okada Y et al., 2001,
Gene,
272:141-8.
Exemplary assays useful for measuring ATPase activity of complex 130a include
but are not limited to those described in Rieger CE et al., 1997, Anal
Biochem, 246:86-
95.

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Exemplary assays useful for measuring sister chromatid cohesion of cells
containing complex 130a include but are not limited to those described in
Megee PC
and Koshland D., 1999, Science, 285:254-7.
Exemplary assays useful for measuring cell survival after DNA damage of cells
containing complex 130a include but are not limited to those described in
Pennaneach
V et al., 2001, Mol Cell, 7:715-27.
Exemplary assays useful for measuring cell cycle progression of cells
containing
complex 130a include but are not limited to those described in Mahalingam S et
al.,
1998, Proc Natl Acad Sci U S A, 95:3419-24.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying a Williams-Beuren syndrome-like phenotype complex 130b include
but
are not limited to those described in Durkin ME et al., 2001, Genomics, 73:20-
7.
Exemplary assays useful for measuring topoisomerase II activity of complex
130b include but are not limited to those described in Okada Y et al., 2001,
Gene,
272:141-8.
Exemplary assays useful for measuring ATPase activity of complex 130b include
but are not limited to those described in Rieger CE et al., 1997, Anal
Biochem, 246:86-
95.
Exemplary assays useful for measuring sister chromatid cohesion of cells
containing complex 130b include but are not limited to those described in
Megee PC
and Koshland D., 1999, Science, 285:254-7.
Exemplary assays useful for measuring cell survival after DNA damage of cells
containing complex 130b include but are not limited to those described in
Pennaneach
V et al., 2001, Mol Cell, 7:715-27.
Exemplary assays useful for measuring cell cycle progression of cells
containing
complex 130b include but are not limited to those described in Mahalingam S et
al.,
1998, Proc Natl Acad Sci U S A, 95:3419-24.
Exemplary assays useful for measuring serine/threonine protein kinase activity
of
complex 131 a include but are not limited to those described in Shiekhattar R
et al.,
1995, Nature, 374:283-7. and/or Fisher RP and Morgan DO., 1994, Cell, 78:713-
24.
Exemplary assays useful for measuring nucleotide excision repair activity of
complex 131 a include but are not limited to those described in Sung P et al.,
1996, J
Biol Chem, 271:10821-6.

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Exemplary assays useful for measuring transcription activity of cells
containing
complex 131 a include but are not limited to those described in Shiekhattar R
et al.,
1995, Nature, 374:283-7.
Exemplary assays useful for measuring transcription assay of complex 131 b
include but are not limited to those described in Hipskind RA and Nordheim A.,
1991, J
Biol Chem, 266:19572-82.
Exemplary assays useful for measuring nucleotide excision repair activity of
complex 131 b include but are not limited to those described in Sung P et al.,
1996, J
Biol Chem, 271:10821-6.
Exemplary assays useful for measuring transcription activity of cells
containing
complex 131 b include but are not limited to those described in Shiekhattar R
et al.,
1995, Nature, 374:283-7.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying systemic sclerosis-like phenotype complex 132a include but are
not
limited to those described in Yamamoto T et al., 1999, J Invest Dermatol,
112:456-62.
and/or Nguyen VA et al., 2000, J Autoimmun, 14:143-9.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying systemic lupus erythematosus-like phenotype complex 132a
include but
are not limited to those described in Kyogoku M et al., 1987, Prog Clin Biol
Res, 229:95-
130.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying Sjogren syndrome-like phenotype complex 132a include but are
not
limited to those described in Haneji N et al., 1994, J Immunol, 153:2769-77.
Exemplary assays useful for measuring RNA stabilizing activity of complex 132a
include but are not limited to those described in McLaren RS et al., 1997, Mol
Cell Biol,
17:3028-36.
Exemplary assays useful for measuring rRNA pseudouridylation activity of cells
containing complex 132a include but are not limited to those described in
Lafontaine DL
et al., 1998, Genes Dev, 12:527-37.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying systemic sclerosis-like phenotype complex 132b include but are
not
limited to those described in Yamamoto T et al., 1999, J Invest Dermatol,
112:456-62.

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Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying aspinal muscular atrophy-like phenotype complex 132b include
but are
not limited to those described in Monani UR et al., 2000, Hum Mol Genet, 9:333-
9.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying systemic sclerosis-like phenotype complex 132b include but are
not
limited to those described in Nguyen VA et al., 2000, J Autoimmun, 14:143-9.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying systemic lupus erythematosus-like phenotype complex 132b
include but
are not limited to those described in Kyogoku M et al., 1987, Prog Clin Biol
Res, 229:95-
130.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying Sjogren syndrome-like phenotype complex 132b include but are
not
limited to those described in Haneji N et al., 1994, J Immunol, 153:2769-77.
Exemplary assays useful for measuring RNA stabilizing activity of complex 132b
include but are not limited to those described in McLaren RS et al., 1997, Mol
Cell Biol,
17:3028-36.
Exemplary assays useful for measuring rRNA pseudouridylation activity of cells
containing complex 132b include but are not limited to those described in
Lafontaine DL
et al., 1998, Genes Dev, 12:527-37.
Exemplary assays useful for measuring the protein folding and translocating
activity of complex 134a include but are not limited to those described in
Gautschi M et
al., 2001, Proc Natl Acad Sci U S A, 98:3762-7.
Exemplary assays useful for measuring RNA stabilizing activity of complex 134a
include but are not limited to those described in Jacobs JS et al., 1998, EMBO
J,
17:1497-506.
Exemplary assays useful for measuring growth of cells containing complex 134a
include but are not limited to those described in hang S et al., 1992, EMBO J,
11:3787-
96.
Exemplary assays useful for measuring translational activity of complex 134b
include but are not limited to those described in Valasek L et al., 2001, EMBO
J, 20:891-
904.
Exemplary assays useful for measuring the protein folding and translocating
activity of complex 134b include but are not limited to those described in
Gautschi M et
al., 2001, Proc Natl Acad Sci U S A, 98:3762-7.

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Exemplary assays useful for measuring RNA stabilizing activity of complex 134b
include but are not limited to those described in Jacobs JS et al., 1998, EMBO
J,
17:1497-506.
Exemplary assays useful for measuring growth of cells containing complex 134b
include but are not limited to those described in Zhang S et al., 1992, EMBO
J, 11:3787-
96.
Exemplary assays useful for measuring protein phosphatase-2A activity of
complex 135a include but are not limited to those described in Cohen P et al.,
1988,
Methods Enzymol, 159:390-408.
Exemplary assays useful for measuring protein phosphatase 4 activity of
complex 135a include but are not limited to those described in Hastie CJ and
Cohen
PT., 1998, FEBS Lett, 431:357-61.
Exemplary assays useful for measuring protein phosphatase-2A activity of
complex 135b include but are not limited to those described in Cohen P et al.,
1988,
Methods Enzymol, 159:390-408.
Exemplary assays useful for measuring protein phosphatase 4 activity of
complex 135b include but are not limited to those described in Hastie CJ and
Cohen
PT., 1998, FEBS Lett, 431:357-61.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice used for the study of ovary development complex 136a include but are not
limited
to those described in Freiman RN et al., 2001, Science, 293:2084-7.
Exemplary assays useful for measuring acetylase activity of complex 136a
include but are not limited to those described in Fischle W et al., 1999, J
Biol Chem,
274:11713-20.
Exemplary assays useful for measuring serine/threonine protein kinase activity
of
complex 136a include but are not limited to those described in Leverson JD et
al., 1998,
Mol Cell, 2:417-25.
Exemplary assays useful for measuring cell cycle progression of cells
containing
complex 136a include but are not limited to those described in Kruhlak MJ et
al., 2001, J
Biol Chem, 276:38307-19.
Exemplary assays useful for measuring apoptosis induction of cells containing
complex 136a include but are not limited to those described in Chen Lf et al.,
2001,
Science, 293:1653-7.

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Exemplary animal models useful for assaying compounds interacting with the
analysis of
genetic complementation during T cell development complex 136b include but are
not
limited to those described in Jacobs H et al., 1999, J Exp Med, 190:1059-68.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice used for the study of ovary development complex 136b include but are not
limited
to those described in Freiman RN et al., 2001, Science, 293:2084-7.
Exemplary assays useful for measuring acetylase activity of complex 136b
include but are not limited to those described in Fischle W et al., 1999, J
Biol Chem,
274:11713-20.
Exemplary assays useful for measuring serine/threonine protein kinase activity
of
complex 136b include but are not limited to those described in Leverson JD et
al., 1998,
Mol Cell, 2:417-25.
Exemplary assays useful for measuring cell cycle progression of cells
containing
complex 136b include but are not limited to those described in Kruhlak MJ et
al., 2001, J
Biol Chem, 276:38307-19.
Exemplary assays useful for measuring apoptosis induction of cells containing
complex 136b include but are not limited to those described in Chen Lf et al.,
2001,
Science, 293:1653-7.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying a human prostate cancer-like phenotype complex 137a include
but are
not limited to those described in Saffran DC et al., 2001, Proc Natl Acad Sci
U S A,
98:2658-63.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice used for the study of ovary development complex 137a include but are not
limited
to those described in Freiman RN et al., 2001, Science, 293:2084-7.
Exemplary assays useful for measuring DNA topoisomerase activity of complex
137a include but are not limited to those described in Merino A et al., 1993,
Nature,
365:227-32. and/or MA D et al., 1996, Proc Natl Acad Sci U S A, 93:6583-8.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice displaying a human prostate cancer-like phenotype complex 137b include
but are
not limited to those described in Saffran DC et al., 2001, Proc Natl Acad Sci
U S A,
98:2658-63.

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Exemplary animal models useful for assaying compounds interacting with
transgenic
mice used for the study of ovary development complex 137b include but are not
limited
to those described in Freiman RN et al., 2001, Science, 293:2084-7.
Exemplary assays useful for measuring casein kinase activity of complex 137b
include but are not limited to those described in Park JW and Bae YS., 1999,
Biochem
Biophys Res Commun, 263:475-81.
Exemplary assays useful for measuring histone deacetylase activity of complex
137b include but are not limited to those described in Hoffmann K et al., 2001
Jan-Feb,
Bioconjug Chem, 12:51-5.
Exemplary assays useful for measuring DNA topoisomerase activity of complex
137b include but are not limited to those described in Merino A et al., 1993,
Nature,
365:227-32. and/or MA D et al., 1996, Proc Natl Acad Sci U S A, 93:6583-8.
Exemplary assays useful for measuring translational initiation activity of
complex
138a include but are not limited to those described in Valasek L et al., 2001,
EMBO J,
20:891-904. and/or Naranda T et al., 1994, J Biol Chem, 269:32286-92.
Exemplary assays useful for measuring viability of cells containing complex
138a
include but are not limited to those described in Das S and Maitra U., 2000,
Mol Cell
Biol, 20:3942-50.
Exemplary assays useful for measuring translational initiation activity of
complex
138b include but are not limited to those described in Valasek L et al., 2001,
EMBO J,
20:891-904. and/or Naranda T et al., 1994, J Biol Chem, 269:32286-92.
Exemplary assays useful for measuring viability of cells containing complex
138b
include but are not limited to those described in Das S and Maitra U., 2000,
Mol Cell
Biol, 20:3942-50.
Exemplary assays useful for measuring DNA helicase activity of complex 139a
include but are not limited to those described in Adamkewicz JI et al., 2000,
J Biol
Chem, 275:21158-68.
Exemplary assays useful for measuring protein kinase activity of complex 139a
include but are not limited to those described in Chen H et al., 2001,
Biochemistry,
40:11851-9.
Exemplary assays useful for measuring in vivo acetyltransferase activity in
CSC12-cells containing complex 139a include but are not limited to those
described in
Hamamori Y et al., 1999, Cell, 96:405-13.

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Exemplary assays useful for measuring DNA helicase activity of complex 139b
include but are not limited to those described in Adamkewicz JI et al., 2000,
J Biol
Chem, 275:21158-68.
Exemplary assays useful for measuring protein kinase activity of complex 139b
include but are not limited to those described in Chen H et al., 2001,
Biochemistry,
40:11851-9.
Exemplary assays useful for measuring RNA polymerase II activity of complex
139b include but are not limited to those described in Majello B and
Napolitano G.,
2001, Front Biosci, 6:1358-68.
Exemplary assays useful for measuring in vivo acetyltransferase activity in
CSC12-cells containing complex 139b include but are not limited to those
described in
Hamamori Y et al., 1999, Cell, 96:405-13.
Exemplary assays useful for measuring translational activity of complex 140a
include but are not limited to those described in Finzi E et al., 1981, J Biol
Chem,
256:11917-22.
Exemplary assays useful for measuring respiration and sensitivity of mtDNA to
damaging agents in cells containing
complex 140a include but are not limited to those described in Ling F et al.,
2000,
Nucleic Acids Res, 28:4956-63.
Exemplary assays useful for measuring respiration activity of cells containing
complex 140a include but are not limited to those described in Levy SB et al.,
1976, N
Engl J Med, 295:583-8.
Exemplary assays useful for measuring translational activity of complex 140b
include but are not limited to those described in Finzi E et al., 1981, J Biol
Chem,
256:11917-22.
Exemplary assays useful for measuring respiration and sensitivity of mtDNA to
damaging agents in cells containing
complex 140b include but are not limited to those described in Ling F et al.,
2000,
Nucleic Acids Res, 28:4956-63.
Exemplary assays useful for measuring respiration activity of cells
containing.
complex 140b include but are not limited to those described in Levy SB et al.,
1976, N
Engl J Med, 295:583-8.

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Exemplary assays usefiul for measuring ATPase activity of complex 141 a
include
but are not limited to those described in Frohlich KU et al., 1995, Biochim
Biophys Acta,
1253:25-32.
Exemplary assays useful for measuring ubiquitin-mediated proteolytic activity
in
yeast cells containing complex 141a include but are not limited to those
described in
Ghislain M et al., 1996, EMBO J, 15:4884-99.
Exemplary assays useful for measuring protein degradation activity of complex
141 b include but are not limited to those described in Wang CW et al., 2001,
J Biol
Chem, 276:30442-51.
Exemplary assays useful for measuring ATPase activity of complex 141 b include
but are not limited to those described in Frohlich KU et al., 1995, Biochim
Biophys Acta,
1253:25-32.
Exemplary assays useful for measuring ubiquitin-mediated proteolytic activity
in
yeast cells containing complex 141 b include but are not limited to those
described in
Ghislain M et al., 1996, EMBO J, 15:4884-99.
Exemplary assays useful for measuring RNA 3'-5' exonuclease activity of
complex 142a include but are not limited to those described in 0
Exemplary assays useful for measuring RNA helicase activity of complex 142a
include but are not limited to those described in Wang Y et al., 1998, Curr
Biol, 8:441-
51.
Exemplary assays useful for measuring Ski7 inhibition of virus propagation in
yeast cells containing complex 142a include but are not limited to those
described in
Benard L et al., 1999, J Virol, 73:2893-900.
Exemplary animal models useful for assaying compounds interacting with EEF1A2,
( the
human homolog of Ski7) transgenic in mice complex 142b include but are not
limited to
those described in Chambers D M et al., 1998, Proc Natl Acad Sci U S A,
95:4463-8.
Exemplary assays useful for measuring RNA 3'-5' exonuclease activity of
complex 142b include but are not limited to those described in Benard L et
al., 1999, J
Virol, 73:2893-900. and/or van Hoof A et al., 2000, Mol Cell Biol, 20:8230-43.
Exemplary assays useful for measuring RNA helicase activity of complex 142b
include but are not limited to those described in Wang Y et al., 1998, Curr
Biol, 8:441-
51.

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Exemplary assays useful for measuring Ski7 inhibition of virus propagation in
yeast cells containing complex 142b include but are not limited to those
described in
Benard L et al., 1999, J Virol, 73:2893-900.
Exemplary assays useful for measuring the effect on eIF4E m7cap-binding
activity of complex 143a include but are not limited to those described in
Altmann M and
Trachsel H., 1989, Nucleic Acids Res, 17:5923-31.
Exemplary assays useful for measuring control of cell growth of yeast cells
containing complex 143a include but are not limited to those described in 0
Exemplary assays useful for measuring control of protein synthesis in human
cells
containing complex 143a include but are not limited to those described in
Jones RM et
al., 1996, Mol Cell Biol, 16:4754-64.
Exemplary animal models useful for assaying compounds interacting with the
analysis
eIF4E level after the induction of global ischaemia in rat brain complex 143b
include but
are not limited to those described in Martin de la Vega C et al., 2001,
Biochem J,
357:819-26.
Exemplary assays useful for measuring the effect on eIF4E m7cap-binding
activity of complex 143b include but are not limited to those described in
Altmann M and
Trachsel H., 1989, Nucleic Acids Res, 17:5923-31.
Exemplary assays useful for measuring control of cell growth of yeast cells
containing complex 143b include but are not limited to those described in
Anthony C et
al., 2001, J Biol Chem, 276:39645-52.
Exemplary assays useful for measuring control of protein synthesis in human
cells
containing complex 143b include but are not limited to those described in
Jones RM et
al., 1996, Mol Cell Biol, 16:4754-64.
Exemplary assays useful for measuring control of cell growth of yeast cells
containing complex 143b include but are not limited to those described in
Sonenberg N
and Gingras AC., 1998, Curr Opin Cell Biol, 10:268-75.
Exemplary assays useful for measuring methyltransferase activity of complex
145a include but are not limited to those described in Aoki A et al., 2001,
Nucleic Acids
Res, 29:3506-12.
Exemplary assays useful for measuring ubiquitylation activity of complex 145a
include but are not limited to those described in Jiang J et al., 2001, J Biol
Chem,
276:42938-44.

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Exemplary assays useful for measuring immortalizing properties of myeloid
progenitors cells containing complex 145a include but are not limited to those
described
in Luo RT et al., 2001, Mol Cell Biol, 21:5678-87.
Exemplary assays useful for measuring methyltransferase activity of complex
145b include but are not limited to those described in Aoki A et al., 2001,
Nucleic Acids
Res, 29:3506-12.
Exemplary assays useful for measuring ubiquitylation activity of complex 145b
include but are not limited to those described in Jiang J et al., 2001, J Biol
Chem,
276:42938-44.
Exemplary assays useful for measuring RNA polymerase II activity of complex
145b include but are not limited to those described in Majello B and
Napolitano G.,
2001, Front Biosci, 6:1358-68.
Exemplary assays useful for measuring immortalizing properties of myeloid
progenitors cells complex 145b include but are not limited to those described
in Luo RT
et al., 2001, Mol Cell Biol, 21:5678-87.
Exemplary assays useful for measuring rRNA processing activity of complex
146a include but are not limited to those described in Colley A et al., 2000,
Mol Cell Biol,
20:7238-46. and/or Tollervey D et al., 1993, Cell, 72:443-57.
Exemplary assays useful for measuring subcellular localization/transport of
precursor rRNA in cells containing complex 146a include but are not limited to
those
described in Dundr M et al., 2000, J Cell Biol, 150:433-46.
Exemplary assays useful for measuring rRNA processing activity of complex
146b include but are not limited to those described in Colley A et al., 2000,
Mol Cell Biol,
20:7238-46. and/or Tollervey D et al., 1993, Cell, 72:443-57.
Exemplary assays useful for measuring subcellular localization/transport of
precursor rRNA in cells containing complex 146b include but are not limited to
those
described in Dundr M et al., 2000, J Cell Biol, 150:433-46.
Exemplary assays useful for measuring Golgi to ER transport activity of
complex
147a include but are not limited to those described in Dogic D et al., 1999,
Eur J Cell
Biol, 78:305-10.
Exemplary assays useful for measuring GAP activity of complex 147a include but
are not limited to those described in Poon PP et al., 1999, EMBO J, 18:555-64.

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Exemplary assays useful for measuring viability of cells containing complex
147a
include but are not limited to those described in Duden R et al., 1994, J Biol
Chem,
269:24486-95.
Exemplary assays useful for measuring Golgi to ER transport activity of
complex
147b include but are not limited to those described in Dogic D et al., 1999,
Eur J Cell
Biol, 78:305-10.
Exemplary assays useful for measuring GAP activity of complex 147b include but
are not limited to those described in Poon PP et al., 1999, EMBO J, 18:555-64.
Exemplary assays useful for measuring viability of cells containing complex
147b
include but are not limited to those described in Duden R et al., 1994, J Biol
Chem,
269:24486-95.
Exemplary animal models useful for assaying compounds interacting with cats
infected
with the feline immunodeficiency virus complex 148a include but are not
limited to those
described in Piedimonte G et al., 1999, Exp Cell Res, 248:381-90.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying an asthma-like phenotype complex 148a include but are not
limited to
those described in Elliott PJ et al., 1999, J Allergy Clin Immunol, 104:294-
300.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a diabetes type 1-like phenotype complex 148a include but are
not
limited to those described in Hayashi T and Faustman D., 1999, Mol Cell Biol,
19:8646-
59.
Exemplary assays useful for measuring protein degradation activity of complex
148a include but are not limited to those described in Kuckelkorn U et al.,
2000 Sep-Oct,
Biol Chem, 381:1017-23. and/or Ugai S et al., 1993, J Biochem (Tokyo), 113:754-
68.
Exemplary assays useful for measuring protein degradation (fluorescence-based
assay) in cells containing complex 148a include but are not limited to those
described in
Andreatta C et al., 2001, Biotechniques, 30:656-60.
Exemplary animal models useful for assaying compounds interacting with cats
infected
with the feline immunodeficiency virus complex 148b include but are not
limited to those
described in Piedimonte G et al., 1999, Exp Cell Res, 248:381-90.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying an asthma-like phenotype complex 148b include but are not
limited to
those described in Elliott PJ et al., 1999, J Allergy Clin Immunol, 104:294-
300.

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Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a diabetes type 1-like phenotype complex 148b include but are
not
limited to those described in Hayashi T and Faustman D., 1999, Mol Cell Biol,
19:8646-
59.
Exemplary assays useful for measuring protein degradation activity of complex
148b include but are not limited to those described in Kuckelkorn U et al.,
2000 Sep-Oct,
Biol Chem, 381:1017-23. and/or Ugai S et al., 1993, J Biochem (Tokyo), 113:754-
68.
Exemplary assays useful for measuring protein degradation (fluorescence-based
assay) in cells containing complex 148b include but are not limited to those
described in
Andreatta C et al., 2001, Biotechniques, 30:656-60.
Exemplary assays useful for measuring DNA helicase activity of complex 149a
include but are not limited to those described in Kanemaki M et al., 1999, J
Biol Chem,
274:22437-44.
Exemplary assays useful for measuring RNAse activity of complex 149a include
but are not limited to those described in Daugeron MC et al., 2001, Nucleic
Acids Res,
29:2448-55.
Exemplary assays useful for measuring DNA endonuclease activity of complex
149a include but are not limited to those described in Zhu FX et al., 1997,
Biochemistry,
36:5947-54.
Exemplary assays useful for measuring mRNA degradation in vivo in cells
containing complex 149a include but are not limited to those described in
Daugeron MC
et al., 2001, Nucleic Acids Res, 29:2448-55.
Exemplary assays useful for measuring DNA helicase activity of complex 149b
include but are not limited to those described in Kanemaki M et al., 1999, J
Biol Chem,
274:22437-44.
Exemplary assays useful for measuring RNAse activity of complex 149b include
but are not limited to those described in Daugeron MC et al., 2001, Nucleic
Acids Res,
29:2448-55.
Exemplary assays useful for measuring DNA endonuclease activity of complex
149b include but are not limited to those described in Zhu FX et al., 1997,
Biochemistry,
36:5947-54.
Exemplary assays useful for measuring mRNA degradation in vivo in cells
containing complex 149b include but are not limited to those described in
Daugeron MC
et al., 2001, Nucleic Acids Res, 29:2448-55.

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Exemplary assays useful for measuring DNA replication activity of complex 150a
include but are not limited to those described in Vashee S et al., 2001, J
Biol Chem,
276:26666-73.
Exemplary assays useful for measuring Epstein Barr Virus plasmid replication
and maintenance in HCT116 colon carcinoma cells containing complex 150a
include but
are not limited to those described in Dhar SK et al., 2001, Cell, 106:287-96.
Exemplary assays useful for measuring DNA replication activity of complex 150b
include but are not limited to those described in Vashee S et al., 2001, J
Biol Chem,
276:26666-73.
Exemplary assays useful for measuring Epstein Barr Virus plasmid replication
and maintenance in HCT116 colon carcinoma cells containing complex 150b
include but
are not limited to those described in Dhar SK et al., 2001, Cell, 106:287-96.
Exem plary assays useful for measuring protein-protein binding activity of
complex 151a include but are not limited to those described in Sontag E et
al., 1999, J
Biol Chem, 274:25490-8.
Exemplary assays useful for measuring protein phosphatase-2A activity of
complex 151 a include but are not limited to those described in Cohen P et
al., 1988,
Methods Enzymol, 159:390-408.
Exemplary animal models useful for assaying compounds interacting with ATR
knocfe out
mice (chromosomal fragmentation and early embryonic lethality phenotypes)
complex
151 b include but are not limited to those described in Brown EJ and Baltimore
D., 2000,
Genes Dev, 14:397-402.
Exemplary assays useful for measuring protein-protein binding activity of
complex 151 b include but are not limited to those described in Sontag E et
al., 1999, J
Biol Chem, 274:25490-8.
Exemplary assays useful for measuring guanine nucleotide exchange factor
activity of complex 151 b include but are not limited to those described in
Sasaki T et al.,
1990, J Biol Chem, 265:2333-7.
Exemplary assays useful for measuring protein phosphatase-2A activity of
complex 151 b include but are not limited to those described in Cohen P et
al., 1988,
Methods Enzymol, 159:390-408.
Exemplary assays useful for measuring guanine nucleotide exchange factor
activity of complex 151 b include but are not limited to those described in
Horiuchi H et
al., 1995, J Biol Chem, 270:11257-62.

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Exemplary assays useful for measuring ATPase of complex 151 b include but are
not limited to those described in Kimura K and Hirano T., 1997, Cell, 90:625-
34.
Exemplary assays useful for measuring exonuclease activity of complex 152a
include but are not limited to those described in Li B and Comai L., 2000, J
Biol Chem,
275:28349-52.
Exemplary assays useful for measuring DNA topoisomerase of complex 152a
include but are not limited to those described in Merino A et al., 1993,
Nature, 365:227-
32.
Exemplary assays useful for measuring genetic complementation of Rad52
mutations in yeast cells containing complex 152a include but are not limited
to those
described in Huang P et al., 2001, Curr Biol, 11:125-9.
Exemplary assays useful for measuring genetic complementation of SGS1
mutations in yeast cells containing complex 152a include but are not limited
to those
described in Kawabe Yi et al., 2001, J Biol Chem, 276:20364-9.
Exemplary assays useful for measuring genetic complementation of Top3
mutations in yeast cells containing complex 152a include but are not limited
to those
described in Chakraverty RK et al., 2001, Mol Cell Biol, 21:7150-62.
Exemplary animal models useful for assaying compounds interacting with Topo
III
defficient mice complex 152b include but are not limited to those described in
Kwan KY
and Wang JC., 2001, Proc Natl Acad Sci U S A, 98:5717-21.
Exemplary animal models useful for assaying compounds interacting with BLM
defficient
mice complex 152b include but are not limited to those described in Chester N
et al.,
1998, Genes Dev, 12:3382-93.
Exemplary assays useful for measuring exonuclease activity of complex 152b
include but are not limited to those described in Li B and Comai L., 2000, J
Biol Chem,
275:28349-52.
Exemplary assays useful for measuring DNA topoisomerase of complex 152b
include but are not limited to those described in Merino A et al., 1993,
Nature, 365:227-
32.
Exemplary assays useful for measuring genetic complementation of Rad52
mutations in yeast cells containing complex 152b include but are not limited
to those
described in Huang P et al., 2001, Curr Biol, 11:125-9.

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Exemplary assays useful for measuring genetic complementation of SGS1
mutations in yeast cells containing complex 152b include but are not limited
to those
described in Kawabe Yi et al., 2001, J Biol Chem, 276:20364-9.
Exemplary assays useful for measuring genetic complementation of Top3
mutations in yeast cells containing complex 152b include but are not limited
to those
described in Chakraverty RK et al., 2001, Mol Cell Biol, 21:7150-62.
Exemplary assays useful for measuring actin polymerization activity of complex
153 include but are not limited to those described in Suzuki T et al., 2000, J
Exp Med,
191:1905-20.
Exemplary assays useful for measuring adhesion properties of cells containing
complex 153 include but are not limited to those described in Liu AX et al.,
2001, Mol
Cell Biol, 21:6906-12.
Exemplary assays useful for measuring protein serine/threonine phosphatase
activity of complex 154a include but are not limited to those described in Li
L et al.,
2000, J Biol Chem, 275:2410-4.
Exemplary assays useful for measuring chromatin remodelling activity of
complex
154a include but are not limited to those described in Kadam S et al., 2000,
Genes Dev,
14:2441-51.
Exemplary assays useful for measuring DNA helicase activity of complex 154a
include but are not limited to those described in Rogers GW et al., 2001, J
Biol Chem,
276:30914-22.
Exemplary assays useful for measuring transcription factor activity of complex
154a include but are not limited to those described in L'Etoile ND et al.,
1994, Proc Natl
Acad Sci U S A, 91:1652-6.
Exemplary assays useful for measuring chromatin remodelling activity of
complex
154a include but are not limited to those described in Wang W et al., 1996,
EMBO J,
15:5370-82.
Exemplary assays useful for measuring rRNA transcription activity of complex
154a include but are not limited to those described in Keener J et al., 1998,
J Biol Chem,
273:33795-802.
Exemplary assays useful for measuring proliferation activity of cells
containing
complex 154a include but are not limited to those described in Sakamoto K et
al., 1991,
J Biol Chem, 266:3031-8.

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Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a systemic sclerosis-like phenotype complex 154b include but
are not
limited to those described in van de Water J and Gershwin ME., 1985, Am J
Pathol,
120:478-82. and/or Siracusa LD et al., 1993, Genomics, 17:748-51.
Exemplary assays useful for measuring protein serine/threonine phosphatase
activity of complex 154b include but are not limited to those described in Li
L et al.,
2000, J Biol Chem, 275:2410-4.
Exemplary assays useful for measuring chromatin remodelling activity of
complex
154b include but are not limited to those described in Kadam S et al., 2000,
Genes Dev,
14:2441-51.
Exemplary assays useful for measuring DNA helicase activity of complex 154b
include but are not limited to those described in Rogers GW et al., 2001, J
Biol Chem,
276:30914-22.
Exemplary assays useful for measuring transcription factor activity of complex
154b include but are not limited to those described in L'Etoile ND et al.,
1994, Proc Natl
Acad Sci U S A, 91:1652-6.
Exemplary assays useful for measuring chromatin remodelling activity of
complex
154b include but are not limited to those described in Wang W et al., 1996,
EMBO J,
15:5370-82.
Exemplary assays useful for measuring rRNA transcription activity of complex
154b include but are not limited to those described in Keener J et al., 1998,
J Biol Chem,
273:33795-802.
Exemplary assays useful for measuring proliferation activity of cells
containing
complex 154b include but are not limited to those described in Sakamoto K et
al., 1991,
J Biol Chem, 266:3031-8.
Exemplary assays useful for measuring mRNA splicing activity of complex 155a
include but are not limited to those described in 0
Exemplary assays useful for measuring pre-mRNA splicing activity of complex
155a include but are not limited to those described in Schwer B and Gross CH.,
1998,
EMBO J, 17:2086-94.
Exemplary assays useful for measuring gene expression of a reporter protein in
cells containing complex 155a include but are not limited to those described
in Baudino
TA et al., 1998, J Biol Chem, 273:16434-41.

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Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a lupus nephritis-like phenotype complex 155b include but are
not limited
to those described in Granholm NA and Cavallo T., 1991, Clin Exp Immunol,
85:270-7.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a systemic lupus erythematosus-like phenotype complex 155b
include
but are not limited to those described in Kyogoku M et al., 1987, Prog Clin
Biol Res,
229:95-130.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a lupus nephritis-like phenotype complex 155b include but are
not limited
to those described in Entani C et al., 1993, Nephron, 64:471-5.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a xeroderma pigmentosum-like phenotype complex 155b include
but are
not limited to those described in Takeuchi S et al., 1998, Cancer Res, 58:641-
6.
Exemplary assays useful for measuring mRNA splicing activity of complex 155b
include but are not limited to those described in Chen CH et al., 2001, J Biol
Chem,
276:488-94. and/or Lin RJ et al., 1985, J Biol Chem, 260:14780-92.
Exemplary assays useful for measuring pre-mRNA splicing activity of complex
155b include but are not limited to those described in Schwer B and Gross CH.,
1998,
EMBO J, 17:2086-94.
Exemplary assays useful for measuring gene expression of a reporter protein in
cells containing complex 155b include but are not limited to those described
in Baudino
TA et al., 1998, J Biol Chem, 273:16434-41.
Exemplary animal models useful for assaying compounds interacting with mice
with a
conditional deletion of a ribosomal protein complex 156a include but are not
limited to
those described in Volarevic S et al., 2000, Science, 288:2045-7.
Exemplary assays useful for measuring casein kinase activity of complex 156a
include but are not limited to those described in Park JW and Bae YS., 1999,
Biochem
Biophys Res Commun, 263:475-81.
Exemplary assays useful for measuring rRNA processing activity of complex
156a include but are not limited to those described in Colley A et al., 2000,
Mol Cell Biol,
20:7238-46. and/or Kressler D et al., 1997, Mol Cell Biol, 17:7283-94.
Exemplary assays useful for measuring cell cycle arrest of cells containing
complex 156a include but are not limited to those described in Pestov DG et
al., 2001,
Mol Cell Biol, 21:4246-55.

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Exemplary assays useful for measuring nuclear export of ribosomal proteins in
cells containing complex 156a include but are not limited to those described
in Hurt E et
al., 1999, J Cell Biol, 144:389-401.
Exemplary animal models useful for assaying compounds interacting with mice
with a
conditional deletion of a ribosomal protein complex 156b include but are not
limited to
those described in Volarevic S et al., 2000, Science, 288:2045-7.
Exemplary assays useful for measuring casein kinase activity of complex 156b
include but are not limited to those described in Park JW and Bae YS., 1999,
Biochem
Biophys Res Commun, 263:475-81.
Exemplary assays useful for measuring rRNA processing activity of complex
156b include but are not limited to those described in Colley A et al., 2000,
Mol Cell Biol,
20:7238-46. andlor Kressler D et al., 1997, Mol Cell Biol, 17:7283-94.
Exemplary assays useful for measuring cell cycle arrest of cells containing
complex 156b include but are not limited to those described in Pestov DG et
al., 2001,
Mol Cell Biol, 21:4246-55.
Exemplary assays useful for measuring nuclear export of ribosomal proteins in
cells containing complex 156b include but are not limited to those described
in Hurt E et
al., 1999, J Cell Biol, 144:389-401.
Exemplary animal models useful for assaying compounds interacting with cats
infected
with the feline immunodeficiency virus complex 157a include but are not
limited to those
described in Piedimonte G et al., 1999, Exp Cell Res, 248:381-90.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying an asthma-like phenotype complex 157a include but are not
limited to
those described in Elliott PJ et al., 1999, J Allergy Clin Immunol, 104:294-
300.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a diabetes type 1-like phenotype complex 157a include but are
not
limited to those described in Hayashi T and Faustman D., 1999, Mol Cell Biol,
19:8646-
59.
Exemplary assays useful for measuring proteasome activity of complex 157a
include but are not limited to those described in Kuckelkorn U et al., 2000
Sep-Oct, Biol
Chem, 381:1017-23. and/or Ugai S et al., 1993, J Biochem (Tokyo), 113:754-68.
Exemplary assays useful for measuring protein degradation via the proteasome
complex 157a include but are not limited to those described in Lightcap ES et
al., 2000,
Clin Chem, 46:673-83.

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Exemplary assays useful for measuring protein degradation (fluorescence-based
assay) in cells containing complex 157a include but are not limited to those
described in
Andreatta C et al., 2001, Biotechniques, 30:656-60.
Exemplary animal models useful for assaying compounds interacting with cats
infected
with the feline immunodeficiency virus complex 157b include but are not
limited to those
described in Piedimonte G et al., 1999, Exp Cell Res, 248:381-90.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying an asthma-like phenotype complex 157b include but are not
limited to
those described in Elliott PJ et al., 1999, J Allergy Clin Immunol, 104:294-
300.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a diabetes type 1-like phenotype complex 157b include but are
not
limited to those described in Hayashi T and Faustman D., 1999, Mol Cell Biol,
19:8646-
59.
Exemplary assays useful for measuring proteasome activity of complex 157b
include but are not limited to those described in Kuckelkorn U et al., 2000
Sep-Oct, Biol
Chem, 381:1017-23. and/or Ugai S et al., 1993, J Biochem (Tokyo), 113:754-68.
Exemplary assays useful for measuring protein degradation via the proteasome
complex 157b include but are not limited to those described in Lightcap ES et
al., 2000,
Clin Chem, 46:673-83.
Exemplary assays useful for measuring protein degradation (fluorescence-based
assay) in cells containing complex 157b include but are not limited to those
described in
Andreatta C et al., 2001, Biotechniques, 30:656-60.
Exemplary assays useful for measuring RNA splicing activity of complex 158a
include but are not limited to those described in Romfo CM et al., 2001, RNA,
7:785-92.
and/or Segault V et al., 1995, EMBO J, 14:4010-21.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a spinal muscular atrophy-like phenotype complex 158b include
but are
not limited to those described in Monani UR et al., 2000, Hum Mol Genet, 9:333-
9.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a spinal lupus nephritis-like phenotype complex 158b include
but are not
limited to those described in Granholm NA and Cavallo T., 1991, Clin Exp
Immunol,
85:270-7.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a systemic lupus erythematosus-like phenotype complex 158b
include

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but are not limited to those described in Kyogoku M et al., 1987, Prog Clin
Biol Res,
229:95-130.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a spinal lupus nephritis-like phenotype complex 158b include
but are not
limited to those described in Entani C et al., 1993, Nephron, 64:471-5.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a xeroderma pigmentosum-like phenotype complex 158b include
but are
not limited to those described in Takeuchi S et al., 1998, Cancer Res, 58:641-
6.
Exemplary assays useful for measuring RNA splicing activity of complex 158b
include but are not limited to those described in Romfo CM et al., 2001, RNA,
7:785-92.
and/or Segault V et al., 1995, EMBO J, 14:4010-21.
Exemplary assays useful for measuring acetylase activity of complex 159a
include but are not limited to those described in Fischle W et al., 1999, J
Biol Chem,
274:11713-20.
Exemplary assays useful for measuring transcription activity of complex 159a
include but are not limited to those described in Kikyo N et al., 2000,
Science, 289:2360-
2.
Exemplary assays useful for measuring protein serine/threonine phosphatase
activity of complex 159a include but are not limited to those described in
Kusuda K et
al., 1998, Biochem J, 332 ( Pt 1 ):243-50.
Exemplary assays useful for measuring protein serine/threonine kinase activity
of
complex 159a include but are not limited to those described in Leverson JD et
al., 1998,
Mol Cell, 2:417-25.
Exemplary assays useful for measuring cell cycle progression of cells
containing
complex 159a include but are not limited to those described in Kruhlak MJ et
al., 2001, J
Biol Chem, 276:38307-19.
Exemplary assays useful for measuring Apoptosis induction of cells containing
complex 159a include but are not limited to those described in Chen Lf et al.,
2001,
Science, 293:1653-7.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice for the study of genetic complementation in T cell during development
complex
159b include but are not limited to those described in Jacobs H et al., 1999,
J Exp Med,
190:1059-68.

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Exemplary animal models useful for assaying compounds interacting with
transgenic
mice for the study of ovary development complex 159b include but are not
limited to
those described in Freiman RN et al., 2001, Science, 293:2084-7.
Exemplary animal models useful for assaying compounds interacting with
transgenic
mice for the study of genetic complementation in lymphomas complex 159b
include but
are not limited to those described in Verbeek S et al., 1991, Mol Cell Biol,
11:1176-9.
Exemplary assays useful for measuring acetylase activity of complex 159b
include but are not limited to those described in Fischle W et al., 1999, J
Biol Chem,
274:11713-20.
Exemplary assays useful for measuring transcription activity of complex 159b
include but are not limited to those described in Kikyo N et al., 2000,
Science, 289:2360-
2.
Exemplary assays useful for measuring protein serine/threonine phosphatase
activity of complex 159b include but are not limited to those described in
Kusuda K et
al., 1998, Biochem J, 332 ( Pt 1 ):243-50.
Exemplary assays useful for measuring protein serine/threonine kinase activity
of
complex 159b include but are not limited to those described in Leverson JD et
al., 1998,
Mol Cell, 2:417-25.
Exemplary assays useful for measuring cell cycle progression of cells
containing
complex 159b include but are not limited to those described in Kruhlak MJ et
al., 2001, J
Biol Chem, 276:38307-19.
Exemplary assays useful for measuring Apoptosis induction of cells containing
complex 159b include but are not limited to those described in Chen Lf et al.,
2001,
Science, 293:1653-7.
Exemplary assays useful for measuring mRNA splicing activity of complex 160a
include but are not limited to those described in Padgett RA et al., 1983,
Cell, 35:101-7.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a spinal muscular atrophy-like phenotype complex 160b include
but are
not limited to those described in Monani UR et al., 2000, Hum Mol Genet, 9:333-
9.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a systemic lupus erythematosus-like phenotype complex 160b
include
but are not limited to those described in Kyogoku M et al., 1987, Prog Clin
Biol Res,
229:95-130.

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Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a xeroderma pigmentosum-like phenotype complex 160b include
but are
not limited to those described in Takeuchi S et al., 1998, Cancer Res, 58:641-
6.
Exemplary assays useful for measuring mRNA splicing activity of complex 160b
include but are not limited to those described in Padgett RA et al., 1983,
Cell, 35:101-7.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a spinal muscular atrophy-like phenotype complex 161a include
but are
not limited to those described in Monani UR et al., 2000, Hum Mol Genet, 9:333-
9.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a systemic lupus erythematosus-like phenotype complex 161 a
include
but are not limited to those described in Kyogoku M et al., 1987, Prog Clin
Biol Res,
229:95-130.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a xeroderma pigmentosum-like phenotype complex 161a include
but are
not limited to those described in Takeuchi S et al., 1998, Cancer Res, 58:641-
6.
Exemplary assays useful for measuring Gcn2 kinase activity of complex 161 a
include but are not limited to those described in Sood R et al., 2000,
Genetics, 154:787-
801.
Exemplary assays useful for measuring mRNA splicing activity of complex 161a
include but are not limited to those described in Behlke MA et al., 2000,
Biotechniques,
29:892-7.
Exemplary assays useful for measuring RNA binding activity of complex 161 a
include but are not limited to those described in lyer RK and Levinger LF.,
1988 Nov-
Dec, Gene Anal Tech, 5:125-9.
Exemplary assays useful for measuring RNA processing activity of complex 161 a
include but are not limited to those described in Seraphin B., 1995, EMBO J,
14:2089-
98.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a spinal muscular atrophy-like phenotype complex 161 b include
but are
not limited to those described in Monani UR et al., 2000, Hum Mol Genet, 9:333-
9.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a systemic lupus erythematosus-like phenotype complex 161 b
include
but are not limited to those described in Kyogoku M et al., 1987, Prog Clin
Biol Res,
229:95-130.

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Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a xeroderma pigmentosum-like phenotype complex 161 b include
but are
not limited to those described in Takeuchi S et al., 1998, Cancer Res, 58:641-
6.
Exemplary assays useful for measuring Gcn2 kinase activity of complex 161b
include but are not limited to those described in Sood R et al., 2000,
Genetics, 154:787-
801.
Exemplary assays useful for measuring mRNA splicing activity of complex 161 b
include but are not limited to those described in Behlke MA et al., 2000,
Biotechniques,
29:892-7.
Exemplary assays useful for measuring RNA binding activity of complex 161 b
include but are not limited to those described in lyer RK and Levinger LF.,
1988 Nov-
Dec, Gene Anal Tech, 5:125-9.
Exemplary assays useful for measuring RNA processing activity of complex 161 b
include but are not limited to those described in Seraphin B., 1995, EMBO J,
14:2089-
98.
Exemplary assays useful for measuring 3' end mRNA processing activity of
complex 162a include but are not limited to those described in Ruegsegger U et
al.,
1996, J Biol Chem, 271:6107-13. and/or Kessler MM et al., 1996, J Biol Chem,
271:27167-75.
Exemplary assays useful for measuring 3' end mRNA processing activity of
complex 162b include but are not limited to those described in Ruegsegger U et
al.,
1996, J Biol Chem, 271:6107-13. and/or Kessler MM et al., 1996, J Biol Chem,
271:27167-75.
Exemplary assays useful for measuring rRNA processing activity of complex
163a include but are not limited to those described in Hong B et al., 1997,
Mol Cell Biol,
17:378-88.
Exemplary assays useful for measuring rRNA localization of cells containing
complex 163a include but are not limited to those described in Jordan P et
al., 1996, J
Cell Biol, 133:225-34.
Exemplary assays useful for measuring nuclear export of ribosomal proteins in
cells containing complex 163a include but are not limited to those described
in Hurt E et
al., 1999, J Cell Biol, 144:389-401.

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Exemplary assays useful for measuring rRNA processing activity of complex
163b include but are not limited to those described in Hong B et al., 1997,
Mol Cell Biol,
17:378-88.
Exemplary assays useful for measuring rRNA localization of cells containing
complex 163b include but are not limited to those described in Jordan P et
al., 1996, J
Cell Biol, 133:225-34. .
Exemplary assays useful for measuring nuclear export of ribosomal proteins in
cells containing complex 163b include but are not limited to those described
in Hurt E et
al., 1999, J Cell Biol, 144:389-401.
Exemplary assays useful for measuring CTD kinase activity of complex 164a
include but are not limited to those described in Morris DP et al., 1997,
Methods,
12:264-75.
Exemplary assays useful for measuring single strand telomeric DNA binding
assay of complex 164b include but are not limited to those described in Lin JJ
and
Zakian VA., 1994, Nucleic Acids Res, 22:4906-13.
Exemplary assays useful for measuring CTD kinase activity of complex 164b
include but are not limited to those described in Morris DP et al., 1997,
Methods,
12:264-75.
Exemplary assays useful for measuring cystathionine beta-synthase activity of
complex 165 include but are not limited to those described in Kraus JP., 1987,
Methods
Enzymol, 143:388-94.
Exemplary assays useful for measuring cystathionine synthase activity of
complex 165 include but are not limited to those described in Kashiwamata S
and
Greenberg DM., 1970, Biochim Biophys Acta, 212:488-500.
Exemplary assays useful for measuring cystathionine synthase activity in
cultured
fibroblasts containing complex 165 include but are not limited to those
described in
Boers GH et al., 1985, Hum Genet, 69:164-9.
Exemplary assays useful for measuring adenylosuccinate lyase activity of
complex 166 include but are not limited to those described in Park ICW et al.,
1980, J
Biochem Biophys Methods, 2:291-7.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a mitochondria) disease-like phenotype complex 167a include
but are not
limited to those described in Wallace DC., 2001 Spring, Am J Med Genet, 106:71-
93.

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Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a Parkinson's disease-like phenotype complex 167a include but
are not
limited to those described in Petroske E et al., 2001, Neuroscience, 106:589-
601.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a diabetes-like phenotype complex 167a include but are not
limited to
those described in Makino S et al., 1980, Jikken Dobutsu, 29:1-13.
Exemplary assays useful for measuring RNA turnover activity of complex 167a
include but are not limited to those described in Min J and Zassenhaus HP.,
1993, J
Bacteriol, 175:6245-53.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a mitochondrial disease-like phenotype complex 167b include
but are not
limited to those described in Wallace DC., 2001 Spring, Am J Med Genet, 106:71-
93.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a Parkinson's disease-like phenotype complex 167b include but
are not
limited to those described in Petroske E et al., 2001, Neuroscience, 106:589-
601.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a diabetes-like phenotype complex 167b include but are not
limited to
those described in Makino S et al., 1980, Jikken Dobutsu, 29:1-13.
Exemplary assays useful for measuring RNA turnover activity of complex 167b
include but are not limited to those described in Min J and Zassenhaus HP.,
1993, J
Bacteriol, 175:6245-53.
Exemplary assays useful for measuring alpha-aminoadipate-semialdehyde
dehydrogenase activity of complex 168a include but are not limited to those
described in
Ehmann DE et al., 1999, Biochemistry, 38:6171-7.
Exemplary assays useful for measuring alcohol dehydrogenase activity of
complex 168a include but are not limited to those described in Chrostek L et
al., 2001,
Hum Exp Toxicol, 20:255-8. and/or Ganzhorn AJ and Plapp BV., 1988, J Biol
Chem,
263:5446-54.
Exemplary assays useful for measuring growth of yeast cells containing complex
168a include but are not limited to those described in Winston MK and
Bhattacharjee
JK., 1982, J Bacteriol, 152:874-9.
Exemplary assays useful for measuring alpha-aminoadipate-semialdehyde
dehydrogenase activity of complex 168b include but are not limited to those
described in
Ehmann DE et al., 1999, Biochemistry, 38:6171-7.

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Exemplary assays useful for measuring nuclear import/export activity of
complex
168b include but are not limited to those described in Lindsay ME et al.,
2001, J Cell
Biol, 153:1391-402, and/or Jakel S and Gorlich D., 1998, EMBO J, 17:4491-502.
Exemplary assays useful for measuring growth of yeast cells containing complex
168b include but are not limited to those described in Winston MK and
Bhattacharjee
JK., 1982, J Bacteriol, 152:874-9.
Exemplary assays useful for measuring actin-binding activity of complex 169a
include but are not limited to those described in Engqvist-Goldstein AE et
al., 1999, J
Cell Biol, 147:1503-18.
Exemplary assays useful for measuring endocytosis activity of complex 169a
include but are not limited to those described in Dulic V et al., 1991,
Methods Enzymol,
194:697-710. and/or Volland C et al., 1994, J Biol Chem, 269:9833-41.
Exemplary assays useful for measuring actin-binding activity of complex 169b
include but are not limited to those described in Engqvist-Goldstein AE et
al., 1999, J
Cell Biol, 147:1503-18.
Exemplary assays useful for measuring kinase activity of complex 169b include
but are not limited to those described in Volonte C et al., 1992,
Biotechniques, 12:854-8.
Exemplary assays useful for measuring endocytosis activity of complex 169b
include but are not limited to those described in Dulic V et al., 1991,
Methods Enzymol,
194:697-710. and/or Volland C et al., 1994, J Biol Chem, 269:9833-41.
Exemplary assays useful for measuring transcription activity of complex 170a
include but are not limited to those described in Schlegel BP et al., 2000,
Proc Natl Acad
Sci U S A, 97:3148-53.
Exemplary assays useful for measuring in vivo chromatin remodeling in yeast
cells containing complex 170a include but are not limited to those described
in Kent NA
et al., 2001, Genes Dev, 15:619-26.
Exemplary assays useful for measuring transcription activity of complex 170b
include but are not limited to those described in Schlegel BP et al., 2000,
Proc Natl Acad
Sci U S A, 97:3148-53.
Exemplary assays useful for measuring protein kinase assay of complex 170b
include but are not limited to those described in Ho Y et al., 1997, Proc Natl
Acad Sci U
S A, 94:581-6.

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Exemplary assays useful for measuring in vivo chromatin remodeling in yeast
cells containing complex 170b include but are not limited to those described
in Kent NA
et al., 2001, Genes Dev, 15:619-26.
Exemplary assays useful for measuring enolase activity of complex 171 include
but are not limited to those described in Baranowski T and Wolna E., 1975,
Methods
Enzymol, 42:335-8. and/or Lilley RM et al., 1985, Anal Biochem, 148:282-7.
Exemplary assays useful for measuring cystathionase activity of complex 172
include but are not limited to those described in Bergad PL and Rathbun WB.,
1986,
Ophthalmic Res, 18:343-8.
Exemplary assays useful for measuring 3-hydroxy-3-methylglutaryl-CoA synthase
activity of complex 173a include but are not limited to those described in
Clinkenbeard
KD et al., 1975, Methods Enzymol, 35:160-7.
Exemplary assays useful for measuring homoisocitric dehydrogenase activity of
complex 173a include but are not limited to those described in Gaillardin CM
et al.,
1982, Eur J Biochem, 128:489-94.
Exemplary assays useful for measuring 3-hydroxy-3-methylglutaryl coenzyme A
synthase activity of complex 173a include but are not limited to those
described in
Rokosz LL et al., 1994, Arch Biochem Biophys, 312:1-13.
Exemplary assays useful for measuring 3-hydroxy-3-methylglutaryl-CoA synthase
activity of complex 173b include but are not limited to those described in
Clinkenbeard
KD et al., 1975, Methods Enzymol, 35:160-7.
Exemplary assays useful for measuring homoisocitric dehydrogenase activity of
complex 173b include but are not limited to those described in Gaillardin CM
et al.,
1982, Eur J Biochem, 128:489-94.
Exemplary assays useful for measuring 3-hydroxy-3-methylglutaryl coenzyme A
synthase activity of complex 173b include but are not limited to those
described in
Rokosz LL et al., 1994, Arch Biochem Biophys, 312:1-13.
Exemplary assays useful for measuring disulfid bond formation activity of
complex 174a include but are not limited to those described in Frand AR and
Kaiser
CA., 1998, Mol Cell, 1:161-70.
Exemplary assays useful for measuring subcellular localisation of a Sec13
marker
protein in cells containing complex 174a include but are not limited to those
described in
Hammond AT and Glick BS., 2000, Mol Biol Cell, 11:3013-30.

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Exemplary assays useful for measuring effects on viability of cells containing
complex 174a include but are not limited to those described in Frand AR and
Kaiser
CA., 1998, Mol Cell, 1:161-70.
Exemplary assays useful for measuring disulfid bond formation activity of
complex 174b include but are not limited to those described in Frand AR and
Kaiser
CA., 1998, Mol Cell, 1:161-70.
Exemplary assays useful for measuring subcellular localisation of a Sec13
marker
protein in cells containing complex 174b include but are not limited to those
described in
Hammond AT and Glick BS., 2000, Mol Biol Cell, 11:3013-30.
Exemplary assays useful for measuring effects on viability of cells containing
complex 174b include but are not limited to those described in Frand AR and
Kaiser
CA., 1998, Mol Cell, 1:161-70.
Exemplary assays useful for measuring GTPase activity of complex 175a include
but are not limited to those described in Esters H et al., 2001, J Mol Biol,
310:141-56.
Exemplary assays useful for measuring subcellular localization/transport of
Sec6
and Sec8 in cells containing complex 175a include but are not limited to those
described
in Charron AJ et al., 2000, J Cell Biol, 149:111-24.
Exemplary assays useful for measuring GTPase activity of complex 175b include
but are not limited to those described in Esters H et al., 2001, J Mol Biol,
310:141-56.
Exemplary assays useful for measuring subcellular localization/transport of
Sec6
and Sec8 in cells containing complex 175b include but are not limited to those
described
in Charron AJ et al., 2000, J Cell Biol, 149:111-24.
Exemplary assays useful for measuring rRNA processing activity of complex
176a include but are not limited to those described in Kressler D et al.,
1997, Mol Cell
Biol, 17:7283-94.
Exemplary assays useful for measuring export of 60S ribosomes in cells
containing complex 176a include but are not limited to those described in
Stage-
Zimmermann T et al., 2000, Mol Biol Cell, 11:3777-89.
Exemplary assays useful for measuring rRNA processing activity of complex
176b include but are not limited to those described in Kressler D et al.,
1997, Mol Cell
Biol, 17:7283-94.
Exemplary assays useful for measuring export of 60S ribosomes in cells
containing complex 176b include but are not limited to those described in
Stage-
Zimmermann T et al., 2000, Mol Biol Cell, 11:3777-89.

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Exemplary assays useful for measuring iron transport activity of complex 178a
include but are not limited to those described in Shingles R et al., 2001,
Anal Biochem,
296:106-13.
Exemplary assays useful for measuring iron uptake by rabbit erythrocytes
containing complex 178a include but are not limited to those described in Chan
RY et
al., 1986, Biochem Int, 13:409-15.
Exemplary animal models useful for assaying compounds interacting with a rat
model of
renal iron transport complex 178b include but are not limited to those
described in
Wareing M et al., 2000, J Physiol, 524 Pt 2:581-6.
Exemplary assays useful for measuring iron transport activity of complex 178b
include but are not limited to those described in Shingles R et al., 2001,
Anal Biochem,
296:106-13.
Exemplary assays useful for measuring iron uptake by rabbit erythrocytes
containing complex 178b include but are not limited to those described in Chan
RY et
al., 1986, Biochem Int, 13:409-15.
Exemplary assays useful for measuring protein secretion activity of complex
180a include but are not limited to those described in Zhdankina O et al.,
2001, Yeast,
18:1-18.
Exemplary assays useful for measuring protein binding activity of complex 180a
include but are not limited to those described in Zhu Y et al., 2001, Science,
292:1716-8.
Exemplary assays useful for measuring subcellular localization of GGA2 in
cells
containing complex 180a include but are not limited to those described in
Hirst J et al.,
2000, J Cell Biol, 149:67-80.
Exemplary assays useful for measuring protein secretion activity of complex
180b include but are not limited to those described in Zhdankina O et al.,
2001, Yeast,
18:1-18.
Exemplary assays useful for measuring protein binding activity of complex 180b
include but are not limited to those described in Zhu Y et al., 2001, Science,
292:1716-8.
Exemplary assays useful for measuring subcellular localization of GGA2 in
cells
containing complex 180b include but are not limited to those described in
Hirst J et al.,
2000, J Cell Biol, 149:67-80.
Exemplary assays useful for measuring protein glycosylation activity of
complex
181 include but are not limited to those described in Sutterlin C et al.,
1998, Biochem J,
332 ( Pt 1 ):153-9.

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Exemplary assays useful for measuring glycolipid labelling in cells containing
complex 181 include but are not limited to those described in Sutterlin C et
al., 1998,
Biochem J, 332 ( Pt 1 ):153-9.
Exemplary assays useful for measuring sumoylation activity of complex 182a
include but are not limited to those described in Okuma T et al., 1999,
Biochem Biophys
Res Commun, 254:693-8.
Exemplary animal models useful for assaying compounds interacting with
transgenic fly
overexpressing UBA2 in the developing eye (retinal degeneration phenotype)
complex
182b include but are not limited to those described in Long X and Griffith
LC., 2000, J
Biol Chem, 275:40765-76.
Exemplary assays useful for measuring sumoylation activity of complex 182b
include but are not limited to those described in Okuma T et al., 1999,
Biochem Biophys
Res Commun, 254:693-8.
Exemplary animal models useful for assaying compounds interacting with mice
injected
with BL6 melanoma cells (metastasis model) complex 183a include but are not
limited to
those described in Nakaji T et al., 1999, Cancer Lett, 147:139-47.(A new
member of the
GTPase superfamily that is upregulated in highly metastatic cells.)
Exemplary assays useful for measuring GTP-binding proteinlGTPase activity of
complex 183a include but are not limited to those described in Ridley AJ et
al., 1993,
EMBO J, 12:5151-60.
Exemplary animal models useful for assaying compounds interacting with mice
injected
with BL6 melanoma cells (metastasis model) complex 183b include but are not
limited to
those described in Nakaji T et al., 1999, Cancer Lett, 147:139-47.(A new
member of the
GTPase superfamily that is upregulated in highly metastatic cells.)
Exemplary assays useful for measuring GTP-binding proteinlGTPase activity of
complex 183b include but are not limited to those described in Ridley AJ et
al., 1993,
EMBO J, 12:5151-60.
Exemplary assays useful for measuring histone deacetylase activity of complex
185a include but are not limited to those described in Grozinger CM et al.,
1999, Proc
Natl Acad Sci U S A, 96:4868-73. and/or HofFmann K et al., 200'1 Jan-Feb,
Bioconjug
Chem, 12:51-5.
Exemplary assays useful for measuring nuclear localization/transport of
retinoic
acid and thyroid hormone receptors (SMRT) in cells containing complex 185a
include
but are not limited to those described in Wu X et al., 2001, J Biol Chem,
276:24177-85.

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Exemplary assays useful for measuring histone deacetylase activity of complex
185b include but are not limited to those described in Grozinger CM et al.,
1999, Proc
Natl Acad Sci U S A, 96:4868-73. and/or Hoffmann K et al., 2001 Jan-Feb,
Bioconjug
Chem, 12:51-5.
Exemplary assays useful for measuring nuclear localization/transport of
retinoic
acid and thyroid hormone receptors (SMRT) in cells containing complex 185b
include
but are not limited to those described in Wu X et al., 2001, J Biol Chem,
276:24177-85.
Exemplary assays useful for measuring homogeneous time-resolved fluorescence
energy transfer activity of complex 186 include but are not limited to those
described in
Zhou G et al., 2001, Methods, 25:54-61.
Exemplary assays useful for measuring protein stabilizing activity of complex
186
include but are not limited to those described in Bigelis R et al., 1981, J
Biol Chem,
256:5144-52.
Exemplary assays useful for measuring arsenite toxicity of cells containing
complex 186 include but are not limited to those described in Solc J et al.,
2001, Cell
Stress Chaperones, 6:6-15.
Exemplary assays useful for measuring proliferation activity of cells
containing
complex 186 include but are not limited to those described in Bencsath M et
al., 1998,
Pathol Oncol Res, 4:121-4.
Exemplary animal models useful for assaying compounds interacting with the
study of
male mating behaviour in Caenorhabditis elegans complex 187a include but are
not
limited to those described in Yoda A et al., 2000, Genes Cells, 5:885-895.
Exemplary assays useful for measuring mRNA decay activity of complex 187a
include but are not limited to those described in Gonzalez CI et al., 2000,
Mol Cell,
5:489-99.
Exemplary animal models useful for assaying compounds interacting with the
study of
male mating behaviour in Caenorhabditis elegans complex 187b include but are
not
limited to those described in Yoda A et al., 2000, Genes Cells, 5:885-895.
Exemplary assays useful for measuring mRNA decay activity of complex 187b
include but are not limited to those described in Gonzalez CI et al., 2000,
Mol Cell,
5:489-99.
Exemplary assays useful for measuring NAD-dependent protein deacetylase
activity of complex 188 include but are not limited to those described in Imai
S et al.,
2000, Nature, 403:795-800.

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Exemplary assays useful for measuring histone deacetylation in senescent
human fibroblasts containing complex 188 include but are not limited to those
described
in Wagner M et al., 2001, FEBS Lett, 499:101-6.
Exemplary assays useful for measuring DNA polymerise activity of complex 189
include but are not limited to those described in Han S et al., 2000, Biochem
Pharmacol,
60:403-11.
Exemplary assays useful.for measuring chromatin remodelling activity of
complex
189 include but are not limited to those described in Brehm A et al., 2000,
EMBO J,
19:4332-41.
Exemplary assays useful for measuring DNA topoisomerase activity of complex
189 include but are not limited to those described in Merino A et al., 1993,
Nature,
365:227-32. and/or MA D et al., 1996, Proc Natl Acad Sci U S A, 93:6583-8.
Exemplary assays useful for measuring RNA polymerise activity of complex 189
include but are not limited to those described in Sturges MR et al., 1999,
Nucleic Acids
Res, 27:690-4.
Exemplary assays useful for measuring differentiation of cells containing
complex
189 include but are not limited to those described in de la Serna IL et al.,
2001, Nat
Genet, 27:187-90.
Exemplary assays useful for measuring centromer DNA binding activity of
complex 190a include but are not limited to those described in Ortiz J et al.,
1999,
Genes Dev, 13:1140-55.
Exemplary assays useful for measuring changes in subcellular localization of
cell
cycle marker proteins in cells containing complex 190a include but are not
limited to
those described in Dalton S and Whitbread L., 1995, Proc Natl Acad Sci U S A,
92:2514-8.
Exemplary assays useful for measuring chromosome transmission in cells
containing complex 190a include but are not limited to those described in
Poddar A et
al., 1999, Mol Microbiol, 31:349-60.
Exemplary assays useful for measuring centromer DNA binding activity of
complex 190b include but are not limited to those described in Ortiz J et al.,
1999,
Genes Dev, 13:1140-55.
Exemplary assays useful for measuring changes in subcellular localization of
cell
cycle marker proteins in cells containing complex 190b include but are not
limited to

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those described in Dalton S and Whitbread L., 1995, Proc Natl Acad Sci U S A,
92:2514-8.
Exemplary assays useful for measuring chromosome transmission in cells
containing complex 190b include but are not limited to those described in
Poddar A et
al., 1999, Mol Microbiol, 31:349-60.
Exemplary assays useful for measuring pyrophosphatase activity of complex
191a include but are not limited to those described in Eriksson J et al.,
2001, Anal
Biochem, 293:67-70.
Exemplary assays useful for measuring ATP sulfurylase activity of complex 191
a
include but are not limited to those described in Daley LA et al., 1986, Anal
Biochem,
157:385-95.
Exemplary animal models useful for assaying compounds interacting with mice
deficient
in plasma cell membrane glycoprotein-1 complex 191 b include but are not
limited to
those described in Rutsch F et al., 2001, Am J Pathol, 158:543-54.
Exemplary assays useful for measuring pyrophosphatase activity of complex
191b include but are not limited to those described in Eriksson J et al.,
2001, Anal
Biochem, 293:67-70.
Exemplary assays useful for measuring GTP exchange activity of complex 191 b
include but are not limited to those described in Sasaki T et al., 1990, J
Biol Chem,
265:2333-7.
Exemplary assays useful for measuring ATP sulfurylase activity of complex 191
b
include but are not limited to those described in Daley LA et al., 1986, Anal
Biochem,
157:385-95.
Exemplary assays useful for measuring VMA1 splicing activity of complex 192
include but are not limited to those described in Kawasaki M et al., 1997, J
Biol Chem,
272:15668-74.
Exemplary assays useful for measuring autophagy on cells containing complex
192 include but are not limited to those described in Kametaka S et al., 1998,
J Biol
Chem, 273:22284-91.
Exemplary assays useful for measuring ATPase activity of complex 193a include
but are not limited to those described in Tsukiyama T et al., 1999, Genes Dev,
13:686-
97.

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Exemplary assays useful for measuring Isw2 ATP-dependent chromatin
remodeling activity of complex 193a include but are not limited to those
described in
Gelbart ME et al., 2001, Mol Cell Biol, 21:2098-106.
Exemplary assays useful for measuring ATPase activity of complex 193b include
but are not limited to those described in Tsukiyama T et al., 1999, Genes Dev,
13:686-
97.
Exemplary assays useful for measuring Isw2 ATP-dependent chromatin
remodeling activity of complex 193b include but are not limited to those
described in
Gelbart ME et al., 2001, Mol Cell Biol, 21:2098-106.
Exemplary assays useful for measuring translation factor activity of complex
195
include but are not limited to those described in Choi SK et al., 1998,
Science,
280:1757-60.
Exemplary assays useful for measuring CD4 internalization of cells containing
complex 195 include but are not limited to those described in Lu X et al.,
1998,
Immunity, 8:647-56.
Exemplary assays useful for measuring aminoacyl synthetase activity of complex
196 include but are not limited to those described in Shiba IC et al., 1997, J
Biol Chem,
272:22809-16. and/or Stark LA and Hay RT., 1998, J Virol, 72:3037-44.
Exemplary assays useful for measuring isopropylmalate dehydratase activity of
complex 197 include but are not limited to those described in Kohlhaw GB.,
1988,
Methods Enzymol, 166:423-9.
Exemplary assays useful for measuring alcohol dehydrogenase activity of
complex 197 include but are not limited to those described in Bennetzen JL and
Hall
BD., 1982, J Biol Chem, 257:3018-25.
Exemplary assays useful for measuring guanine nucleotide exchange factor
activity of complex 198a include but are not limited to those described in
Sasaki T et al.,
1990, J Biol Chem, 265:2333-7. and/or Horiuchi H et al., 1995, J Biol Chem,
270:11257-
62.
Exemplary assays useful for measuring guanine nucleotide exchange factor
activity of complex 198b include but are not limited to those described in
Sasaki T et al.,
1990, J Biol Chem, 265:2333-7. and/or Horiuchi H et al., 1995, J Biol Chem,
270:11257-
62.

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Exemplary assays useful for measuring mitochondria) protein translocation
activity
of complex 201 a include but are not limited to those described in Gordon DM
et al.,
1999, Hum Mol Genet, 8:2255-62.
Exemplary assays useful for measuring protease activity and mitochondria)
protein import activity of complex 201a include but are not limited to those
described in
Geli V et al., 1990, J Biol Chem, 265:19216-22. and/or Folsch H et al., 1998,
EMBO J,
17:6508-15.
Exemplary assays useful for measuring proliferation activity of cells
containing
complex 201a include but are not limited to those described in Kissova I et
al., 2000,
FEBS Lett, 471:113-8.
Exemplary assays useful for measuring mitochondria) protein translocation
activity
of complex 201 b include but are not limited to those described in Gordon DM
et al.,
1999, Hum Mol Genet, 8:2255-62.
Exemplary assays useful for measuring protease activity and mitochondria)
protein import activity of complex 201 b include but are not limited to those
described in
Geli V et al., 1990, J Biol Chem, 265:19216-22. and/or Folsch H et al., 1998,
EMBO J,
17:6508-15.
Exemplary assays useful for measuring proliferation activity of cells
containing
complex 201 b include but are not limited to those described in Kissova I et
al., 2000,
FEBS Lett, 471:113-8.
Exemplary assays useful for measuring C 1-tetrahydrofolate synthase activity
of
complex 203a include but are not limited to those described in Paukert JL and
Rabinowitz JC., 1980, Methods Enzymol, 66:616-26.
Exemplary assays useful for measuring subcellular localization/transport of
mannose-6-phosphate receptor in cells containing complex 203a include but are
not
limited to those described in Meyer C et al., 2000, EMBO J, 19:2193-203.
Exemplary assays useful for measuring trafficking of AP-1 using YFP-tagged
mu1A subunit of AP-1 in cells containing complex 203a include but are not
limited to
those described in Huang F et al., 2001, TrafFic, 2:345-57.
Exemplary animal models useful for assaying compounds interacting with mice
deficient
in gamma-adaptin (model for AP-1 function) complex 203b include but are not
limited to
those described in Zizioli D et al., 1999, J Biol Chem, 274:5385-90.
Exemplary animal models useful for assaying compounds interacting with mice
deficient
in mu1A-adaptin (model for impaired endosome to TGN trafficking) complex 203b

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include but are not limited to those described in Meyer C et al., 2000, EMBO
J, 19:2193-
203.
Exemplary assays useful for measuring C1-tetrahydrofolate synthase activity of
complex 203b include but are not limited to those described in Paukert JL and
Rabinowitz JC., 1980, Methods Enzymol, 66:616-26.
Exemplary assays useful for measuring subcellular localization/transport of
mannose-6-phosphate receptor in cells containing complex 203b include but are
not
limited to those described in Meyer C et al., 2000, EMBO J, 19:2193-203.
Exemplary assays useful for measuring trafficking of AP-1 using YFP-tagged
mu1A subunit of AP-1 in cells containing complex 203b include but are not
limited to
those described in Huang F et al., 2001, Traffic, 2:345-57.
Exemplary assays useful for measuring receptor protein translocation activity
of
complex 204a include but are not limited to those described in Hill K et al.,
1998, Nature,
395:516-21.]
Exemplary assays useful for measuring motility and morphology of mitochondria
in cells containing complex 204a include but are not limited to those
described in
Boldogh I et al., 1998, J Cell Biol, 141:1371-81.
Exemplary assays useful for measuring receptor protein translocation activity
of
complex 204b include but are not limited to those described in Hill IC et al.,
1998, Nature,
395:516-21.]
Exemplary assays useful for measuring motility and morphology of mitochondria
in cells containing complex 204b include but are not limited to those
described in
Boldogh I et al., 1998, J Cell Biol, 141:1371-81.
Exemplary assays useful for measuring mRNA binding activity of complex 205
include but are not limited to those described in Katahira J et al., 1999,
EMBO J,
18:2593-609.
Exemplary assays useful for measuring mRNA binding and mRNA export activity
of complex 205 include but are not limited to those described in Semmes OJ et
al.,
1998, J Virol, 72:9526-34.
Exemplary assays useful for measuring RNA export in yeast cells containing
complex 205 include but are not limited to those described in ICadowaki T et
al., 1994, J
Cell Biol, 126:649-59.

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Exemplary assays useful for measuring RNA export using HIV rev in HeL_a cells
containing complex 205 include but are not limited to those described in
Kimura T et al.,
1996, Biochimie, 78:1075-80.
Exemplary animal models useful for assaying compounds interacting with nude
mice
injected with phospholipase D transformed cells complex 206a include but are
not
limited to those described in Min DS et al., 2001, Carcinogenesis, 22:1641-7.
Exemplary assays useful for measuring phospholipase D activity of complex
206a include but are not limited to those described in Brown HA et al., 1993,
Cell,
75:1137-44. and/or Hammond SM et al., 1995, J Biol Chem, 270:29640-3.
Exemplary assays useful for measuring phospholipase D activity of complex
206a include but are not limited to those described in Rudge SA et al., 1998,
J Cell Biol,
140:81-90.
Exemplary assays useful for measuring phopholipase D induced anchorage-
independent growth in fibroblasts containing complex 206a include but are not
limited to
those described in Min DS et al., 2001, Carcinogenesis, 22:1641-7.
Exemplary animal models useful for assaying compounds interacting with nude
mice
injected with phospholipase D transformed cells complex 206b include but are
not
limited to those described in Min DS et al., 2001, Carcinogenesis, 22:1641-7.
Exemplary assays useful for measuring phospholipase D activity of complex
206b include but are not limited to those described in Brown HA et al., 1993,
Cell,
75:1137-44. and/or Hammond SM et al., 1995, J Biol Chem, 270:29640-3.
Exemplary assays useful for measuring phospholipase D activity of complex
206b include but are not limited to those described in Rudge SA et al., 1998,
J Cell Biol,
140:81-90.
Exemplary assays useful for measuring phopholipase D induced anchorage-
independent growth in fibroblasts containing complex 206b include but are not
limited to
those described in Min DS et al., 2001, Carcinogenesis, 22:1641-7.
Exemplary animal models useful for assaying compounds interacting with EMK
knock
out mice complex 207a include but are not limited to those described in
Bessone S et
al., 1999, Dev Biol, 214:87-101.(EMK protein kinase-null mice: dwarfism and
hypofertility
associated with alterations in the somatotrope and prolactin pathways.)
Exemplary assays useful for measuring protein serine/threonine kinase activity
of
complex 207a include but are not limited to those described in Illenberger S
et al., 1996,
J Biol Chem, 271:10834-43.

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Exemplary assays useful for measuring chromatin assembly activity of complex
207a include but are not limited to those described in McQuibban GA et al.,
1998, J Biol
Chem, 273:6582-90.
Exemplary animal models useful for assaying compounds interacting with EMK
knock
out mice complex 207b include but are not limited to those described in
Bessone S et
al., 1999, Dev Biol, 214:87-101.(EMK protein kinase-null mice: dwarfism and
hypofertility
associated with alterations in the somatotrope and prolactin pathways.)
Exemplary assays useful for measuring protein serine/threonine kinase activity
of
complex 207b include but are not limited to those described in Illenberger S
et al., 1996,
J Biol Chem, 271:10834-43.
Exemplary assays useful for measuring chromatin assembly activity of complex
207b include but are not limited to those described in McQuibban GA et al.,
1998, J Biol
Chem, 273:6582-90.
Exemplary assays useful for measuring GTP-binding and GTPase activity of
complex 208 include but are not limited to those described in Zahraoui A et
al., 1989, J
Biol Chem, 264:12394-401.
Exemplary assays useful for measuring ATPase activity of complex 208 include
but are not limited to those described in Navarro Izquierdo A et al., 1977,
Rev Clin Esp,
147:47-53.]
Exemplary assays useful for measuring translation factor activity of complex
209a include but are not limited to those described in Remacha M et al., 1992,
J Biol
Chem, 267:12061-7.
Exemplary assays useful for measuring RNA binding and translation activity of
complex 209a include but are not limited to those described in Gustafson WC et
al.,
1998, Biochem J, 331 ( Pt 2):387-93.
Exemplary assays useful for measuring effects on nucleolar localization of
marker
proteins in cells containing complex 209a include but are not limited to those
described
in Freeman JW et al., 1991, Cancer Res, 51:1973-8.
Exemplary assays useful for measuring translation factor activity of complex
209b include but are not limited to those described in Remacha M et al., 1992,
J Biol
Chem, 267:12061-7.
Exemplary assays useful for measuring RNA binding and translation activity of
complex 209b include but are not limited to those described in Gustafson WC et
al.,
1998, Biochem J, 331 ( Pt 2):387-93.

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Exemplary assays useful for measuring effects on nucleolar localization of
marker
proteins in cells containing complex 209b include but are not limited to those
described
in Freeman JW et al., 1991, Cancer Res, 51:1973-8.
Exemplary assays useful for measuring protein degradation activity of complex
210a include but are not limited to those described in Wang CW et al., 2001, J
Biol
Chem, 276:30442-51.
Exemplary assays useful for measuring alpha-mannosidase activity of complex
210a include but are not limited to those described in Opheim DJ., 1978,
Biochim
Biophys Acta, 524:121-30.
Exemplary assays useful for measuring autophagy (peroxisome levels) in cells
containing complex 210a include but are not limited to those described in Wang
CW et
al., 2001, J Biol Chem, 276:30442-51.
Exemplary assays useful for measuring protein degradation activity of complex
210b include but are not limited to those described in Wang CW et al., 2001, J
Biol
Chem, 276:30442-51.
Exemplary assays useful for measuring alpha-mannosidase activity of complex
210b include but are not limited to those described in Opheim DJ., 1978,
Biochim
Biophys Acta, 524:121-30.
Exemplary assays useful for measuring autophagy (peroxisome levels) in cells
containing complex 210b include but are not limited to those described in Wang
CW et
al., 2001, J Biol Chem, 276:30442-51.
Exemplary assays useful for measuring sterol lipid biosynthesis activity of
complex 211 a include but are not limited to those described in Beh CT et al.,
2001,
Genetics, 157:1117-40.
Exemplary assays useful for measuring subcellular localization of GFP-fusion
proteins in cells containing complex 211 a include but are not limited to
those described
in Levine TP and Munro S., 2001, Mol Biol Cell, 12:1633-44.
Exemplary assays useful for measuring sterol lipid biosynthesis activity of
complex 211 b include but are not limited to those described in Beh CT et al.,
2001,
Genetics, 157:1117-40.
Exemplary assays useful for measuring subcellular localization of GFP-fusion
proteins in cells containing complex 211 b include but are not limited to
those described
in Levine TP and Munro S., 2001, Mol Biol Cell, 12:1633-44.

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Exemplary assays useful for measuring protein serine/threonine kinase activity
of
complex 212 include but are not limited to those described in Blasina A et
al., 1999, Curr
Biol, 9:1-10.
Exemplary assays useful for measuring activation of DNA damage checkpoints of
cells containing complex 212 include but are not limited to those described in
Tominaga
K et al., 1999, J Biol Chem, 274:31463-7.
Exemplary assays useful for measuring N-acetylglucosamine-phosphate mutase
activity of complex 214 include but are not limited to those described in
Hofmann M et
al., 1994, Eur J Biochem, 221:741-7.
Exemplary animal models useful for assaying compounds interacting with p44
MAPK
knock out mice complex 215a include but are not limited to those described in
Pages G
et al., 1999, Science, 286:1374-7.(Defective thymocyte maturation in p44 MAP
kinase
(Erk 1) knockout mice.)
Exemplary assays useful for measuring protein serine/threonine kinase activity
of
complex 215a include but are not limited to those described in Boulton TG et
al., 1991,
Biochemistry, 30:278-86. and/or Tedford K et al., 1997, Curr Biol, 7:228-38.
Exemplary animal models useful for assaying compounds interacting with p44
MAPK
knock out mice complex 215b include but are not limited to those described in
Pages G
et al., 1999, Science, 286:1374-7.(Defective thymocyte maturation in p44 MAP
kinase
(Erk 1 ) knockout mice.)
Exemplary assays useful for measuring protein serine/threonine kinase activity
of
complex 215b include but are not limited to those described in Boulton TG et
al., 1991,
Biochemistry, 30:278-86. and/or Tedford K et al., 1997, Curr Biol, 7:228-38.
Exemplary assays useful for measuring NAD+-specific isocitrate dehydrogenase
activity of complex 217 include but are not limited to those described in Keys
DA and
McAlister-Henn L., 1990, J Bacteriol, 172:4280-7.
Exemplary assays useful for measuring protein kinase C activity of complex 218
include but are not limited to those described in Antonsson B et al., 1994, J
Biol Chem,
269:16821-8.
Exemplary assays useful for measuring transformation activity of cells
containing
complex 218 include but are not limited to those described in Wang XY et al.,
1999, Exp
Cell Res, 250:253-63.

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Exemplary assays useful for measuring sensitivity to hypo-osmolarity of cells
containing complex 218 include but are not limited to those described in
Shimizu J et
al., 1994, Mol Gen Genet, 242:641-8.
Exemplary assays useful for measuring DNA replication activity of complex 219a
include but are not limited to those described in Pasero P et al., 1999,
Methods, 18:368-
76. and/or Biswas EE et al., 1993, Biochemistry, 32:3013-9.
Exemplary assays useful for measuring DNA replication of cells containing
complex 219a include but are not limited to those described in Cooley M and
Mishra
NC., 2000, Curr Genet, 38:256-63.
Exemplary assays useful for measuring DNA replication activity of complex 219b
include but are not limited to those described in Pasero P et al., 1999,
Methods, 18:368-
76. and/or Biswas EE et al., 1993, Biochemistry, 32:3013-9.
Exemplary assays useful for measuring transcriptional assay of complex 219b
include but are not limited to those described in Machado AK et al., 1997, J
Biol Chem,
272:17045-54.
Exemplary assays useful for measuring DNA replication of cells containing
complex 219b include but are not limited to those described in Cooley M and
Mishra
NC., 2000, Curr Genet, 38:256-63.
Exemplary assays useful for measuring protein serine/threonine phosphatase
activity of complex 221 include but are not limited to those described in
Volonte C et al.,
1992, Biotechniques, 12:854-8.
Exemplary assays useful for measuring heat-shock induced huntingtin protein
aggregation in COS cells containing complex 221 include but are not limited to
those
described in Sittler A et al., 2001, Hum Mol Genet, 10:1307-15.
Exemplary assays useful for measuring gamma-Glutamate kinase activity of
complex 222 include but are not limited to those described in Seddon AP et
al., 1989, J
Biol Chem, 264:11326-35.
Exemplary assays useful for measuring nuclear export of mRNA of cells
containing complex 222 include but are not limited to those described in
Pritchard CE et
al., 1999, J Cell Biol, 145:237-54.
Exemplary assays useful for measuring pyrroline-5-carboxylate synthase
activity
of complex 223 include but are not limited to those described in Wakabayashi Y
et al.,
1991, Arch Biochem Biophys, 291:1-8.

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Exemplary assays useful for measuring gammma-glutamyl phosphate reductase
activity of complex 223 include but are not limited to those described in
Brandriss MC.,
1979, J Bacteriol, 138:816-22.
Exemplary assays useful for measuring protein ser/thr phosphatase activity of
complex 223 include but are not limited to those described in Robinson MK and
Phizicky
EM., 1998, Methods Mol Biol, 93:235-42.
Exemplary assays useful for measuring effects of heterologous expression of
human pyrroline-5-carboxylate synthase (PSCS) in cells containing complex 223
include
but are not limited to those described in Hu CA et al., 1999, J Biol Chem,
274:6754-62.
Exemplary assays useful for measuring protein phosphatase 2C activity of
complex 224a include but are not limited to those described in Cheng A et al.,
2000, J
Biol Chem, 275:34744-9.
Exemplary assays useful for measuring Ptc1/Tpd1 protein phosphatase 2C
activity of complex 224a include but are not limited to those described in
Robinson MK
and Phizicky EM., 1998, Methods Mol Biol, 93:235-42.
Exemplary assays useful for measuring protein phosphatase 2C activity of
complex 224b include but are not limited to those described in Cheng A et al.,
2000, J
Biol Chem, 275:34744-9.
Exemplary assays useful for measuring Ptc1/Tpd1 protein phosphatase 2C
activity of complex 224b include but are not limited to those described in
Robinson MK
and Phizicky EM., 1998, Methods Mol Biol, 93:235-42.
Exemplary assays useful for measuring protein phosphatase 2C activity of
complex 225a include but are not limited to those described in Robinson MK and
Phizicky EM., 1998, Methods Mol Biol, 93:235-42.
Exemplary assays useful for measuring protein phosphatase 2C activity of
complex 225b include but are not limited to those described in Robinson MK and
Phizicky EM., 1998, Methods Mol Biol, 93:235-42.
Exemplary assays useful for measuring RNA stabilizing activity of complex 226a
include but are not limited to those described in Ruiz-Echevarria MJ and Peltz
SW.,
2000, Cell, 101:741-51.
Exemplary assays useful for measuring DNA fragmentation activity of complex
226a include but are not limited to those described in Tian Q et al., 1991,
Cell, 67:629-
39.

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Exemplary assays useful for measuring transcription termination activity of
complex 226a include but are not limited to those described in Gottlieb E and
Steitz JA.,
1989, EMBO J, 8:851-61.
Exemplary assays useful for measuring translation factor activity of complex
226a include but are not limited to those described in Ohlmann T et al., 1995,
Nucleic
Acids Res, 23:334-40.
Exemplary assays useful for measuring induction of apoptosis in cells
containing
complex 226a include but are not limited to those described in Barry M et al.,
2000,
Methods Enzymol, 322:40-6.
Exemplary animal models useful for assaying compounds interacting with ataxia-
telangiectasia transgenic mice complex 226b include but are not limited to
those
described in Inoue T et al., 1986, Basic Life Sci, 39:323-35.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a Sjogren's syndrome-like phenotype complex 226b include but
are not
limited to those described in Haneji N et al., 1994, J Immunol, 153:2769-77.
Exemplary assays useful for measuring RNA stabilizing activity of complex 226b
include but are not limited to those described in Ruiz-Echevarria MJ and Peltz
SW.,
2000, Cell, 101:741-51.
Exemplary assays useful for measuring DNA fragmentation activity of complex
226b include but are not limited to those described in Tian Q et al., 1991,
Cell, 67:629-
39.
Exemplary assays useful for measuring transcription termination activity of
complex 226b include but are not limited to those described in Gottlieb E and
Steitz JA.,
1989, EMBO J, 8:851-61.
Exemplary assays useful for measuring translation factor activity of complex
226b include but are not limited to those described in Ohlmann T et al., 1995,
Nucleic
Acids Res, 23:334-40.
Exemplary assays useful for measuring induction of apoptosis in cells
containing
complex 226b include but are not limited to those described in Barry M et al.,
2000,
Methods Enzymol, 322:40-6.
Exemplary assays useful for measuring pseudouridinylation activity of complex
227a include but are not limited to those described in Arluison V et al.,
1999, J Mol Biol,
289:491-502.

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Exemplary assays useful for measuring pseudouridylation of rRNA in cells
containing complex 227a include but are not limited to those described in
Zebarjadian Y
et al., 1999, Mol Cell Biol, 19:7461-72.
Exemplary assays useful for measuring pseudouridinylation activity of complex
227b include but are not limited to those described in Arluison V et al.,
1999, J Mol Biol,
289:491-502.
Exemplary assays useful for measuring pseudouridylation of rRNA in cells
containing complex 227b include but are not limited to those described in
Zebarjadian Y
et al., 1999, Mol Cell Biol, 19:7461-72.
Exemplary assays useful for measuring sister chromatid cohesion activity of
complex 228a include but are not limited to those described in Losada A and
Hirano T.,
2001, Curr Biol, 11:268-72.
Exemplary assays useful for measuring mitotic aster assembly activity of
complex 228a include but are not limited to those described in Gregson HC et
al., 2001,
J Biol Chem, 276:47575-82.
Exemplary assays useful for measuring ATPase/motor protein activity of complex
228a include but are not limited to those described in Kimura K and Hirano T.,
1997,
Cell, 90:625-34.
Exemplary assays useful for measuring sister chromatid cohesion in cells
containing complex 228a include but are not limited to those described in
Megee PC
and Koshland D., 1999, Science, 285:254-7.
Exemplary assays useful for measuring metaphase arrest of cells containing
complex 228a include but are not limited to those described in Geley S et al.,
2001, J
Cell Biol, 153:137-48.
Exemplary assays useful for measuring sister chromatid cohesion activity of
complex 228b include but are not limited to those described in Losada A and
Hirano T.,
2001, Curr Biol, 11:268-72.
Exemplary assays useful for measuring mitotic aster assembly activity of
complex 228b include but are not limited to those described in Gregson HC et
al., 2001,
J Biol Chem, 276:47575-82.
Exemplary assays useful for measuring ATPase/motor protein activity of complex
228b include but are not limited to those described in Kimura K and Hirano T.,
1997,
Cell, 90:625-34.

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Exemplary assays useful for measuring sister chromatid cohesion in cells
containing complex 228b include but are not limited to those described in
Megee PC ,
and Koshland D., 1999, Science, 285:254-7.
Exemplary assays useful for measuring metaphase arrest of cells containing
complex 228b include but are not limited to those described in Geley S et al.,
2001, J
Cell Biol, 153:137-48.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a skin cancer-like phenotype complex 229a include but are not
limited to
those described in Hanausek M et al., 2001, Proc Natl Acad Sci U S A, 98:11551-
6.
Exemplary assays useful for measuring DNA helicase activity of complex 229a
include but are not limited to those described in Nanduri B et al., 2001,
Nucleic Acids
Res, 29:2829-35.
Exemplary assays useful for measuring lyase activity of complex 229a include
but are not limited to those described in Garcia-Diaz M et al., 2001, J Biol
Chem,
276:34659-63.
Exemplary assays useful for measuring DNA damage in cells containing complex
229a include but are not limited to those described in Samper E et al., 2001,
J Cell Biol,
154:49-60.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a skin cancer-like phenotype complex 229b include but are not
limited to
those described in Hanausek M et al., 2001, Proc Natl Acad Sci U S A, 98:11551-
6.
Exemplary assays useful for measuring DNA helicase activity of complex 229b
include but are not limited to those described in Nanduri B et al., 2001,
Nucleic Acids
Res, 29:2829-35.
Exemplary assays useful for measuring lyase activity of complex 229b include
but are not limited to those described in Garcia-Diaz M et al., 2001, J Biol
Chem,
276:34659-63.
Exemplary assays useful for measuring DNA damage in cells containing complex
229b include but are not limited to those described in Samper E et al., 2001,
J Cell Biol,
154:49-60.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a trichothiodystrophy (basal transcription/DNA repair
syndrome)-like
phenotype complex 230a include but are not limited to those described in de
Boer J et
al., 1998, Mol Cell, 1:981-90.

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Exemplary assays useful for measuring DNA helicase activity of complex 230a
include but are not limited to those described in Vindigni A et al., 2001,
Nucleic Acids
Res, 29:1061-7.
Exemplary assays useful for measuring ATPase activity of complex 230a include
but are not limited to those described in Ozsoy AZ et al., 2001, Nucleic Acids
Res,
29:2986-93.
Exemplary assays useful for measuring recombination in mouse pJS3-10 and
pJS4.7.1 cells containing complex 230a include but are not limited to those
described in
Saintigny Y et al., 2001, EMBO J, 20:3861-70.
Exemplary animal models useful for assaying compounds interacting with
transgenic
nice displaying a trichothiodystrophy (basal transcription/DNA repair
syndrome)-like
phenotype complex 230b include but are not limited to those described in de
Boer J et
al., 1998, Mol Cell, 1:981-90.
Exemplary assays useful for measuring DNA helicase activity of complex 230b
include but are not limited to those described in Vindigni A et al., 2001,
Nucleic Acids
Res, 29:1061-7.
Exemplary assays useful for measuring ATPase activity of complex 230b include
but are not limited to those described in Ozsoy AZ et al., 2001, Nucleic Acids
Res,
29:2986-93.
Exemplary assays useful for measuring recombination in mouse pJS3-10 and
pJS4.7.1 cells containing complex 230b include but are not limited to those
described in
Saintigny Y et al., 2001, EMBO J, 20:3861-70.
Exemplary animal models useful for assaying compounds interacting with
systemic lupus
erythematosus transgenic mice complex 231 a include but are not limited to
those
described in Talal N., 1975, J Rheumatol, 2:130-4.
Exemplary assays useful for measuring protein serine/threonine phosphatase
activity of complex 231 a include but are not limited to those described in
Gee KR et al.,
1999, Anal Biochem, 273:41-8.
Exemplary assays useful for measuring 5'-->3' RNA exonuclease activity of
complex 231 a include but are not limited to those described iri Kenna M et
al., 1993, Mol
Cell Biol, 13:341-50.
Exemplary animal models useful for assaying compounds interacting with
systemic lupus
erythematosus transgenic mice complex 231 b include but are not limited to
those
described in Talal N., 1975, J Rheumatol, 2:130-4.

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Exemplary assays useful for measuring protein serine/threonine phosphatase
activity of complex 231 b include but are not limited to those described in
Gee KR et al.,
1999, Anal Biochem, 273:41-8.
Exemplary assays useful for measuring guanine nucleotide exchange factor
activity of complex 231 b include but are not limited to those described in
Kiyono M et
al., 2000, J Biol Chem, 275:29788-93.
Exem plary assays useful for measuring GTP binding/GTPase activity of complex
231 b include but are not limited to those described in Zahraoui A et al.,
1989, J Biol
Chem, 264:12394-401.
Exemplary assays useful for measuring guanine nucleotide exchange factor
activity of complex 231 b include but are not limited to those described in
Haney SA and
Broach JR., 1994, J Biol Chem, 269:16541-8.
Exemplary assays useful for measuring 5'-->3' RNA exonuclease activity of
complex 231 b include but are not limited to those described in Kenna M et
al., 1993, Mol
Cell Biol, 13:341-50.
Exemplary animal models useful for assaying compounds interacting with GSK3
beta
knocfe out mice complex 232 include but are not limited to those described in
Hoeflich
KP et al., 2000, Nature, 406:86-90.(Requirement for glycogen synthase kinase-
3beta in
cell survival and NF-kappaB activation.)
Exemplary assays useful for measuring Rim11 kinase activity of complex 232
include but are not limited to those described in Zhan XL et al., 2000, Mol
Biol Cell,
11:663-76.
Exemplary assays useful for measuring GSK3 beta kinase activity of complex
232 include but are not limited to those described in Orena SJ et al., 2000, J
Biol Chem,
275:15765-72.
Exemplary assays useful for measuring glycogen synthase kinase-3 activity of
complex 232 include but are not limited to those described in Cross D., 2001,
Methods
Mol Biol, 124:147-59.
Exemplary assays useful for measuring cell survival /apoptosis induction in
cells
containing complex 232 include but are not limited to those described in Cross
DA et
al., 2001, J Neurochem, 77:94-102.
Exemplary assays useful for measuring MICROTUBULE NUCLEATION of
complex 233 include but are not limited to those described in Lingle WL and
Salisbury
JL., 2001, Methods Cell Biol, 67:325-36.

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Exemplary assays useful for measuring PHOSPHOFRUCTOKINASE of complex
233 include but are not limited to those described in Klinder A et al., 1998,
Yeast,
14:323-34.
Exemplary animal models useful for assaying compounds interacting with
zebrafish
mutant in spt5 gene complex 238 include but are not limited to those described
in Guo
S et al., 2000, Nature, 408:366-9.
Exemplary assays useful for measuring transcriptional assay of complex 238
include but are not limited to those described in Kikyo N et al., 2000,
Science, 289:2360-
2.
Exemplary assays useful for measuring methyl group transfer to guanosine base
activity of complex 238 include but are not limited to those described in Mao
X et al.,
1995, Mol Cell Biol, 15:4167-74.
Exemplary assays useful for measuring mutation of orf complex 238 include but
are not limited to those described in Hartzog GA et al., 1998, Genes Dev,
12:357-69.
Exemplary assays useful for measuring protein-protein-binding activity of
complex 250 include but are not limited to those described in Keen JH and Beck
KA.,
1989, Biochem Biophys Res Commun, 158:17-23.
Exemplary assays useful for measuring ATPase activity of complex 257 include
but are not limited to those described in Norcum MT., 1996, Protein Sci,
5:1366-75.
Exemplary assays useful for measuring NO deoxygenation of complex 262
include but are not limited to those described in Gardner PR et al., 2000, J
Biol Chem,
275:31581-7.
Exemplary assays useful for measuring aminopeptidase of complex 262 include
but are not limited to those described in Basten DE et al., 2001,
Microbiology, 147:2045-
50.
Exemplary assays useful for measuring atpase of complex 262 include but are
not limited to those described in Nadeau K et al., 1993, J Biol Chem, 268:1479-
87.
Exemplary assays useful for measuring transcription inhibition/repression of
complex 265 include but are not limited to those described in Oberholzer U and
Collart
MA., 1998, Gene, 207:61-9.
Exemplary assays useful for measuring Functional complementation complex
265 include but are not limited to those described in Albert TK et al., 2000,
Nucleic Acids
Res, 28:809-17.

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Exemplary assays useful for measuring transcription assay of complex 274
include but are not limited to those described in Schlegel BP et al., 2000,
Proc Natl Acad
Sci U S A, 97:3148-53.
Exemplary assays useful for measuring protein kinase assay of complex 274
include but are not limited to those described in Chen H et al., 2001,
Biochemistry,
40:11851-9.
Exemplary animal models useful for assaying compounds interacting with mouse
conditional ko of small ribosomal protein S6 complex 281 include but are not
limited to
those described in Volarevic S et al., 2000, Science, 288:2045-7.
Exemplary assays useful for measuring rRNA processing of complex 281 include
but are not limited to those described in Colley A et al., 2000, Mol Cell
Biol, 20:7238-46.
and/or Kressler D et al., 1997, Mol Cell Biol, 17:7283-94.
Exemplary assays useful for measuring nuclear export of ribosomal protein
complex 281 include but are not limited to those described in Hurt E et al.,
1999, J Cell
Biol, 144:389-401.
Exemplary assays useful for measuring DNA binding of complex 309 include but
are not limited to those described in Koering CE et al., 2000, Nucleic Acids
Res,
28:2519-26.
Exemplary assays useful for measuring ATPase of complex 309 include but are
not limited to those described in Norcum MT., 1996, Protein Sci, 5:1366-75.
Exemplary assays useful for measuring RNA binding of complex 351 include but
are not limited to those described in Kessler MM et al., 1997, Genes Dev,
11:2545-56.
Exemplary assays useful for measuring nuclear import activity of complex 351
include but are not limited to those described in Truant R et al., 1998, Mol
Cell Biol,
18:1449-58.
Exemplary assays useful for measuring Endosom to Golgi Transport of complex
363 include but are not limited to those described in Edgar AJ and Polak JM.,
2000,
Biochem Biophys Res Commun, 277:622-30.
Exemplary assays useful for measuring transcription activity of complex 364
include but are not limited to those described in Lim CR et al., 2000, J Biol
Chem,
275:22409-17.
Exemplary assays useful for measuring acylation of lysophosphatidic acid
activity
of complex 364 include but are not limited to those described in Athenstaedt K
and
Daum G., 1997, J Bacteriol, 179:7611-6.

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Exemplary assays useful for measuring inosine-5'-monophosphate
dehydrogenase assay of complex 366 include but are not limited to those
described in
Metz S et al., 2001, Endocrinology, 142:193-204.
Exemplary assays useful for measuring RNA binding assay of complex 366
include but are not limited to those described in lyer RK and Levinger LF.,
1988 Nov-
Dec, Gene Anal Tech, 5:125-9.
Exemplary assays useful for measuring single-stranded-DNA endonuclease of
complex 367 include but are not limited to those described in Tomkinson AE et
al., 1994,
Biochemistry, 33:5305-11. and/or Tomkinson AE et al., 1993, Nature, 362:860-2.
Exemplary assays useful for measuring exonuclease assay of complex 369
include but are not limited to those described in Brouwer R et al., 2001, J
Biol Chem,
276:6177-84.
Exemplary assays useful for measuring endonuclease assay of complex 369
include but are not limited to those described in Goldstein JN and Weller SK.,
1998,
Virology, 244:442-57.
Exemplary assays useful for measuring carbamylphosphate synthetase activity of
complex 373 include but are not limited to those described in Kaseman DS and
Meister
A., 1985, Methods Enzymol, 113:305-26.
Exemplary assays useful for measuring methionine adenosyl transferase activity
of complex 373 include but are not limited to those described in Cabrero C et
al., 1987,
Eur J Biochem, 170:299-304.
Exemplary assays useful for measuring carbamylphosphate synthetase activity of
complex 373 include but are not limited to those described in Pierson DL and
Brien JM.,
1980, J Biol Chem, 255:7891-5.
Exemplary assays useful for measuring CTP synthetase of complex 373 include
but are not limited to those described in Hashimoto H et al., 1997, J Biol
Chem,
272:16308-14.
Exemplary animal models useful for assaying compounds interacting with
Increased
insulin sensitivity and hypoglycaemia in mice lacking the p85-alpha subunit of
phosphoinositide 3-kinase complex 376 include but are not limited to those
described in
Terauchi Y et al., 1999, Nat Genet, 21:230-5.
Exemplary assays useful for measuring protein kinase of complex 376 include
but are not limited to those described in Mallory JC and Petes TD., 2000, Proc
Natl Acad
Sci U S A, 97:13749-54.

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Exemplary assays useful for measuring inosine-5'-monophosphate
dehydrogenase assay of complex 376 include but are not limited to those
described in
Metz S et al., 2001, Endocrinology, 142:193-204.
Exemplary assays useful for measuring cleavage of L-allo-threonine and L-
threonine to glycine of complex 376 include but are not limited to those
described in Liu
JQ et al., 1997, Eur J Biochem, 245:289-93.
Exemplary assays useful for measuring ATPase activity of complex 386 include
but are not limited to those described in Cairns BR et al., 1996, Cell,
87:1249-60.
Exemplary assays useful for measuring protein phosphatase assay of complex
406 include but are not limited to thos a described in Taylor GS et al., 1997,
J Biol Chem,
272:24054-63.
Exemplary assays useful for measuring DNA binding assay of complex 407
include but are not limited to those described in Aparicio OM et al., 1997,
Cell, 91:59-69.
5.6.1. CANDIDATE MOLECULES
Any molecule known in the art can be tested for its ability to modulate
(increase or decrease) the amount of, activity of, or protein component
composition of a
complex of the present invention as detected by a change in the amount of,
activity of, or
protein component composition of, said complex. By way of example, a change in
the
amount of the complex can be detected by detecting a change in the amount of
the
complex that can be isolated from a cell expressing the complex machinery. For
identifying a molecule that modulates complex activity, candidate molecules
can be
directly provided to a cell expressing the complex machinery, or, in the case
of candidate
proteins, can be provided by providing their encoding nucleic acids under
conditions in
which the nucleic acids are recombinantly expressed to produce the candidate
proteins
within the cell expressing the complex machinery, the complex is then isolated
from the
cell and the isolated complex is assayed for activity using methods well known
in the art,
not limited to those described, supra.
This embodiment of the invention is well suited to screen chemical libraries
for molecules which modulate, e.g., inhibit, antagonize, or agonize, the
amount of,
activity of, or protein component composition of the complex. The chemical
libraries can
be peptide libraries, peptidomimetic libraries, chemically synthesized
libraries,

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recombinant, e.g., phage display libraries, and in vitro translation-based
libraries, other
non-peptide synthetic organic libraries, etc.
Exemplary libraries are commercially available from several sources
(ArQule, Tripos/PanLabs, ChemDesign, Pharmacopoeia). In some cases, these
chemical libraries are generated using combinatorial strategies that encode
the identity
of each member of the library on a substrate to which the member compound is
attached, thus allowing direct and immediate identification of a molecule that
is an
effective modulator. Thus, in many combinatorial approaches, the position on a
plate of
a compound specifies that compound's composition. Also, in one example, a
single
plate position may have from 1-20 chemicals that can be screened by
administration to a
well containing the interactions of interest. Thus, if modulation is detected,
smaller and
smaller pools of interacting pairs can be assayed for the modulation activity.
By such
methods, many candidate molecules can be screened.
Many diversity libraries suitable for use are known in the art and can be
used to provide compounds to be tested according to the present invention.
Alternatively, libraries can be constructed using standard methods. Chemical
(synthetic)
libraries, recombinant expression libraries, or polysome-based libraries are
exemplary
types of libraries that can be used.
The libraries can be constrained or semirigid (having some degree of
structural rigidity), or linear or nonconstrained. The library can be a cDNA
or genomic
expression library, random peptide expression library or a chemically
synthesized
random peptide library, or non-peptide library. Expression libraries are
introduced into
the cells in which the assay occurs, where the nucleic acids of the library
are expressed
to produce their encoded proteins.
In one embodiment, peptide libraries that can be used in the present
invention may be libraries that are chemically synthesized in vitro. Examples
of such
libraries are given in Houghten et al., 1991, Nature 354:84-86, which
describes mixtures
of free hexapeptides in which the first and second residues in each peptide
were
individually and specifically defined; Lam et al., 1991, Nature 354:82-84,
which describes
a "one bead, one peptide" approach in which a solid phase split synthesis
scheme
produced a library of peptides in which each bead in the collection had
immobilized
thereon a single, random sequence of amino acid residues; Medynski, 1994,
Bio/Technology 12:709-710, which describes split synthesis and T-bag synthesis
methods; and Gallop et al., 1994, J. Medicinal Chemistry 37(9):1233-1251.
Simply by

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way of other examples, a combinatorial library may be prepared for use,
according to the
methods of Ohlmeyer et al., 1993, Proc. Natl. Acad. Sci. USA 90:10922-10926;
Erb et
al., 1994, Proc. Natl. Acad. Sci. USA 91:11422-11426; Houghten et al., 1992,
Biotechniques 13:412; Jayawickreme et al., 1994, Proc. Natl. Acad. Sci. USA
91:1614-1618; or Salmon et al., 1993, Proc. Natl. Acad. Sci. USA 90:11708-
11712. PCT
Publication No. WO 93/20242 and Brenner and Lerner, 1992, Proc. Natl. Acad.
Sci. USA
89:5381-5383 describe "encoded combinatorial chemical libraries," that contain
oligonucleotide identifiers for each chemical polymer library member.
In a preferred embodiment, the library screened is a biological expression
library that is a random peptide phage display library, where the random
peptides are
constrained (e.g., by virtue of having disulfide bonding).
Further, more general, structurally constrained, organic diversity (e.g.,
nonpeptide) libraries, can also be used. By way of example, a benzodiazepine
library
(see e.g., Bunin et al., 1994, Proc. Natl. Acad. Sci. USA 91:4708-4712) may be
used.
Conformationally constrained libraries that can be used include but are not
limited to those containing invariant cysteine residues which, in an oxidizing
environment,
cross-link by disulfide bonds to form cystines, modified peptides (e.g.,
incorporating
fluorine, metals, isotopic labels, are phosphorylated, etc.), peptides
containing one or
more non-naturally occurring amino acids, non-peptide structures, and peptides
containing a significant fraction of xarboxyglutamic acid.
Libraries of non-peptides, e.g., peptide derivatives (for example, that
contain one or more non-naturally occurring amino acids) can also be used. One
example of these are peptoid libraries (Simon et al., 1992, Proc. Natl. Acad.
Sci. USA
89:9367-9371 ). Peptoids are polymers of non-natural amino acids that have
naturally
occurring side chains attached not to the alpha carbon but to the backbone
amino
nitrogen. Since peptoids are not easily degraded by human digestive enzymes,
they are
advantageously more easily adaptable to drug use. Another example of a library
that
can be used, in which the amide functionalities in peptides have been
permethylated to
generate a chemically transformed combinatorial library, is described by
Ostresh et al.,
1994, Proc. Natl. Acad. Sci. USA 91:11138-11142).
The members of the peptide libraries that can be screened according to
the invention are not limited to containing the 20 naturally occurring amino
acids. In
particular, chemically synthesized libraries and polysome based libraries
allow the use of
amino acids in addition to the 20 naturally occurring amino acids (by their
inclusion in the

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precursor pool of amino acids used in library production). In specific
embodiments, the
library members contain one or more non-natural or non-classical amino acids
or cyclic
peptides. Non-classical amino acids include but are not limited to the D-
isomers of the
common amino acids, ?amino isobutyric acid, 4-aminobutyric acid, Abu, 2-amino
butyric
acid; ?Abu, ~Ahx, 6-amino hexanoic acid; Aib, 2-amino isobutyric acid; 3-amino
propionic
acid; ornithine; norleucine; norvaline, hydroxyproline, sarcosine, citrulline,
cysteic acid, t-
butylglycine, t-butylalanine, phenylglycine, cyclohexylalanine, f3-alanine,
designer amino
acids such as f3-methyl amino acids, C~nethyl amino acids, N~nethyl amino
acids,
fluoro-amino acids and amino acid analogs in general. Furthermore, the amino
acid can
be D (dextrorotary) or L (levorotary).
In a specific embodiment, fragments and/or analogs of complexes of the
invention, or protein components thereof, especially peptidomimetics, are
screened for
activity as competitive or non-competitive inhibitors of complex activity or
formation.
In another embodiment of the present invention, combinatorial chemistry
can be used to identify modulators of a the complexes. Combinatorial chemistry
is
capable of creating libraries containing hundreds of thousands of compounds,
many of
which may be structurally similar. While high throughput screening programs
are
capable of screening these vast libraries for affinity for known targets, new
approaches
have been developed that achieve libraries of smaller dimension but which
provide
maximum chemical diversity. (See e.g., Matter, 1997, Journal of Medicinal
Chemistry
40:1219-1229).
One method of combinatorial chemistry, affinity fingerprinting, has
previously been used to test a discrete library of small molecules for binding
affinities for
a defined panel of proteins. The fingerprints obtained by the screen are used
to predict
the affinity of the individual library members for other proteins or receptors
of interest (in
the instant invention, the protein complexes of the present invention and
protein
components thereof.) The fingerprints are compared with fingerprints obtained
from
other compounds known to react with the protein of interest to predict whether
the library
compound might similarly react. For example, rather than testing every ligand
in a large
library for interaction with a complex or protein component, only those
ligands having a
fingerprint similar to other compounds known to have that activity could be
tested. (See,
e.g., Kauvar et al., 1995, Chemistry and Biology 2:107-118; Kauvar, 1995,
Affinity
fingerprinting, Pharmaceutical Manufacturing International. 8:25-28; and
Kauvar, Toxic-
Chemical Detection by Pattern Recognition in New Frontiers in Agrochemical

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Immunoassay, D. Kurtz. L. Stanker and J.H. Skerritt. Editors, 1995, AOAC:
Washington,
D.C., 305-312).
Kay et al., 1993, Gene 128:59-65 (Kay) discloses a method of constructing
peptide libraries that encode peptides of totally random sequence that are
longer than
those of any prior conventional libraries. The libraries disclosed in Kay
encode totally
synthetic random peptides of greater than about 20 amino acids in length. Such
libraries
can be advantageously screened to identify complex modulators. (See also U.S.
Patent
No. 5,498,538 dated March 12, 1996; and PCT Publication No. WO 94/18318 dated
August 18, 1994).
A comprehensive review of various types of peptide libraries can be found
in Gallop et al., 1994, J. Med. Chem. 37:1233-1251.
5.7. PHARMACEUTICAL COMPOSITIONS AND THERAPEUTIC/PROPHYLACTIC
ADMINISTRATION
The invention provides methods of treatment (and prophylaxis) by
administration to a subject of an effective amount of a Therapeutic of the
invention. In a
preferred aspect, the Therapeutic is substantially purified. The subject is
preferably an
animal including, but not limited to animals such as cows, pigs, horses,
chickens, cats,
dogs, etc., and is preferably a mammal, and most preferably human. In a
specific
embodiment, a non-human mammal is the subject.
Various delivery systems are known and can be used to administer a
Therapeutic of the invention, e.g., encapsulation in liposomes,
microparticles, and
microcapsules: use of recombinant cells capable of expressing the Therapeutic,
use of
receptor-mediated endocytosis (e.g., Wu and Wu, 1987, J. Biol. Chem. 262:4429-
4432);
construction of a Therapeutic nucleic acid as part of a retroviral or other
vector, etc.
Methods of introduction include but are not limited to intradermal,
intramuscular,
intraperitoneal, intravenous, subcutaneous, intranasal, epidural, and oral
routes. The
compounds may be administered by any convenient route, for example by
infusion, by
bolus injection, by absorption through epithelial or mucocutaneous linings
(e.g., oral,
rectal and intestinal mucosa, etc.), and may be administered together with
other
biologically active agents. Administration can be systemic or local. In
addition, it may be
desirable to introduce the pharmaceutical compositions of the invention into
the central
nervous system by any suitable route, including intraventricular and
intrathecal injection;
intraventricular injection may be facilitated by an intraventricular catheter,
for example,

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attached to a reservoir, such as an Ommaya reservoir. Pulmonary administration
can
also be employed, e.g., by use of an inhaler or nebulizer, and formulation
with an
aerosolizing agent.
In a specific embodiment, it may be desirable to administer the
pharmaceutical compositions of the invention locally to the area in need of
treatment.
This may be achieved by, for example, and not by way of limitation, local
infusion during
surgery, topical application, e.g., in conjunction with a wound dressing after
surgery, by
injection, by means of a catheter, by means of a suppository, or by means of
an implant,
said implant being of a porous, non-porous, or gelatinous material, including
membranes,
such as sialastic membranes, or fibers. In one embodiment, administration can
be by
direct injection at the site (or former site) of a malignant tumor or
neoplastic or pre-
neoplastic tissue.
In another embodiment, the Therapeutic can be delivered in a vesicle, in
particular a liposome (Langer, 1990, Science 249:1527-1533; Treat et al.,
1989, In:
Liposomes in the Therapy of Infectious Disease and Cancer, Lopez-Berestein and
Fidler,
eds., Liss, New York, pp. 353-365; Lopez-Berestein, ibid., pp. 317-327; see
generally
ibid.)
In yet another embodiment, the Therapeutic can be delivered via a
controlled release system. In one embodiment, a pump may be used (Langer,
supra;
Sefton, 1987, CRC Crit. Ref. Biomed. Eng. 14:201-240; Buchwald et al., 1980,
Surgery
88:507-516; Saudek et al., 1989, N. Engl. J. Med. 321:574-579). In another
embodiment, polymeric materials can be used (Medical Applications of
Controlled
Release, Langer and Wise, eds., CRC Press, Boca Raton, Florida, 1974;
Controlled
Drug Bioavailability, Drug Product Design and Performance, Smolen and Ball,
eds.,
Wiley, New York, 1984; Ranger and Peppas, 1983, Macromol. Sci. Rev. Macromol.
Chem. 23:61; Levy et al., 1985, Science 228:190-192; During et al., 1989, Ann.
Neurol.
25:351-356; Howard et al., 1989, J. Neurosurg. 71:858-863). In yet another
embodiment, a controlled release system can be placed in proximity of the
therapeutic
target, i.e., the brain, thus requiring only a fraction of the systemic dose
(e.g., Goodson,
1984, In: Medical Applications of Controlled Release, supra, Vol. 2, pp. 115-
138). Other
controlled release systems are discussed in the review by Langer (1990,
Science
249:1527-1533).
In a specific embodiment where the Therapeutic is a nucleic acid encoding
a protein Therapeutic, the nucleic acid can be administered in vivo to promote

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expression of its encoded protein, by constructing it as part of an
appropriate nucleic acid
expression vector and administering it so that it becomes intracellular, e.g.,
by use of a
retroviral vector (U.S. Patent No. 4,980,286), or by direct injection, or by
use of
microparticle bombardment (e.g., a gene gun; Biolistic, Dupont), or by coating
it with
lipids, cell-surface receptors or transfecting agents, or by administering it
in linkage to a
homeobox like peptide which is known to enter the nucleus (e.g., Joliot et
al., 1991, Proc.
Natl. Acad. Sci. USA 88:1864-1868), etc. Alternatively, a nucleic acid
Therapeutic can
be introduced intracellularly and incorporated by homologous recombination
within host
cell DNA for expression.
The present invention also provides pharmaceutical compositions. Such
compositions comprise a therapeutically effective amount of a Therapeutic, and
a
pharmaceutically acceptable carrier. In a specific embodiment, the term
"pharmaceutically acceptable" means approved by a regulatory agency of the
Federal or
a state government or listed in the U.S. Pharmacopeia or other generally
recognized
pharmacopeia for use in animals, and more particularly, in humans. The term
"carrier"
refers to a diluent, adjuvant, excipient, or vehicle with which the
therapeutic is
administered. Such pharmaceutical carriers can be sterile liquids, such as
water and
oils, including those of petroleum, animal, vegetable or synthetic origin,
including but not
limited to peanut oil, soybean oil, mineral oil, sesame oil and the like.
Water is a
preferred carrier when the pharmaceutical composition is administered orally.
Saline and
aqueous dextrose are preferred carriers when the pharmaceutical composition is
administered intravenously. Saline solutions and aqueous dextrose and glycerol
solutions are preferably employed as liquid carriers for injectable solutions.
Suitable
pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin,
malt, rice,
flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium
chloride,
dried skim milk, glycerol, propylene, glycol, water, ethanol and the like. The
composition,
if desired, can also contain minor amounts of wetting or emulsifying agents,
or pH
buffering agents. These compositions can take the form of solutions,
suspensions,
emulsions, tablets, pills, capsules, powders, sustained-release formulations
and the like.
The composition can be formulated as a suppository, with traditional binders
and carriers
such as triglycerides. Oral formulation can include standard carriers such as
pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium
saccharine, cellulose, magnesium carbonate, etc. Examples of suitable
pharmaceutical
carriers are described in "Remington's Pharmaceutical Sciences" by E.W.
Martin. Such

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compositions will contain a therapeutically effective amount of the
Therapeutic,
preferably in purified form, together with a suitable amount of carrier so as
to provide the
form for proper administration to the patient. The formulation should suit the
mode of
administration.
In a preferred embodiment, the composition is formulated, in accordance
with routine procedures, as a pharmaceutical composition adapted for
intravenous
administration to human beings. Typically, compositions for intravenous
administration
are solutions in sterile isotonic aqueous buffer. Where necessary, the
composition may
also include a solubilizing agent and a local anesthetic such as lidocaine to
ease pain at
the site of the injection. Generally, the ingredients are supplied either
separately or
mixed together in unit dosage form, for example, as a dry lyophilized powder
or water-
free concentrate in a hermetically sealed container such as an ampoule or
sachette
indicating the quantity of active agent. Where the composition is to be
administered by
infusion, it can be dispensed with an infusion bottle containing sterile
pharmaceutical
grade water or saline. Where the composition is administered by injection, an
ampoule
of sterile water or saline for injection can be provided so that the
ingredients may be
mixed prior to administration.
The Therapeutics of the invention can be formulated as neutral or salt
forms. Pharmaceutically acceptable salts include those formed with free
carboxyl groups
such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric
acids, etc.,
those formed with free amine groups such as those derived from isopropylamine,
triethylamine, 2-ethylamino ethanol, histidine, procaine, etc., and those
derived from
sodium, potassium, ammonium, calcium, and ferric hydroxides, etc.
The amount of the Therapeutic of the invention which will be effective in
the treatment of a particular disorder or condition will depend on the nature
of the
disorder or condition, and can be determined by standard clinical techniques.
In
addition, in vitro assays may optionally be employed to help identify optimal
dosage
ranges. The precise dose to be employed in the formulation will also depend on
the
route of administration, and the seriousness of the disease or disorder, and
should be
decided according to the judgment of the practitioner and each patient's
circumstances.
However, suitable dosage ranges for intravenous administration are generally
about 20-
500 micrograms of active compound per kilogram body weight. Suitable dosage
ranges
for intranasal administration are generally about 0.01 pg/kg body weight to 1
mg/kg body

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weight. Effective doses may be extrapolated from dose-response curves derived
from in
vitro or animal model test systems.
Suppositories generally contain active ingredient in the range of 0.5% to
10% by weight; oral formulations preferably contain 10% to 95% active
ingredient.
The invention also provides a pharmaceutical pack or kit comprising one or
more containers filled with one or more of the ingredients of the
pharmaceutical
compositions of the invention. Optionally associated with such containers) can
be a
notice in the form prescribed by a governmental agency regulating the
manufacture, use
or sale of pharmaceuticals or biological products, which notice reflects
approval by the
agency of manufacture, use or sale for human administration.
The invention also provides a pharmaceutical pack or kit comprising one or
more containers filled with one or more of the ingredients of the
pharmaceutical
compositions of the invention. For example, the kit can comprise in one or
more
containers a first protein, or a functionally active fragment or functionally
active derivative
thereof, which first protein is selected from the group consisting of
proteins listed in table 1, third column of a given complex, or a functionally
active
fragment or functionally active derivative thereof, or a homologue thereof or
a variant
encoded by a nucleic acid of any of said proteins.
The kits of the present invention can also contain expression vectors
encoding the essential components of the complex machinery, which components
after
being expressed can be reconstituted in order to form a biologically active
complex.
Such a kit preferably also contains the required buffers and reagents.
Optionally
associated with such containers) can be instructions for use of the kit and/or
a notice in
the form prescribed by a governmental agency regulating the manufacture, use
or sale of
pharmaceuticals or biological products, which notice reflects approval by the
agency of
manufacture, use or sale for human administration.
5.8 ANIMAL MODELS
The present invention also provides animal models. In one embodiment,
animal models for diseases and disorders involving the protein complexes of
the present
invention are provided. These animal models are well known in the art. These
animal
models include, but are not limited to those which are listed in the section
5.6 (supra) as
exemplary animald models to study any of the complexes provided in the
invention. Such
animals can be initially produced by promoting homologous recombination or
insertional

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mutagenesis between genes encoding the protein components of the complexes in
the
chromosome, and exogenous genes encoding the protein components of the
complexes
that have been rendered biologically inactive or deleted (preferably by
insertion of a
heterologous sequence, e.g., an antibiotic resistance gene). In a preferred
aspect,
homologous recombination is carried out by transforming embryo-derived stem
(ES) cells
with one or more vectors containing one or more insertionally inactivated
genes, such
that homologous recombination occurs, followed by injecting the transformed ES
cells
into a blastocyst, and implanting the blastocyst into a foster mother,
followed by the birth
of the chimeric animal ("knockout animal") in which a gene encoding a
component
protein from table 1, third column of a given complex, or a functionally
active fragment or
functionally active derivative thereof, or a homologue thereof or a variant
encoded by a
nucleic acid of any of said proteins, has been inactivated or deleted
(Capecchi, 1989,
Science 244:1288-1292)..
The chimeric animal can be bred to produce additional knockout animals.
Such animals can be mice, hamsters, sheep, pigs, cattle, etc., and are
preferably non-
human mammals. In a specific embodiment, a knockout mouse is produced.
Such knockout animals are expected to develop, or be predisposed to
developing, diseases or disorders associated with mutations involving the
protein
complexes of the present invention, and thus, can have use as animal models of
such
diseases and disorders, e.g., to screen for or test molecules (e.g., potential
Therapeutics) for such diseases and disorders.
In a different embodiment of the invention, transgenic animals that have
incorporated and express (or over-express or mis-express) a functional gene
encoding a
protein component of the complex, e.g. by introducing the a gene encoding one
or more
of the components of the complex under the control of a heterologous promoter
(i.e., a
promoter that is not the native promoter of the gene) that either over-
expresses the
protein or proteins, or expresses them in tissues not normally expressing the
complexes
or proteins, can have use as animal models of diseases and disorders
characterized by
elevated levels of the protein complexes. Such animals can be used to screen
or test
molecules for the ability to treat or prevent the diseases and disorders cited
supra.
In one embodiment, the present invention provides a recombinant non-
human animal in which an endogenous gene encoding a first protein, or a
functionally
active fragment or functionally active derivative thereof, which first protein
is selected

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from the group of proteins of table 1, third column of a given complex, or a
functionally
active fragment or functionally active derivative thereof, or a homologue
thereof or a
variant encoded by a nucleic acid of any of said proteins has been deleted or
inactivated
by homologous recombination or insertional mutagenesis of said animal or an
ancestor
thereof.
In another embodiment, the present invention provides a recombinant non-
human animal in which an endogenous gene encoding a first protein, or a
functionally
active fragment or functionally active derivative thereof, which first protein
is selected
from the group consisting of proteins of table 1, third column of a given
complex, or a
functionally active fragment or functionally active derivative thereof, or a
homologue
thereof or a variant encoded by a nucleic acid of any of said proteins.
The following series of examples are presented by way of illustration and
not by way of limitation on the scope of the invention.
EXAM PLES
In order to systematically purify multiprotein complexes, the strategy
depicted in Fig. 1
was developed. Gene-specific PCR-generated cassettes containing the tandem
affinity
purification tag (TAP) (Rigaut, G. et al., Nat Biotechnol 17, 1030-2 (1999))
were inserted
by homologous recombination at the 3' end of the genes (Fig. 2). The focus was
on
1,143 yeast genes representing eul<aryotic orthologs (Lander, E.S. et al.,
Nature 409,
860-921 (2001)). Orthologs, by definition, have evolved by vertical descent
from a
common ancestor (Fitch, W.M., Syst Zool 19, 99-113 (1970)) and are presumed to
carry
out similar function. As a comparison to the orthologs, also a non-orthologous
set of 596
genes from chromosome 1, 2 and 4 was targeted. In order to perform the
analysis in the
absence of the wild-type allele, haploid cells were used. A library of 1,167
yeast strains
expressing the tagged proteins was generated. After growing cells to mid-log
phase, TAP
assemblies were purified from total cellular lysates under mild conditions
(Rigaut, G. et
al., Nat Biotechnol 17, 1030-2 (1999)). The purified protein assemblies were
separated
by denaturing gel electrophoresis, bands digested with trypsin, analyzed by
MALDI-TOF-
MS and identified by database search algorithms. 240 proteins were localized
at
membranes (integral and peripherally associated) (Costanzo, M. C. et al. YPD,
Nucleic
Acids Res 29, 75-9 (2001)). Of the soluble proteins that could not be tagged,
one third

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was detected in multiprotein complexes using another tagged protein as "entry
point".
Within the set of 418 essential genes (Costanzo, M. C. et al. YPD, Nucleic
Acids Res 29,
75-9 (2001)), only 18% did not result in viable strains, suggesting that in
the majority of
cases, the C-terminal TAP tag does not interfere with protein function. The
proteins
found associated to the 589 successfully purified tagged proteins were
analyzed. This
generated 20,946 samples for mass spectrometry and a subsequent identification
of
16,830 proteins. Of these, 1,440 were distinct gene products, representing
more than
30% of the proteome as estimated from transcripts expressed under similar
conditions
(Holstege, F. C. et al., Cell95, 717-28 (1998)). The analysis covers proteins
of various
subcellular compartments, suggesting that the strategy has general validity
Of all the successfully purified tagged proteins, 78% presented associated
partners,
suggesting an unexpectedly high level of interactivity and complex cohesion.
Different
complex entry points often lead to the purification of very similar
assemblies. A
sequential approach to integrate the 589 different purifications into a
reduced number of
curated TAP-complexes was taken. All subsequent statistical analysis is based
on that
set. 245 purifications overlapped with 98 known multiprotein complexes as
described in
the YPD literature database (Costanzo, M. C. et al., Nucleic Acids Res 29, 75-
9. (2001 )).
Among the set of complexes that were assigned to YPD complexes, coverage of
components was very high. 102 proteins were not detected in association with
any other
protein, neither when used directly for purification nor as part of other
complexes. The
remaining 242 purifications were assembled manually into 134 novel complexes.
Of all
232 curated TAP complexes, only 9% had no novel constituents (Tab. 1). The
size of the
TAP complexes varied from 2 to 83 components, with an average of 12 components
per
complex. Cellular roles were ascribed to complexes by computing functional
assignments of the individual components as found in YPD (Costanzo, M. C. et
al.,
Nucleic Acids Res 29, 75-9. (2001)) and by literature mining (Tab. 1). In
general terms,
there is a wide functional distribution of complexes over nine categories,
except for
membrane-associated complexes that are underrepresented due to the reduced
number
of TAP membrane proteins used for purification. Orthologous gene products are
thought
to be responsible for essential cellular activities. It was found that
orthologous proteins
preferentially interact with complexes enriched with other orthologs. This
confirms the
existence of an "orthologous proteome" that may represent core functions for
the
eukaryotic cell (Rubin, G. M. et al. Science 287, 2204-15. (2000).) A
particular complex is

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not necessarily of invariable composition nor are all its building blocks
uniquely
associated with that specific complex. A given protein may be only transiently
associated with a complex depending on physiological conditions or subcellular
compartment. Using several distinct tagged proteins as entry points to purify
a complex,
core components can be identified and validated systematically, while more
dynamic,
perhaps regulatory components may be present differentially. The dynamics of
complex
composition is well illustrated by the cellular signaling complexes formed
around the
protein phosphatase 2A (yTAP-C151). Tagging different PP2A components resulted
in
the purification of the known trimeric complexes containing Tpd3 (the
regulatory A
subunit), either of the two catalytic subunits, Pph21 or Pph22, and either of
the two
regulatory B subunits, Cdc55 or Rts1. The Cdc55-containing complexes were
found to
additionally contain the Zds1 and/or Zds2 proteins, cell-cycle regulators,
revealing
preferences among the different "sub-complexes" and a link to cell-cycle
checkpoints.
Additional plasticity of the PP2A complexes is apparent by the interaction
with three
proteins implicated in bud shape and morphogenesis (Lte1, Kel1 and YBL104c).
This
analysis shows that also the interactions of a signaling enzyme may be
sufficiently strong
to allow the detection of distinct cellular complexes and thus be diagnostic
for a role of
this enzyme in different cellular activities.
An example of a large, cohesive complex is given by the polyadenylation
machinery
(infra).
This example shows that complexes are often sufficiently strong to show high
composition integrity even when purified using different entry points.
Moreover, the
example shows that the TAP method reveals novel components even in well-
studied
cellular machinery.
The results presented herein show that orthologous proteins are more likely to
associate
with each other than to non-orthologous proteins. Comparison to several human
complexes showed that indeed, complexes built around yeast orthologs have
counterparts in human. To analyze if the TAP strategy can be applied to
retrieve
orthologous multiprotein complexes from human cells, complexes from distinct
subcellular compartments were purified:

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Human complexes analyzed are the Arp2/3.complex, the CCR4-NOT-complex (more
fully described below), a nuclear assembly and the TRAPP-complex, a Golgi-
associated
complex (more fully described below).
The Arp2/3 complex, a cytoskeleton-associated complex, is a stable multi-
protein
assembly required for the nucleation of actin filaments in all eukaryotic
cells and consists
of 7 proteins in human and yeast (Higgs, H. N. & Pollard, T. D., Annu Rev
Biochem 70,
649-676. (2001)). Tandem affinity purification of Arp2 in yeast (yTAP-C153)
and ARPC2
in human (Higgs, H. N. & Pollard, T. D., Annu Rev Biochem 70, 649-676. (2001),
respectively, resulted in the isolation and identification of all known
components. This
demonstrates that the TAP-based approach combined with LC-MS/MS is an
efficient and
sensitive way to retrieve and characterize human multiprotein complexes (Fig.
3).
Taken together, these examples show that the analysis of the yeast com plex is
predictive
of novel components in the human counterparts, suggesting that the large-scale
yeast
analysis has immediate functional relevance for human biology.
To assign cellular functions to novel, non-annotated gene products, as well as
understanding the context within which proteins operate, several large-scale
approaches
have been undertaken. These include mRNA expression monitoring (chips and
SAGE)
(Lockhart, D. J. & Winzeler, E. A., Nature 405, 827-36. (2000)) loss-of
function
approaches combined with subcellular localization screens in yeast (Lockhart,
D. J. &
Winzeler, E. A., Nature 405, 827-36. (2000) and Ross-Macdonald, P. et al.,
Nature 402,
413-8. (1999)), RNAi in C. elegans (Fraser, A. G. et al., Nature 408, 325-30.
(2000) and
Gonczy, P. et al., Nature 408, 331-6. (2000)), gene trap in mice (Friedrich,
G. & Soriano,
P., Genes Dev 5, 1513-23. (1991) and Leighton, P. A. et al., Nature 410, 174-
9. (2001))
in silico methods (based on homology or genomic context, such as gene fusion
and
neighbourhood (Eisenberg, D., Marcotte, E. M., Xenarios, I. & Yeates, T. O.,
Nature 405,
823-6. (2000) and Huynen, M., Snel, B., Lathe, W., 3rd & Bork, P., Genome Res
10,
1204-10. (2000)) as well as extensive two-hybrid screens (Fromont-Racine, M.,
Rain, J.
C. & Legrain, P., Nat Genet 16, 277-82. (1997), P. et al., Nature 403, 623-7.
(2000) and
Ito, T. et al., Proc Natl Acad Sci U S A 98, 4569-74. (2001 ).

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The TAP-based approach (Rigaut, G. et al., Nat Biotechnol 17, 1030-2 (1999))
proved
invaluable for the purification of complexes from different cellular
compartments,
including complexes associated with cellular membranes. The approach also
allows for
the efficient identification of low abundance proteins that would not be
detectable by
expression proteomic approaches. Further, the TAP procedure allows the
purification of
very large complexes. For example, we have been able to purify yTAP-C116
(IN080), a
complex reported to be approximately 1-1.5 MDa in size (Shen, X., Mizuguchi,
G.,
Hamiche, A. & Wu, C., Nature 406, 541-4. (2000)), of which we identified all
known and
several novel interactors. This work presents the first examples of TAP
purifications of
mammalian complexes. Side-by-side comparison with selected yeast complexes
show
that, as in yeast, the technique is efficient and shows little or no
background.
We sought to gauge the reliability of our data by comparison of our
experimental results
to those in the published literature. If normalized for the proteins analyzed
in this study, It
was found that the present data covers 56% of the data present in the YPD
protein
complex database. In comparison, large-scale yeast two-hybrid approaches
(Fromont-
Racine, M., Rain, J. C. & Legrain, P., Nat Genet 16, 277-82. (1997), Uetz, P.
et al.,
Nature 403, 623-7. (2000), Ito, T. et al., Proc Natl Acad Sci U S A 98, 4569-
74. (2001 ))
cover approximately 10% of the YPD complex database (Ito, T. et al., Proc Natl
Acad Sci
U S A 98, 4569-74. (2001 ), demonstrating that the TAP/MS strategy is
particularly well
suited for the characterization of multiprotein complexes. Previous approaches
to tag
large numbers of yeast ORFs for biochemical studies have relied on protein
overexpression from heterologous promoters (Martzen, M. R. et al., Science
286, 1153-
5. (1999) and Heyman, J. A. et al., Genome Res 9, 383-92. (1999)).
The success of the present approach relies on the conditions used for the
assembly and
retrieval of the complexes. These include maintaining protein concentration,
localisation
and postranslational modifications in a manner that closely approximate normal
physiology.
Complex stoichiometry was not analyzed. Yet it is obvious by the intensity of
the different
protein bands stained after electrophoresis, that there is variability in the
amount of
purified proteins. This may indicate different affinities and abundance of the
individual
proteins, but also the possibility that several complexes may co-purify. When
size

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exclusion chromatography was performed to test complex integrity, we detected
instances of pronounced complex cohesion as well as cases where different sub-
complexes could be distinguished. Finally, TAP-purified complexes from this
collection
may be used to produce protein chips containing physiological protein
complexes (Zhu,
H. et al. Science26, 26 (2001)) and for assessment of biochemical activity of
proteins
within their molecular environment (Martzen, M. R. et al., Science 286, 1153-
5. (1999)).
Another interesting outcome of the present invention is the ease and the
frequency by
which protein complexes can be retrieved from cells. These biophysical
properties of
protein complexes may suggest co-operative binding. Bridging factors,
postranslational
modifications, allosteric structural changes, binding of ions and metabolites
can all co-
operate to increase the number of short range interactions between individual
proteins in
an assembly. Moreover, several proteins with critical regulatory functions are
non-
globular or intrinsically unstructured (Wright, P. E. & Dyson, H. J., J Mol
Biol 293, 321-31.
(1999)).
Folding into ordered structures only occurs upon binding to other proteins,
offering the
opportunity for control over the thermodynamics of the binding process. Many
of the
complexes identified in this study will be useful for structural studies.
The statistical analysis of the large-scale yeast approach shows a clear
tendency of
proteins that are part of the set of metazoan orthologs to bind to other
proteins of the
same set. Moreover, a high propensity to associate is also observed among the
products
of essential genes. There is a significant overlap between complexes
containing
orthologs and essential proteins. This experimental observation confirms the
proposition
that the products of essential genes are also more likely to represent central
components
in the protein network (Jeong, H., Mason, S. P., Barabasi, A. L. & Oltvai, Z.
N., Nature
411, 41-2. (2001)).
Thus, "orthologous complexes" may well represent the building blocks of a
eukaryotic
core proteome (Rubin, G. M. et al. Science 287, 2204-15. (2000) and Jeong, H.,
Mason,
S. P., Barabasi, A. L. & Oltvai, Z. N., Nature411, 41-2. (2001)).
A significant number of the yeast complexes described here has human
equivalents
which may form the basis for understanding multifactorial diseases. Through
the "guilt by
association" concept we are able to propose testable cellular roles for
proteins that had
no previous functional annotation and novel roles for known proteins.
Assessment of the

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physiological molecular context of proteins, as described here, may be one of
the most
efficient and unambiguous routes towards the assignment of gene identity and
function.
The present analysis allowed us to group cellular proteins into approximately
200
complexes. These are connected to each other by sharing components. The
network
that results is a functional description of the eukaryotic proteome at an
unprecedented
level of organization. Such higher order maps will bring increasing quality to
our
appreciation of biological systems. This provides drug discovery programs with
a
molecular context for the choice and evaluation of drug targets.
The Cleavage-Polyadenylation Machinery (Complex No. 162)
Polyadenylation of precursor mRNA (pre-mRNAs) is an obligatory step in the
maturation
of most eukaryotic transcripts. The addition of poly(A) (polyadenosine) tails
promote
transcription termination and export of the mRNA from the nucleus.
Furthermore, the
poly(A) tails have the function to increase the efficiency of translation
initiation and to
help to stabilize mRNAs. Polyadenylation occurs posttranscriptionally in the
nucleus of
eukaryotic cells in two tightly coupled steps: the endonucleolytic cleavage of
the
precursor and the addition of a poly(A) tail.
In the yeast Saccharomyces cerevisiae, the pre-mRNA 3'-end processing signals
are not
as well conserved as in mammalian cells (see below). In addition to the
cleavage and
polyadenylation site, two cis-acting elements, called the efficiency element
and the
positioning element, are found upstream of the cleavage site. Efficiency
elements contain
the sequence UAUAUA (or close variants thereof) and are often repeated. The
sequence
AAUAAA and several related sequences can function as a positioning element.
Fractionation of yeast extracts led to the separation of protein factors that
are required
for mRNA 3'-end formation in vitro. The cleavage reaction requires cleavage
factors I and
II (CF I and CF II), whereas polyadenylation involves CF I, polyadenylation
factor I (PF I)
and poly(A) polymerase (Pap1 ).
CF I can be separated into two activities, CF IA and CF IB. CF IA is needed
for both
processing steps and is a heterotetrameric protein with subunits of 38, 50, 70
and 76
kDa that are encoded by the RNAS, CLP1, PCF11 and RNA14 genes. Rna14 shares

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significant sequence similarity to the 77 kDa subunit of mammalian cleavage
stimulation
factor (CstF) and Rna15 contains a RNA-binding domain homologous to that of
the 64
kDa subunit of CstF.
In addition to the above mentioned four CFI subunits, Pab1 (poly(A) binding
protein) was
identified in purified CFI fractions. Both biochemical and genetic data
indicate an
involvement of Pab1 in poly(A) length control. CF IB consists of a single
protein called
Nab4/Hrp1 and is required for cleavage site selection and polyadenylation.
A multiprotein complex which has CFII-PF I (= CPF) activity consists of nine
polypeptides: Pap1 (poly(A) polymerase), Pta1, Pfs1, Pfs2, Fip1, Cft1/Yhh1,
Cft2/Ydh1,
Ysh1/BrrS, and Yth1. Pap1, a 64 kDa protein, was the first component of the
yeast 3'-end
formation complex to be purified to homogeneity. Pta1 is a 90 kDa protein
which is
required for both cleavage and polyadenylation of mRNA precursors. Pfs2 is a
53 kDa
protein that contains seven WD40 repeats. Pfs2 has been shown to directly
interact with
subunits of CFII-PF1 and CFIA and is thought to function in the assembly and
stabilization of the 3'-end processing complex. Fip1 has been demonstrated to
physically
interact with Pap1, Yth1 and Rna14 and it is believed that it tethers Pap1 to
its substrate
during polyadenylation. Cft1/Yhh1, Cft2/Ydh1, Ysh1lBrr5, and Yth1 are the
counterparts
of the four subunits of the mammalian cleavage and polyadenylation specificity
factor,
CPSF160, CPSF100, CPSF73 and CPSF30, respectively.
For the mammalian system, various data have been presented which have given
evidence both for a conserved mechanism and also showed some differences
between
the yeast and the mammalian structures.
The composition and function of the mammalian complex based on the data to
date is as
follows:
The cleavage and polyadenylation factor (CPSF) is composed of 4 subunits:
CPSF160 (involved in mRNA and poly(A) polymerase (PAP) binding), CPSF100, CPSF
73 and CPSF30 (involved in mRNA and PABII binding).
CPSF binds the AAUAAA hexanucleotides. CPSF links the mRNA 3'-end processing
to
the transcription. CPSF exists as a stable complex with the transcription
factor TFIID

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complex. The 160 kDa subunit of CPSF binds to several hTAFII. TFIID recruits
CPSF to
the RNA polymerise II pre-initiation complex. Upon transcriptional activation
CPSF
dissociates from TFII and associates with the elongating RNA pol II (CTD
carboxy-
terminal domain of the largest subunit of the RNA polymerise II). CPSF is
thought to
travel with RNA pol II until they reach the polyadenylation site, where CPSF
can bind the
AAUAAA element. CPSF is required for the termination of transcription.
The interaction between CPSF and the AAUAAA element is weak and not so
specific.
The binding of CPSF to the hexanucleotide is greatly enhanced by a 2nd
component of
the poly-adenylation machinery, the cleavage stimulation factor (CstF), which
binds the
G-U rich motif. CstF also binds the RNA pol II through its 50 kDa subunit
(CstF50).
Furthermore, CstF50 binds another component of the transcriptional machinery:
BRCA1
associated RING domain protein (BARD1). BARD1 also interacts with RNA pol II.
BARD1-CstF50 interaction inhibits polyadenylation in vitro and may prevent
inappropriate mRNA processing during transcription. CstF is composed of 3
subunits:
CstF64 (binds mRNA and symplekin (yeast homolog: Pta1), CstF77 (binds CPSF160,
CstF64, CstF50) and CstF50 (binds RNA pol II and BARD1). The co-operative
binding of
CPSF and CstF to the polyadenylation site forms a ternary complex, which
functions to
recruit the other components of the polyadenylation machinery to the cleavage
site: the
two cleavage factors (CFIm and CFllm) and the poly(A) polymerise (PAP).
CFIm is an heterodimer of 4 subunits 72, 68, 59, 25 components: one essential,
CFIImA
and one stimulatory, CFIIB. CFIImA contains hPCF11p and hClp1p (binds cPSF and
CF
I). CF IImB contains no factors previously shown to be involved in 3'-end
processing and
may be a new 3'-end processing factor. Although the identity of the proteins
that perform
the cleavage step is still unknown, it is well established that both CFIm and
CFllm are
required. The reaction products of the cleavage suggest that a metal ion is
involved.
Surprisingly, PAP (but not its catalytic activity) is required for the
cleavage.
After the cleavage step CstF, CFIm and CFllm are dispensable. PAP bound to
CPSF
(through its 160 kD subunit) can start polyadenylating the cleaved 3'-end, but
at that
step, the process is very inefficient. The poly(A) binding protein II (PAB II)
can bind the
nascent poly(A) chain as soon as it reaches a minimal length of 10 poly(A).
PAB II also
interacts with the CPSF30. The binding of PAB II greatly stabilizes PAP at the
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the mRNA, supporting the progressive synthesis of a long poly(A) tail. In the
nucleus,
the length of the poly(A) tail is restricted to about 250 poly(A). This size
restriction is
probably achieved through stoichiometric binding of multiple PAB II. It is not
yet known
how the incorporation of a certain amount of PAB II in the complex termhates
processive
elongation.
CstF is part of the mammalian 3'-end processing complex and is a
heterotrimeric protein
with subunits of 77, 64 and 50 kDa. CstF-50 has been shown to interact with
the BRCA1-
associated protein BARD1 and this interaction suppresses the nuclear mRNA
polyadenylation machinery in vivo. In a recent study it was found that
treatment of cells
with DNA damage-inducing agents causes a transient, but specific, inhibition
of mRNA
3'-end processing in cell extracts. This inhibition reflects the BARD1/CstF
interaction and
involves enhanced formation of a CstF/BARD1/BRCA1 complex. A tumor-associated
germline mutation in BARD1 decreases binding to CstF-50 and renders the
protein
inactive in polyadenylation inhibition. These results support the existence of
a link
between mRNA 3'-end formation and DNA repair/tumor suppression. The in vivo
function
of these interactions may be to inhibit the cleavage and polyadenylation of
pre-mRNAs
on polymerase molecules that are stalled at sites of DNA repair.
Cleavage stimulation factor (CstF) is one of the multiple factors required for
mRNA
polyadenylation in mammalians. CstF-64 may play a role in regulating gene
expression
and cell growth in B cells. The concentration of one CstF subunit (CstF-64)
increases
during activation of B cells, and this is sufficient to switch IgM heavy chain
mRNA
expression from membrane- bound to secreted form. Reduction in CstF-64 causes
reversible cell cycle arrest in GO/G1 phase, while depletion results in
apoptotic cell death.
In contrast to what is observed in yeast, the sequence elements in mammals,
which
specify the site of cleavage and polyadenylation, flank the site of
endonucleolytic attack.
One is the hexanucleotide AAUAAA found 10-30 bases upstream of the
cleavage/polyadenylation site. The second is a G-U-rich motif located 20-40
bases
downstream of the cleavage/polyadenylation site. These two elements and their
spacing
determine the site of cleavagelpolyadenylation and also the strength of the
polyadenylation signal.

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Some other elements, like sequences upstream of the AAUAAA (upstream sequence
elemenfis, USEs) play regulatory roles.
A schematic presentation of the motifs underlying mammalian polyadenylation
and yeast
polyadenylation are shown in Fig. 4. A review on the formation of mRNA 3'-ends
in
eukaryotes is given in Zhao, Hyman and Moore in Microbiology and Molecular
Biology
Reviews, 1999, pp. 405-445. A comparison of mammalian and yeast pre-mRNA 3'-
end
processing is also given in Keller and Minvielle-Sebastia in Nucleus and gene
expression
in Current Opinion in Cell Biology, 1997, Vol. 9, pp. 329-336.
There are diseases which involve defects in the function of the
polyadenylation
machinery.
Many viruses interact directly with components of the mRNA processing
machinery.
The herpes simplex virus type 1 (HSV 1) immediate early (alpha) protein ICP27
is an
essential regulatory protein that is involved in the shutoff of host protein
synthesis,. It
affects mRNA processing at the level of both polyadenylation and splicing.
During
polyadenylation, ICP27 appears to stimulate 3' mRNA processing at selected
poly(A)
sites. The opposite effect occurs on host cell splicing. That is, during HSV 1
infection, an
inhibition in host cell splicing requires ICP27 expression. This contributes
to the shutoff of
host protein synthesis by decreasing levels of spliced cellular mRNAs
available for
translation. A redistribution of splicing factors regulated by ICP27 has also
been seen.
Epstein-Barr virus BMLF1 gene product EB2 seems to affect mRNA nuclear export
of
intronless mRNAs and pre-mRNA 3' processing. EB2 contains an Arg-X Pro
tripeptide
repeated eight times, similar to that described as an mRNA-binding domain in
the herpes
simplex virus type 1 protein US11.
Interestingly, both viruses have been found to precede the onset of lymphomas.
Influenza A virus NS1A protein binds the 30 kDa subunit of the cleavage and
polyadenylation specificity factor (CPSF), NS1 protein (NS1A protein) via its
effector
domain targets the poly(A)-binding protein II (PABII) of the cellular 3'-end
processing
machinery. In vitro the NS1A protein binds the PABII protein, and in vivo
causes PABII

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protein molecules to relocalize from nuclear speckles to a uniform
distribution throughout
the nucleoplasm. In vitro the NS1A protein inhibits the ability of PABII to
stimulate the
processive synthesis of long poly(A) tails catalyzed by poly(A) polymerase
(PAP). Such
inhibition also occurs in vivo in influenza virus-infected cells.
Consequently, although the
NS1A protein also binds the 30 kDa subunit of the cleavage and polyadenylation
specificity factor (CPSF), 3' cleavage of some cellular pre-mRNAs still occurs
in virus-
infected cells, followed by the PAP-catalyzed addition of short poly(A) tails.
Subsequent
elongation of these short poly(A) tails is blocked because the NS1A protein
inhibits PABII
function. The NS1 effector domain functionally interacts with the cellular 30
kDa subunit
of CPSF, an essential component of the 3' end processing machinery of cellular
pre-
mRNAs.
Metachromatic leukodystrophy (MLD) is a lysosomal storage disorder caused by
the
deficiency of arylsulfatase A (ASA). A substantial ASA deficiency has also
been
described in clinically healthy persons, a condition for which the term
pseudodeficiency
was introduced. The mutations characteristic for the pseudodeficiency (PD)
allele have
been identified. Sequence analysis revealed two /~G transitions. One of them
changes
the first polyadenylation signal downstream of the stop codon from AATAAC to
AGTAAC.
This causes a severe deficiency of a 2.1-kilobase (kb) mRNA species. The
deficiency of
the 2.1-kb RNA species provides an explanation for the diminished synthesis of
ASA
seen in pseudodeficiency fibroblasts.
MLD patients have been identified who are homozygous for the ASArPD allele and
it is
thought that the allele might play a role in the development and progression
of disease.
There is a tight link between cell cycle control and polyadenylation machinery
suggesting
an important role of this machinery in the development of cancer. Cyclin-
dependent
enzymes seem to regulate the activity of the polyadenylation machinery. The
amounts of
some factors of the mRNA 3' processing machinery (CstF) increase in
mitotically active
cells in phases of the cell cycle preceding DNA synthesis. The amount of the
64-kDa
subunit CstF-64 increases 5-fold during the GO to S phase transition and
concomitant
proliferation induced by serum in 3T6 fi-broblasts. The increase in CstF-64 is
associated
with the GO to S phase transition. Cdc2-cyclin B phosphorylates PAP at the Ser-
Thr-rich
region.

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However, as it seems now, most diseases associated with defects in mRNA
processing
are caused by mutations in cis-acting elements that disrupt sequences
essential for pre-
mRNA splicing. These can be canonical sequences at the intron-exon border or
located
within an exon. They directly affect the expression of a single mutated gene.
Approximately 15% of the nucleotide substitutions that cause human diseases
disrupt
pre-mRNA splicing. Thus these diseases do not seem to be directly caused by
alterations in the polyadenyation/cleavage-machinery.
However, since recently evidence for a number of interrelationships between
polyadenylation/cleavage and splicing is accumulating (for review see ~hao,
Hyman and
Moore in Microbiology and Molecular Biology Reviews, 1999, pp. 405-445), it
might very
well be that alterations in the 3'-end processing machinery contribute to the
etiology of
these diseases.
Examples of diseases caused by incorrect splicing are mentioned below:
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease involving
degeneration of cortical motor neurons and spinal/bulbar motor neurons. In the
sporadic
form of the disease, the neuron degeneration is caused by excessive
extracellular
glutamate. The glutamate transporter functional in the CNS is the astrocyte
EAAT2 which
is altered in ALS. The pre-mRNA for EAAT2 is aberrantly spliced in the brain
regions
affected. The reason for this is still unknown, but the defect lies probably
in one or a few
auxiliary splicing factors that regulate the splicing of a sub-set of pre-mRNA
in these
cells. The factors have not yet been identified.
The human papillomavirus (HPV) E2 protein plays an important role in
transcriptional
regulation of viral genes as well as in viral DNA replication. HPV 5 (an EV
epidermodysplasia verruciformis-HPV) protein can specifically interact with
cellular
splicing factors including a set of prototypical SR proteins and t~nio snRNP-
associated
proteins (Lai, Teh et al. 1999, J. Biol. Chem. 274, pages 11832-41).
Interestingly all
these three viruses have been associated with cancer progression.
Papillomavirus
infection precedes cervical cancer, whereas EBV and HSV 8 have been described
in
association with lymphomas.

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In hepatocellular carcinoma, there is a defect in mRNA splicing. In this
disease, there are
anti-nuclear antibodies to a 64 kD protein, which has splicing factor motifs.
A defect in
the regulatory subunit 3 of the protein phosphatase 1(PP1) has been found in
haematological malignancies and in lung, ovarian, colorectal and gastric
cancers. Low
PP1 activity has been observed also in acute myelogenous leukaemia.
Heterogeneous nuclear ribonucleoproteins (hnRNP) associate with pre-mRNA and
have
a role in RNA processing and splice site selection. HnRNP A2 shows a marked
overexpression in lung cancer and brain tumours and has thus been used as a
biomarker for these tumor types.
The development of antinuclear antibodies (ANA) in malignancies has been
described
but its mechanism is still not understood. A great diversity of ANA
specificities is found in
hepatocellular carcinoma. In hepatoma sera antibodies co-localize with non-
snRNP
splicing factor SC35, suggesting that the antigenic targets might be involved
in mRNA
splicing. Hepatocellular carcinoma has a significantly higher frequency of ANA
than
chronic hepatitis C, chronic hepatitis B, alcoholic liver cirrhosis or healthy
donors.
In some autoimmune diseases, a possible link has been detected to a preceding
virus
infection, like Epstein-Barr virus in SLE. Furthermore it seems that even
vaccination is
potentially dangerous: a candidate for cytomegalovirus CMV vaccine is
glycoprotein gB
(UL55). Immunization with an adenovirus-gB construct (Ad-gB) not only induces
a
significant anti-viral response, but a significant IgG auto-antibody response
(p > 0.005)
to the U1-70 kDa spliceosome protein. Auto-antibodies to U1-70 kDa are part of
the anti-
ribonucleoprotein response seen in systemic lupus erythematosus and mixed
connective
tissue disease.
At least two molecules which are also part of the complex are known to be
inhibited by
natural toxins or treatment against various diseases.
Protein phosphatase 1 is inhibited by several natural product toxins.

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The marine toxins include the cyanobacteria-derived cyclic heptapeptide
microcystin-LR
and the polyether fatty acid okadaic acid from dinoflagellate sources. They
bind to a
common site on PP1. The dephosphorylation of PP1 is inhibited ( among other
serine/threonine phosphatases PP2A, PP2B, PP2C and PP5/T/K/H ) by Fumonisin B1
(FB1), a mycotoxin produced by the fungus Fusarium moniliforme. This is a
common
contaminant of corn, and is suspected to be a cause of human esophageal
cancer. FB1
is hepatotoxic and hepatocarcinogenic in rats, although the mechanisms
involved have
not been clarified.
Viral proteins are able to interfere with PP1 activity:
The transcription factor EBNA2 of the Epstein-Barr virus induces the
expression of LMP1
onco-gene in human B- cells. EBNA2Afrom an EBV-immortalized B-cell line co-
immunopurifies with a PP1-like protein. A PP1-like activity in nuclear
extracts from EBV
immortalized B-cell line can be inhibited by a GST-EBNA2A fusion product.
Poly(A)polymerase (PAP) is affected by anticancer drugs and is inhibited by
some
antiviral agents.
Anticancer drugs:
Most anticancer drugs act through the mechanism of apoptosis. Apoptosis may be
regulated at all levels of gene expression including the addition of the
poly(A) tail to the 3'
end of mRNAs. Drug combinations are more effective than single drugs and
various
chemotherapeutic strategies have therefore been developed. Dimethylsulfoxide
(DMSO)
in combination with interferon (IFN) results in pronounced PAP
dephosphorylation,
activity reduction and apoptosis of HeLa cells.
Purine and pyrimidine analogues often affect PAP activity. They are
potentially useful
agents for chemotherapy of cancer diseases. The anticancer drugs 5-
Fluorouracil (5-
FU), interferon and tamoxifen mediate both partial dephos phorylation and
inactivation of
poly(A) polymerise (PAP).
PAP (from isolated hepatic nuclei) is inhibited by cordycepin 5'-
triphosphate.The
nucleoside analogue cordycepin is a therapeutic agent for TdT+ (terminal

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deoxynucleotidyl transferase positive) leukemia. In the presence of an
adenosine
deaminase inhibitor, deoxycoformycin (dCF), cordycepin is cytotoxic to
leukemic TdT+
cells. A cordycepin analog of (2'-5') oligo(A) which can be synthesized
enzymatically
from cordycepin 5'-triphosphate and the core cordycepin analog can replace
human
fibroblast interferon in preventing the transformation of human lymphocytes
after
infection with Epstein-Barr virus B95-8 (EBV). The core cordycepin analog is
not
cytotoxic to uninfected lymphocytes and proliferating lymphoblasts.
Not only is PAP affected by anticancer drugs, but it has a possible use as a
tumor
marker involved in cell commitment and/or induction of apoptosis and could be
used to
evaluate tumor cell sensitivity to anticancer treatment.
Antiviral drugs:
Ara-ATP (arabinofuranosyladenosine triphosphate) is an antiherpetic drug that
inhibits
herpes simplex virus replication. It inhibits poly(A) polymerase activity by
competing with
ATP. It blocks both cleavage and polyadenylation reactions by interacting with
the ATP-
binding site on poly(A) polymerase, the activity of which is essential for the
cleavage
reaction.
Purine and pyrimidine analogues are also used as antiviral agents. As an
example, the
most extensively used drug against HSV is idoxyuridine, the 5'-amino analog of
thymidine.
A decrease in herpes simplex virus transcription and perturbation of RNA
polyadenylation is induced by 5'-amino-5'-deoxythymidine (AdThd).
The cleavage stimulation factor (CSTF)
Treatment with hydroxyurea or ultraviolet light strongly, but transiently,
inhibits 3'
cleavage. This is accompanied by increased amounts of a CstF/BARD1/BRCA1
complex, though the amount of these proteins remains the same.

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Despite the large body of information already available from the prior art
concerning the
cleavage/polyadenylation machinery of precursor mRNA up to now not all
components of
the machinery are known not to speak of the composition of the complex as a
whole.
This invention relates to a component of the cleavage/polyadenylation m
achinery of
precursor mRNA as listed in table 1, ninth colum of the respective complex
(No. 162 alb)
By applying the process according to the invention to the isolation of the
polyadenylation/cleavage machinery from yeast, which is further described
below, thirty-
two new proteins could be identified in said yeast complex
Purifications have been done using different proteins as bait according to the
protocols
stated further below.
Below is a more detailed list of the newly identified components of the
polyadenylation
complex (see also Tab. 1). The Accession-Number stated is the GenBank
Accession
number for the protein.
Protein patterns for some of the purifications are shown in Figures 3 and 4.
Act1: Is a known and essential protein (GenBank Acc. No. BAA21512.1), which
has been
shown to be involved in Pol II transcription and has been found to be
associated with
histone acetylation. It serves as a structural protein.
Cka1: Is a known and non-essential protein (GenBank Acc. No. CAA86916.1),
which has
been found to be involved in Polymerase III transcription and has been found
to be
associated with the Casein kinase II complex.
Eft2: The translation elongation factor EF-2 is a known protein involved in
protein
synthesis (GenBank AAB64827.1)
Eno2: Is a known and essential protein (GenBank Acc. No. AAB68019.1). It has
been
shown to have lyase activity and is known to be involved in carbohydrate
metabolism.

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GIc7 (YER133w) is also a known protein (GenBank Acc. No. AAC03231.1). It is
also an
essential protein and is a Type I protein serine threonine phosphatase which
has been
implicated in distinct cellular roles, such as carbohydrate metabolism,
meiosis, mitosis
and cell polarity. Its occurrence in the cleavage/polyadenylation machinery
has not. been
known before.
Gpm1: This protein is a phosphoglycerate mutase that converts 2-
phosphoglyvcerate to
3-phosphoglycerate in glycolysis. It is an essential protein (GenBank:
CAA81994.1)
Hhf2: Is a known and non-essential protein (GenBank Acc. No. CAA95892.1) which
has
been shown to be involved in DNA-binding. It has previously been linked to
Histone
octamer and the RNA polymerase I upstream activation factor.
Hta1: Is a known and non-essential protein (GenBank Acc. No. CAA88505.1) which
has
DNA binding capability and has been shown to be involved in polymerase II
transcription.
Hsc82: Is a non-essential protein so far being associated with protein
folding. (GenBank
Acc. No: CAA89919.1 )
Imd2: Is an Inosine-5°-monophosphate dehydrogenase so far being
associated with
nucleotide metabolism. It is non-essential. (GenBank Acc: No.: AAB69728.1)
Imd4: Is a non-essential protein with similiarity to Imd2 so far being
associated with
nucleotide metabolism (GenBank Acc-No.: CAA86719.1)
Meth: Is a homocysteine methyltransferase so far being associated with amino-
acid
metabolism (GenBank Acc: No.: AAB64646.1)
Pdc1: Is a pyruvate decarboxylase isozyme1 so far being associated with
carbohydrate
metabolism (GenBank Acc.-No.: CAA97573.1)
Pfk1: Is a known protein (GenBank Acc. No. CAA97268.1) which has previously
been
described as part of the phosphofructokinase complex.

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Ref2 (YDR195w) is a known protein (GenBank Acc. No. CAA88708.1). It is a non=
essential gene product. It has been shown to be involved in 3'-end formation
prior to the
final polyadenylation step. However, Ref2 has never been identified before as
a
component of the 3'-end processing machinery. Ref2 has been shown to interact
with
GIc7, another new component of the cleavage/polyadenylation machinery.
Sec13: Is a known and essential protein (GenBank Acc. No AAB67426.1).
Sec31: Is a known and essential protein (GenBank Acc. No. CAA98772.1)
Ssa3: Is a known and non-essential protein (GenBank Acc. No. CAA84896.1) which
so
far has been implicated with protein folding/protein transport.
Ssu72 (YNL222w) is also a known protein (GenBank Acc. No. CAA96125.1) and is
an
essential phylogenetically conserved protein which has been shown to interact
with the
general transcription factor TFIIB (Sua7). TFIIB is an essential component of
the RNA
polymerase II (RNAP II) core transcriptional machinery. It is thought that
this interaction
plays a role in the mechanism of start site selection by RNAP II. The finding
according to
the present invention that Ssu72 is associated with Pta1 is likely to be
relevant since it is
believed that mRNA 3'-end formation is linked with other nuclear processes
like
transcription, capping and splicing. Furthermore, Ssu 72 has also been clearly
identified
in a "reverse tagging experiment" as explained herein below by using some of
the Pta1
associated proteins as bait. However, when Ssu72 itself was used as a bait
associated
proteins were not found most likely due to the fact that the addition of a C-
terminal tag
renders Ssu72 non-functional.
Taf60: Is a known and essential protein (GenBank Acc. No. CAA96819.1 ) which
has
been shown to be involved in Polymerase II transcription.
Tkl1: Is a non-essential transketolase so far being associated with amino-acid
metabolism and carbohydrate metabolism (GenBank Acc-No.: CAA89191.1)

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Tsa1: Translation initiation factor eIF5 which so far has been to shown to
catalyze
hydrolysis of GTP on the 40S ribosomal subunit-initiation complex followed by
joining to
60S ribosomal subunit. (GenBank Acc: No.: CAA92145.1)
Tye7: Is a known protein (GenBank Acc. No. CAA99671.1). It has been shown to
be a
basic helix loop-helix transcription factor.
Vid24: Is a known and non-essential protein (GenBank Acc. No. CAA89320.1)
which has
previously been associated with protein degradation and vesicular transport.
Vps53: Is a known protein (GenBank Acc. No. CAA89320.1) which has been found
to
play a role in protein sorting.
YCL046w: Is a non-essential protein (GenBank Acc. No. CAA42371.1).
YGR156w is the protein product of an essential gene. This protein also
contains a RNA
binding motif. (GenBank Acc. No. CAA97170.1).
YHL035c: Is a known and non-essential protein (GenBank Acc. No. AAB65047.1).
It is a
member of the ATP-binding cassette superfamily.
YKL018w is also an essential protein containing a WD40 domain which is a
typical
protein binding domain. (GenBank Acc. No. CAA81853.1)
YLR221c: Is a protein of unknown function (GenBank Acc. No.AAB67410.1)
YML030w: Is a protein of unknown function (GenBank Acc. No. CAA86625.1)
YOR179c shows significant sequence similarity to Ysh1 (GenBank Acc. No.
CAA99388.1 )
Two further proteins for which binary interactions with members of the
polyadenylation
complex as known so far have been shown before have also been purified with
the
complex:

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YKL059c: is the product of an essential gene and is a zinc binding profiein
containing a
C2HC Zinc finger. The presence of this domain predicts a RNA binding function
of
YKL059c. We believe the corresponding gene product is identical to Pfs1, a
protein
which has been mentioned in several publications, but which has never been
annotated
in the databases (for review see Keller, W. and Minvielle-Sebastia (1997).
Curr Opin Cell
Biol 11: 352-357). (GenBank Acc. No. CAA81896.1)
Tif4632: Is a known and non-essential protein (GenBank Acc. No. CAA96751.1)
which
has been shown to have an RNA binding/translation factor activity and is
involved in
protein synthesis.
The present invention further relates to the following embodiments relating to
the
polyadenylation complex:
1. A protein complex selected from complex (I) and comprising
(a) at least one first protein selected from the group consisting of:
(i) "CFT1" (SEQ ID No:2837) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CFT1", the
variant being
encoded by a nucleic acid that hybridizes to the "CFT1" nucleic acid (SEQ ID
No:2838 )
or its complement under low stringency conditions,
(ii) "CFT2" (SEQ ID No:1529) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CFT2", the
variant being
encoded by a nucleic acid that hybridizes to the "CFT2" nucleic acid (SEQ ID
No:1530 )
or its complement under low stringency conditions,
(iii) "CLP1" (SEQ ID No:2839) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "CLP1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "CLP1" nucleic acid (SEQ ID
No:2840 )
or its complement under low stringency conditions,
(iv) "FIP1" (SEQ ID No:1531) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "FIP1", the
variant being
encoded by a nucleic acid that hybridizes to the "FIP1" nucleic acid (SEQ ID
No:1532 )
or its complement under low stringency conditions,

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(v) "GLC7" (SEQ ID No:929) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "GLC7", the
variant being
encoded by a nucleic acid that hybridizes to the "GLC7" nucleic acid (SEQ ID
No:930 ) or
its complement under low stringency conditions,
(vi) "PAP1" (SEQ ID No:1541) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "PAP1", the
variant being
encoded by a nucleic acid that hybridizes to the "PAP1" nucleic acid (SEQ ID
No:1542 )
or its complement under low stringency conditions,
(vii) "PCF11" (SEQ ID No:2843) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PCF11", the
variant being encoded by a nucleic acid that hybridizes to the "PCF11" nucleic
acid (SEQ
ID No:2844 ) or its complement under low stringency conditions,
(viii) "PFS2" (SEQ ID No:1543) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "PFS2", the
variant being
encoded by a nucleic acid that hybridizes to the "PFS2" nucleic acid (SEQ ID
No:1544 )
or its complement under low stringency conditions,
(ix) "PTA1" (SEQ ID No:1545) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "PTA1", the
variant being
encoded by a nucleic acid that hybridizes to the "PTA1" nucleic acid (SEQ ID
No:1546 )
or its complement under low stringency conditions,
(x) "REF2" (SEQ ID No:1547) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "REF2", the
variant being
encoded by a nucleic acid that hybridizes to the "REF2" nucleic acid (SEQ ID
No:1548 )
or its complement under low stringency conditions,
(xi) "RNA14" (SEQ ID No:1549) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"RNA14", the
variant being encoded by a nucleic acid that hybridizes to the "RNA14" nucleic
acid
(SEQ ID No:1550 ) or its complement under low stringency conditions,
(xii) "RNA15" (SEQ ID No:2845) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"RNA15", the
variant being encoded by a nucleic acid that hybridizes to the "RNA15" nucleic
acid
(SEQ ID No:2846 ) or its complement under low stringency conditions,
(xiii) "SEC13" (SEQ ID No:1171) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SEC13", the

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variant being encoded by a nucleic acid that hybridizes to the "SEC13" nucleic
acid (SEQ
ID No:1172 ) or its complement under low stringency conditions,
(xiv) "SEC31" (SEQ ID No:1177) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SEC31 ", the
variant being encoded ~by a nucleic acid that hybridizes to the "SEC31"
nucleic acid (SEQ
ID No:1178 ) or its complem ent under low stringency conditions,
(xv) "YKL059C" (SEQ ID No:2861) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YKL059C",
the variant being encoded by a nucleic acid that hybridizes to the "YKL059C"
nucleic
acid (SEQ ID No:2862 ) or its complement under low stringency conditions,
(xvi) "YSH1" (SEQ ID No:1561) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YSH1", the
variant being encoded by a nucleic acid that hybridizes to the "YSH1" nucleic
acid (SEQ
ID No:1562 ) or its complement under low stringency conditions,
(xvii) "YTH1" (SEQ ID No:2847) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YTH1", the
variant being encoded by a nucleic acid that hybridizes to the "YTH1" nucleic
acid (SEQ
ID No:2848 ) or its complement under low stringency conditions,
(xviii) "PAB1" (SEQ ID No:2841) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PAB1 ", the
variant being encoded by a nucleic acid that hybridizes to the "PAB1" nucleic
acid (SEQ
ID No:2842 ) or its complement under low stringency conditions, and
(xix) "HHF2" (SEQ ID No:555) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "HHF2", the
variant being
encoded by a nucleic acid that hybridizes to the "HHF2" nucleic acid (SEQ ID
No:556 ) or
its complement under low stringency conditions,
and
(b) at least one second protein, which second protein is selected from the
group
consisting of:
(i) "ACT1" (SEQ ID No:681) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "ACT1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "ACT1" nucleic acid (SEQ ID
No:682 ) or
its complement under low stringency conditions,

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(ii) "CKA1" (SEQ ID No:133) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CKA1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "CKA1" nucleic acid (SEQ ID
No:134 ) or
its complement under low stringency conditions,
(iii) "EFT2" (SEQ ID No:39) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "EFT2", the
variant being
encoded by a nucleic acid that hybridizes to the "EFT2" nucleic acid (SEQ ID
No:40 ) or
its complement under low stringency conditions,
(iv) "ENO2" (SEQ ID No:293) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "EN02", the
variant
being encoded by a nucleic acid that hybridizes to the "EN02" nucleic acid
(SEQ ID
No:294 ) or its complement under low stringency conditions,
(v) "GPM1" (SEQ ID No:597) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "GPM1", the
variant
being encoded by a nucleic acid that hybridizes to the "GPM1" nucleic acid
(SEQ ID
No:598 ) or its complement under low stringency conditions,
(vi) "HTA1" (SEQ ID No:1029) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "HTA1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "HTA1" nucleic acid (SEQ ID
No:1030 )
or its complement under low stringency conditions,
(vii) "IMD2" (SEQ ID No:259) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "IMD2", the
variant being
encoded by a nucleic acid that hybridizes to the "IMD2" nucleic acid (SEQ ID
No:260 ) or
its complement under low stringency conditions,
(viii) "IMD4" (SEQ ID No:41) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "IMD4", the
variant being
encoded by a nucleic acid that hybridizes to the "IMD4" nucleic acid (SEQ ID
No:42 ) or
its complement under low stringency conditions,
(ix) "METE" (SEQ ID No:1921) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "METE", the
variant being
encoded by a nucleic acid that hybridizes to the "METE" nucleic acid (SEQ ID
No:1922 )
or its complement under low stringency conditions,
(x) "PFK1" (SEQ ID No:143) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "PFK1 ", the
variant being

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encoded by a nucleic acid that hybridizes to the "PFI<1" nucleic acid (SEQ ID
No:144 ) or
its complement under low stringency conditions,
(xi) "PT11" (SEQ ID No:1597) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "PT11 ", the
variant being
encoded by a nucleic acid that hybridizes to the "PT11" nucleic acid (SEQ ID
No:1598 )
or its complement under low stringency conditions,
(xii) "RSA3" (SEQ ID No:2849) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "RSA3", the
variant being
encoded by a nucleic acid that hybridizes to the "RSA3" nucleic acid (SEQ ID
No:2850 )
or its complement under low stringency conditions,
(xiii) "SSA3" (SEQ ID No:723) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "SSA3", the
variant being
encoded by a nucleic acid that hybridizes to the "SSA3" nucleic acid (SEQ ID
No:724 ) or
its complement under low stringency conditions,
(xiv) "SSU72" (SEQ ID No:2851) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SSU72", the
variant being encoded by a nucleic acid that hybridizes to the "SSU72" nucleic
acid (SEQ
ID No:2852 ) or its complement under low stringency conditions,
(xv) "SWD2" (SEQ ID No:1455) or a functionally active derivative thereof, or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SWD2", the
variant being encoded by a nucleic acid that hybridizes to the "SWD2" nucleic
acid (SEQ
ID No:1456 ) or its complement under low stringency conditions,
(xvi) "TAF60" (SEQ ID No:825) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "TAF60", the
variant
being encoded by a nucleic acid that hybridizes to the "TAF60" nucleic acid
(SEQ ID
No:826 ) or its complement under low stringency conditions,
(xvii) "TIF4632" (SEQ ID No:195) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TIF4632",
the variant being encoded by a nucleic acid that hybridizes to the "TIF4632"
nucleic acid
(SEQ ID No:196 ) or its complement under low stringency conditions,
(xviii) "TICL1" (SEQ ID No:379) or a functionally active derivative thereof,
or a functionally
active fragment thereof, or a homologue thereof, or a variant of "TKL1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "TKL1" nucleic acid (SEQ ID
No:380 ) or
its complement under low stringency conditions,

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(xix) "TSA1" (SEQ ID No:733) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "TSA1", the
variant being
encoded by a nucleic acid that hybridizes to the "TSA1" nucleic acid (SEQ ID
No:734 ) or
its complement under low stringency conditions,
(xx) "TYE7" (SEQ ID No:2853) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "TYE7", the
variant being
encoded by a nucleic acid that hybridizes to the "TYE7" nucleic acid (SEQ ID
No:2854 )
or its complement under low stringency conditions,
(xxi) "VID24" (SEQ ID No:2855) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"VID24", the
variant being encoded by a nucleic acid that hybridizes to the "VID24" nucleic
acid (SEQ
ID No:2856 ) or its complement under low stringency conditions,
(xxii) "VPS53" (SEQ ID No:1233) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"VPS53", the
variant being encoded by a nucleic acid that hybridizes to the "VPS53" nucleic
acid (SEQ
ID No:1234 ) or its complement under low stringency conditions,
(xxiii) "YCL046W" (SEQ ID No:2857) or a functionally active derivative
thereof, or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YCL046W",
the variant being encoded by a nucleic acid that hybridizes to the "YCL046W"
nucleic
acid (SEQ ID No:2858 ) or its complement under low stringency conditions,
(xxiv) "YHL035C" (SEQ ID No:2859) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YHL035C",
the variant being encoded by a nucleic acid that hybridizes to the "YHL035C"
nucleic
acid (SEQ ID No:2860 ) or its complement under low stringency conditions,
(xxv) "YML030W" (SEQ ID No:2863) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YML030W",
the variant being encoded by a nucleic acid that hybridizes to the "YML030W"
nucleic
acid (SEQ ID No:2864 ) or its complement,under low stringency conditions, and
(xxvi) "YOR179C" (SEQ ID No:2865) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YOR179C",
the variant being encoded by a nucleic acid that hybridizes to the "YOR179C"
nucleic
acid (SEQ ID No:2866 ) or its complement under low stringency conditions,
and a complex (II) comprising at least two of said second proteins, wherein
said low
stringency conditions comprise hybridization in a buffer comprising 35%
formamide, 5X

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SSC, 50 mM Tris-HCI (pH 7.5), 5 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.2% BSA,
100
ug/ml denatured salmon sperm DNA, and 10% (wt/vol) dextran sulfate for 18-20
hours at
40° C, washing in a buffer consisting of 2X SSC, 25 mM Tris-HCI (pH
7.4), 5 mM EDTA,
and 0.1 % SDS for 1.5 hours at 55° C, and washing in a buffer
consisting of 2X SSC, 25
mM Tris-HCI (pH 7.4), 5 mM EDTA, and 0.1 % SDS for 1.5 hours at 60° C.
2. The protein complex selected from complex (I) and comprising the following
proteins:
(i) "ACT1" (SEQ ID No:681) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "ACT1", the
variant being,
encoded by a nucleic acid that hybridizes to the "ACT1" nucleic acid (SEQ ID
No:682 ) or -
its complement under low stringency conditions,
(ii) "CFT1" (SEQ ID No:2837) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CFT1", the
variant being
encoded by a nucleic acid that hybridizes to the "CFT1" nucleic acid (SEQ ID
No:2838 )
or its complement under low stringency conditions,
(iii) "CFT2" (SEQ ID No:1529) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "CFT2", the
variant being
encoded by a nucleic acid that hybridizes to the "CFT2" nucleic acid (SEQ ID
No:1530 )
or its complement under low stringency conditions,
(iv) "CKA1" (SEQ ID No:133) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CKA1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "CKA1" nucleic acid (SEQ ID
No:134 ) or
its complement under low stringency conditions,
(v) "CLP1" (SEQ ID No:2839) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CLP1", the
variant being
encoded by a nucleic acid that hybridizes to the "CLP1" nucleic acid (SEQ ID
No:2840 )
or its complement under low stringency conditions,
(vi) "EFT2" (SEQ ID No:39) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "EFT2", the
variant being
encoded by a nucleic acid that hybridizes to the "EFT2" nucleic acid (SEQ ID
No:40 ) or
its complement under low stringency conditions,
(vii) "EN02" (SEQ ID No:293) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "EN02", the
variant

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being encoded by a nucleic acid that hybridizes to the "EN02" nucleic acid
(SEQ ID
No:294 ) or its complement under low stringency conditions,
(viii) "FIP1" (SEQ ID No:1531) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "FIP1", the
variant being
encoded by a nucleic acid that hybridizes to the "FIP1" nucleic acid (SEQ ID
No:1532 )
or its complement under low stringency conditions,
(ix) "GLC7" (SEQ ID No:929) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "GLC7", the
variant being
encoded by a nucleic acid that hybridizes to the "GLC7" nucleic acid (SEQ ID
No:930 ) or
its complement under low stringency conditions,
(x) "GPM1" (SEQ ID No:597) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "GPM1", the
variant
being encoded by a nucleic acid that hybridizes to the "GPM1" nucleic acid
(SEQ ID
No:598 ) or its complement under low stringency conditions,
(xi) "HTA1" (SEQ ID No:1029) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "HTA1", the
variant being
encoded by a nucleic acid that hybridizes to the "HTA1" nucleic acid (SEQ ID
No:1030 )
or its complement under low stringency conditions,
(xii) "IMD2" (SEQ ID No:259) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "IMD2", the
variant being
encoded by a nucleic acid that hybridizes to the "IMD2" nucleic acid (SEQ ID
No:260 ) or
its complement under low stringency conditions,
(xiii) "IMD4" (SEQ ID No:41) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "IMD4", the
variant being
encoded by a nucleic acid that hybridizes to the "IMD4" nucleic acid (SEQ ID
No:42 ) or
its complement under low stringency conditions,
(xiv) "METE" (SEQ ID No:1921) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"METE", the
variant being encoded by a nucleic acid that hybridizes to the "METE" nucleic
acid (SEQ
ID No:1922 ) or its complement under low stringency conditions,
(xv) "PAP1" (SEQ ID No:1541) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "PAP1", the
variant being
encoded by a nucleic acid that hybridizes to the "PAP1" nucleic acid (SEQ ID
No:1542 )
or its complement under low stringency conditions,

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(xvi) "PCF11" (SEQ ID No:2843) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PCF11", the
variant being encoded by a nucleic acid that hybridizes to the "PCF11" nucleic
acid (SEQ
ID No:2844 ) or its complement under low stringency conditions,
(xvii) "PFK1" (SEQ ID No:143) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "PFK1", the
variant being
encoded by a nucleic acid that hybridizes to the "PFK1" nucleic acid (SEQ ID
No:144 ) or
its complement under low stringency conditions,
(xviii)."PFS2" (SEQ ID No:1543) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PFS2", the
variant being encoded by a nucleic acid that hybridizes to the "PFS2" nucleic
acid (SEQ
ID No:1544 ) or its complement under low stringency conditions,
(xix) "PTA1" (SEQ ID No:1545) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PTA1 ", the
variant being encoded by a nucleic acid that hybridizes to the "PTA1" nucleic
acid (SEQ
ID No:1546 ) or its complement under low stringency conditions,
(xx) "PTI1" (SEQ ID No:1597) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "PT11", the
variant being
encoded by a nucleic acid that hybridizes to the "PT11" nucleic acid (SEQ ID
No:1598 )
or its complement under low stringency conditions,
(xxi) "REF2" (SEQ ID No:1547) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"REF2", the
variant being encoded by a nucleic acid that hybridizes to the "REF2" nucleic
acid (SEQ
ID No:1548 ) or its complement under low stringency conditions,
(xxii) "RNA14" (SEQ ID No:1549) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"RNA14", the
variant being encoded by a nucleic acid that hybridizes to the "RNA14" nucleic
acid
(SEQ ID No:1550 ) or its complement under low stringency conditions,
(xxiii) "RNA15" (SEQ ID No:2845) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a~homologue thereof, or a variant of
"RNA15", the
variant being encoded by a nucleic acid that hybridizes to the "RNA15" nucleic
acid
(SEQ ID No:2846 ) or its complement under low stringency conditions,
(xxiv) "RSA3" (SEQ ID No:2849) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"RSA3", the

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variant being encoded by a nucleic acid that hybridizes to the "RSA3" nucleic
acid (SEQ
ID No:2850 ) or its complement under low stringency conditions,
(xxv) "SEC13" (SEQ ID No:1171) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SEC13", the
variant being encoded by a nucleic acid that hybridizes to the "SEC13" nucleic
acid (SEQ
ID No:1172 ) or its complement under low stringency conditions,
(xxvi) "SEC31" (SEQ ID No:1177) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SEC31 ", the
variant being encoded by a nucleic acid that hybridizes to the "SEC31" nucleic
acid (SEQ
ID No:1178 ) or its complement under low stringency conditions,
(xxvii) "SSA3" (SEQ ID No:723) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SSA3", the
variant being encoded by a nucleic acid that hybridizes to the "SSA3" nucleic
acid (SEQ
ID No:724 ) or its complement under low stringency conditions,
(xxviii) "SSU72" (SEQ ID No:2851) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SSU72", the
variant being encoded by a nucleic acid that hybridizes to the "SSU72" nucleic
acid (SEQ
ID No:2852 ) or its complement under low stringency conditions,
(xxix) "SWD2" (SEQ ID No:1455) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SWD2", the
variant being encoded by a nucleic acid that hybridizes to the "SWD2" nucleic
acid (SEQ
ID No:1456 ) or its complement under low stringency conditions,
(xxx) "TAF60" (SEQ ID No:825) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TAF60", the
variant being encoded by a nucleic acid that hybridizes to the "TAF60" nucleic
acid (SEQ
ID No:826 ) or its complement under low stringency conditions,
(xxxi) "TIF4632" (SEQ ID No:195) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TIF4632",
the variant being encoded by a nucleic acid that hybridizes to the "TIF4632"
nucleic acid
(SEQ ID No:196 ) or its complement under low stringency conditions,
(xxxii) "TKL1" (SEQ ID No:379) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TKL1", the
variant being encoded by a nucleic acid that hybridizes to the "TKL1" nucleic
acid (SEQ
ID No:380 ) or its complement under low stringency conditions,

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(xxxiii) "TSA1" (SEQ ID No:733) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TSA1 ", the
variant being encoded by a nucleic acid that hybridizes to the "TSA1" nucleic
acid (SEQ
ID No:734 ) or its complement under low stringency conditions,
(xxxiv) "TYE7" (SEQ ID No:2853) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TYE7", the
variant being encoded by a nucleic acid that hybridizes to the "TYE7" nucleic
acid (SEQ
ID No:2854 ) or its complement under low stringency conditions,
(xxxv) "VID24" (SEQ ID No:2855) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"VID24", the
variant being encoded by a nucleic acid that hybridizes to the "VID24" nucleic
acid (SEQ
ID No:2856 ) or its complement under low stringency conditions,
(xxxvi) "VPS53" (SEQ ID No:1233) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"VPS53", the
variant being encoded by a nucleic acid that hybridizes to the "VPS53" nucleic
acid (SEQ
ID No:1234 ) or its complement under low stringency conditions,
(xxxvii) "YCL046W" (SEQ ID No:2857) or a functionally active derivative
thereof, or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YCL046W",
the variant being encoded by a nucleic acid that hybridizes to the "YCL046W"
nucleic
acid (SEQ ID No:2858 ) or its complement under low stringency conditions,
(xxxviii) "YHL035C" (SEQ ID No:2859) or a functionally active derivative
thereof, or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YHL035C",
the variant being encoded by a nucleic acid that hybridizes to the "YHL035C"
nucleic
acid (SEQ ID No:2860 ) or its complement under low stringency conditions,
(xxxix) "YKL059C" (SEQ ID No:2861) or a functionally active derivative
thereof, or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YKL059C",
the variant being encoded by a nucleic acid that hybridizes to the "YKL059C"
nucleic
acid (SEQ ID No:2862 ) or its complement under low stringency conditions,
(xl) "YML030W" (SEQ ID No:2863) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YML030W",
the variant being encoded by a nucleic acid that hybridizes to the "YML030W"
nucleic
acid (SEQ ID No:2864 ) or its complement under low stringency conditions,
(xli) "YOR179C" (SEQ ID No:2865) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YOR179C",

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the variant being encoded by a nucleic acid that hybridizes to the "YOR179C"
nucleic
acid (SEQ ID No:2866 ) or its complement under low stringency conditions,
(xlii) "YSH1" (SEQ ID No:1561) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YSH1", the
variant being encoded by a nucleic acid that hybridizes to the "YSH1" nucleic
acid (SEQ
ID No:1562 ) or its complement under low stringency conditions,
(xliii) "YTH1" (SEQ ID No:2847) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YTH1", the
variant being encoded by a nucleic acid that hybridizes to the "YTH1" nucleic
acid (SEQ
ID No:2848 ) or its complement under low stringency conditions, and
(xliv) "PAB1" (SEQ ID No:2841) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PAB1", the
variant being encoded by a nucleic acid that hybridizes to the "PAB1" nucleic
acid (SEQ
ID No:2842 ) or its complement under low stringency conditions,
and a protein complex selected from complex (II) and comprising the following
proteins:
(i) "ACT1" (SEQ ID No:681) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "ACT1", the
variant being
encoded by a nucleic acid that hybridizes to the "ACT1" nucleic acid (SEQ ID
No:682 ) or
its complement under low stringency conditions,
(ii) "CFT1" (SEQ ID No:2837) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CFT1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "CFT1" nucleic acid (SEQ ID
No:2838 )
or its complement under low stringency conditions,
(iii) "CFT2" (SEQ ID No:1529) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "CFT2", the
variant being
encoded by a nucleic acid that hybridizes to the "CFT2" nucleic acid (SEQ ID
No:1530 )
or its complement under low stringency conditions,
(iv) "CIOA1" (SEQ ID No:133) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CI<A1", the
variant being
encoded by a nucleic acid that hybridizes to the "C4CA1" nucleic acid (SEQ ID
No:134 ) br
its complement under low stringency conditions,
(v) "CLP1" (SEQ ID No:2839) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CLP1", the
variant being

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encoded by a nucleic acid that hybridizes to the "CLP1" nucleic acid (SEQ ID
No:2840 )
or its complement under low stringency conditions,
(vi) "EFT2" (SEQ ID No:39) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "EFT2", the
variant being
encoded by a nucleic acid that hybridizes to the "EFT2" nucleic acid (SEQ ID
No:40 ) or
its complement under low stringency conditions,
(vii) "EN02" (SEQ ID No:293) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "EN02", the
variant
being encoded by a nucleic acid that hybridizes to the "EN02" nucleic acid
(SEQ ID
No:294 ) or its complement under low stringency conditions,
(viii) "FIP1" (SEQ ID No:1531) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "FIP1", the
variant being
encoded by a nucleic acid that hybridizes to the "FIP1" nucleic acid (SEQ ID
No:1532 )
or its complement under low stringency conditions,
(ix) "GLC7" (SEQ ID No:929) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "GLC7", the
variant being
encoded by a nucleic acid that hybridizes to the "GLC7" nucleic acid (SEQ ID
No:930 ) or
its complement under low stringency conditions,
(x) "GPM1" (SEQ ID No:597) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "GPM1", the
variant
being encoded by a nucleic acid that hybridizes to the "GPM1" nucleic acid
(SEQ ID
No:598 ) or its complement under low stringency conditions,
(xi) "PAP1" (SEQ ID No:1541) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "PAP1", the
variant being
encoded by a nucleic acid that hybridizes to the "PAP1" nucleic acid (SEQ ID
No:1542 )
or its complement under low stringency conditions,
(xii) "PCF11" (SEQ ID No:2843) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PCF11", the
variant being encoded by a nucleic acid that hybridizes to the "PCF11" nucleic
acid (SEQ
ID No:2844 ) or its complement under low stringency conditions,
(xiii) "PFK1" (SEQ ID No:143) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "PFK1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "PFK1" nucleic acid (SEQ ID
No:144 ) or
its complement under low stringency conditions,

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(xiv) "PFS2" (SEQ ID No:1543) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PFS2", the
variant being encoded by a nucleic acid that hybridizes to the "PFS2" nucleic
acid (SEQ
ID No:1544 ) or its complement under low stringency conditions,
(xv) "PTA1" (SEQ ID No:1545) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "PTA1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "PTA1" nucleic acid (SEQ ID
No:1546 )
or its complement under low stringency conditions,
(xvi) "REF2" (SEQ ID No:1547) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"REF2", the
variant being encoded by a nucleic acid that hybridizes to the "REF2" nucleic
acid (SEQ
ID No:1548 ) or its complement under low stringency conditions,
(xvii) "RNA14" (SEQ ID No:1549) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"RNA14", the
variant being encoded by a nucleic acid that hybridizes to the "RNA14" nucleic
acid
(SEQ ID No:1550 ) or its complement under low stringency conditions,
(xviii) "RNA15" (SEQ ID No:2845) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"RNA15", the
variant being encoded by a nucleic acid that hybridizes to the "RNA15" nucleic
acid
(SEQ ID No:2846 ) or its complement under low stringency conditions,
(xix) "RSA3" (SEQ ID No:2849) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"RSA3", the
variant being encoded by a nucleic acid that hybridizes to the "RSA3" nucleic
acid (SEQ
ID No:2850 ) or its complement under low stringency conditions,
(xx) "SEC13" (SEQ ID No:1171) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SEC13", the
variant being encoded by a nucleic acid that hybridizes to the "SEC13" nucleic
acid (SEQ
ID No:1172 ) or its complement under low stringency conditions,
(xxi) "SEC31" (SEQ ID No:1177) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SEC31 ", the
variant being encoded by a nucleic acid that hybridizes to the "SEC31" nucleic
acid (SEQ
ID No:1178 ) or its complement under low stringency conditions,
(xxii) "SSA3" (SEQ ID No:723) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "SSA3", the
variant being

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encoded by a nucleic acid that hybridizes to the "SSA3" nucleic acid (SEQ ID
No:724 ) or
its complement under low stringency conditions,
(xxiii) "SSU72" (SEQ ID No:2851) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SSU72", the
variant being encoded by a nucleic acid that hybridizes to the "SSU72" nucleic
acid (SEQ
ID No:2852 ) or its complement under low stringency conditions,
(xxiv) "TAF60" (SEQ ID No:825) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TAF60", the
variant being encoded by a nucleic acid that hybridizes to the "TAF60" nucleic
acid (SEQ
ID No:826 ) or its complement under low stringency conditions,
(xxv) "TIF4632" (SEQ ID No:195) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TIF4632",
the variant being encoded by a nucleic acid that hybridizes to the "TIF4632"
nucleic acid
(SEQ ID No:196 ) or its complement under low stringency conditions,
(xxvii) "TKL1" (SEQ ID No:379) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TKL1", the
variant being encoded by a nucleic acid that hybridizes to the "TKL1" nucleic
acid (SEQ
ID No:380 ) or its complement under low stringency conditions,
(xxviii) "TSA1" (SEQ ID No:733) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TSA1 ", the
variant being encoded by a nucleic acid that hybridizes to the "TSA1" nucleic
acid (SEQ
ID No:734 ) or its complement under low stringency conditions,
(xxix) "TYE7" (SEQ ID No:2853) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TYE7", the
variant being encoded by a nucleic acid that hybridizes to the "TYE7" nucleic
acid (SEQ
ID No:2854 ) or its complement under low stringency conditions,
(xxx) "VID24" (SEQ ID No:2855) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"VID24", the
variant being encoded by a nucleic acid that hybridizes to the "VID24" nucleic
acid (SEQ
ID No:2856 ) or its complement under low stringency conditions,
(xxxi) "VPS53" (SEQ ID No:1233) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"VPS53", the
variant being encoded by a nucleic acid that hybridizes to the "VPS53" nucleic
acid (SEQ
ID No:1234 ) or its complement under low stringency conditions,

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(xxxii) "YCL046W" (SEQ ID No:2857) or a functionally active derivative
thereof, or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YCL046W",
the variant being encoded by a nucleic acid that hybridizes to the "YCL046W"
nucleic
acid (SEQ ID No:2858 ) or its complement under low stringency conditions,
(xxxiii) "YHL035C" (SEQ ID No:2859) or a functionally active derivative
thereof, or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YHL035C",
the variant being encoded by a nucleic acid that hybridizes to the "YHL035C"
nucleic
acid (SEQ ID No:2860 ) or its complement under low stringency conditions,
(xxxiv) "YKL059C" (SEQ ID No:2861) or a functionally active derivative
thereof, or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YKL059C",
the variant being encoded by a nucleic acid that hybridizes to the "YKL059C"
nucleic
acid (SEQ ID No:2862 ) or its complement under low stringency conditions,
(xxxv) "YML030W" (SEQ ID No:2863) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YML030W",
the variant being encoded by a nucleic acid that hybridizes to the "YML030W"
nucleic
acid (SEQ ID No:2864 ) or its complement under low stringency conditions,
(xxxvi) "YOR179C" (SEQ ID No:2865) or a functionally active derivative
thereof, or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YOR179C",
the variant being encoded by a nucleic acid that hybridizes to the "YOR179C"
nucleic
acid (SEQ ID No:2866 ) or its complement under low stringency conditions,
(xxxvii) "YSH1" (SEQ ID No:1561) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YSH1", the
variant being encoded by a nucleic acid that hybridizes to the "YSH1" nucleic
acid (SEQ
ID No:1562 ) or its complement under low stringency conditions,
(xxxviii) "YTH1" (SEQ ID No:2847) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YTH1", the
variant being encoded by a nucleic acid that hybridizes to the "YTH1" nucleic
acid (SEQ
ID No:2848 ) or its complement under low stringency conditions, and
(xlix) "PAB1" (SEQ ID No:2841) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PAB1", the
variant being encoded by a nucleic acid that hybridizes to the "PAB1" nucleic
acid (SEQ
ID No:2842 ) or its complement under low stringency conditions,
(xl) "HHF2" (SEQ ID No:555) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "HHF2", the
variant being

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encoded by a nucleic acid that hybridizes to the "HHF2" nucleic acid (SEQ ID
No:556 ) or
its complement under low stringency conditions,
3. The protein complex according to No. 1 comprising all but 1 - 27 of the
following
proteins:
(i) "ACT1" (SEQ ID No:681) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "ACT1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "ACT1" nucleic acid (SEQ ID
No:682 ) or
its complement under low stringency conditions,
(ii) "CFT1" (SEQ ID No:2837) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CFT1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "CFT1" nucleic acid (SEQ ID
No:2838 )
or its complement under low stringency conditions,
(iii) "CFT2" (SEQ ID No:1529) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "CFT2", the
variant being
encoded by a nucleic acid that hybridizes to the "CFT2" nucleic acid (SEQ ID
No:1530 )
or its complement under low stringency conditions,
(iv) "CKA1" (SEQ ID No:133) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CKA1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "CKA1" nucleic acid (SEQ ID
No:134 ) or
its complement under low stringency conditions,
(v) "CLP1" (SEQ ID No:2839) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CLP1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "CLP1" nucleic acid (SEQ ID
No:2840 )
or its complement under low stringency conditions,
(vi) "EFT2" (SEQ ID No:39) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "EFT2", the
variant being
encoded by a nucleic acid that hybridizes to the "EFT2" nucleic acid (SEQ ID
No:40 ) or
its complement under low stringency conditions,
(vii) "EN02" (SEQ ID No:293) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "EN02", the
variant
being encoded by a nucleic acid that hybridizes to the "EN02" nucleic acid
(SEQ ID
No:294 ) or its complement under low stringency conditions,

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(viii) "FIP1" (SEQ ID No:1531) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "FIP1", the
variant being
encoded by a nucleic acid that hybridizes to the "FIP1" nucleic acid (SEQ ID
No:1532
or its complement under low stringency conditions,
(ix) "GLC7" (SEQ ID No:929) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "GLC7", the
variant being
encoded by a nucleic acid that hybridizes to the "GLC7" nucleic acid (SEQ ID
No:930 ) or
its complement under low stringency conditions,
(x) "GPM1" (SEQ ID No:597) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "GPM1", the
variant
being encoded by a nucleic acid that hybridizes to the "GPM1" nucleic acid
(SEQ ID
No:598 ) or its complement under low stringency conditions,
(xi) "HTA1" (SEQ ID No:1029) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "HTA1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "HTA1" nucleic acid (SEQ ID
No:1030 )
or its complement under low stringency conditions,
(xii) "IMD2" (SEQ ID No:259) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "IMD2", the
variant being
encoded by a nucleic acid that hybridizes to the "IMD2" nucleic acid (SEQ ID
No:260 ) or
its complement under low stringency conditions,
(xiii) "IMD4" (SEQ ID No:41) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "IMD4", the
variant being
encoded by a nucleic acid that hybridizes to the "IMD4" nucleic acid (SEQ ID
No:42 ) or
its complement under low stringency conditions,
(xiv) "METE" (SEQ ID No:1921) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"METE", the
variant being encoded by a nucleic acid that hybridizes to the "METE" nucleic
acid (SEQ
ID No:1922 ) or its complement under low stringency conditions,
(xv) "PAP1" (SEQ ID No:1541) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "PAP1", the
variant being
encoded by a nucleic acid that hybridizes to the "PAP1" nucleic acid (SEQ ID
No:1542 )
or its complement under low stringency conditions,
(xvi) "PCF11" (SEQ ID No:2843) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PCF11", the

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variant being encoded by a nucleic acid that hybridizes to the "PCF11" nucleic
acid (SEQ
ID No:2844 ) or its complement under low stringency conditions,
(xvii) "PFK1" (SEQ ID No:143) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "PFK1", the
variant being
encoded by a nucleic acid that hybridizes to the "PFK1" nucleic acid (SEQ ID
No:144 ) or
its complement under low stringency conditions,
(xviii) "PFS2" (SEQ ID No:1543) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PFS2", the
variant being encoded by a nucleic acid that hybridizes to the "PFS2" nucleic
acid (SEQ
ID No:1544 ) or its complement under low stringency conditions,
(xix) "PTA1" (SEQ ID No:1545) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PTA1 ", the
variant being encoded by a nucleic acid that hybridizes to the "PTA1" nucleic
acid (SEQ
ID No:1546 ) or its complement under low stringency conditions,
(xx) "PT11" (SEQ ID No:1597) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "PT11 ", the
variant being
encoded by a nucleic acid that hybridizes to the "PT11" nucleic acid (SEQ ID
No:1598 )
or its complement under low stringency conditions,
(xxi) "REF2" (SEQ ID No:1547) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"REF2", the
variant being encoded by a nucleic acid that hybridizes to the "REF2" nucleic
acid (SEQ
ID No:1548 ) or its complement under low stringency conditions,
(xxii) "RNA14" (SEQ ID No:1549) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"RNA14", the
variant being encoded by a nucleic acid that hybridizes to the "RNA14" nucleic
acid
(SEQ ID No:1550 ) or its complement under low stringency conditions,
(xxiii) "RNA15" (SEQ ID No:2845) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"RNA15", the
variant being encoded by a nucleic acid that hybridizes to the "RNA15" nucleic
acid
(SEQ ID No:2846 ) or its complement under low stringency conditions,
(xxiv) "RSA3" (SEQ ID No:2849) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"RSA3", the
variant being encoded by a nucleic acid that hybridizes to the "RSA3" nucleic
acid (SEQ
ID No:2850 ) or its complement under low stringency conditions,

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(xxv) "SEC13" (SEQ ID No:1171) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SEC13", the
variant being encoded by a nucleic acid that hybridizes to the "SEC13" nucleic
acid (SEQ
ID No:1172 ) or its complement under low stringency conditions,
(xxvi) "SEC31" (SEQ ID No:1177) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SEC31 ", the
variant being encoded by a nucleic acid that hybridizes to the "SEC31" nucleic
acid (SEQ
ID No:1178 ) or its complement under low stringency conditions,
(xxvii) "SSA3" (SEQ ID No:723) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SSA3", the
variant being encoded by a nucleic acid that hybridizes to the "SSA3" nucleic
acid (SEQ
ID No:724 ) or its complement under low stringency conditions,
(xxviii) "SSU72" (SEQ ID No:2851) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SSU72", the
variant being encoded by a nucleic acid that hybridizes to the "SSU72" nucleic
acid (SEQ
ID No:2852 ) or its complement under low stringency conditions,
(xxix) "SWD2" (SEQ ID No:1455) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SWD2", the
variant being encoded by a nucleic acid that hybridizes to the "SWD2" nucleic
acid (SEQ
ID No:1456 ) or its complement under low stringency conditions,
(xxx) "TAF60" (SEQ ID No:825) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TAF60", the
variant being encoded by a nucleic acid that hybridizes to the "TAF60" nucleic
acid (SEQ
ID No:826 ) or its complement under low stringency conditions,
(xxxi) "TIF4632" (SEQ ID No:195) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TIF4632",
the variant being encoded by a nucleic acid that hybridizes to the "TIF4632"
nucleic acid
(SEQ ID No:196 ) or its complement under low stringency conditions,
(xxxii) "TKL1" (SEQ ID No:379) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TKL1", the
variant being encoded by a nucleic acid that hybridizes to the "TKL1" nucleic
acid (SEQ
ID No:380 ) or its complement under low stringency conditions,
(xxxiii) "TSA1" (SEQ ID No:733) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TSA1", the

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variant being encoded by a nucleic acid that hybridizes to the "TSA1" nucleic
acid (SEQ
ID No:734 ) or its complement under low stringency conditions,
(xxxiv) "TYE7" (SEQ ID No:2853) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TYE7", the
variant being encoded by a nucleic acid that hybridizes to the "TYE7" nucleic
acid (SEQ
ID No:2854 ) or its complement under low stringency conditions,
(xxxv) "VID24" (SEQ ID No:2855) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"VID24", the
variant being encoded by a nucleic acid that hybridizes to the "VID24" nucleic
acid (SEQ
ID No:2856 ) or its complement under low stringency conditions,
(xxxvi) "VPS53" (SEQ ID No:1233) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"VPS53", the
variant being encoded by a nucleic acid that hybridizes to the "VPS53" nucleic
acid (SEQ
ID No:1234 ) or its complement under low stringency conditions,
(xxxvii) "YCL046W" (SEQ ID No:2857) or a functionally active derivative
thereof, or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YCL046W",
the variant being encoded by a nucleic acid that hybridizes to the "YCL046W"
nucleic
acid (SEQ ID No:2858 ) or its complement under low stringency conditions,
(xxxviii) "YHL035C" (SEQ ID No:2859) or a functionally active derivative
thereof, or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YHL035C",
the variant being encoded by a nucleic acid that hybridizes to the "YHL035C"
nucleic
acid (SEQ ID No:2860 ) or its complement under low stringency conditions,
(xxxix) "YKL059C" (SEQ ID No:2861) or a functionally active derivative
thereof, or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YKL059C",
the variant being encoded by a nucleic acid that hybridizes to the "YKL059C"
nucleic
acid (SEQ ID No:2862 ) or its complement under low stringency conditions,
(xl) "YML030W" (SEQ ID No:2863) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YML030W",
the variant being encoded by a nucleic acid that hybridizes to the "YML030W"
nucleic
acid (SEQ ID No:2864 ) or its complement under low stringency conditions,
(xli) "YOR179C" (SEQ ID No:2865) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YOR179C",
the variant being encoded by a nucleic acid that hybridizes to the "YOR179C"
nucleic
acid (SEQ ID No:2866 ) or its complement under low stringency conditions,

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(xlii) "YSH1" (SEQ ID No:1561) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YSH1", the
variant being encoded by a nucleic acid that hybridizes to the "YSH1" nucleic
acid (SEQ
ID No:1562 ) or its complement under low stringency conditions, . .
(xliii) "YTH1" (SEQ ID No:2847) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YTH1", the
variant being encoded by a nucleic acid that hybridizes to the "YTH1" nucleic
acid (SEQ
ID No:2848 ) or its complement under low stringency conditions,
(xliv) "PAB1" (SEQ ID No:2841) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PAB1", the
variant being encoded by a nucleic acid that hybridizes to the "PAB1" nucleic
acid (SEQ
ID No:2842 ) or its complement under low stringency conditions, and
(xlv) "HHF2" (SEQ ID No:555) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "HHF2", the
variant being
encoded by a nucleic acid that hybridizes to the "HHF2" nucleic acid (SEQ ID
No:556 ) or
its complement under low stringency conditions.
4. The complex of any of No. 1 - 3 comprising a functionally active derivative
of said first
protein and/or a functionally active derivative of said second protein,
wherein the
functionally active derivative is a fusion protein comprising said first
protein or said
second protein fused to an amino acid sequence different from the first
protein or second
protein, respectively.
5. The complex of No. 4 wherein the functionally active derivative is a fusion
protein
comprising said first protein or said second protein fused to an affinity tag
or label.
6. The complex of any of No. 1 - 3 comprising a fragment of said first protein
and/or a
fragment of said second protein, which fragment binds to another protein
component of
said complex.
7. The complex of any of No. 1 -6 that is involved in the 3' end mRNA
processing activity
3' end mRNA processing activity .

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8. A process for preparing complex of any of No. 1 - 7 and optionally the
components
thereof comprising the following steps:
Expressing a protein (bait) of the complex, preferably the tagged protein, in
a target cell,
or a tissue or an organ, isolating the protein complex which is attached to
the bait
protein, and optionally disassociating the protein complex and isolating the
individual
complex members.
9. The process according to No. 8 wherein the tagged protein comprises two
different
tags which allow two separate affinity purification steps.
10. The process according to any of No. 8 - 9 wherein the two tags are
separated by a
cleavage site for a protease.
11. Component of the polyadenylation complex obtainable by a process according
to any
of No. 8 - 10.
12. Protein of the polyadenylation complex selected from
(i) "YCL046W" (SEQ ID No:2857) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YCL046W",
the variant being encoded by a nucleic acid that hybridizes to the "YCL046W"
nucleic
acid (SEQ ID No:2858 ) or its complement under low stringency conditions,
(ii) "YHL035C" (SEQ ID No:2859) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YHL035C",
the variant being encoded by a nucleic acid that hybridizes to the "YHL035C"
nucleic
acid (SEQ ID No:2860 ) or its complement under low stringency conditions,
(iii) "YKL059C" (SEQ ID No:2861) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YKL059C",
the variant being encoded by a nucleic acid that hybridizes to the "YKL059C"
nucleic
acid (SEQ ID No:2862 ) or its complement under low stringency conditions,
(iv) "YML030W" (SEQ ID No:2863) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YML030W",
the variant being encoded by a nucleic acid that hybridizes to the "YML030W"
nucleic
acid (SEQ ID No:2864 ) or its complement under low stringency conditions, and

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(v) "YOR179C" (SEQ ID No:2865) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YOR179C",
the variant being encoded by a nucleic acid that hybridizes to the "YOR179C"
nucleic
acid (SEQ ID No:2866 ) or its complement under low stringency conditions,
wherein said
low stringency conditions comprise hybridization in a buffer comprising 35%
formamide,
5X SSC, 50 mM Tris-HCI (pH 7.5), 5 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.2% BSA,
100 ug/ml denatured salmon sperm DNA, and 10% (wt/vol) dextran sulfate for 18-
20
hours at 40° C, washing in a buffer consisting of 2X SSC, 25 mM Tris-
HCI (pH 7.4), 5
mM EDTA, and 0.1 % SDS for 1.5 hours at 55° C, and washing in a buffer
consisting of
2X SSC, 25 mM Tris-HCI (pH 7.4), 5 mM EDTA, and 0.1 % SDS for 1.5 hours at
60° C.
13. Nucleic acid encoding a protein according to No. 12.
14. Construct, preferably a vector construct, comprising
(a) a nucleic acid according to No. 13 and at least one further nucleic acid
which is
normally not associated with said nucleic acid, or
(b) at least two separate nucleic acid sequences each encoding a different
protein, or a
functionally active fragment or a functionally active derivative thereof at
least one of said
proteins, or functionally active fragments or functionally active derivative
thereof being
selected from the first group of proteins according to No. 1 (a) and at least
one of said
proteins, or functionally active fragments or functionally active derivative
thereof being
selected from the second group of proteins according to No. 1 (b) or
(c)at least two separate nucleic acid sequences each encoding a different
protein, or a
functionally active fragment or a functionally active derivative thereof, or a
homologue or
a variant thereof, said proteins being selected from the proteins of complex
(II) according
to No. 1.
15. Host cell containing a vector comprising at least the nucleic acid of No.
13 and/or a
construct of No. 14 or containing several vectors each comprising at least one
nucleic
acid sequence encoding at least one of the proteins, or functionally active
fragments or
functionally active derivatives thereof selected from the first group of
proteins according
to No. 1 (a) and the proteins, or functionally active fragments or
functionally active
derivatives thereof selected from the second group of proteins according to
No. 1 (b).

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16. An antibody or a fragment of said antibody containing the binding domain
thereof,
selected from an antibody or fragment thereof, which binds the complex of any
of No. 1 -
7 and which does not bind any of the proteins of said compleX ~ivhen
uncomplexed and
an antibody or a fragment of said antibody which binds to any of the proteins
according
to No. 12.
17. A kit comprising in one or more container:
(a) the complex of any of No. 1 - 7 and/or the proteins of No. 12 and/or
(b) an antibody according to No. 16 and/or
(c) a nucleic acid encoding a protein of the complex of any of No. 1 - 7
and/or a protein of
No. 12 and/or
(d) cells expressing the complex of any of No. 1 - 7 and/or the proteins of
No. 12 and
optionally
(e) further components such as reagents and working instructions.
18. A kit according to No. 17 for processing a substrate of said complex.
19. A kit according to No. 17 for the diagnosis or prognosis of a disease or a
disease
risk, preferentially for a disease or disorder such as viral infections such
as herpes
simplex infections, Epstein-Barr-infections, influenza; metabolic diseases
such as
metachromatic leukodystrophy; neurodegenerative disorders such as amyotrophic
lateral
sclerosis; cancer.
20. Array, preferably a microarray, in which at least a complex according to
any of No. 1 -
7 andlor at least one antibody according to No. 16 is attached to a solid
carrier.
21. A process for modifying a physiological substrate of the complex
comprising the step
of bringing into contact a complex of any of No. 1 - 7 with said substrate,
such that said
substrate is modified.
22. A pharmaceutical composition comprising the protein complex of any of No.
1 - 7
and/or any of the following the proteins:
(i) "YCL046W" (SEQ ID No:2857) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YCL046W",

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the variant being encoded by a nucleic acid that hybridizes to the "YCL046W"
nucleic
acid (SEQ ID No:2858 ) or its complement under low stringency conditions,
(ii) "YHL035C" (SEQ ID No:2859) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YHL035C",
the variant being encoded by a nucleic acid that hybridizes to the "YHL035C"
nucleic
acid (SEQ ID No:2860 ) or its complement under low stringency conditions,
(iii) "YKL059C" (SEQ ID No:2861) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YKL059C",
the variant being encoded by a nucleic acid that hybridizes to the "YKL059C"
nucleic
acid (SEQ ID No:2862 ) or its complement under low stringency conditions,
(iv) "YML030W" (SEQ ID No:2863) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YML030W",
the variant being encoded by a nucleic acid that hybridizes to the "YML030W"
nucleic
acid (SEQ ID No:2864 ) or its complement under low stringency conditions,
and/or
(v) "YOR179C" (SEQ ID No:2865) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YOR179C",
the variant being encoded by a nucleic acid that hybridizes to the "YOR179C"
nucleic
acid (SEQ ID No:2866 ) or its complement under low stringency conditions,
and a pharmaceutical acceptable carrier.
23. A pharmaceutical composition according to No. 22 for the treatment of
diseases and
disorders such as viral infections such as herpes simplex infections, Epstein-
Barr-
infections, influenza; metabolic diseases such as metachromatic
leukodystrophy;
neurodegenerative disorders such as amyotrophic lateral sclerosis; cancer.
24. A method for screening for a molecule that binds to a complex of anyone of
No. 1 - 7
and/or any of the following proteins:
(i) "YCL046W" (SEQ ID No:2857) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YCL046W",
the variant being encoded by a nucleic acid that hybridizes to the "YCL046W"
nucleic
acid (SEQ ID No:2858 ) or its complement under low stringency conditions,
(ii) "YHL035C" (SEQ ID No:2859) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YHL035C",

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the variant being encoded by a nucleic acid that hybridizes to the "YHL035C"
nucleic
acid (SEQ ID No:2860 ) or its complement under low stringency conditions,
(iii) "YKL059C" (SEQ ID No:2861) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YKL059C",
the variant being encoded by a nucleic acid that hybridizes~to the "YKL059C"
nucleic
acid (SEQ ID No:2862 ) or its complement under low stringency conditions,
(iv) "YML030W" (SEQ ID No:2863) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YML030W",
the variant being encoded by a nucleic acid that hybridizes to the "YML030W"
nucleic
acid (SEQ ID No:2864 ) or its complement under low stringency conditions,
and/or
(v) "YOR179C" (SEQ ID No:2865) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YOR179C",
the variant being encoded by a nucleic acid that hybridizes to the "YOR179C"
nucleic
acid (SEQ ID No:2866 ) or its complement under low stringency conditions,
comprising the steps of
(a) exposing said complex, or a cell or organism containing same to one or
more
candidate molecules; and
(b) determining whether said candidate molecule is bound to the complex or
protein.
25. A method for screening for a molecule that modulates directly or
indirectly the
function, activity, composition or formation of the complex of any one of No.
1 - 7
comprising the steps of
(a) exposing said complex, or a cell or organism containing polyadenylation
complex to
one or more candidate molecules; and
(b) determining the amount of activity of protein components of, and/or
intracellular
localization of, said complex andlor the transcription level of a gene
regulated by the
complex and/or the abundance and/or activity of a protein or protein complex
dependend
on the function of the complex and/or product of a gene dependent on the
complex in the
presence of the one or more candidate molecules, wherein a change in said
amount,
activity, protein components or intracellular localization relative to said
amount, activity,
protein components and/or intracellular localization and/or a change in the
transcription
level of a gene dependend on the complex and/or the abundance and/or activity
of a
protein or protein complex dependent on the function of the complex and/or
product of a

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gene dependent on the complex in the absence of said candidate molecules
indicates
that the molecule modulates function, activity or composition of said complex.
26. The method of No. 25, wherein the amount of said complex is determined.
27. The method of No. 25, wherein the activity of said complex is determined.
28. The method of No. 27, wherein said determining step comprises isolating
from the
cell or organism said complex to produce said isolated complex and contacting
said
isolated complex in the presence or absence of a candidate molecule with a
substrate of
said complex and determining the processing of said substrate is modified in
the
presence of said candidate molecule.
29. The method of No. 25, wherein the amount of the individual protein
components of
said complex are determined.
30. The method of No. 29, wherein said determining step comprises determining
whether
(i) "ACT1" (SEQ ID No:681) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "ACT1", the
variant being
encoded by a nucleic acid that hybridizes to the "ACT1" nucleic acid (SEQ ID
No:682 ) or
its complement under low stringency conditions,and/or
(ii) "CFT1" (SEQ ID No:2837) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CFT1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "CFT1" nucleic acid (SEQ ID
No:2838 )
or its complement under low stringency conditions,and/or
(iii) "CFT2" (SEQ ID No:1529) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "CFT2", the
variant being
encoded by a nucleic acid that hybridizes to the "CFT2" nucleic acid (SEQ ID
No:1530 )
or its complement under low stringency conditions,and/or
(iv) "CKA1" (SEQ ID No:133) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CKA1", the
variant being
encoded by a nucleic acid that hybridizes to the "CKA1" nucleic acid (SEQ ID
No:134 ) or
its complement under low stringency conditions,and/or

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(v) "CLP1" (SEQ ID No:2839) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CLP1", the
variant being
encoded by a nucleic acid that hybridizes to the "CLP1" nucleic acid (SEQ ID
No:2840 )
or its complement under low stringency conditions,and/or
(vi) "EFT2" (SEQ ID No:39) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "EFT2", the
variant being
encoded by a nucleic acid that hybridizes to the "EFT2" nucleic acid (SEQ ID
No:40 ) or
its complement under low stringency conditions,and/or
(vii) "EN02" (SEQ ID No:293) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "ENO2", the
variant
being encoded by a nucleic acid that hybridizes to the "EN02" nucleic acid
(SEQ ID
No:294 ) or its complement under low stringency conditions,and/or
(viii) "FIP1" (SEQ ID No:1531) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "FIP1", the
variant being
encoded by a nucleic acid that hybridizes to the "FIP1" nucleic acid (SEQ ID
No:1532 )
or its complement under low stringency conditions,and/or
(ix) "GLC7" (SEQ ID No:929) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "GLC7", the
variant being
encoded by a nucleic acid that hybridizes to the "GLC7" nucleic acid (SEQ ID
No:930 ) or
its complement under low stringency conditions,and/or
(x) "GPM1" (SEQ ID No:597) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "GPM1", the
variant
being encoded by a nucleic acid that hybridizes to the "GPM1" nucleic acid
(SEQ ID
No:598 ) or its complement under low stringency conditions,and/or
(xi) "HTA1" (SEQ ID No:1029) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "HTA1", the
variant being
encoded by a nucleic acid that hybridizes to the "HTA1" nucleic acid (SEQ ID
No:1030 )
or its complement under low stringency conditions,and/or
(xii) "IMD2" (SEQ ID No:259) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "IMD2", the
variant being
encoded by a nucleic acid that hybridizes to the "IMD2" nucleic acid (SEQ ID
No:260 ) or
its complement under low stringency conditions,and/or
(xiii) "IMD4" (SEQ ID No:41) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "IMD4", the
variant being

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encoded by a nucleic acid that hybridizes to the "IMD4" nucleic acid (SEQ ID
No:42 ) or
its complement under low stringency conditions,and/or
(xiv) "METE" (SEQ ID No:1921) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"METE", the
variant being encoded by a nucleic acid that hybridizes to the "METE" nucleic
acid (SEQ
ID No:1922 ) or its complement under low stringency conditions,and/or
(xv) "PAP1" (SEQ ID No:1541) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "PAP1", the
variant being
encoded by a nucleic acid that hybridizes to the "PAP1" nucleic acid (SEQ ID
No:1542 )
or its complement under low stringency conditions,and/or
(xvi) "PCF11" (SEQ ID No:2843) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PCF11", the
variant being encoded by a nucleic acid that hybridizes to the "PCF11" nucleic
acid (SEQ
ID No:2844 ) or its complement under low stringency conditions,and/or
(xvii) "PFK1" (SEQ ID No:143) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "PFK1", the
variant being
encoded by a nucleic acid that hybridizes to the "PFK1" nucleic acid (SEQ ID
No:144 ) or
its complement under low stringency conditions,and/or
(xviii) "PFS2" (SEQ ID No:1543) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PFS2", the
variant being encoded by a nucleic acid that hybridizes to the "PFS2" nucleic
acid (SEQ
ID No:1544 ) or its complement under low stringency conditions,and/or
(xix) "PTA1" (SEQ ID No:1545) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PTA1 ", the
variant being encoded by a nucleic acid that hybridizes to the "PTA1" nucleic
acid (SEQ
ID No:1546 ) or its complement under low stringency conditions,and/or
(xx) "PT11" (SEQ ID No:1597) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "PTI1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "PT11" nucleic acid (SEQ ID
No:1598 )
or its complement under low stringency conditions,and/or
(xxi) "REF2" (SEQ ID No:1547) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"REF2", the
variant being encoded by a nucleic acid that hybridizes to the "REF2" nucleic
acid (SEQ
ID No:1548 ) or its complement under low stringency conditions,and/or

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(.xxii) "RNA14" (SEQ ID No:1549) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"RNA14", the
variant being encoded by a nucleic acid that hybridizes to the "RNA14" nucleic
acid
(SEQ ID No:1550 ) or its complement under low stringency conditions,and/or
(xxiii) "RNA15" (SEQ ID No:2845) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"RNA15", the
variant being encoded by a nucleic acid that hybridizes to the "RNA15" nucleic
acid
(SEQ ID No:2846 ) or its complement under low stringency conditions,and/or
(xxiv) "RSA3" (SEQ ID No:2849) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"RSA3", the
variant being encoded by a nucleic acid that hybridizes to the "RSA3" nucleic
acid (SEQ
ID No:2850 ) or its complement under low stringency conditions,and/or
(xxv) "SEC13" (SEQ ID No:1171) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SEC13", the
variant being encoded by a nucleic acid that hybridizes to the "SEC13" nucleic
acid (SEQ
ID No:1172 ) or its complement under low stringency conditions,and/or
(xxvi) "SEC31" (SEQ ID No:1177) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SEC31", the
variant being encoded by a nucleic acid that hybridizes to the "SEC31" nucleic
acid (SEQ
ID No:1178 ) or its complement under low stringency conditions,and/or
(xxvii) "SSA3" (SEQ ID No:723) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SSA3", the
variant being encoded by a nucleic acid that hybridizes to the "SSA3" nucleic
acid (SEQ
ID No:724 ) or its complement under low stringency conditions,and/or
(xxviii) "SSU72" (SEQ ID No:2851) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SSU72", the
variant being encoded by a nucleic acid that hybridizes to the "SSU72" nucleic
acid (SEQ
ID No:2852 ) or its complement under low stringency conditions,and/or
(xxix) "SWD2" (SEQ ID No:1455) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SWD2", the
variant being encoded by a nucleic acid that hybridizes to the "SWD2" nucleic
acid (SEQ
ID No:1456 ) or its complement under low stringency conditions,and/or
(xxx) "TAF60" (SEQ ID No:825) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TAF60", the

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variant being encoded by a nucleic acid that hybridizes to the "TAF60" nucleic
acid (SEQ
ID No:826 ) or its complement under low stringency conditions,and/or
(xxxi) "TIF4632" (SEQ ID No:195) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TIF4632",
the variant being encoded by a nucleic acid that hybridizes to the 'TIF4632"
nucleic acid
(SEQ ID No:196 ) or its complement under low stringency conditions,and/or
(xxxii) "TKL1" (SEQ ID No:379) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TKL1 ", the
variant being encoded by a nucleic acid that hybridizes to the "TKL1" nucleic
acid (SEQ
ID No:380 ) or its complement under low stringency conditions,and/or
(xxxiii) "TSA1" (SEQ ID No:733) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TSA1", the
variant being encoded by a nucleic acid that hybridizes to the "TSA1" nucleic
acid (SEQ
ID No:734 ) or its complement under low stringency conditions,and/or
(xxxiv) "TYE7" (SEQ ID No:2853) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TYE7", the
variant being encoded by a nucleic acid that hybridizes to the "TYE7" nucleic
acid (SEQ
ID No:2854 ) or its complement under low stringency conditions,and/or
(xxxv) "VID24" (SEQ ID No:2855) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"VID24", the
variant being encoded by a nucleic acid that hybridizes to the "VID24" nucleic
acid (SEQ
ID No:2856 ) or its complement under low stringency conditions,and/or
(xxxvi) "VPS53" (SEQ ID No:1233) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"VPS53", the
variant being encoded by a nucleic acid that hybridizes to the "VPS53" nucleic
acid (SEQ
ID No:1234 ) or its complement under low stringency conditions,and/or
(xxxvii) "YCL046W" (SEQ ID No:2857) or a functionally active derivative
thereof, or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YCL046W",
the variant being encoded by a nucleic acid that hybridizes to the "YCL046W"
nucleic
acid (SEQ ID No:2858 ) or its complement under low stririgency
conditions,and/or
(xxxviii) "YHL035C" (SEQ ID No:2859) or a functionally active derivative
thereof, or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YHL035C",
the variant being encoded by a nucleic acid that hybridizes to the "YHL035C"
nucleic
acid (SEQ ID No:2860 ) or its complement under low stringency
conditions,and/or

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(xxxix) "YKL059C" (SEQ ID No:2861) or a functionally active derivative
thereof, or a
functionally active fragment thereof, or a hom ologue thereof, or a variant of
"YKL059C",
the variant being encoded by a nucleic acid that hybridizes to the "YKL059C"
nucleic
acid (SEQ ID No:2862 ) or its complement under low stringency
conditions,and/or
(xl) "YML030W" (SEQ ID No:2863) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YML030W",
the variant being encoded by a nucleic acid that hybridizes to the "YML030W"
nucleic
acid (SEQ ID No:2864 ) or its complement under low stringency
conditions,and/or
(xli) "YOR179C" (SEQ ID No:2865) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YOR179C",
the variant being encoded by a nucleic acid that hybridizes to the "YOR179C"
nucleic
acid (SEQ ID No:2866 ) or its complement under low stringency
conditions,and/or
(xlii) "YSH1" (SEQ ID No:1561) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YSH1", the
variant being encoded by a nucleic acid that hybridizes to the "YSH1" nucleic
acid (SEQ
ID No:1562 ) or its complement under low stringency conditions, and/or
(xliii) "YTH1" (SEQ ID No:2847) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YTH1", the
variant being encoded by a nucleic acid that hybridizes to the "YTH1" nucleic
acid (SEQ
ID No:2848 ) or its complement under low stringency conditions, and/or
(xliv) "PAB1" (SEQ ID No:2841) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PAB1 ", the
variant being encoded by a nucleic acid that hybridizes to the "PAB1" nucleic
acid (SEQ
ID No:2842 ) or its complement under low stringency conditions, and/or
(xlv) "HHF2" (SEQ ID No:555) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "HHF2", the
variant being
encoded by a nucleic acid that hybridizes to the "HHF2" nucleic acid (SEQ ID
No:556 ) or
its complement under low stringency conditions,
is present in the complex.
31. The method of any of No. 25 - 30, wherein said method is a method of
screening for
a drug for treatment or prevention of a disease or disorder such as viral
infections such
as herpes simplex infections, Epstein-Barr-infections, influenza; metabolic
diseases such

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as metachromatic leukodystrophy; neurodegenerative disorders such as
amyotrophic
lateral sclerosis; cancer.
32. Use of a molecule that modulates the amount of, activity of, or the
protein
components of the complex of any one of No. 1 - 7 for the manufacture of a
medicament
for the treatment or prevention of a disease or disorder such as viral
infections such as
herpes simplex infections, Epstein-Barr-infections, influenza; metabolic
diseases such as
metachromatic leukodystrophy; neurodegenerative disorders such as amyotrophic
lateral
sclerosis; cancer.
33. A method for the production of a pharmaceutical composition comprising
carrying out
the method of any of No. 1 - 7 to identify a molecule that modulates the
function, activity,
composition or formation of said complex, and further comprising mixing the
identified
molecule with a pharmaceutically acceptable carrier.
34. A method for diagnosing or screening for the presence of a disease or
disorder or a
predisposition for developing a disease or disorder in a subject, which
disease or
disorder is characterized by an aberrant amount of, activity of, or component
composition
of, or intracellular localization of the complex of any one of the No. 1 - 7,
comprising
determining the amount of, activity of, protein components of, and/or
intracellular
localization of, said complex and/or the transcription level of a gene
dependend on the
complex and/or the abundance and/or activity of a protein or protein complex
dependend
on the function of the complex and/or product of a gene dependent on the
complex in a
comparative sample derived from a subject, wherein a difference in said
amount, activity,
or protein components of, said complex in a corresponding sample from a
subject not
having the disease or disorder or predisposition indicates the presence in the
subject of
the disease or disorder or predisposition in the subject.
35. The method of No. 34, wherein the amount of said complex is determined.
36. The method of No. 34, wherein the activity of said complex is determined.
37. The method of No. 36, wherein said determining step comprises isolating
from the
subject said complex to produce said isolated complex and contacting said
isolated

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complex in the presence or absence of a candidate molecule with a substrate of
said
complex and determining whether said substrate is processed in the absence of
the
candidate molecule and whether the processing of said substrate is modified in
the
presence of said candidate molecule.
38. The method of No. 34, wherein the amount of the individual protein
components of
said complex are determined.
39. The method of No. 38, wherein said determining step comprises determining
whether
(i) "ACT1" (SEQ ID No:681) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "ACT1", the
variant being
encoded by a nucleic acid that hybridizes to the "ACT1" nucleic acid (SEQ ID
No:682 ) or
its complement under low stringency conditions, and/or
(ii) "CFT1" (SEQ ID No:2837) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CFT1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "CFT1" nucleic acid (SEQ ID
No:2838 )
or its complement under low stringency conditions, and/or
(iii) "CFT2" (SEQ ID No:1529) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "CFT2", the
variant being
encoded by a nucleic acid that hybridizes to the "CFT2" nucleic acid (SEQ ID
No:1530 )
or its complement under low stringency conditions, and/or
(iv) "CKA1" (SEQ ID No:133) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CKA1", the
variant being
encoded by a nucleic acid that hybridizes to the "CKA1" nucleic acid (SEQ ID
No:134 ) or
its complement under low stringency conditions, and/or
(v) "CLP1" (SEQ ID No:2839) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CLP1", the
variant being
encoded by a nucleic acid that hybridizes to the "CLP1" nucleic acid (SEQ ID
No:2840 )
or its complement under low stringency conditions, and/or
(vi) "EFT2" (SEQ ID No:39) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "EFT2", the
variant being
encoded by a nucleic acid that hybridizes to the "EFT2" nucleic acid (SEQ ID
No:40 ) or
its complement under low stringency conditions, and/or

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(vii) "EN02" (SEQ ID No:293) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "EN02", the
variant
being encoded by a nucleic acid that hybridizes to the "EN02" nucleic acid
(SEQ ID
No:294 ) or its complement under low stringency conditions, and/or
(viii) "FIP1" (SEQ ID No:1531) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "FIP1", the
variant being
encoded by a nucleic acid that hybridizes to the "FIP1" nucleic acid (SEQ ID
No:1532 )
or its complement under low stringency conditions, and/or
(ix) "GLC7" (SEQ ID No:929) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "GLC7", the
variant being
encoded by a nucleic acid that hybridizes to the "GLC7" nucleic acid (SEQ ID
No:930 ) or
its complement under low stringency conditions, and/or
(x) "GPM1" (SEQ ID No:597) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "GPM1", the
variant
being encoded by a nucleic acid that hybridizes to the "GPM1" nucleic acid
(SEQ ID
No:598 ) or its complement under low stringency conditions, and/or
(xi) "HTA1" (SEQ ID No:1029) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "HTA1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "HTA1" nucleic acid (SEQ ID
No:1030 )
or its complement under low stringency conditions, and/or
(xii) "IMD2" (SEQ ID No:259) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "IMD2", the
variant being
encoded by a nucleic acid that hybridizes to the "IMD2" nucleic acid (SEQ ID
No:260 ) or
its complement under low stringency conditions, and/or
(xiii) "IMD4" (SEQ ID No:41) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "IMD4", the
variant being
encoded by a nucleic acid that hybridizes to the "IMD4" nucleic acid (SEQ ID
No:42 ) or
its complement under low stringency conditions, and/or
(xiv) "METE" (SEQ ID No:1921) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"METE", the
variant being encoded by a nucleic acid that hybridizes to the "METE" nucleic
acid (SEQ
ID No:1922 ) or its complement under low stringency conditions, and/or
(xv) "PAP1" (SEQ ID No:1541) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "PAP1", the
variant being

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encoded by a nucleic acid that hybridizes to the "PAP1" nucleic acid (SEQ ID
No:1542 )
or its complement under low stringency conditions, and/or
(xvi) "PCF11" (SEQ ID No:2843) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PCF11", the
variant being encoded by a nucleic acid that hybridizes to the "PCF11" nucleic
acid (SEQ
ID No:2844 ) or its complement under low stringency conditions, and/or
(xvii) "PFK1" (SEQ ID No:143) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "PFK1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "PFK1" nucleic acid (SEQ ID
No:144 ) or
its complement under low stringency conditions, and/or
(xviii) "PFS2" (SEQ ID No:1543) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PFS2", the
variant being encoded by a nucleic acid that hybridizes to the "PFS2" nucleic
acid (SEQ
ID No:1544 ) or its complement under low stringency conditions, and/or
(xix) "PTA1" (SEQ ID No:1545) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PTA1", the
variant being encoded by a nucleic acid that hybridizes to the "PTA1" nucleic
acid (SEQ
ID No:1546 ) or its complement under low stringency conditions, and/or
(xx) "PT11" (SEQ ID No:1597) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "PT11 ", the
variant being
encoded by a nucleic acid that hybridizes to the "PT11" nucleic acid (SEQ ID
No:1598 )
or its complement under low stringency conditions, and/or
(xxi) "REF2" (SEQ ID No:1547) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"REF2", the
variant being encoded by a nucleic acid that hybridizes to the "REF2" nucleic
acid (SEQ
ID No:1548 ) or its complement under low stringency conditions, and/or
(xxii) "RNA14" (SEQ ID No:1549) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"RNA14", the
variant being encoded by a nucleic acid that hybridizes to the "RNA14" nucleic
acid
(SEQ ID No:1550 ) or its complement under lov~i stringency conditions, and/or
(xxiii) "RNA15" (SEQ ID No:2845) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"RNA15", the
variant being encoded by a nucleic acid that hybridizes to the "RNA15" nucleic
acid
(SEQ ID No:2846 ) or its complement under low stringency conditions, and/or

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(xxiv) "RSA3" (SEQ ID No:2849) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"RSA3", the
variant being encoded by a nucleic acid that hybridizes to the "RSA3" nucleic
acid (SEQ
ID No:2850 ) or its complement under low stringency conditions, and/or
(xxv) "SEC13" (SEQ ID No:1171) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SEC13", the
variant being encoded by a nucleic acid that hybridizes to the "SEC13" nucleic
acid (SEQ
ID No:1172 ) or its complement under low stringency conditions, and/or
(xxvi) "SEC31" (SEQ ID No:1177) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SEC31", the
variant being encoded by a nucleic acid that hybridizes to the "SEC31" nucleic
acid (SEQ
ID No:1178 ) or its complement under low stringency conditions, and/or
(xxvii) "SSA3" (SEQ ID No:723) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SSA3", the
variant being encoded by a nucleic acid that hybridizes to the "SSA3" nucleic
acid (SEQ
ID No:724 ) or its complement under low stringency conditions, andlor
(xxviii) "SSU72" (SEQ ID No:2851) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SSU72", the
variant being encoded by a nucleic acid that hybridizes to the "SSU72" nucleic
acid (SEQ
ID No:2852 ) or its complement under low stringency conditions, andlor
(xxix) "SWD2" (SEQ ID No:1455) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SWD2", the
variant being encoded by a nucleic acid that hybridizes to the "SWD2" nucleic
acid (SEQ
ID No:1456 ) or its complement under low stringency conditions, and/or
(xxx) "TAF60" (SEQ ID No:825) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TAF60", the
variant being encoded by a nucleic acid that hybridizes to the "TAF60" nucleic
acid (SEQ
ID No:826 ) or its complement under low stringency conditions, and/or
(xxxi) "TIF4632" (SEQ ID No:195) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TIF4632",
the variant being encoded by a nucleic acid that hybridizes to the "TIF4632"
nucleic acid
(SEQ ID No:196 ) or its complement under low stringency conditions, and/or
(xxxii) "TKL1" (SEQ ID No:379) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TKL1", the

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variant being encoded by a nucleic acid that hybridizes to the "TKL1" nucleic
acid (SEQ
ID No:380 ) or its complement under low stringency conditions, and/or
(xxxiii) "TSA1" (SEQ ID No:733) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TSA1", the
variant being encoded by a nucleic acid that hybridizes to the "TSA1" nucleic
acid (SEQ
ID No:734 ) or its complement under low stringency conditions, and/or
(xxxiv) "TYE7" (SEQ ID No:2853) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TYE7", the
variant being encoded by a nucleic acid that hybridizes to the "TYE7" nucleic
acid (SEQ
ID No:2854 ) or its complement under low stringency conditions, and/or
(xxxv) "VID24" (SEQ ID No:2855) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"VID24", the
variant being encoded by a nucleic acid that hybridizes to the "VID24" nucleic
acid (SEQ
ID No:2856 ) or its complement under low stringency conditions, and/or
(xxxvi) "VPS53" (SEQ ID No:1233) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"VPS53", the
variant being encoded by a nucleic acid that hybridizes to the "VPS53" nucleic
acid (SEQ
ID No:1234 ) or its complement under low stringency conditions, andlor
(xxxvii) "YCL046W" (SEQ ID No:2857) or a functionally active derivative
thereof, or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YCL046W",
the variant being encoded by a nucleic acid that hybridizes to the "YCL046W"
nucleic
acid (SEQ ID No:2858 ) or its complement under low stringency conditions,
and/or
(xxxviii) "YHL035C" (SEQ ID No:2859) or a functionally active derivative
thereof, or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YHL035C",
the variant being encoded by a nucleic acid that hybridizes to the "YHL035C"
nucleic
acid (SEQ ID No:2860 ) or its complement under low stringency conditions,
and/or
(xxxix) "YKL059C" (SEQ ID No:2861) or a functionally active derivative
thereof, or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YKL059C",
the variant being encoded by a nucleic acid that hybridizes to the "YKL059C"
nucleic
acid (SEQ ID No:2862 ) or its complement under low stringency conditions,
and/or
(xl) "YML030W" (SEQ ID No:2863) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YML030W",
the variant being encoded by a nucleic acid that hybridizes to the "YML030W"
nucleic
acid (SEQ ID No:2864 ) or its complement under low stringency conditions,
and/or

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(xli) "YOR179C" (SEQ ID No:2865) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YOR179C",
the variant being encoded by a nucleic acid that hybridizes to the "YOR179C"
nucleic
acid (SEQ ID No:2866 ) or its complement under low stringency conditions,
and/or
(xlii) ."YSH1" (SEQ ID No:1561) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YSH1", the
variant being encoded by a nucleic acid that hybridizes to the "YSH1" nucleic
acid (SEQ
ID No:1562 ) or its complement under low stringency conditions, and/or
(xliii) "YTH1" (SEQ ID No:2847) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YTH1", the
variant being encoded by a nucleic acid that hybridizes to the "YTH1" nucleic
acid (SEQ
ID No:2848 ) or its complement under low stringency conditions, andlor
(xliv) "PAB1" (SEQ ID No:2841) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PAB1", the
variant being encoded by a nucleic acid that hybridizes to the "PAB1" nucleic
acid (SEQ
ID No:2842 ) or its complement under low stringency conditions, and/or
(xlv) "HHF2" (SEQ ID No:555) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "HHF2", the
variant being
encoded by a nucleic acid that hybridizes to the "HHF2" nucleic acid (SEQ ID
No:556 ) or
its complement under low stringency conditions.
is present in the complex.
40. The complex of any one of No. 1 - 7, or proteins of No. 12 or the antibody
or
fragment of No. 16, for use in a method of diagnosing a disease or disorder
such as viral
infections such as herpes simplex infections, Epstein-Barr-infections,
influenza;
metabolic diseases such as metachromatic leukodystrophy; neurodegenerative
disorders
such as amyotrophic lateral sclerosis; cancer.
41. A method for treating or preventing a disease or disorder characterized by
an
aberrant amount of, activity or component composition of or intracellular
localization of,
the complex of anyone of No. 1 - 7, comprising administering to a subject in
need of such
treatment or prevention a therapeutically effective amount of one or more
molecules that
modulate the amount of, 3' end mRNA processing activity ; 3' end mRNA
processing
activity , or protein composition of, said complex.

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42. The method according to No. 41, wherein said disease or disorder involves
decreased levels of the amount or activity of said complex.
43. The method according to No. 41 , wherein said disease or disorder involves
increased levels of the amount or activity of said complex.
44. Complex of any of No. 1 - 7 and/or protein selected from the following
proteins
(i) "ACT1" (SEQ ID No:681) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "ACT1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "ACT1" nucleic acid (SEQ ID
No:682 ) or
its complement under low stringency conditions,and
(ii) "CFT1" (SEQ ID No:2837) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CFT1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "CFT1" nucleic acid (SEQ ID
No:2838 )
or its complement under low stringency conditions,and
(iii) "CFT2" (SEQ ID No:1529) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "CFT2", the
variant being
encoded by a nucleic acid that hybridizes to the "CFT2" nucleic acid (SEQ ID
No:1530 )
or its complement under low stringency conditions,and
(iv) "CKA1" (SEQ ID No:133) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CKA1", the
variant being
encoded by a nucleic acid that hybridizes to the "C4CA1" nucleic acid (SEQ ID
No:134 ) or
its complement under low stringency conditions,and
(v) "CLP1" (SEQ ID No:2839) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CLP1", the
variant being
encoded by a nucleic acid that hybridizes to the "CLP1" nucleic acid (SEQ ID
No:2840 )
or its complement under low stringency conditions,and
(vi) "EFT2" (SEQ ID No:39) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "EFT2", the
variant being
encoded by a nucleic acid that hybridizes to the "EFT2" nucleic acid (SEQ ID
No:40 ) or
its complement under low stringency conditions,and
(vii) "EN02" (SEQ ID No:293) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "ENO2", the
variant

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being encoded by a nucleic acid that hybridizes to the "EN02" nucleic acid
(SEQ ID
No:294 ) or its complement under low stringency conditions,and
(viii) "FIP1" (SEQ ID No:1531) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof,~or a variant of "FIP1", the
variant being
encoded by a nucleic acid that hybridizes to the "FIP1" nucleic acid (SEQ ID
No:1532 )
or its complement under low stringency conditions,and
(ix) "GLC7" (SEQ ID No:929) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "GLC7", the
variant being
encoded by a nucleic acid that hybridizes to the "GLC7" nucleic acid (SEQ ID
No:930 ) or
its complement under low stringency conditions,and
(x) "GPM1" (SEQ ID No:597) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "GPM1", the
variant
being encoded by a nucleic acid that hybridizes to the "GPM1" nucleic acid
(SEQ ID
No:598 ) or its complement under low stringency conditions,and
(xi) "HTA1" (SEQ ID No:1029) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "HTA1", the
variant being
encoded by a nucleic acid that hybridizes to the "HTA1" nucleic acid (SEQ ID
No:1030 )
or its complement under low stringency conditions,and
(xii) "IMD2" (SEQ ID No:259) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "IMD2", the
variant being
encoded by a nucleic acid that hybridizes to the "IMD2" nucleic acid (SEQ ID
No:260 ) or
its complement under low stringency conditions,and
(xiii) "IMD4" (SEQ ID No:41) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "IMD4", the
variant being
encoded by a nucleic acid that hybridizes to the "IMD4" nucleic acid (SEQ ID
No:42 ) or
its complement under low stringency conditions,and
(xiv) "METE" (SEQ ID No:1921) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"METE", the
variant being encoded by a nucleic acid that hybridizes to the "METE" nucleic
acid (SEQ
ID No:1922 ) or its complement under low stringency conditions,and
(xv) "PAP1" (SEQ ID No:1541) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "PAP1", the
variant being
encoded by a nucleic acid that hybridizes to the "PAP1" nucleic acid (SEQ ID
No:1542 )
or its complement under low stringency conditions,and

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(xvi) "PCF11" (SEQ ID No:2843) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PCF11", the
variant being encoded by a nucleic acid that hybridizes to the "PCF11" nucleic
acid (SEQ
ID No:2844 ) or its complement under low stringency conditions,and
(xvii) "PFK1" (SEQ ID No:143) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "PFK1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "PFK1" nucleic acid (SEQ ID
No:144 ) or
its complement under low stringency conditions,and
(xviii) "PFS2" (SEQ ID No:1543) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PFS2", the
variant being encoded by a nucleic acid that hybridizes to the "PFS2" nucleic
acid (SEQ
ID No:1544 ) or its complement under low stringency conditions,and
(xix) "PTA1" (SEQ ID No:1545) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PTA1", the
variant being encoded by a nucleic acid that hybridizes to the "PTA1" nucleic
acid (SEQ
ID No:1546 ) or its complement under low stringency conditions,and
(xx) "PT11" (SEQ ID No:1597) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "PT11 ", the
variant being
encoded by a nucleic acid that hybridizes to the "PT11" nucleic acid (SEQ ID
No:1598 )
or its complement under low stringency conditions,and
(xxi) "REF2" (SEQ ID No:1547) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"REF2", the
variant being encoded by a nucleic acid that hybridizes to the "REF2" nucleic
acid (SEQ
ID No:1548 ) or its complement under low stringency conditions,and
(xxii) "RNA14" (SEQ ID No:1549) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"RNA14", the
variant being encoded by a nucleic acid that hybridizes to the "RNA14" nucleic
acid
(SEQ ID No:1550 ) or its complement under low stringency conditions,and
(xxiii) "RNA15" (SEQ ID No:2845) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"RNA15", the
variant being encoded by a nucleic acid that hybridizes to the "RNA15" nucleic
acid
(SEQ ID No:2846 ) or its complement under low stringency conditions,and
(xxiv) "RSA3" (SEQ ID No:2849) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"RSA3", the

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variant being encoded by a nucleic acid that hybridizes to the "RSA3" nucleic
acid (SEQ
ID No:2850 ) or its complement under low stringency conditions,and
(xxv) "SEC13" (SEQ ID No:1171) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SEC13", the
variant being encoded by a nucleic acid that hybridizes to the "SEC13" nucleic
acid (SEQ
ID No:1172 ) or its complement under low stringency conditions,and
(xxvi) "SEC31" (SEQ ID No:1177) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SEC31", the
variant being encoded by a nucleic acid that hybridizes to the "SEC31" nucleic
acid (SEQ
ID No:1178 ) or its complement under low stringency conditions,and
(xxvii) "SSA3" (SEQ ID No:723) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SSA3", the
variant being encoded by a nucleic acid that hybridizes to the "SSA3" nucleic
acid (SEQ
ID No:724 ) or its complement under low stringency conditions,and
(xxviii) "SSU72" (SEQ ID No:2851) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SSU72", the
variant being encoded by a nucleic acid that hybridizes to the "SSU72" nucleic
acid (SEQ
ID No:2852 ) or its complement under low stringency conditions,and
(xxix) "SWD2" (SEQ ID No:1455) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SWD2", the
variant being encoded by a nucleic acid that hybridizes to the "SWD2" nucleic
acid (SEQ
ID No:1456 ) or its complement under low stringency conditions,and
(xxx) "TAF60" (SEQ ID No:825) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TAF60", the
variant being encoded by a nucleic acid that hybridizes to the "TAF60" nucleic
acid (SEQ
ID No:826 ) or its complement under low stringency conditions,and
(xxxi) "TIF4632" (SEQ ID No:195) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TIF4632",
the variant being encoded by a nucleic acid that hybridizes to the "TIF4632"
nucleic acid
(SEQ ID No:196 ) or its complement under low stringency conditions,and
(xxxii) "TKL1" (SEQ ID No:379) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TKL1", the
variant being encoded by a nucleic acid that hybridizes to the "TKL1" nucleic
acid (SEQ
ID No:380 ) or its complement under low stringency conditions,and

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(xxxiii) "TSA1" (SEQ ID No:733) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TSA1 ", the
variant being encoded by a nucleic acid that hybridizes to the "TSA1" nucleic
acid (SEQ
ID No:734 ) or its complement under low stringency conditions,and
(xxxiv) "TYE7" (SEQ ID No:2853) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"TYE7", the
variant being encoded by a nucleic acid that hybridizes to the "TYE7" nucleic
acid (SEQ
ID No:2854 ) or its complement under low stringency conditions,and
(xxxv) "VID24" (SEQ ID No:2855) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"VID24", the
variant being encoded by a nucleic acid that hybridizes to the "VID24" nucleic
acid (SEQ
ID No:2856 ) or its complement under low stringency conditions,and
(xxxvi) "VPS53" (SEQ ID No:1233) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"VPS53", the
variant being encoded by a nucleic acid that hybridizes to the "VPS53" nucleic
acid (SEQ
ID No:1234 ) or its complement under low stringency conditions,and
(xxxvii) "YCL046W" (SEQ ID No:2857) or a functionally active derivative
thereof, or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YCL046W",
the variant being encoded by a nucleic acid that hybridizes to the "YCL046W"
nucleic
acid (SEQ ID No:2858 ) or its complement under low stringency conditions,and
(xxxviii) "YHL035C" (SEQ ID No:2859) or a functionally active derivative
thereof, or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YHL035C",
the variant being encoded by a nucleic acid that hybridizes to the "YHL035C"
nucleic
acid (SEQ ID No:2860 ) or its complement under low stringency conditions,and
(xxxix) "YICL059C" (SEQ ID No:2861) or a functionally active derivative
thereof, or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YKL059C",
the variant being encoded by a nucleic acid that hybridizes to the "YICL059C"
nucleic
acid (SEQ ID No:2862 ) or its complement under low stringency conditions,and
(xl) "YML030W" (SEQ ID No:2863) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YML030W",
the variant being encoded by a nucleic acid that hybridizes to the "YML030W"
nucleic
acid (SEQ ID No:2864 ) or its complement under low stringency conditions,and
(xli) "YOR179C" (SEQ ID No:2865) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YOR179C",

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the variant being encoded by a nucleic acid that hybridizes to the "YOR179C"
nucleic
acid (SEQ ID No:2866 ) or its complement under low stringency conditions,and
(xlii) "YSH1" (SEQ ID No:1561) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YSH1", the
variant being encoded by a nucleic acid that hybridizes to the "YSH1" nucleic
acid (SEQ
ID No:1562 ) or its complement under low stringency conditions, and/or
(xliii) "YTH1" (SEQ ID No:2847) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YTH1", the
variant being encoded by a nucleic acid that hybridizes to the "YTH1" nucleic
acid (SEQ
ID No:2848 ) or its complement under low stringency conditions, and/or
(xliv) "PAB1" (SEQ ID No:2841) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PAB1", the
variant being encoded by a nucleic acid that hybridizes to the "PAB1" nucleic
acid (SEQ
ID No:2842 ) or its complement under low stringency conditions, and/or
(xlv) "HHF2" (SEQ ID No:555) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "HHF2", the
variant being
encoded by a nucleic acid that hybridizes to the "HHF2" nucleic acid (SEQ ID
No:556 ) or
its complement under low stringency conditions,
as a target for an active agent of a pharmaceutical, preferably a drug target
in the
treatment or prevention of a disease or disorder such as viral infections such
as herpes
simplex infections, Epstein-Barr-infections, influenza; metabolic diseases
such as
metachromatic leukodystrophy; neurodegenerative disorders such as amyotrophic
lateral
sclerosis; cancer.
In a preferred embodiment of the present invention, the protein
components of the complex are vertebrate homologs of the yeast proteins, or a
mixture
of yeast and vertebrate homolog proteins. In a more preferred embodiment the
present
invention relates to a complex which is useful for cleaving and/or
polyadenylating a
nucleic acid. In a more preferred embodiment, the protein components of the
complex
are mammalian homologs of the yeast proteins, or a mixture of yeast and
mammalian
homolog proteins. In particular aspects,n the native component proteins, or
derivatives
or fragments of the complex are obtained from a mammal such as mouse, rat,
pig, cow,
dog, monkey, human, sheep or horse. In another preferred embodiment, the
protein
components of the complex are human homologs of the yeast proteins, or a
mixture of

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yeast and human homolog proteins. In yet another preferred embodiment, the
protein
components of the complex are a mixture of yeast, vertebrate, mammalian and/or
human
proteins.
As used herein, a "functionally active complex" refers to that material
displaying one or more known functional attributes of a wild type complex,
including but
not limited to binding to a complex specific antibody or physiological
function (for
physiological functions of the protein complexes of the present invention,
A specific embodiment of the present invention is directed to a complex
comprising of a fragment of a component protein that can be bound by an anti-
component protein antibody or bound by an antibody specific for the protein
complex or
wherein the fragment is able to bind another component protein of the complex.
In
another specific embodiments, the present invention is directed to a complex
comprisng
a fragment of one or more members of the complex. Fragments, or proteins
comprising
fragments, lacking a region of a member of the complex, are also provided.
Nucleic
acids encoding the foregoing are also provided in the present invention.
The present invention is also directed to methods for production of a
protein complex of the present invention and derivatives of the complex and/or
fragments
and/or derivatives of individual component proteins or the complex e. g. by
the TAP-
method described further below. Pharmaceutical compositions are also provided.
The present invention is further directed to complexes comprising a fusion
protein which comprises a component of the complex or a fragment thereof
linked via a
covalent bond to an amino acid sequence different from said component protein,
as well
as nucleic acids encoding the protein, fusions and fragments thereof. For
example, the
non-component protein portion of the fusion protein, which can be added to the
N-
terminal, the C-terminal or inserted into the amino acid sequence of the
complex
component can comprise a few amino acids, which provide an epitope that is
used as a
target for affinity purification of the fusion protein and/or complex.
The invention is further directed to methods for modulating (i.e., inhibiting
or enhancing) the amount of, the cleavage and/or polyadenylating activity of
RNA of, or
the identity of the protein components of, a complex of the present invention.
The
protein components of a complex of the present invention have been implicated
in many
physiological processes. The present invention is also directed to methods for
screening
a complex, as well as a derivative of the complex, for the ability to alter a
cell function,

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particularly a cell function in which the complex and/or a component protein
of the
complex has been implicated.
Moreover, the present invention provides a process for the identification
and/or
preparation of an effector of a composition according to the invention which
process
comprises the steps of bringing into contact the composition of the invention
or of a
component thereof with a compound, a mixture of compounds or a library of
compounds
and determining whether the compounds or certain compounds of the mixture or
library
bind to the composition of the invention and/or a component thereof and/or
affects the
cleavage and/or polyadenylation of nucleic acid activity of such a composition
or
component and then optionally further purifying the compound positively tested
as
effector by such a process.
A major application of the composition according to the invention results in
the
identification of an active agent capable of binding thereto. Hence, the
compositions of
the invention are useful tools in screening for new pharmaceutical drugs.
The present invention is also directed to a method for isolating the
complex and the component proteins comprising tagging a protein of the complex
with a
sequence that allows affinity purification of the tagged protein, expressing
such protein in
a target cell, isolating the protein complex which is attached to the tagged
protein, and
optionally disassociating the protein complex and isolating the individual
complex
members.
The present invention further relates to a composition, preferably a protein
complex, which is obtainable by the method comprising the following steps:
tagging a
protein as defined above, i.e. a protein which forms part of a protein
complex, with a
moiety, preferably an amino acid sequence, that allows affinity purification
of the tagged
protein and expressing such protein in a target cell and isolating the protein
complex
which is attached to the tagged protein. The details of such purification are
described in
WO 00/09716 and in Rigaut, G. et al. (1999), Nature Biotechnology, Vol. 17
(10): 1030-
1032 and further herein below. The tagging can essentially be performed with
any
moiety which is capable of providing a specific interaction with a further
moiety, e.g. in
the sense of a ligand receptor interaction, antigen antibody interaction or
the like. The
tagged protein can also be expressed in an amount in the target cell which
comes close
to the physiological concentration in order to avoid a complex formation
merely due to
high concentration of the expressed protein but not reflecting the natural
occurring
complex.

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In a further preferred embodiment, the composition is obtained by using a
tagged protein which comprises two different tags which allow two different
affinity
purification steps. This measure allows a higher degree of purification of the
composition
in question.
In a further preferred embodiment the tagged protein comprises two tags that
are
separated by a cleavage site for a protease. This allows a step-by-step
purification on
affinity columns.
The present invention is also directed to therapeutic and prophylactic, as
well as diagnostic, prognostic, and screening methods and compositions based
upon the
complex (and the nucleic acids encoding the individual proteins that
participate in the
complex). Therapeutic compounds of the invention include, but are not limited
to, a
complex of the invention, and a complex where one or more members of the
complex is
a derivative or fragment thereof. The present invention is also directed to
complex
specific antibodies to and nucleic acids encoding the foregoing; and antisense
nucleic
acids to the nucleotide sequences encoding the complex components. Diagnostic,
prognostic and screening kits are also provided.
The present invention further relates to a kit comprising a composition as
described above, optionally together with further reagents and working
instructions. The
further reagents may be, for example, buffers, substrates for enzymes but also
carrier
material such as beads, filters, microarrays and other solid carries. The
working
instructions may indicate how to use the ingredients of the kit in order to
perform a
desired assay.
The present invention further relates to a nucleic acid encoding a
component of a composition as defined above. Such a nucleic acid may be used
for
example to express a desired tagged protein in a given cell for the isolation
of a complex
or component according to the invention. Such a nucleic acid may also be used
for the
identification and isolation of genes from other organisms by cross species
hybridization.
The present invention further relates to a construct, preferably a vector
construct, which comprises a nucleic acid as described above. Such constructs
may
comprise expression controlling elements such as promoters, enhancers and
terminators
in order to express the nucleic acids in a given host cell, preferably under
conditions
which resemble the physiological concentrations.
The present invention further relates to a host cell containing a construct
as defined above. Such a host cell can be, e.g., any eukaryotic cell such as
yeast, plant

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or mammalian, whereas human cells are preferred. Such host cells may form the
starting material for isolation of a complex according to the present
invention.
Animal models and methods of screening for modulators (i.e., agonists,
and antagonists) of the amount of, activity of, or protein component
composition of, a
complex of the present invention are also provided.
The present invention further relates to a kit comprising a composition as
described above, optionally together with further reagents and working
instructions. The
further reagents may be, for example, buffers, substrates for enzymes but also
carrier
material such as beads, filters, microarrays and other solid carries. The
working
instructions may indicate how to use the ingredients of the kit in order to
perform a
desired assay.
The following examples further illustrate the invention as it relates to the
polyadenylation
complex.
Construction of a yeast strain expressing TAP-tagged Pta1: see Tab. 6
Purification of proteins associated with Pta1:
The TAP-technology, which is more fully described in WO 00/09716 and in
Rigaut, G. et.
al. (1999), Nature Biotechnology. Vol. 17 (10): 1030-1032 respectively was
used for
protein complex purification. The Pta1 protein was C-terminally tagged with a
TAP-tag
which consists of calmodulin-binding peptide (CBP), a cleavage site for TEV
protease
followed by two IgG-binding units of protein A (Rigaut, G. et. al. (1999),
Nature
Biotechnology. Vol. 17 (10): 1030-1032). Pta1 is an essential protein which
has been
reported to be a component of PFI. Pta1-TAP was used as a bait to identify
associated
partners from cell lysates using the two-step TAP purification procedure.
Proteins were
separated by 1 D gel electrophoresis and visualized by staining with
Coomassie. More
than a total of 20 bands could be detected on the gel (see Fig. 5). The
identity of the
proteins was determined by mass spectrometry. 13 of these are known components
of
the pre-mRNA processing machinery: Cft1, Cft2, Ysh, Pta1, Rna14, Pab1, Pcf11,
Pap1,
CIp1, Pfs2, Fip1, Rna15 and Yth1. The remaining seven proteins (see Fig 5)
have not
previously been found associated with Pta1: Ref2, YK059c, YGR156w, YICL018w,
GIc7,
Ssu72 and YOR179c. Further experiments using the TAP-technology using
different

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baits have identified additional 18 proteins which have now found to be
associated with
the complex, thus increasing the size of the complex to 38 proteins in total
(as described
further above).
Validation of interactions found with Pta1:
A reciprocal experiment to the one described above was performed. For this
purpose a
subset of the interactors found in the above described Pta purification (both
known and
novel interactors) were chosen as a bait for a further round of purification.
In the case of
some proteins the C-terminally tagged versions could not be recovered. The
likely
reason for this is that the addition of the TAP tag at the C-terminus
interferes with the
function of these proteins (a selection of the reciprocal experiments
undertaken is shown
in Fig. 6)
Results for the polyadenylation complex thus show, that, complexes are often
sufficiently
strong to show high composition integrity even when purified using different
entry points.
Moreover, the example shows that the TAP method reveals novel components even
in
well-studied cellular machinery .
Sequence analysis of members of the complex:
The process of mRNA processing is highly conserved in eukaryotes. Accordingly,
for
significant proportion of the yeast proteins, human orthologs could be found.
This
illustrates that many of the functions found in the yeast complex can be
transferred to
humans. Also the enzymatic activity of this complex has long been known, the
enzymatically active member could not yet be unraveled. Using extensive
sequence
similarity searches it could be shown that Ysh1 is homologous to a class of
bacterial
beta-lactamases. The active center of this protein family contains 2 zinc ions
which are
bound by histidines. As these residues are conserved in Ysh1 and it was shown
that
enzymatic activity of the yeast complex is zinc dependent predicted that Ysh1
is
responsible for the catalytic activity of the complex: Two other proteins
found in the
complex, Cft2 and YOR179c, are homologous to the Ysh1 N- and C-terminus,
respectively. Though Cft2 is homologous to the enzymatic region of Ysh1 it
misses the
zinc binding histidines indicating that it lacks enzymatic activity. Thus, Cft
2 and
YOR179c could compete with Ysh1 for the same binding slot of the complex,
suggesting

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a novel type of regulation of polyadenylation. A similar way of regulation
might be used in
the case of Pfs2 and YKL018w, which both consist of multiple WD40 domains.
Prediction of mammalian proteins:
To allow the transfer of function information from yeast to human proteins, we
did not
only use an identity cutoff, but also the 'orthology' concept. Orthology
defines genes
which arose via a speciation event, in contrast to genes which arose via gene
duplication. Orthologs genes are supposed to perform the same function in
different
organisms, therefore more detailed function information can be transferred.
The
algorithm for the detection of orthologous gene pairs from yeast and human
uses the
whole genome of these organisms. First, pairwise best hits were retrieved,
using a full
Smith-Waterman alignment of predicted proteins. To further improve reli-
ability, these
pairs were clustered with pairwise best hits involving Drosophila melanogaster
and
Caenorhabditis elegans proteins. See "Initial sequencing and analysis of the
human
genome", Nature 2001 Feb 15; 409(6822):860-921 for a detailed description of
the
analysis.
Bioinformatic analysis of the Complex:
Functional domains of all members of the complex were analyzed using SMART
(SMART: a web-based tool for the study of genetically mobile domains. Nucleic
Acids
Res 2000 Jan 1; 28(1):231-4) and Pfam (Pfam: protein families database,
Nucleic Acids
Res 2000 Jan 1; 28(1):263-6).
Comparison of the yeast and mammalian polyadenylation complex:
The sequence of many of the polypeptides which have been proposed to be
involved in
3'-end formation so far are conserved form yeast to mammals, although the
sequence
elements on the substrate pre-mRNA differ (see Tab. 7).
Purification of the protein complexes from yeast using Pta1 as a bait:

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Yeast strain Sc0051 expressing TAP-tagged Pta1 was cultured in 4 I of YPD
medium to
an OD600 of 2. After harvesting, the cell pellet was frozen in liquid nitrogen
and stored at
-80°C. All further manipulations were done at 4°C except where
noted. For preparation of
protein lysates the cells were resuspended in lysis buffer (50 mM Tris-HCI pH
7.5, 100
mM NaCI, 0.15 % NP-40, 1.5 mM MgCl2, 0.5 mM DTT, protease inhibitors) and
subjected to mechanical disruption with glass beads. Lysates were clarified by
two
successive centrifugation steps at 20.000 x g for 10 min and 100.000 x g for 1
hour. After
addition of glycerol to 5 % final concentration the lysates were frozen in
liquid nitrogen
and stored at -80°C.
For the first purification step 500 pl of rabbit IgG-Agarose (50:50 slurry,
Sigma A2909)
pre-equilibrated in lysis buffer were added to the lysate and the sample was
rotated for 2
hours. The unbound fraction was discarded and the beads with the bound
material were
transferred to a 0.8 ml column (MoBiTec M1002, 90 Nm filter). The beads were
washed
with 10 ml of lysis buffer followed by 5 ml of TEV cleavage buffer (10 mM Tris-
HCI pH
8.0, 100 mM NaCI, 0.1 % NP-40, 0.5 mM EDTA, 1 mM DTT).
150 pl of TEV cleavage buffer and 4 pl of TEV protease were added to the
column and
the sample was incubated on a shaker at 16 °C for 2 hours. The eluate
was recovered by
pressing with a syringe.
150 NI of Calmodulin dilution buffer (10 mM Tris-HCI pH 8.0, 100 mM NaCI, 0.1
% NP-40,
2 mM MgAc, 2 mM imidazole, 4 mM CaCl2, 1 mM DTT) was added to the previous
eluate and this mixture was transferred to a MoBiTec column containing 300 pl
(bead
volume) of Calmodulin affinity resin (Stratagene #214303) which was prewashed
in
Calmodulin wash buffer (10 mM Tris-HCI pH 8.0, 100 mM NaCI, 0.1 % NP-40, 1 mM
MgAc, 1 mM imidazole, 2 mM CaCl2, 1 mM DTT). The samples were rotated for 1
hour
at 4 °C.
After washing of the beads with 10 ml of Calmodulin wash buffer, protein
complexes
were eluted with 600 NI of elution buffer (10 mM Tris-HCI pH 8.0, 5 mM EDTA).
The
samples were concentrated in siliconised tubes in a speed vac to a final
volume of 10-20
pl. Proteins were detected by polyacrylamide gel electrophoresis followed by
staining
with colloidal Coomassie blue.

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The following preferred embodiments can be obtained and characterized with the
methodology as explained above for the polyadenylation complex as well as the
respective protocols for yeast as described in section °protocols'
(infra) (There, also
protocols for mammalian cells and membrane proteins are given). Basically, the
same
steps are applied to each complex with the exception that different baits are
used for the
isolation of different complexes.
The Ccr4-Not-complex (complex 149)
Gene regulation plays a crucial role in every physiological aspect of all
organisms.
Transcription activation and repression is at the heart of highly regulated
processes like
development, adaptation, differentiation, aging, etc.
The CCR4-NOT complex plays a critical role in the yeast adaptation process to
utilize
different carbon sources. The mechanism by which alters gene expression is not
clear
yet multiple genetic interactions with the basal transcription machinery have
been
described (Collart, M.A., 1996, Mol. Cell. Biol. 16: 6668-6676 and Collart,
M.A. and
Struhl K, 1994, Genes Dev 8: 525-37) . This complex was first identified by
genetic
means (Collart, M.A. and Struhl K, 1994, Genes Dev 8: 525-37) and later on
biochemically as a 1 MDa complex in yeast cell extracts (Liu, H et al, 1998,
EMBO J. 17:
1096-106). The genetic isolation of yNOTs was based on suppression of the
defect of a
mutant GCN4 transcriptional activator and on the yeast HIS3 promoter.
Subsequent
analysis showed that all suppressors were loss-of function alleles leading to
an up-
regulation of the low, constitutive level of HIS3 transcription rather than
enhancing
function of the defective GCN4 allele. Whereas mutations in NOTs de-repress
constitutive HIS3 transcription, mutations in subunits of TFIID have the
opposite effect
(Collart, M.A., 1996, Mol. Cell. Bioo. 16: 6668-6676 and Moqtaderi, Z et al,
1996, Nature
383: 188-191). Biochemical fractionation and characterization of yNOT proteins
(NOT1 to
5) showed that they reside in a multi-subunit complex also harboring yCCR4 and
yCAF1,
which are also global regulators of transcription. Biochemical and genetic
evidences
have proposed a model for the architecture of this complex. CAF1 is presumed
to bind to
residues 667 to 1152 of NOT1, CCR4 binds to CAF1, and NOT2 and NOT5 interact
with
the Gterminal residues 1490 to 2108 of NOT1 in no particular order. NOT4 is
placed on
the periphery of NOT2 and NOTS, and it is presumed that NOT3 makes contacts
with

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NOT2, NOT5 or NNOT4 and the N~terminus of NOT1 (Bai, Y et al, 1999, Mol Cell
Biol
19: 6642-6651). At least two additional subunits have also been proposed to be
part of
the CCR4/NOT complex, Dhh1 p and DBF2, however they seem to be part of a
larger 1.9
MDa complex.
Potential human orthologues for hNOT2, hNOT3, hNOT4 and CALIF (a CAF1-like
protein) have been identified and cloned (Albert, T.K. et al, 2000, Nucl Acid
Res 28: 809-
817). As expected, multiple two-hybrid interactions exists between the human
NOTs and
that hNOT4 and hNOT4 can cross-complement their yeast orthologues yet no data
supporting a higher complex has been described.
In order to better understand the function of the CCR4-NOT multi-protein
complex, we
decided to TAP tag the yeast CCR4 and the human Not2 subunit of this
regulatory
complex of RNA Polymerase II transcription. Caf40, and Caf130, two novel
components
of the yeast CCR4/NOT complex were identified. Interestingly, Rqcd1, a human
homologue of Caf40, was conversely identified as a novel component of the
human
CCR4/NOT complex. Other human orthologues of Not1 (KIAA1007), CCR4 (KIAA1194),
were also identified as components of the human CCR4/Not complex. Here we show
for
the first time that CALIF and CAF1, which represent the counterpart of CAF1 in
yeast,
are also part of this complex together with hNot2 and hNot3.
Despite the large body of information already available from the prior art
concerning the
Ccr4-Not complex up to now not all components of the complex are known not to
speak
of the composition of the complex as a whole.
This invention relates to a component of the Ccr4-Not-complex selected from:
Yeast proteins
YDR214w
functionally active fragements or functionally active derivatives thereof, the
mammalian
homologs thereof, or variants thereof encoded by a nucleic acid that
hybridizes to any of
the above proteins or their complements under low stringency conditions.

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By applying the process according to the invention to the isolation of the
Ccr4/Not
complex from yeast thirteen new proteins could be identified in said yeast
complex.
The proteins are listed below (see also Tab. 2). The Accession-Number is the
GenBank
Accession number for the protein.
Atp11: Is a known and essential protein (GenBank Acc. No.: CAA96245.1)). It
has been
previously linked to roles in protein complex assembly.
Caf130: Is a non-essential protein of unknown function (GenBank Acc. NO.:
CAA97147.1 )
Caf40: Is a non-essential protein of unknown function (GenBank Acc. NO.:
CAA96205.1 )
Cct6: Is an essential protein having ATPase/Chaperonin-function which has been
shown
to be involved in protein folding (GenBank Acc. NO.: CAA86694.1)
Fas2: Is an essential protein with oxidoreductaseltransferase activity which
has been
shown to be involved in lipid-, fatty-acid and sterol metabolism (GenBank Acc.
NO.:
CAA97948.1 )
Gcn1: Is a known and non-essential protein which has been shown to be involved
in
amino-acid metabolism (GenBank Acc. No.: CAA96907.1)
Pdc1: Is a known and non-essential protein which has lyase-activity and has
been shown
to be involved in carbohydrate metabolism (GenBank Acc. No. CAA97573.1)
Rvb2: Is a known and essential protein which has been shown to be involved in
Pol II
transcription and RNA processing/modification. It has Helicase activity
(GenBank Acc.
No.: CAA97952.1)
Sam1: Is a known and non-essential protein (GenBank Acc. No.: AAB67461.1)
which
has transferase activity and has been shown to be involved in amino-acid
metabolism.

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Tfc1: Is a known and essential protein which has been shown to be involved in
RNA pol
III transcription initiation (GenBank Acc. No.: CAA85080.1).
Vma1: Is a known and non-essential protein which has been shown to be involved
in
small molecule transport and has Hydrolase/ATPase activity (GenBank Acc. No.:
CAA98761.1). Catalytic subunit (subunit A) of the vacuolar H(+) ATPase V1
complex.
Ydr214w: Is a non-essential protein of unknown function (GenBank Acc. No.:
CAA92357.1 )
Yra1: Is a known and essential protein with RNA:RNA annealing activity,
involved in
mRNA packaging for export from the nucleus (GenBank Acc. No.: AAC09951.1)
In addition, the invention relates to the human Ccr4-Not-complex
The previously uncharacterised human Ccr4-Not-complex was - by applying the
protocols for protein complex isolation in mammalian cells as described in
section
'Protocols' (infra) and using hNot2 as a bait - found to be composed of the
following
proteins (see Fig. 7 and Tab. 2b):
KIAA1007 (homolog of yNot1): GenBank Acc. No of protein: NP_057368
KIAA1194 (homolog of yCcr4): GenBank Acc. No. of protein: XP_003851
hNot2: GenBank Acc. No. of protein: NP_055330
hCaf1 (homolog of yCaf1): GenBank Acc. No. of protein NP_037486
Calif (homolog of yCaf1): GenBank Acc. No. of protein NP_004770
Rqcd (homolog of Caf40); GenBank Acc. No. of protein NP_005435
AAH02928: GenBank Acc. No. of protein AAH02928
So far, for the mammalian proteins, only two-hybrid interactions between Calif
and hNot2
as well as Calif and KIAA1194 have been described.
Components of the complex are believed to be involved in the 5q-syndrome. The
5q-
syndrome is a myelodysplastic syndrome associated with an interstitial
deletion of the

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5q31-33 region. Fiedler et al (Fiedler et al, 1999, Genomics 56: 134-136)
found that the
human POP2 (CALIF) gene is located within this region. The predicted 292-amino-
acid
human protein shares 75%, 44% and 38% sequence identity with mouse Caf1,
C.elegans Caf1 and yeast POP2, respectively. Northern blot analysis revealed
that
human POP2 was expressed as an approximately 2,5 kb mRNA in all tissues
tested. The
authors concluded that POP2 is a candidate for the tumor suppressor gene
associated
with the development of 5q-syndrome.
Furthermore, the complex is a potential drug target for the treatment of forms
of cancer
such as leukaemia and prostate cancer. The complex is a potential entry point
for agents
affecting the regulation of aging processes.
The present invention further relates to complex 149a
1. A protein complex selected from complex (I) and comprising
(a) at least one first protein selected from the group consisting of:
(i) "CCR4" (SEQ ID No:2587) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CCR4", the
variant
being encoded by a nucleic acid that hybridizes to the "CCR4" nucleic acid
(SEQ ID
No:2588 ) or its complement under low stringency conditions,
(ii) "CDC36" (SEQ ID No:2589) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"CDC36", the
variant being encoded by a nucleic acid that hybridizes to the "CDC36" nucleic
acid
(SEQ ID No:2590 ) or its complement under low stringency conditions,
(iii) "CDC39" (SEQ ID No:1695) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"CDC39", the
variant being encoded by a nucleic acid that hybridizes to the "CDC39" nucleic
acid
(SEQ ID No:1696 ) or its complement under low stringency conditions,
(iv) "COP1" (SEQ ID No:2379) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "COP1", the
variant
being encoded by a nucleic acid that hybridizes to the "COP1" nucleic acid
(SEQ ID
No:2380 ) or its complement under low stringency conditions,
(v) "NOT3" (SEQ ID No:2591) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "NOT3", the
variant being

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encoded by a nucleic acid that hybridizes to the "NOT3" nucleic acid (SEQ ID
No:2592 )
or its complement under low stringency conditions,
(vi) "NOTS" (SEQ ID No:2593) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "NOT5", the
variant being
encoded by a nucleic acid that hybridizes to the "NOTS" nucleic acid (SEQ ID
No:2594 )
or its complement under low stringency conditions,
(vii) "POL1" (SEQ ID No:2595) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "POL1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "POL1" nucleic acid (SEQ ID
No:2596 )
or its complement under low stringency conditions,
(viii) "POL12" (SEQ ID No:2597) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"POL12", the
variant being encoded by a nucleic acid that hybridizes to the "POL12" nucleic
acid (SEQ
ID No:2598 ) or its complement under low stringency conditions,
(ix) "POP2" (SEQ ID No:2599) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "POP2", the
variant being
encoded by a nucleic acid that hybridizes to the "POP2" nucleic acid (SEQ ID
No:2600 )
or its complement under low stringency conditions,
(x) "PR11" (SEQ ID No:2601) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "PR11", the
variant being
encoded by a nucleic acid that hybridizes to the "PRI1" nucleic acid (SEQ ID
No:2602 )
or its complement under low stringency conditions,
(xi) "PRI2" (SEQ ID No:2603) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "PRI2", the
variant being
encoded by a nucleic acid that hybridizes to the "PRI2" nucleic acid (SEQ ID
No:2604
or its complement under low stringency conditions,
(xii) "SEC27" (SEQ ID No:1245) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SEC27", the
variant being encoded by a nucleic acid that hybridizes to the "SEC27" nucleic
acid (SEQ
ID No:1246 ) or its complement under low stringency conditions, and
(xiii) "SIG1" (SEQ ID No:2605) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SIG1", the
variant being encoded by a nucleic acid that hybridizes to the "SIG1" nucleic
acid (SEQ
ID No:2606 ) or its complement under low stringency conditions,

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and
(b) at least one second protein, which second protein is selected from the
group
consisting of:
(i) "ATP11" (SEQ ID No:2607) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "ATP11 ", the
variant
being encoded by a nucleic acid that hybridizes to the "ATP11" nucleic acid
(SEQ ID
No:2608 ) or its complement under low stringency conditions,
(ii) "CAF130" (SEQ ID No:2609) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"CAF130",
the variant being encoded by a nucleic acid that hybridizes to the "CAF130"
nucleic acid
(SEQ ID No:2610 ) or its complement under low stringency conditions,
(iii) "CAF40" (SEQ ID No:2611) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"CAF40", the
variant being encoded by a nucleic acid that hybridizes to the "CAF40" nucleic
acid (SEQ
ID No:2612 ) or its complement under low stringency conditions,
(iv) "CCT6" (SEQ ID No:347) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CCT6", the
variant being
encoded by a nucleic acid that hybridizes to the "CCT6" nucleic acid (SEQ ID
No:348 ) or
its complement under low stringency conditions,
(v) "FAS2" (SEQ ID No:573) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "FAS2", the
variant being
encoded by a nucleic acid that hybridizes to the "FAS2" nucleic acid (SEQ ID
No:574 ) or
its complement under low stringency conditions,
(vi) "GCN1" (SEQ ID No:853) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "GCN1", the
variant
being encoded by a nucleic acid that hybridizes to the "GCN1" nucleic acid
(SEQ ID
No:854 ) or its complement under low stringency conditions,
(vii) "PDC1" (SEQ ID No:359) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "PDC1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "PDC1" nucleic acid (SEQ ID
No:360 )
or its complement under low stringency conditions,
(viii) "RVB2" (SEQ ID No:515) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "RVB2", the
variant being

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encoded by a nucleic acid that hybridizes to the "RVB2" nucleic acid (SEQ ID
No:516 ) or
its complement under low stringency conditions,
(ix) "SAM1" (SEQ ID No:449) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "SAM1", the
variant
being encoded by a nucleic acid that hybridizes to the "SAM1" nucleic acid
(SEQ ID
No:450 ) or its complement under low stringency conditions,
(x) "TFC7" (SEQ ID No:9) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "TFC7", the
variant being
encoded by a nucleic acid that hybridizes to the "TFC7" nucleic acid (SEQ ID
No:10 ) or
its complement under low stringency conditions,
(xi) "VMA1" (SEQ ID No:275) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "VMA1 ", the
variant
being encoded by a nucleic acid that hybridizes to the "VMA1" nucleic acid
(SEQ ID
No:276 ) or its complement under low stringency conditions,
(xii) "YDR214W" (SEQ ID No:337) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YDR214W",
the variant being encoded by a nucleic acid that hybridizes to the "YDR214W"
nucleic
acid (SEQ ID No:338 ) or its complement under low stringency conditions, and
(xiii) "YRA1" (SEQ ID No:1195) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YRA1 ", the
variant being encoded by a nucleic acid that hybridizes to the "YRA1" nucleic
acid (SEQ
ID No:1196 ) or its complement under low stringency conditions,
and a complex (II) comprising at least two of said second proteins, wherein
said low
stringency conditions comprise hybridization in a buffer comprising 35%
formamide, 5X
SSC, 50 mM Tris-HCI (pH 7.5), 5 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.2% BSA,
100
ug/ml denatured salmon sperm DNA, and 10% (wt/vol) dextran sulfate for 18-20
hours at
40° C, washing in a buffer consisting of 2X SSC, 25 mM Tris-HCI (pH
7.4), 5 mM EDTA,
and 0.1 % SDS for 1.5 hours at 55° C, and washing in a buffer
consisting of 2X SSC, 25
mM Tris-HCI (pH 7.4), 5 mM EDTA, and 0.1 % SDS for 1.5 hours at 60° C.
2. The protein complex comprising the following proteins:
(i) "ATP11" (SEQ ID No:2607) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "ATP11 ", the
variant

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being encoded by a nucleic acid that hybridizes to the "ATP11" nucleic acid
(SEQ ID
No:2608 ) or its complement under low stringency conditions,
(ii) "CAF130" (SEQ ID No:2609) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"CAF130",
the variant being encoded by a nucleic acid that hybridizes to the "CAF130"
nucleic acid
(SEQ ID No:2610 ) or its complement under low stringency conditions,
(iii) "CAF40" (SEQ ID No:2611) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"CAF40", the
variant being encoded by a nucleic acid that hybridizes to the "CAF40" nucleic
acid (SEQ
ID No:2612 ) or its complement under low stringency conditions,
(iv) "CCR4" (SEQ ID No:2587) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CCR4", the
variant
being encoded by a nucleic acid that hybridizes to the "CCR4" nucleic acid
(SEQ ID
No:2588 ) or its complement under low stringency conditions,
(v) "CCT6" (SEQ ID No:347) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CCT6", the
variant being
encoded by a nucleic acid that hybridizes to the "CCT6" nucleic acid (SEQ ID
No:348 ) or
its complement under low stringency conditions,
(vi) "CDC36" (SEQ ID No:2589) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"CDC36", the
variant being encoded by a nucleic acid that hybridizes to the "CDC36" nucleic
acid
(SEQ ID No:2590 ) or its complement under low stringency conditions,
(vii) "CDC39" (SEQ ID No:1695) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"CDC39", the
variant being encoded by a nucleic acid that hybridizes to the "CDC39" nucleic
acid
(SEQ ID No:1696 ) or its complement under low stringency conditions,
(viii) "COP1" (SEQ ID No:2379) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"COP1", the
variant being encoded by a nucleic acid that hybridizes to the "COP1" nucleic
acid (SEQ
ID No:2380 ) or its complement under low stringency conditions,
(ix) "FAS2" (SEQ ID No:573) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "FAS2", the
variant being
encoded by a nucleic acid that hybridizes to the "FAS2" nucleic acid (SEQ ID
No:574 ) or
its complement under low stringency conditions,

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(x) "GCN1" (SEQ ID No:853) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "GCN1", the
variant
being encoded by a nucleic acid that hybridizes to the "GCN1" nucleic acid
(SEQ ID
No:854 ) or its complement under low stringency conditions,
(xi) "NOT3" (SEQ ID No:2591) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "NOT3", the
variant being
encoded by a nucleic acid that hybridizes to the "NOT3" nucleic acid (SEQ ID
No:2592 )
or its complement under low stringency conditions,
(xii) "NOT5" (SEQ ID No:2593) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "NOT5", the
variant being
encoded by a nucleic acid that hybridizes to the "NOTS" nucleic acid (SEQ ID
No:2594 )
or its complement under low stringency conditions,
(xiii) "PDC1" (SEQ ID No:359) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "PDC1", the
variant being
encoded by a nucleic acid that hybridizes to the "PDC1" nucleic acid (SEQ ID
No:360 )
or its complement under low stringency conditions,
(xiv) "POL1" (SEQ ID No:2595) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"POL1", the
variant being encoded by a nucleic acid that hybridizes to the "POL1" nucleic
acid (SEQ
ID No:2596 ) or its complement under low stringency conditions,
(xv) "POL12" (SEQ ID No:2597) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"POL12", the
variant being encoded by a nucleic acid that hybridizes to the "POL12" nucleic
acid (SEQ
ID No:2598 ) or its complement under low stringency conditions,
(xvi) "POP2" (SEQ ID No:2599) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"POP2", the
variant being encoded by a nucleic acid that hybridizes to the "POP2" nucleic
acid (SEQ
ID No:2600 ) or its complement under low stringency conditions,
(xvii) "PRI1" (SEQ ID No:2601) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof; or a variant of "PRI1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "PR11" nucleic acid (SEQ ID
No:2602 )
or its complement under low stringency conditions,
(xviii) "PRI2" (SEQ ID No:2603) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PRI2", the

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variant being encoded by a nucleic acid that hybridizes to the "PR12" nucleic
acid (SEQ
ID No:2604 ) or its complement under low stringency conditions,
(xix) "RVB2" (SEQ ID No:515) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "RVB2", the
variant being
encoded by a nucleic acid that hybridizes to the "RVB2" nucleic acid (SEQ ID
No:516 ) or
its complement under low stringency conditions,
(xx) "SAM1" (SEQ ID No:449) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "SAM1", the
variant
being encoded by a nucleic acid that hybridizes to the "SAM1" nucleic acid
(SEQ ID
No:450 ) or its complement under low stringency conditions,
(xxi) "SEC27" (SEQ ID No:1245) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SEC27", the
variant being encoded by a nucleic acid that hybridizes to the "SEC27" nucleic
acid (SEQ
ID No:1246 ) or its complement under low stringency conditions,
(xxii) "SIG1" (SEQ ID No:2605) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SIG1", the
variant being encoded by a nucleic acid that hybridizes to the "SIG1" nucleic
acid (SEQ
ID No:2606 ) or its complement under low stringency conditions,
(xxiii) "TFC7" (SEQ ID No:9) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "TFC7", the
variant being
encoded by a nucleic acid that hybridizes to the "TFC7" nucleic acid (SEQ ID
No:10 ) or
its complement under low stringency conditions,
(xxiv) "VMA1" (SEQ ID No:275) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"VMA1", the
variant being encoded by a nucleic acid that hybridizes to the "VMA1" nucleic
acid (SEQ
ID No:276 ) or its complement under low stringency conditions,
(xxv) "YDR214W" (SEQ ID No:337) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YDR214W",
the variant being encoded by a nucleic acid that hybridizes to the "YDR214W"
nucleic
acid (SEQ ID No:338 ) or its complement under low stringency conditions, and
(xxvi) "YRA1" (SEQ ID No:1195) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YRA1", the
variant being encoded by a nucleic acid that hybridizes to the "YRA1" nucleic
acid (SEQ
ID No:1196 ) or its complement under low stringency conditions,.

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3. The protein complex according to No. 1 comprising all but 1 - 12 of the
following
proteins:
(i) "ATP11" (SEQ ID No:2607) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "ATP11 ", the
variant
being encoded by a nucleic acid that hybridizes to the "ATP11" nucleic acid
(SEQ ID
No:2608 ) or its complement under low stringency conditions,
(ii) "CAF130" (SEQ ID No:2609) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"CAF130",
the variant being encoded by a nucleic acid that hybridizes to the "CAF130"
nucleic acid
(SEQ ID No:2610 ) or its complement under low stringency conditions,
(iii) "CAF40" (SEQ ID No:2611) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"CAF40", the
variant being encoded by a nucleic acid that hybridizes to the "CAF40" nucleic
acid (SEQ
ID No:2612 ) or its complement under low stringency conditions,
(iv) "CCR4" (SEQ ID No:2587) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CCR4", the
variant
being encoded by a nucleic acid that hybridizes to the "CCR4" nucleic acid
(SEQ ID
No:2588 ) or its complement under low stringency conditions,
(v) "CCT6" (SEQ ID No:347) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "CCT6", the
variant being
encoded by a nucleic acid that hybridizes to the "CCT6" nucleic acid (SEQ ID
No:348 ) or
its complement under low stringency conditions,
(vi) "CDC36" (SEQ ID No:2589) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"CDC36", the
variant being encoded by a nucleic acid that hybridizes to the "CDC36" nucleic
acid
(SEQ ID No:2590 ) or its complement under low stringency conditions,
(vii) "CDC39" (SEQ ID No:1695) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"CDC39", the
variant being encoded by a nucleic acid that hybridizes to the "CDC39" nucleic
acid
(SEQ ID No:1696 ) or its complement under low stringency conditions,
(viii) "COP1" (SEQ ID No:2379) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"COP1", the

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variant being encoded by a nucleic acid that hybridizes to the "COP1" nucleic
acid (SEQ
ID No:2380 ) or its complement under low stringency conditions,
(ix) "FAS2" (SEQ ID No:573) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "FAS2", the
variant being
encoded by a nucleic acid that hybridizes to the "FAS2" nucleic acid (SEQ ID
No:574 ) or
its complement under low stringency conditions,
(x) "GCN1" (SEQ ID No:853) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "GCN1", the
variant
being encoded by a nucleic acid that hybridizes to the "GCN1" nucleic acid
(SEQ ID
No:854 ) or its complement under low stringency conditions,
(xi) "NOT3" (SEQ ID No:2591) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "NOT3", the
variant being
encoded by a nucleic acid that hybridizes to the "NOT3" nucleic acid (SEQ ID
No:2592 )
or its complement under low stringency conditions,
(xii) "NOTS" (SEQ ID No:2593) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "NOT5", the
variant being
encoded by a nucleic acid that hybridizes to the "NOTS" nucleic acid (SEQ ID
No:2594 )
or its complement under low stringency conditions,
(xiii) "PDC1" (SEQ ID No:359) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "PDC1", the
variant being
encoded by a nucleic acid that hybridizes to the "PDC1" nucleic acid (SEQ ID
No:360 )
or its complement under low stringency conditions,
(xiv) "POL1" (SEQ ID No:2595) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"POL1", the
variant being encoded by a nucleic acid that hybridizes to the "POL1" nucleic
acid (SEQ
ID No:2596 ) or its complement under low stringency conditions,
(xv) "POL12" (SEQ ID No:2597) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"POL12", the
variant being encoded by a nucleic acid that hybridizes to the "POL12" nucleic
acid (SEQ
ID No:2598 ) or its complement under low stringency conditions,
(xvi) "POP2" (SEQ ID No:2599) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"POP2", the
variant being encoded by a nucleic acid that hybridizes to the "POP2" nucleic
acid (SEQ
ID No:2600 ) or its complement under low stringency conditions,

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(xvii) "PR11" (SEQ ID No:2601) or a functionally active derivative thereof, or
a functionally
active fragment thereof, or a homologue thereof, or a variant of "PRI1 ", the
variant being
encoded by a nucleic acid that hybridizes to the "PR11" nucleic acid (SEQ ID
No:2602 )
or its complement under low stringency conditions,
(xviii) "PRI2" (SEQ ID No:2603) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"PRI2", the
variant being encoded by a nucleic acid that hybridizes to the "PRI2" nucleic
acid (SEQ
ID No:2604 ) or its complement under low stringency conditions,
(xix) "RVB2" (SEQ ID No:515) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "RVB2", the
variant being
encoded by a nucleic acid that hybridizes to the "RVB2" nucleic acid (SEQ ID
No:516 ) or
its complement under low stringency conditions,
(xx) "SAM1" (SEQ ID No:449) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "SAM1", the
variant
being encoded by a nucleic acid that hybridizes to the "SAM1" nucleic acid
(SEQ ID
No:450 ) or its complement under low stringency conditions,
(xxi) "SEC27" (SEQ ID No:1245) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SEC27", the
variant being encoded by a nucleic acid that hybridizes to the "SEC27" nucleic
acid (SEQ
ID No:1246 ) or its complement under low stringency conditions,
(xxii) "SIG1" (SEQ ID No:2605) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"SIG1", the
variant being encoded by a nucleic acid that hybridizes to the "SIG1" nucleic
acid (SEQ
ID No:2606 ) or its complement under low stringency conditions,
(xxiii) "TFC7" (SEQ ID No:9) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "TFC7", the
variant being
encoded by a nucleic acid that hybridizes to the "TFC7" nucleic acid (SEQ ID
No:10 ) or
its complement under low stringency conditions,
(xxiv) "VMA1" (SEQ ID No:275) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"VMA1 ", the
variant being encoded by a nucleic acid that hybridizes to the "VMA1" nucleic
acid (SEQ
ID No:276 ) or its complement under low stringency conditions,
(xxv) "YDR214W" (SEQ ID No:337) or a functionally active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YDR214W",

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the variant being encoded by a nucleic acid that hybridizes to the "YDR214W"
nucleic
acid (SEQ ID No:338 ) or its complement under low stringency conditions, and
(xxvi) "YRA1" (SEQ ID No:1195) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YRA1 ", the
variant being encoded by a nucleic acid that hybridizes to the "YRA1" nucleic
acid (SEQ
ID No:1196 ) or its complement under low stringency conditions.
4. The complex of any of No. 1 - 3 comprising a functionally active derivative
of said first
protein and/or a functionally active derivative of said second protein,
wherein the
functionally active derivative is a fusion protein comprising said first
protein or said
second protein fused to an amino acid sequence different from the first
protein or second
protein, respectively.
5. The complex of No. 4 wherein the functionally active derivative is a fusion
protein
comprising said first protein or said second protein fused to an affinity tag
or label.
6. The complex of any of No. 1 - 3 comprising a fragment of said first protein
and/or a
fragment of said second protein, which fragment binds to another protein
component of
said complex.
7. The complex of any of No. 1 -6 that is involved in the DNA endonuclease
activity
and/or DNA helicase activity and/or RNAs a activity.
8. A process for preparing complex of any of No. 1 - 7 and optionally the
components
thereof comprising the following steps:
Expressing a protein (bait) of the complex, preferably the tagged protein, in
a target cell,
or a tissue or an organ, isolating the protein complex which is attached to
the bait
protein, and optionally disassociating the protein complex and isolating the
individual
complex members.
9. The process according to No. 8 wherein the tagged protein comprises two
different
tags which allow two separate affinity purification steps.

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10. The process according to any of No. 8 - 9 wherein the two tags are
separated by a
cleavage site for a protease.
11. Component of the CCR4-NOT-subcomplex obtainable by a process according to
any
of No. 8 - 10.
12. Protein of the CCR4-NOT-subcomplex selected from
(i) "YDR214W" (SEQ ID No:337) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YDR214W",
the variant being encoded by a nucleic acid that hybridizes to the "YDR214W"
nucleic
acid (SEQ ID No:338 ) or its complement under low stringency conditions,
wherein said
low stringency conditions comprise hybridization in a buffer comprising 35%
formamide,
5X SSC, 50 mM Tris-HCI (pH 7.5), 5 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.2% BSA,
100 ug/ml denatured salmon sperm DNA, and 10% (wt/vol) dextran sulfate for 18-
20
hours at 40° C, washing in a buffer consisting of 2X SSC, 25 mM Tris-
HCI (pH 7.4), 5
mM EDTA, and 0.1 % SDS for 1.5 hours at 55° C, and washing in a buffer
consisting of
2X SSC, 25 mM Tris-HCI (pH 7.4), 5 mM EDTA, and 0.1 % SDS for 1.5 hours at
60° C.
13. Nucleic acid encoding a protein according to No. 12.
14. Construct, preferably a vector construct, comprising
(a) a nucleic acid according to No. 13 and at least one further nucleic acid
which is
normally not associated with said nucleic acid, or
(b) at least two separate nucleic acid sequences each encoding a different
protein, or a
functionally active fragment or a functionally active derivative thereof at
least one of said
proteins, or functionally active fragments or functionally active derivative
thereof being
selected from the first group of proteins according to No. 1 (a) and at least
one of said
proteins, or functionally active fragments or functionally active derivative
thereof being
selected from the second group of proteins according to No. 1 (b) or
(c)at least two separate nucleic acid sequences each encoding a different
protein, or a
functionally active fragment or a functionally active derivative thereof, or a
homologue or
a variant thereof, said proteins being selected from the proteins of complex
(II) according
to No. 1.

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15. Host cell containing a vector comprising at least the nucleic acid of No.
13 and/or a
construct of No. 14 or containing several vectors each comprising at least one
nucleic
acid sequence encoding at least one of the proteins, or functionally active
fragments or
functionally active derivatives thereof selected from the first group of
proteins according
to No. 1 (a) and the proteins, or functionally active fragments or
functionally active
derivatives thereof selected from the second group of proteins according to
No. 1 (b).
16. An antibody or a fragment of said antibody containing the binding domain
thereof,
selected from an antibody or fragment thereof, which binds the complex of any
of No. 1 -
7 and which does not bind any of the proteins of said complex when uncomplexed
and
an antibody or a fragment of said antibody which binds to any of the proteins
according
to No. 12.
17. A kit comprising in one or more container:
(a) the complex of any of No. 1 - 7 and/or the proteins of No. 12 and/or
(b) an antibody according to No. 16 and/or
(c) a nucleic acid encoding a protein of the complex of any of No. 1 - 7
and/or a protein of
No. 12 and/or
(d) cells expressing the complex of any of No. 1 - 7 and/or the proteins of
No. 12 and
optionally
(e) further components such as reagents and working instructions.
1~. A kit according to No. 17 for processing a substrate of said complex.
19. A kit according to No. 17 for the diagnosis or prognosis of a disease or a
disease
risk, preferentially for a disease or disorder such as cancer such as
leukemia, prostate
cancer; target for affecting the regulation of aging processes.
20. Array, preferably a microarray, in which at least a complex according to
any of No. 1 -
7 and/or at least one antibody according to No. 16 is attached to a solid
carrier.
21. A process for modifying a physiological substrate of the complex
comprising the step
of bringing into contact a complex of any of No. 1 - 7 with said substrate,
such that said
substrate is modified.

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22. A pharmaceutical composition comprising the protein complex of any of No.
1 - 7
and/or any of the following the proteins:
(i) "YDR214W" (SEQ ID No:337) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YDR214W",
the variant being encoded by a nucleic acid that hybridizes to the "YDR214W"
nucleic
acid (SEQ ID No:338 ) or its complement under low stringency conditions,
and a pharmaceutical acceptable carrier.
23. A pharmaceutical composition according to No. 22 for the treatment of
diseases and
disorders such as cancer such as leukemia, prostate cancer; target for
affecting the
regulation of aging processes.
24. A method for screening for a molecule that binds to a complex of anyone of
No. 1 - 7
and/or any of the following proteins:
(i) "YDR214W" (SEQ ID No:337) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"YDR214W",
the variant being encoded by a nucleic acid that hybridizes to the "YDR214W"
nucleic
acid (SEQ ID No:338 ) or its complement under low stringency conditions,
comprising the steps of
(a) exposing said complex, or a cell or organism containing same to one or
more
candidate molecules; and
(b) determining whether said candidate molecule is bound to the complex or
protein.
25. A method for screening for a molecule that modulates directly or
indirectly the
function, activity, composition or formation of the complex of any one of No.
1 - 7
comprising the steps of
(a) exposing said complex, or a cell or organism containing CCR4-NOT-
subcomplex to
one or more candidate molecules; and
(b) determining the amount of activity of protein components of, andlor
intracellular
localization of, said complex and/or the transcription level of a gene
regulated by the
complex and/or the abundance and/or activity of a protein or protein complex
dependend
on the function of the complex andlor product of a gene dependent on the
complex in the
presence of the one or more candidate molecules, wherein a change in said
amount,

CA 02471307 2004-06-18
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277
activity, protein components or intracellular localization relative to said
amount, activity,
protein components and/or intracellular localization and/or a change in the
transcription
level of a gene dependend on the complex and/or the abundance and/or activity
of a
protein or protein complex dependent on the function of the complex andlor
product of a
gene dependent on the complex in the absence of said candidate molecules
indicates
that the molecule modulates function, activity or composition of said complex.
26. The method of No. 25, wherein the amount of said complex is determined.
27. The method of No. 25, wherein the activity of said complex is determined.
28. The method of No. 27, wherein said determining step comprises isolating
from the
cell or organism said complex to produce said isolated complex and contacting
said
isolated complex in the presence or absence of a candidate molecule with a
substrate of
said complex and determining the processing of said substrate is modified in
the
presence of said candidate molecule.
29. The method of No. 25, wherein the amount of the individual protein
components of
said complex are determined.
30. The method of No. 29, wherein said determining step comprises determining
whether
(i) "ATP11" (SEQ ID No:2607) or a functionally active derivative thereof, or a
functionally
active fragment thereof, or a homologue thereof, or a variant of "ATP11", the
variant
being encoded by a nucleic acid that hybridizes to the "ATP11" nucleic acid
(SEQ ID
No:2608 ) or its complement under low stringency conditions,and/or
(ii) "CAF130" (SEQ ID No:2609) or a functionally active derivative thereof, or
a
functionally active fragment thereof, or a homologue thereof, or a variant of
"CAF130",
the variant being encoded by a nucleic acid that hybridizes to the "CAF130"
nucleic acid
(SEQ ID No:2610 ) or its complement under low stringency conditions,and/or
(iii) "CAF40" (SEQ ID No:2611) or a functionally 'active derivative thereof,
or a
functionally active fragment thereof, or a homologue thereof, or a variant of
"CAF40", the
variant being encoded by a nucleic acid that hybridizes to the "CAF40" nucleic
acid (SEQ
ID No:2612 ) or its complement under low stringency conditions,and/or

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