Note: Descriptions are shown in the official language in which they were submitted.
~
CA 02584021 2007-04-18
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CORYNEBACTERIUM GLUTAMICUM GENES ENCODING PROTEINS
INVOLVED IN CARBON METABOLISM AND ENERGY PRODUCTION
This application is a divisional application of Canadian Application Serial
No. 2,383,875 filed June 23, 2000.
1 i. IYIN
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Background of the Invention
Certain products and by-products of naturally-occurring metabolic processes in
cells have utility in a wide array of industries, including the food, feed,
cosmetics, and
pharmaceutical industries. These molecules, collectively tetxned 'fine
chemicals',
include organic acids, both proteinogenic and non-proteinogenic amino acids,
nucleotides and nucleosides, lipids and fatty acids, diols, carbohydrates,
aromatic
compounds, vitamins and cofactors, and enzymes. Their production is most
conveniently performed through the large-scale culture of bacteria developed
to produce
and secrete large quantities of one or more desired molecules. One
particularly useful
organism for this purpose is Corynebacterium glutamicum, a gram positive,
nonpathogenic bacterium. Through strain selection, a number of mutant strains
have
been developed which produce an array of desirable compounds. However,
selection of
strains improved for the production of a particular molecule is a time-
consuming and
difficult process.
Summary of the Invention
The invention provides novel bacterial nucleic acid molecules which have a
variety of uses. These uses include the identification of microorganisms which
can be
used to produce fine chemicals, the modulation of fine chemical production in
C.
glutamicum or related bacteria, the typing or identification of C. glutamicum
or related
bacteria, as reference points for mapping the C. glutamicum genome, and as
markers for
transformation. These novel nucleic acid molecules encode proteins, referred
to herein
as sugar metabolism and oxidative phosphoryl,ation (SMP) proteins.
C. glutamicum is a gram positive, aerobic bacterium which is commonly used in
industry for the large-scale production of a variety of fine chemicals, and
also for the
degradation of hydrocarbons (such as in petroleum spills) and for the
oxidation of
terpenoids. The SMP nucleic acid molecules of the invention, therefore, can be
used to
identify microorganisms which can be used to produce fine chemicals, e.g., by
fermentation processes. Modulation of the expression of the SMP nucleic acids
of the
invention, or modification of the sequence of the SMP nucleic acid molecules
of the
invention, can be used to modulate the production of one or more fine
chemicals from a
i iI14.
CA 02584021 2007-04-18
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microorganism (e.g., to improve the yield or production of one or more fine
chemicals
from a Corynebacterium or Brevibacterium species).
The SMP nucleic acids of the invention may also be used to identify an
organism
as being Corynebacteriurn glutamicum or a close relative thereof, or to
identify the
presence of C. glutamicum or a relative thereof in a mixed population of
microorganisms. The invention provides the nucleic acid sequences of a number
of C.
glutamicum genes; by probing the extracted genomic DNA of a culture of a
unique or
mixed population of microorganisms under stringent conditions with a probe
spanning a
region of a C. glutamicum gene which is unique to this organism, one can
ascertain
whether this organism is present. Although Corynebacterium glutamicum itself
is
nonpathogenic, it is related to species pathogenic in humans, such as
Corynebacterium
diphtheriae (the causative agent of diphtheria); the detectiori of such
organisms is of
significant clinical relevance.
The SMP nucleic acid molecules of the invention may also serve as reference
points for mapping of the C. glutamicum genome, or of genomes of related
organisms.
Similarly, these molecules, or variants or portions thereof, may serve as
markers for
genetically engineered Corynebacterium or Brevibacterium species.
The SMP ptoteins encoded by the novel nucleic acid molecules of the invention
are capable of, for example, performing a function involved in the metabolism
of carbon
compounds such as sugars or in the generation of energy molecules by processes
such as
oxidative phosphorylation in Corynebacterium glutamicum. Given the
availability of
cloning vectors for use in Corynebacterium glutamicum, such as those disclosed
in
Sinskey et al., U.S. Patent No. 4,649,119, and techniques for genetic
manipulation of C.
glutamicum and the related Brevibacterium species (e.g., lactofermentum)
(Yoshihama
et al, J. Bacteriol. 162: 591-597 (1985); Katsumata et al., J. Bacteriol. 159:
306-311
(1984); and Santamaria et al., J. Gen. Microbiol. 130: 2237-2246 (1984)), the
nucleic
acid molecules of the invention may be utilized in the genetic engineering of
this
organism to make it a better or more efficient producer of one or more fine
chemicals.
This improved production or efficiency of production of a fine chemical may be
due to a
direct effect of manipulation of a gene of the invention, or it may be due to
an indirect
effect of such manipulation.
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There are a number of mechanisms by which the alteration of an SMP protein of
the invention may directly affect the yield, production, andlor efficiency of
production
of a fine chemical from a C. glutamicum strain incorporating such an altered
protein.
The degradation of high-energy carbon molecules such as sugars, and the
conversion of
compounds such as NADH and FADH2 to compounds containing high energy phosphate
bonds via oxidative phosphorylation results in a number of compounds which
themselves may be desirable fine chemicals, such as pyruvate, ATP, NADH, and a
number of intermediate sugar compounds. Further, the energy molecules (such as
ATP)
and the reducing equivalents (such as NADH or NADPH) produced by these
metabolic
pathways are utilized in the cell to drive reactions which would otherwise be
energetically unfavorable. Such unfavorable reactions include many
biosynthetic
pathways for fine chemicals. By improving the ability of the cell to utilize a
particular
sugar (e.g., by manipulating the genes encoding enzymes involved in the
degradation
and conversion of that sugar into energy for the cell), one may increase the
amount of
energy available to permit unfavorable, yet desired metabolic reactions (e.g.,
the
biosynthesis of a desired fine chemical) to occur.
The mutagenesis of one or more SMP genes of the invention may also result in
SMP proteins having altered activities which indirectly impact the production
of one or
more desired fine chemicals from C. glutamicum. For example, by increasing the
efficiency of utilization of one or more sugars (such that the conversion of
the sugar to
useful energy molecules is improved), or by increasing the efficiency of
conversion of
reducing equivalents to useful energy molecules (e.g., by improving the
efficiency of
oxidative phosphorylation, or the activity of the ATP synthase), one can
increase the
amount of these high-energy compounds available to the cell to drive nornaally
unfavorable metabolic processes. These processes include the construction of
cell walls,
transcription, translation, and the biosynthesis of compounds necessary for
growth and
division of the cells (e.g., nucleotides, amino acids, vitamins, lipids, etc.)
(Lengeler et al.
(1999) Biology of Prokaryotes, Thieme Verlag: Stuttgart, p. 88-109; 913-918;
875-899).
By improving the growth and multiplication of these engineered cells, it is
possible to
increase both the viability of the cells in large-scale culture, and also to
improve their
rate of division, such that a relatively larger number of cells can survive in
fermentor
culture. The yield, production, or efficiency of production may be increased,
at least
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due to the presence of a greater number of viable cells, each producing the
desired fine
chemical. Also, many of the degradation products produced during sugar
metabolism
are utilized by the cell as precursors or intermediates in the production of
other desirable
products, such as fine chemicals. So, by increasing the ability of the cell to
metabolize
sugars, the number of these degradation products available to the cell for
other processes
should also be increased.
The invention provides novel nucleic acid molecules which encode proteins,
refen;ed to herein as SMP proteins, which are capable of, for example,
performing a
function involved in the metabolism of carbon compounds such as sugars and the
generation of energy molecules by processes such as oxidative phosphorylation
in
Corynebacterium glutamicum. Nucleic acid molecules encoding an SMP protein are
referred to herein as SMP nucleic acid molecules. In a preferred embodiment,
the SMP
protein participates in the conversion of carbon molecules and degradation
products
thereof to energy which is utilized by the cell for metabolic processes.
Examples of
such proteins include those encoded by the genes set forth in Table 1.
Accordingly, one aspect of the invention pertains to isolated nucleic acid
molecules (e.g., cDNAs, DNAs, or RNAs) comprising a nucleotide sequence
encoding
an SMP protein or biologically active portions thereof, as well as nucleic
acid fragments
suitable as primers or hybridization probes for the detection or amplification
of SMP-
encoding nucleic acid (e.g., DNA or mRNA). In particularly preferred
embodiments,
the isolated nucleic acid molecule comprises one of the nucleotide sequences
set forth as
the odd-numbered SEQ ID NOs in the Sequence Listing (e.g., SEQ ID NO:1, SEQ ID
NO:3, SEQ ID NO:5, SEQ ID NO:7....), or the coding region or a complement
thereof
of one of these nucleotide sequences. In other particularly preferred
embodiments, the
isolated nucleic acid molecule of the invention comprises a nucleotide
sequence which
hybridizes to or is at least about 50%, preferably at least about 60 /a, more
preferably at
least about 70%, 80% or 90%, and even more preferably at least about 95%, 96%,
97%,
98%, 99% or more homologous to a nucleotide sequence set forth as an odd-
numbered
SEQ ID NO in the Sequence Listing (e.g., SEQ ID NO:1, SEQ ID NO:3, SEQ ID
NO:5,
SEQ ID NO:7....), or a portion thereof. In other preferred embodiments, the
isolated
nucleic acid molecule encodes one of the amino acid sequences set forth as an
even-
numbered SEQ ID NO in the Sequence Listing (e.g., SEQ ID NO:2, SEQ ID NO:4,
SEQ
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ID NO:6, SEQ ID NO:8....).. The preferred SMP proteins of the present
invention also
preferably possess at least one of the SMP activities described herein.
In another embodiment, the isolated nucleic acid molecule encodes a protein or
portion thereof wherein the protein or portion thereof includes an amino acid
sequence
which is sufficiently homologous to an amino acid sequence of the invention
(e.g., a
sequence having an even-numbered SEQ ID NO: in the Sequence Listing), e.g.,
suf~iciently homologous to an amino acid sequence of the invention such that
the protein
or portion thereof maintains an SMP activity. Preferably, the protein or
portion thereof
encoded by the nucleic acid molecule maintains the ability to perform a
function
involved in the metabolism of carbon compounds such as sugars or the
generation of
energy molecules (e.g., ATP) by processes such as oxidative phosphorylation in
Corynebacterium glutamicum. In one embodiment, the protein encoded by the
nucleic
acid molecule is at least about 50%, preferably at least about 60%, and more
preferably
at least about 70%, 80%, or 90% and most preferably at least about 95%, 96%,
97%,
98%, or 99% or more homologous to an amino acid sequence of the invention
(e.g_, an
entire amino acid sequence selected those having an even-numbered SEQ ID NO in
the
Sequence Listing). In another preferred embodiment, the protein is a full
length C.
glutamicum protein which is substantially homologous to an entire amino acid
sequence
of the invention (encoded by an open reading frame shown in the corresponding
odd-
numbered SEQ ID NOs in the Sequence Listing (e.g., SEQ ID NO:1, SEQ ID NO:3,
SEQ ID NO:5, SEQ ID NO:7....).
In another preferred embodiment, the isolated nucleic acid molecule is derived
from C. glutamicum and encodes a protein (e.g., an SMP fusion protein) which
includes
a biologically active domain which is at least about 50% or more homologous to
one of
the amino acid sequences of the invention (e.g., a sequence of one of the even-
numbered
SEQ ID NOs in the Sequence Listing) and is able to perform a function involved
in the
metabolism of carbon compounds such as sugars or the generation of energy
molecules
(e.g., ATP) by processes such as oxidative phosphorylation in Corynebacterium
glutamicum, or has one or more of the activities set forth in Table 1, and
which also
includes heterologous nucleic acid sequences encoding a heterologous
polypeptide or
regulatory regions.
. li II I xf
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In another embodiment, the isolated nucleic acid molecule is at least 15
nucleotides in length and hybridizes under stringent conditions to a nucleic
acid
molecule comprising a nucleotide sequence of the invention (e.g., a sequence
of an odd-
numbered SEQ ID NO in the Sequence Listing) A. Preferably, the isolated
nucleic acid
molecule corresponds to a naturally-occurring nucleic acid molecule. More
preferably,
the isolated nucleic acid encodes a naturally-occurring C. glutamicum SMP
protein, or a
biologically active portion thereof.
Another aspect of the invention pertains to vectors, e.g., recombinant
expression
vectors, containing the nucleic acid molecules of the invention, and host
cells into which
such vectors have been introduced. In one embodiment, such a host cell is used
to
produce an SMP protein by culturing the host cell in a suitable medium. The
SMP
protein can be then isolated from the medium or the host cell.
Yet another aspect of the invention pertains to a genetically altered
microorganism in which an SMP gene has been introduced or altered. In one
embodiment, the genome of the microorganism has been altered by introduction
of a
nucleic acid molecule of the invention encoding wild-type or mutated SMP
sequence as
a transgene. In another embodiment, an endogenous SMP gene within the genome
of
the microorganism has been altered, e.g., functionally disrupted, by
homologous
recombination with an altered SMP gene. In another embodiment, an endogenous
or
20; introduced SMP gene in a microorganism has been altered by one or more
point
mutations, deletions, or inversions, but still encodes a functional SMP
protein. In still
another embodiment, one or more of the regulatory regions (e.g., a promoter,
repressor,
or inducer) of an SMP gene in a microorganism has been altered (e.g., by
deletion,
truncation, inversion, or point mutation) such that the expression of the SMP
gene is
modulated. In a preferred embodiment, the microorganism belongs to the genus
Corynebacterium or Brevibacterium, with Corynebacterium glutamicum being
particularly preferred. In a preferred embodiment, the microorganism is also
utilized for
the production of a desired compound, such as an amino acid, with lysine being
particularly preferred.
In another aspect, the invention provides a method of identifying the presence
or
activity of Cornyebacterium diphtheriae in a subject. This method includes
detection of
one or more of the nucleic acid or amino acid sequences of the invention
(e.g., the
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CA 02584021 2007-04-18
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sequences set forth in the Sequence Listing as SEQ ID NOs 1 through 782) in a
subject,
thereby detecting the presence or activity of Corynebacterium diphtheriae in
the subject.
Still another aspect of the invention pertains to an isolated SMP protein or a
portion, e.g., a biologically active portion, thereof. In a preferred
embodiment, the
isolated SMP protein or portion thereof is capable of performing a function
involved in
the metabolism of carbon compounds such as sugars or in the generation of
energy
molecules (e.g., ATP) by processes such as oxidative phosphorylation in
Corynebacterium glutamicum. In another preferred embodiment, the isolated SMP
protein or portion thereof is sufficiently homologous to an amino acid
sequence of the
invention (e.g., a sequence of an even-numbered SEQ ID NO: in the Sequence
Listing)
such that the protein or portion thereof maintains the ability to perform a
function
involved in the metabolism of.carbon compounds such as sugars or in the
generation of
energy molecules (e.g., ATP) by processes such as oxidative phosphorylation in
Corynebacterium glutamicum.
The invention also provides an isolated preparation of an SMP protein. In
preferred embodiments, the SMP protein comprises an amino acid sequence of the
invention (e.g., a sequence of an even-numbered SEQ ID NO: of the Sequence
Listing).
In another preferred embodiment, the invention pertains to an isolated full
length protein
which is substantially homologous to an entire amino acid sequence of the
invention
(e.g., a sequence of an even-numbered SEQ ID NO: of the Sequence Listing)
(encoded
by an open reading frame set forth in a corresponding odd-numbered SEQ ID NO:
of the
Sequence Listing). In yet another embodiment, the protein is at least about
50%,
preferably at least about 60%, and more preferably at least about 70%, 80%, or
90%,
and most preferably at least about 95%, 96%, 97%, 98%, or 99% or more
homologous
to an entire amino acid sequence of the invention (e.g., a sequence of an even-
numbered
SEQ ID NO: of the Sequence Listing). In other embodiments, the isolated SMP
protein
comprises an amino acid sequence which is at least about 50% or more
homologous to
one of the amino acid sequences of the invention (e.g., a sequence of an even-
numbered
SEQ ID NO: of the Sequence Listing) and is able to perform a function involved
in the
metabolism of carbon compounds such as sugars or in the generation of energy
molecules (e.g., ATP) by processes such as oxidative phosphorylation in
Corynebacterium glutamicum, or has one or more of the activities set forth in
Table 1.
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Alternatively, the isolated SMP protein can comprise an amino acid sequence
which is encoded by a nucleotide sequence which hybridizes, e.g., hybridizes
under
stringent conditions, or is at least about 50%, preferably at least about 60%,
more
preferably at least about 70%, 80%, or 90%, and even more preferably at least
about
:5 95%, 96%, 97%, 98,%, or 99% or more homologous to a nucleotide sequence of
one of
the even-numbered SEQ ID NOs set forth in the Sequence Listing. It is also
preferred
that the preferred forms of SMP proteins also have one or more of the SMP
bioactivities
described herein.
The SMP potypeptide, or a biologically active portion thereof, can be
operatively
linked to a non-SMP polypeptide to form a fusion protein. In preferred
embodiments,
this fusion protein has an activity which differs from that of the SMP protein
alone. In
other preferred embodiments, this fusion protein performs a function involved
in the
metabolism of carbon compounds such as sugars or in the generation of energy
molecules (e.g., ATP) by processes such as oxidative phosphorylation in
Corynebacterium glutamicum. In particularly preferred embodiments, integration
of this
fusion protein into a host cell modulates production of a desired compound
from the
cell.
In another aspect, the invention provides methods for screening molecules
which
modulate the activity of an SMP protein, either by interacting with the
protein itself or a
substrate or binding partner of the SMP protein, or by modulating the
transcription or
translation of an SMP nucleic acid molecule of the invention.
Another aspect of the invention pertains to a method for producing a fine
chemical. This method involves the culturing of a cell containing a vector
directing the
expression of an SMP nucleic acid molecule of the invention, such that a fine
chemical
is produced. In a preferred embodiment, this method further includes the step
of
obtaining a cell containing such a vector, in which a cell is transfected with
a vector
directing the expression of an SMP nucleic acid. In another preferred
embodiment, this
method further includes the step of recovering the fine chemical from the
culture. In a
particularly preferred embodiment, the cell is from the genus Corynebacterium
or
Brevibacterium, or is selected from those strains set forth in Table 3.
Another aspect of the invention pertains to methods for modulating production
of
a molecule from a microorganism. Such methods include contacting the cell with
an
~. õ
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agent which modulates SMP protein activity or SMP nucleic acid expression such
that a
cell associated activity is altered relative to this same activity in the
absence of the
agent. In a preferred embodiment, the cell is modulated for one or more C.
glutamicum
carbon metabolism pathways or for the production of energy through processes
such as
:5 oxidative phosphorylation, such that the yields or rate of production of a
desired fine
chemical by this microorganism is improved. The agent which modulates SMP
protein
activity can be an agent which stimulates SMP protein activity or SMP nucleic
acid
expression. Examples of agents which stimulate SMP protein activity or SMP
nucleic
acid expression include small molecules, active SMP proteins, and nucleic
acids
11) encoding SMP proteins that have been introduced into the cell. Examples of
agents
which inhibit SMP activity or expression include small molecules and antisense
SMP
nucleic acid molecules.
Another aspect of the invention pertains to methods for modulating yields of a
desired compound from a cell, involving the introduction of a wild-type or
mutant SMP
15 gene into a cell, either maintained on a separate plasmid or integrated
into the genome of
the host cell. If integrated into the genome, such integration can be random,
or it can
take place by homologous recombination such that the native gene is replaced
by the
introduced copy, causing the production of the desired compound from the cell
to be
modulated. In a preferred embodiment, said yields are increased. In another
preferred
20 embodiment, said chemical is a fine chemical. In a particularly preferred
embodiment,
said fine chemical is an amino acid. In especially preferred embodiments, said
amino
acid is L-lysine.
Detailed Description of the Invention
25 The present invention provides SMP nucleic acid and protein molecules which
are involved in the metabolism of carbon compounds such as sugars and the
generation
of energy molecules by processes such as oxidative phosphorylation in
Corynebacterium glutamicum. The molecules of the invention may be utilized in
the
modulation of production of fine chemicals from microorganisms, such as C.
30 glutamicum, either directly (e.g., where overexpression or optimization of
a glycolytic
pathway protein has a direct impact on the yield, production, and/or
efficiency of
production of, e.g., pyruvate from modified C. glutamicum), or may have an
indirect
I I I N IIM
CA 02584021 2007-04-18
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impact which nonetheless results in an increase of yield, production, and/or
efficiency of
production of the desired compound (e.g., where modulation of proteins
involved in
oxidative phosphorylation results in alterations in the amount of energy
available to
perform necessary metabolic processes and other cellular functions, such as
nucleic acid
and protein biosynthesis and transcription/translation). Aspects of the
invention are
further explicated below.
1. Fine Chemicals
The term 'fine chemical' is art-recognized and includes molecules produced by
an organism which have applications in various industries, such as, but not
limited to,
the pharmaceutical, agriculture, and cosmetics industries. Such compounds
include
organic acids, such as tartaric acid, itaconic acid, and diaminopimelic acid,
both
proteinogenic and non-proteinogenic amino acids, purine and pyrimidine bases,
nucleosides, and nucleotides (as described e.g. in Kuninaka, A. (1996)
Nucleotides and
related compounds, p. 56 i-612, in Biotechnology vol. 6, Rehm et al., eds.
VCH:
Weinheim, and references contained therein), lipids, both saturated and
unsaturated fatty
acids (e.g., arachidonic acid), diols (e.g., propane diol, and butane diol),
carbohydrates
(e.g., hyaluronic acid and trehalose), aromatic compounds (e.g., aromatic
amines,
vanillin, and indigo), vitamins and cofactors (as described in Ullmann's
Encyclopedia of
Industrial Chemistry, vol. A27, "Vitamins", p. 443-613 (1996) VCH: Weinheim
and
references therein; and Ong, A.S., Niki, E. & Packer, L. (1995) "Nutrition,
Lipids,
Health, and Disease" Proceedings of the UNESCO/Confederation of Scientific and
Technological Associations in Malaysia, and the Society for Free Radical
Research -
Asia, held Sept. 1-3, 1994 at Penang, Malaysia, AOCS Press, (1995)), enzymes,
polyketides (Cane el al. (1998) Science 282: 63-68), and all other chemicals
described in
Gutcho (1983) Chemicals by Fermentation, Noyes Data Corporation, ISBN:
0818805086 and references therein. The metabolism and uses of certain of these
fine
chemicals are further explicated below.
A. Amino Acid Metabolism and Uses
Amino acids comprise the basic structural units of all proteins, and as such
are
essential for normal cellular functioning in all organisms. The term "amino
acid" is art-
I. IaI1Mi
CA 02584021 2007-04-18
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recognized. The proteinogenic amino acids, of which there are 20 species,
serve as
structural units for proteins, in which they are linked by peptide bonds,
while the
nonproteinogenic amino acids (hundreds of which are known) are not normally
found in
proteins (see Ulmann's Encyclopedia of Industrial Chemistry, vol. A2, p. 57-97
VCH:
Weinheim (1985)). Amino acids may be in the D- or L- optical configuration,
though L-
amino acids are generally the only type found in naturally-occurring proteins.
Biosynthetic and degradative pathways of each of the 20 proteinogenic amino
acids
have been well characterized in both prokaryotic and eukaryotic cells (see,
for example,
Stryer, L. Biochemistry, 3rd edition, pages 578-590 (1988)). The 'essential'
amino acids
liD (histidine, isoleucine, leucine, lysine, methionine, phenytalanine,
threonine, tryptophan,
and valine), so named because they are generally a nutritional requirement due
to the
complexity of their biosyntheses, are readily converted by simple biosynthetic
pathways
to the remaining 11 'nonessential' amino acids (alanine, arginine, asparagine,
aspartate,
cysteine, glutamate, glutamine, glycine, proline, serine, and tyrosine).
Higher animals
do retain the ability to synthesize some of these amino acids, but the
essential amino
acids must be supplied from the diet in order for normal protein synthesis to
occur.
Aside from their function in protein biosynthesis, these amino acids are
interesting chemicals in their own right, and many have been found to have
various
applications in the food, feed, chemical, cosmetics, agriculture, and
pharmaceutical
industries. Lysine is an important amino acid in the nutrition not only of
humans, but
also of monogastric animals such as poultry and swine. Glutamate is most
commonly
used as a flavor additive (mono-sodium glutamate, MSG) and is widely used
throughout
the food industry, as are aspartate, phenylalanine, glycine, and cysteine.
Glycine, L-
methionine and tryptophan are all utilized in the pharmaceutical industry.
Glutamine,
valine, leucine, isoleucine, histidine, arginine, proline, serine and alanine
are of use in
both the pharmaceutical and cosmetics industries. Threonine, tryptophan, and
D/ L-
methionine are common feed additives. (Leuchtenberger, W. (1996) Amino aids -
technical production and use, p. 466-502 in Rehm et al. (eds.) Biotechnology
vol. 6,
chapter 14a, VCH: Weinheim). Additionally, these amino acids have been found
to be
useful as precursors for the synthesis of synthetic amino acids and proteins,
such as N-
acetylcysteine, S-carboxymethyl-L-cysteine, (S)-5-hydroxytryptophan, and
others
IYIILCA 02584021 2007-04-18
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described in Ulmann's Encyclopedia of Industrial Chemistry, vol. A2, p. 57-97,
VCH:
Weinheim, 1985.
The biosynthesis of these natural amino acids in organisms capable of
producing them, such as bacteria, has been well characterized (for review of
bacterial
'i amino acid biosynthesis and regulation thereof, see Umbarger, H.E.(1978)
Ann. Rev.
Biochem. 47: 533-606). Glutamate is synthesized by the reductive amination of
a-
ketoglutarate, an intermediate in the citric acid cycle. Glutamine, proline,
and arginine
are each subsequently produced from glutamate. The biosynthesis of serine is a
three-
step process beginning with 3-phosphoglycerate (an intermediate in
glycolysis), and
resulting in this amino acid after oxidation, transamination, and hydrolysis
steps. Both
cysteine and glycine are produced from serine; the former by the condensation
of
homocysteine with serine, and the latter by the transferal of the side-chain R-
carbon
atom to tetrahydrofolate, in a reaction catalyzed by serine
transhydroxymethylase.
Phenylalanine, and tyrosine are synthesized from the glycolytic and pentose
phosphate
pathway precursors erythrose 4-phosphate and phosphoenolpyruvate in a 9-step
biosynthetic pathway that differ only at the final two steps after synthesis
of prephenate.
Tryptophan is also produced from these two initial molecules, but its
synthesis is an 11-
step pathway. Tyrosine may also be synthesized from phenylalanine, in a
reaction
catalyzed by phenylalanine hydroxylase. Alanine, valine, and leucine are all
biosynthetic products of pyruvate, the final product of glycolysis. Aspartate
is fonmed
from oxaloacetate, an intermediate of the citric acid cycle. Asparagine,
methionine,
threonine, and lysine are each produced by the conversion of aspartate.
Isoleucine is
formed from threonine. A complex 9-step pathway results in the production of
histidine
from 5-phosphoribosyl-l-pyrophosphate, an activated sugar.
Amino acids in excess of the protein synthesis needs of the cell cannot be
stored,
and are instead degraded to provide intermediates for the major metabolic
pathways of
the cell (for review see Stryer, L. Biochemistry 3d ed. Ch. 21 "Amino Acid
Degradation
and the Urea Cycle" p. 495-516 (1988)). Although the cell is able to convert
unwanted
amino acids into useful metabolic intermediates, amino acid production is
costly in
terms of energy, precursor molecules, and the enzymes necessary to synthesize
them.
Thus it is not surprising that amino acid biosynthesis is regulated by
feedback inhibition,
in which the presence of a particular amino acid serves to slow or entirely
stop its own
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production (for overview of feedback mechanisms in amino acid biosynthetic
pathways,
see Stryer, L. Biochemistry, 3'd ed. Ch. 24: "Biosynthesis of Amino Acids and
Heme" p.
575-600 (1988)). Thus, the output of any particular amino acid is limited by
the amount
of that amino acid present in the cell.
:5
B. Vitamin, Cofactor, and Nutraceutical Metabolism and Uses
Vitamins, cofactors, and nutraceuticals comprise another group of molecules
which the higher animals have lost the ability to synthesize and so must
ingest, although
they are readily synthesized by other organisms such as bacteria. These
molecules are
either bioactive substances themselves, or are precursors of biologically
active
substances which may serve as electron carriers or inten.nediates in a variety
of
metabolic pathways. Aside from their nutritive value, these compounds also
have
significant industrial value as coloring agents, antioxidants, and catalysts
or other
processing aids. (For an overview of the structure, activity, and industrial
applications
of these compounds, see, for example, Ullman's Encyclopedia of Industrial
Chemistry,
"Vitamins" vol. A27, p. 443-613, VCH: Weinheim, 1996.) The term "vitamin" is
art-
recognized, and includes nutrients which are required by an organism for
normal
functioning, but which that organism cannot synthesize by itself. The group of
vitamins
may encompass cofactors and nutraceutical compounds. The language "cofactor"
includes nonproteinaceous compounds required for a normal enzymatic activity
to
occur. Such compounds may be organic or inorganic; the cofactor molecules of
the
invention are preferably organic. The term "nutraceutical" includes dietary
supplements
having health benefits in plants and animals, particularly humans. Examples of
such
molecules are vitamins, antioxidants, and also certain lipids (e.g.,
polyunsaturated fatty
acids).
The biosynthesis of these molecules in organisms capable of producing them,
such as bacteria, has been largely characterized (Ullman's Encyclopedia of
Industrial
Chemistry, "Vitamins" vol. A27, p. 443-613, VCH: Weinheim, 1996; Michal, G.
(1999)
Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology, John
Wiley
& Sons; Ong, A.S., Niki, E. & Packer, L. (1995) "Nutrition, Lipids, Health,
and
Disease" Proceedings of the UNESCO/Confederation of Scientific and
Technological
I I. IMIN.
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Associations in Malaysia, and the Society for Free Radical Research - Asia,
held Sept.
1-3, 1994 at Penang, Malaysia, AOCS Press: Champaign, IL X, 374 S).
Thiamin (vitamin B1) is produced by the chemical coupling of pyrimidine and
thiazole moieties. Riboflavin (vitamin BZ) is synthesized from guanosine-5'-
triphosphate
(GTP) and ribose-5'-phosphate. Riboflavin, in turn, is utilized for the
synthesis of flavin
mononucleotide (FMN) and flavin adenine dinucleotide (FAD). The family of
compounds collectively termed 'vitamin B6' (e.g., pyridoxine, pyridoxamine,
pyridoxa-
5'-phosphate, and the commercially used pyridoxin hydrochloride) are all
derivatives of
the common structural unit, 5-hydroxy-6-methylpyridine. Pantothenate
(pantothenic
acid, (R)-(+)-N-(2,4-dihydroxy-3,3-dimethyl-1 -oxobutyl)-(3-alanine) can be
produced
either by chemical synthesis or by fermentation. The final steps in
pantothenate
biosynthesis consist of the ATP-driven condensation of a-alanine and pantoic
acid. The
enzymes responsible for the biosynthesis steps for the conversion to pantoic
acid, to 0-
alanine and for the condensation to panthotenic acid are known. The
metabolically
active form of pantothenate is Coenzyme A, for which the biosynthesis proceeds
in 5
enzymatic steps. Pantothenate, pyridoxal-5'-phosphate, cysteine and ATP are
the
precursors of Coenzyme A. These enzymes not only catalyze the formation of
panthothante, but also the production of (R)-pantoic acid, (R)-pantolacton,
(R)-
panthenol (provitamin B5), pantetheine (and its derivatives) and coenzyme A.
Biotin biosynthesis from the precursor molecule pimeloyl-CoA in
microorganisms has been studied in detail and several of the genes involved
have been
identified. Many of the corresponding proteins have been found to also be
involved in
Fe-cluster synthesis and are members of the nif5 class of proteins. Lipoic
acid is
derived from octanoic acid, and serves as a coenzyme in energy metabolism,
where it
becomes part of the pyruvate dehydrogenase complex and the a-ketoglutarate
dehydrogenase complex. The folates are a group of substances which are all
derivatives
of folic acid, which is turn is derived from L-glutamic acid, p-amino-benzoic
acid and 6-
methylpterin. The biosynthesis of folic acid and its derivatives, starting
from the
metabolism intermediates guanosine-5'-triphosphate (GTP), L-glutamic acid and
p-
amino-benzoic acid has been studied in detail in certain microorganisms.
Corrinoids (such as the cobalamines and particularly vitamin Bj2) and
porphyrines belong to a group of chemicals characterized by a tetrapyrole ring
system.
I_~.
I I 1 . 111
CA 02584021 2007-04-18
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The biosynthesis of vitamin B 12 is sufficiently complex that it has not yet
been
completely characterized, but many of the enzymes and substrates involved are
now
known. Nicotinic acid (nicotinate), and nicotinamide are pyridine derivatives
which are
also termed 'niacin'. Niacin is the precursor of the important coenzymes NAD
(nicotinamide adenine dinucleotide) and NADP (nicotinamide adenine
dinucleotide
phosphate) and their reduced forms.
The large-scale production of these compounds has largely relied on cell-free
chemical syntheses, though some of these chemicals have also been produced by
large-
scale culture of microorganisms, such as riboflavin, Vitamin B6, pantothenate,
and
biotin. Only Vitamin BiZ is produced solely by fennentation, due to the
complexity of
its synthesis. In vitro methodologies require significant inputs of materials
and time,
often at great cost.
C. Purine, Pyrimidine, Nucleoside and Nucleotide Metabolism and Uses
Purine and pyrimidine metabolism genes and their corresponding proteins are
important targets for the therapy of tumor diseases and viral infections. The
language
"purine" or "pyrimidine" includes the nitrogenous bases which are constituents
of
nucleic acids, co-enzymes, and nucleotides. The term "nucleotide" includes the
basic
structural units of nucleic acid molecules, which are comprised of a
nitrogenous base, a
pentose sugar (in the case of RNA, the sugar is ribose; in the case of DNA,
the sugar is
D-deoxyribose), and phosphoric acid. The language "nucleoside" includes
molecules
which serve as precursors to nucleotides, but which are lacking the phosphoric
acid
moiety that nucleotides possess. By inhibiting the biosynthesis of these
molecules, or
their mobilization to form nucleic acid molecules, it is possible to inhibit
RNA and DNA
synthesis; by inhibiting this activity in a fashion targeted to cancerous
cells, the ability
of tumor cells to divide and replicate may be inhibited. Additionally, there
are
nucleotides which do not form nucleic acid molecules, but rather serve as
energy stores
(t.e., AMP) or as coenzymes (i.e., FAD and NAD).
Several publications have described the use of these chemicals for these
medical
indications, by influencing purine and/or pyrimidine metabolism (e.g.
Christopherson,
R.I. and Lyons, S.D. (1990) "Potent inhibitors of de novo pyrimidine and
purine
biosynthesis as chemotherapeutic agents." Med. Res. Reviews 10: 505-548).
Studies of
CA 02584021 2007-04-18
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enzymes involved in purine and pyrimidine metabolism have been focused on the
development of new drugs which can be used, for example, as immunosuppressants
or
anti-proliferants (Smith, J.L., (1995) "Enzymes in nucleotide synthesis."
Curr. Opin.
Struct. Biol. 5: 752-757; (1995) Biochem Soc. Transact. 23: 877-902). However,
purine
and pyrimidine bases, nucleosides and nucleotides have other utilities: as
intenmediates
in the biosynthesis of several fine chemicals (e.g., thiamine, S-adenosyl-
methionine,
folates, or riboflavin), as energy carriers for the cell (e.g., ATP or GTP),
and for
chemicals themselves, commonly used as flavor enhancers (e.g., IMP or GMP) or
for
several medicinal applications (see, for example, Kuninaka, A. (1996)
Nucleotides and
1() Related Compounds in Biotechnology vol. 6, Rehm et al., eds. VCH:
Weinheim, p. 561-
612). Also, enzymes involved in purine, pyrimidine, nucleoside, or nucleotide
metabolism are increasingly serving as targets against which chemicals for
crop
protection, including fungicides, herbicides and insecticides, are developed.
The metabolism of these compounds in bacteria has been characterized (for
reviews see, for example, Zalkin, H. and Dixon, J.E. (1992) "de novo purine
nucleotide
biosynthesis", in: Progress in Nucleic Acid Research and Molecular Biology,
vol. 42,
Academic Press:, p. 259-287; and Michal, G. (1999) "Nucleotides and
Nucleosides",
Chapter 8 in: Biochemical Pathways: An Atlas of Biochemistry and Molecular
Biology,
Wiley: New York). Purine metabolism has been the subject of intensive
research, and is
essential to the normal functioning of the cell. Impaired purine metabolism in
higher
animals can cause severe disease, such as gout. Purine nucleotides are
synthesized from
ribose-5-phosphate, in a series of steps through the intermediate compound
inosine-5'-
phosphate (IMP), resulting in the production of guanosine-5'-monophosphate
(GMP) or
adenosine-5'-monophosphate (AMP), from which the triphosphate forms utilized
as
nucleotides are readily formed. These compounds are also utilized as energy
stores, so
their degradation provides energy for many different biochemical processes in
the cell.
Pyrimidine biosynthesis proceeds by the formation of uridine-5'-monophosphate
(UMP)
from ribose-5-phosphate. UMP, in turn, is converted to cytidine-5'-
triphosphate (CTP).
The deoxy- forms of all of these nucleotides are produced in a one step
reduction
reaction from the diphosphate ribose form of the nucleotide to the diphosphate
deoxyribose form of the nucleotide. Upon phosphorylation, these molecules are
able to
participate in DNA synthesis.
I . II .
CA 02584021 2007-04-18
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D. Trehalose Metabolism and Uses
Trehalose consists of two glucose molecules, bound in a, a-1,l linkage. It is
commonly used in the food industry as a sweetener, an additive for dried or
frozen
foods, and in beverages. However, it also has applications in the
phamlaceutical,
cosmetics and biotechnology industries (see, for example, Nishimoto et al.,
(1998) U.S.
Patent No. 5,759,610; Singer, M.A. and Lindquist, S. (1998) Trends Biolech.
16: 460-
467; Paiva, C.L.A. and Panek, A.D. (1996) Biotech. Ann. Rev. 2: 293-314; and
Shiosaka, M. (1997) J. Japan 172: 97-102). Trehalose is produced by enzymes
from
many microorganisms and is naturally released into the surrounding medium,
from
which it can be collected using methods known in the art.
II. Sugar and Carbon Molecule Utilization and Oxidative Phosphorylation
Carbon is a critically important element for the formation of all organic
compounds, and thus is a nutritional requirement not only for the growth and
division of
C. glutamicum, but also for the overproduction of fine chemicals from this
microorganism. Sugars, such as mono-, di-, or polysaccharides, are
particularly good
carbon sources, and thus standard growth media typically contain one or more
of:
glucose, fructose, mannose, galactose, ribose, sorbose, ribulose, lactose,
maltose,
sucrose, raffinose, starch, or cellulose (Ullmann's Encyclopedia of Industrial
Chemistry
(1987) vol. A9, "Enzymes", VCH: Weinheim). Alternatively, more complex forms
of
sugar may be utilized in the media, such as molasses, or other by-products of
sugar
refinement. Other compounds aside from the sugars may be used as alternate
carbon
sources, including alcohols (e.g., ethanol or methanol), alkanes, sugar
alcohols, fatty
acids, and organic acids (e.g., acetic acid or lactic acid). For a review of
carbon sources
and their utilization by microorganisms in culture, see: Ullman's Encyclopedia
of
Industrial Chemistry (1987) vol. A9, "Enzymes", VCH: Weinheim; Stoppok, E. and
Buchholz, K. (1996) "Sugar-based raw materials for fermentation applications"
in
Biotechnology (Rehm, H.J. et al., eds.) vol. 6, VCH: Weinheim, p. 5-29; Rehm,
H.J.
(1980) Industrielle Mikrobiologie, Springer: Berlin; Bartholomew, W.H., and
Reiman,
H.B. (1979). Economics of Fermentation Processes, in: Peppler, H.J. and
Perlman, D.,
eds. Microbial Technology 2"d ed., vol. 2, chapter 18, Academic Press: New
York; and
N i li ,
CA 02584021 2007-04-18
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Kockova-Kratachvilova, A. (1981) Characteristics of Industrial Microorganisms,
in:
Rehm, H.J. and Reed, G., eds. Handbook of Biotechnology, vol. 1, chapter 1,
Verlag
Chemie: Weinheim.
After uptake, these energy-rich carbon molecules must be processed such that
they are able to be degraded by one of the major sugar metabolic pathways.
Such
pathways lead directly to useful degradation products, such as ribose-5-
phosphate and
phosphoenolpyruvate, which may be subsequently converted to pyruvate. Three of
the
most important pathways in bacteria for sugar metabolism include the Embden-
Meyerhotff Parnas (EMP) pathway (also known as the glycolytic or fructose
bisphosphate pathway), the hexosemonophosphate (HMP) pathway (also known as
the
pentose shunt or pentose phosphate pathway), and the Entner-Doudoroff (ED)
pathway
(for review, see Michal, G. (1999) Biochemical Pathways: An Atlas of
Biochemistry
and Molecular Biology, Wiley: New York, and Stryer, L. (1988) Biochemistry,
Chapters
13-19, Freeman: New York, and references therein).
The EMP pathway converts hexose molecules to pyruvate, and in the process
produces 2 molecules of ATP and 2 molecules of NADH. Starting with glucose-l-
phosphate (which may be either directly taken up from the medium, or
altematively may
be generated from glycogen, starch, or cellulose), the glucose molecule is
isomerized to
fructose-6-phosphate, is phosphorylated, and split into two 3-carbon molecules
of
glyceraldehyde-3-phosphate. After dehydrogenation, phosphorylation, and
successive
rearrangements, pyruvate results.
The HMP pathway converts glucose to reducing equivalents, such as NADPH,
and produces pentose and tetrose compounds which are necessary as
intenmediates and
precursors in a number of other metabolic pathways. In the HMP pathway,
glucose-6-
phosphate is converted to ribulose-5-phosphate by two successive dehydrogenase
reactions (which also release two NADPH molecules), and a carboxylation step.
Ribulose-5-phosphate may also be converted to xyulose-5-phosphate and ribose-5-
phosphate; the former can undergo a series of biochemical steps to glucose-6-
phosphate,
which may enter the EMP pathway, while the latter is commonly utilized as an
intermediate in other biosynthetic pathways within the cell.
The ED pathway begins with the compound glucose or gluconate, which is
subsequently phosphorylated and dehydrated to form 2-dehydro-3-deoxy-6-P-
gluconate.
I d 111.
CA 02584021 2007-04-18
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Glucuronate and galacturonate may also be converted to 2-dehydro-3-deoxy-6-P-
gluconate through more complex biochemical pathways. This product molecule is
subsequently cleaved into glyceraldehyde-3-P and pyruvate; glyceraldehyde-3-P
may
itself also be converted to pyruvate.
:5 The EMP and HMP pathways share many features, including intermediates and
enzymes. The EMP pathway provides the greatest amount of ATP, but it does not
produce ribose-5-phosphate, an important precursor for, e.g., nucleic acid
biosynthesis,
nor does it produce erythrose-4-phosphate, which is important for amino acid
biosynthesis. Microorganisms that are capable of using only the EMP pathway
for
glucose utilization are thus not able to grow on simple media with glucose as
the sole
carbon source. They are referred to as fastidious organisms, and their growth
requires
inputs of complex organic compounds, such as those found in yeast extract.
In contrast, the HMP pathway produces all of the precursors necessary for both
nucleic acid and amino acid biosynthesis, yet yields only half the amount of
ATP energy
that the EMP pathway does. The HMP pathway also produces NADPH, which may be
used for redox reactions in biosynthetic pathways. The HMP pathway does not
directly
produce pyruvate, however, and thus these microorganisms must also possess
this
portion of the EMP pathway. It is therefore not surprising that a number of
microorganisms, particularly the facultative anerobes, have evolved such that
they
possess both of these pathways.
The ED pathway has thus far has only been found in bacteria. Although this
pathway is linked partly to the HMP pathway in the reverse direction for
precursor
formation, the ED pathway directly forms pyruvate by the aldolase cleavage of
3-
ketodeoxy-6-phosphogluconate. The ED pathway can exist on its own and is
utilized by
the majority of strictly aerobic microorganisms. The net result is similar to
that of the
HMP pathway, although one mole of ATP can be formed only if the carbon atoms
are
converted into pyruvate, instead of into precursor molecules.
The pyruvate molecules produced through any of these pathways can be readily
converted into energy via the Krebs cycle (also known as the citric acid
cycle, the citrate
cycle, or the tricarboxylic acid cycle (TCA cycle)). In this process, pyruvate
is first
decarboxylated, resulting in the production of one molecule of NADH, 1
molecule of
acetyl-CoA, and I molecule of COZ. The acetyl group of acetyl CoA then reacts
with
1 ~
I I = . I Y 14.=
CA 02584021 2007-04-18
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the 4 carbon unit, oxaolacetate, leading to the formation of citric acid, a 6
carbon
organic acid. Dehydration and two additional CO2 molecules are released.
Ultimately,
oxaloacetate is regenerated and can serve again as an acetyl acceptor, thus
completing
the cycle. The electrons released during the oxidation of intermediates in the
TCA cycle
are transferred to NAD+ to yield NADH.
During respiration, the electrons from NADH are transferred to molecular
oxygen or other terminal electron acceptors. This process is catalyzed by the
respiratory
chain, an electron transport system containing both integral membrane proteins
and
membrane associated proteins. This system serves two basic functions: first,
to accept
electrons from an electron donor and to transfer them to an electron acceptor,
and
second, to conserve some of the energy released during electron transfer by
the synthesis
of ATP. Several types of oxidation-reduction enzymes and electron transport
proteins
are known to be involved in such processes, including the NADH dehydrogenases,
flavin-containing electron carriers, iron sulfur proteins, and cytochromes.
The NADH
dehydrogenases are located at the cytoplasmic surface of the plasma membrane,
and
transfer hydrogen atoms fi-om NADH to flavoproteins, in turn accepting
electrons from
NADH. The flavoproteins are a group of electron carriers possessing a flavin
prosthetic
group which is altemately reduced and oxidized as it accepts and transfers
electrons.
Three flavins are known to participate in these reactions: riboflavin, flavin-
adenine
dinucleotide (FAD) and flavin-mononucleotide (FMN). Iron sulfur proteins
contain a
cluster of iron and sulfur atoms which are not bonded to a heme group, but
which still
are able to participate in dehydration and rehydration reactions. Succinate
dehydrogenase and aconitase are exemplary iron-sulfur proteins; their iron-
sulfur
complexes serve to accept and transfer electrons as part of the overall
electron-transport
chain. The cytochromes are proteins containing an iron porphyrin ring (heme).
There
are a number of different classes of cytochromes, differing in their reduction
potentials.
Functionally, these cytochromes fonn pathways in which electrons may be
transferred to
other cytochromes having increasingly more positive reduction potentials. A
further
class of non-protein electron carriers is known: the lipid-soluble quinones
(e.g.,
coenzyme Q). These molecules also serve as hydrogen atom acceptors and
electron
donors.
I Y I lw
CA 02584021 2007-04-18
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The action of the respiratory chain generates a proton gradient across the
cell
membrane, resulting in proton motive force. This force is utilized by the cell
to
synthesize ATP, via the membrane-spanning enzyme, ATP synthase. This enzyme is
a
multiprotein complex in which the transport of H+ molecules through the
membrane
results in the physical rotation of the intracellular subunits and concomitant
phosphorylation of ADP to form ATP (for review, see Fillingame, R.H. and
Divall, S.
(1999) Novartis Found. Symp. 221: 218-229, 229-234).
Non-hexose carbon substrates may also serve as carbon and energy sources for
cells. Such substrates may first be converted to hexose sugars in the
gluconeogenesis
11) pathway, where glucose is first synthesized by the cell and then is
degraded to produce
energy. The starting material for this reaction is phosphoenolpyruvate (PEP),
which is
one of the key intermediates in the glycolytic pathway. PEP may be formed from
substrates other than sugars, such as acetic acid, or by decarboxylation of
oxaloacetate
(itself an intermediate in the TCA cycle). By reversing the glycolytic pathway
(utilizing
a cascade of enzymes different than those of the original glycolysis pathway),
glucose-6-
phosphate may be formed. The conversion of pyruvate to glucose requires the
utilization of 6 high energy phosphate bonds, whereas glycolysis only produces
2 ATP
in the conversion of glucose to pyruvate. However, the complete oxidation of
glucose
(glycolysis, conversion of pyruvate into acetyl CoA, citric acid cycle, and
oxidative
phosphorylation) yields between 36-38 ATP, so the net loss of high energy
phosphate
bonds experienced during gluconeogenesis is offset by the overall greater gain
in such
high-energy molecules produced by the oxidation of glucose.
III. Elements and Methods of the Invention
The present invention is based, at least in part, on the discovery of novel
molecules, referred to herein as SMP nucleic acid and protein molecules, which
participate in the conversion of sugars to useful degradation products and
energy (e.g.,
ATP) in C. glutamicum or which may participate in the production of useful
energy-rich
molecules (e.g., ATP) by other processes, such as oxidative phosphorylation.
In one
embodiment, the SMP molecules participate in the metabolism of carbon
compounds
such as sugars or the generation of energy molecules (e.g., ATP) by processes
such as
oxidative phosphorylation in Corynebacterium glutamicum. In a preferred
embodiment,
I Y I Y i:
CA 02584021 2007-04-18
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the activity of the SMP molecules of the present invention to contribute to
carbon
metabolism or energy production in C. glutamicum has an impact on the
production of a
desired fine chemical by this organism. In a particularly preferred
embodiment, the SMP
molecules of the invention are modulated in activity, such that the C.
glutamicum
metabolic and energetic pathways in which the SMP proteins of the invention
participate
are modulated in yield, production, and/or efficiency of production, which
either directly
or indirectly modulates the yield, production, and/or efficiency of production
of a
desired fine chemical by C. glutamicum.
The language, "SMP protein" or "SMP polypeptide" includes proteins which are
capable of performing a function involved in the metabolism of carbon
compounds such
as sugars and the generation of energy molecules by processes such as
oxidative
phosphorylation in Corynebacterium glutamicum. Examples of SMP proteins
include
those encoded by the SMP genes set forth in Table l and by the odd-numbered
SEQ ID
NOs. The terms "SMP gene" or "SMP nucleic acid sequence" include nucleic acid
sequences encoding an SMP protein, which consist of a coding region and also
corresponding untranslated 5' and 3' sequence regions. Examples of SMP genes
include
those set forth in Table 1. The terms "production" or "productivity" are art-
recognized
and include the concentration of the fermentation product (for example, the
desired fine
chemical) formed within a given time and a given fermentation volume (e.g., kg
product
per hour per liter). The term "efficiency of production" includes the time
required for a.
particular level of production to be achieved (for example, how long it takes
for the cell
to attain a particular rate of output of a fine chemical). The term "yield" or
"product/carbon yield" is art-recognized and includes the efficiency of the
conversion of
the carbon source into the product (f.e., fine chemical). This is generally
written as, for
example, kg product per kg carbon source. By increasing the yield or
production of the
compound, the quantity of recovered molecules, or of useful recovered
molecules of that
compound in a given amount of culture over a given amount of time is
increased. The
terms "biosynthesis" or a "biosynthetic pathway" are art-recognized and
include the
synthesis of a compound, preferably an organic compound, by a cell from
intermediate
compounds in what may be a multistep and highly regulated process. The terms
"degradation" or a "degradation pathway" are art-recognized and include the
breakdown of a compound, preferably an organic compound, by a cell to
degradation
I I. IYIY..
CA 02584021 2007-04-18
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products (generally speaking, smaller or less complex molecules) in what may
be a
multistep and highly regulated process. The term "degradation product" is art-
recognized and includes breakdown products of a compound. Such products may
themselves have utility as precursor (starting point) or intermediate
molecules necessary
for the biosynthesis of other compounds by the cell. The language "metabolism"
is art-
recognized and includes the totality of the biochemical reactions that take
place in an
organism. The metabolism of a particular compound, then, (e.g., the metabolism
of an
amino acid such as glycine) comprises the overall biosynthetic, modification,
and
degradation pathways in the cell related to this compound.
110 In another embodiment, the SMP molecules of the invention are capable of
modulating the production of a desired molecule, such as a fine chemical, in a
microorganism such as C. glutamicum. There are a number of mechanisms by which
the alteration of an SMP protein of the invention may directly affect the
yield,
production, and/or efficiency of production of a fine chemical from a C.
glutamicum
1:5 strain incorporating such an altered protein. The degradation of high-
energy carbon
molecules such as sugars, and the conversion of compounds such as NADH and
FADH2
to more useful forms via oxidative phosphorylation results in a number of
compounds
which themselves may be desirable fine chemicals, such as pyruvate, ATP, NADH,
and
a number of intermediate sugar compounds. Further, the energy molecules (such
as
20 ATP) and the reducing equivalents (such as NADH or NADPH) produced by these
metabolic pathways are utilized in the cell to drive reactions which would
otherwise be
energetically unfavorable. Such unfavorable reactions include many
biosynthetic
pathways for fine chemicals. By improving the ability of the cell to utilize a
particular
sugar (e.g., by manipulating the genes encoding enzymes involved in the
degradation
25 and conversion of that sugar into energy for the cell), one may increase
the amount of
energy available to permit unfavorable, yet desired metabolic reactions (e.g.,
the
biosynthesis of a desired fine chemical) to occur.
The mutagenesis of one or more SMP genes of the invention may also result in
SMP proteins having altered activities which indirectly impact the production
of one or
30 more desired fine chemicals from C. glutamicum. For example, by increasing
the
efficiency of utilization of one or more sugars (such that the conversion of
the sugar to
useful energy molecules is improved), or by increasing the efficiency of
conversion of
I I
CA 02584021 2007-04-18
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reducing equivalents to useful energy molecules (e.g., by improving the
efficiency of
oxidative phosphorylation, or the activity of the ATP synthase), one can
increase the
amount of these high-energy compounds available to the cell to drive normally
unfavorable metabolic processes. These processes include the construction of
cell walls,
transcription, translation, and the biosynthesis of compounds necessary for
growth and
division of the cells (e.g., nucleotides, amino acids, vitamins, lipids, etc.)
(Lengeler et al.
(1999) Biology of Prokaryotes, Thieme Verlag: Stuttgart, p. 88-109; 913-918;
875-899).
By improving the growth and multiplication of these engineered cells, it is
possible to
increase both the viability of the cells in large-scale culture, and also to
improve their
rate of division, such that a relatively larger number of cells can survive in
fermentor
culture. The yield, production, or efficiency of production may be increased,
at least
due to the presence of a greater number of viable cells, each producing the
desired fine
chemical. Further, a number of the degradation and intermediate compounds
produced
during sugar metabolism are necessary precursors and intermediates for other
biosynthetic pathways throughout the cell. For example, many amino acids are
synthesized directly from compounds normally resulting from glycolysis or the
TCA
cycle (e.g., serine is synthesized from 3-phosphoglycerate, an intermediate in
glycolysis). Thus, by increasing the efficiency of conversion of sugars to
useful energy
molecules, it is also possible to increase the amount of useful degradation
products as
well.
The isolated nucleic acid sequences of the invention are contained within the
genome of a Corynebacterium glutamicum strain available through the American
Type
Culture Collection, given designation ATCC 13032. The nucleotide sequence of
the
isolated C. glutamicum SMP DNAs and the predicted amino acid sequences of the
C.
glutamicum SMP proteins are shown in the Sequence Listing as odd-numbered SEQ
ID
NOs and even-numbered SEQ ID NOs, respectively. Computational analyses
were performed which classified and/or identified these nucleotide sequences
as
sequences which encode proteins having a function involved in the metabolism
of
carbon compounds such as sugars or in the generation of energy molecules by
processes
such as oxidative phosphorylation in Corynebacterium glutamicum.
The present invention also pertains to proteins which have an amino acid
sequence which is substantially homologous to an amino acid sequence of the
invention
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(e.g., the sequence of an even-numbered SEQ ID NO of the Sequence Listing). As
used
herein, a protein which has an amino acid sequence which is substantially
homologous
to a selected amino acid sequence is least about 50% homologous to the
selected amino
acid sequence, e.g., the entire selected amino acid sequence. A protein which
has an
amino acid sequence which is substantially homologous to a selected amino acid
sequence can also be least about 50-60%, preferably at least about 60-70%, and
more
preferably at least about 70-80%, 80-90%, or 90-95%, and most preferably at
least about
96%, 97%, 98%, 99% or more homologous to the selected amino acid sequence.
An SMP protein or a biologically active portion or fragment thereof of the
invention can participate in the metabolism of carbon compounds such as sugars
or in
the generation of energy molecules (e.g., ATP) by processes such as oxidative
phosphorylation in Corynebacterium glutamicum, or can have one or more of the
activities set forth in Table 1.
Various aspects of the invention are described in further detail in the
following
1.5 subsections:
A. Isolated Nucleic Acid Molecules
One aspect of the invention pertains to isolated nucleic acid molecules that
encode SMP polypeptides or biologically active portions thereof, as well as
nucleic acid
fragments sufficient for use as hybridization probes or primers for the
identification or
amplification of SMP-encoding nucleic acid (e.g., SMP DNA). As used herein,
the term
"nucleic acid molecule" is intended to include DNA molecules (e.g., cDNA or
genomic
DNA) and RNA molecules (e.g., mRNA) and analogs of the DNA or RNA generated
using nucleotide analogs. This term also encompasses untranslated sequence
located at
both the 3' and 5' ends of the coding region of the gene: at least about 100
nucleotides
of sequence upstream from the 5' end of the coding region and at least about
20
nucleotides of sequence downstream from the 3'end of the coding region of the
gene.
The nucleic acid molecule can be single-stranded or double-stranded, but
preferably is
double-stranded DNA. An "isolated" nucleic acid molecule is one which is
separated
from other nucleic acid molecules which are present in the natural source of
the nucleic
acid. Preferably, an "isolated" nucleic acid is free of sequences which
naturally flank
the nucleic acid (i.e., sequences located at the 5' and 3' ends of the nucleic
acid) in the
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genomic DNA of the organism from which the nucleic acid is derived. For
example, in
various embodiments, the isolated SMP nucleic acid molecule can contain less
than
about 5 kb, 4kb, 3kb, 2kb, 1 kb, 0.5 kb or 0.1 kb of nucleotide sequences
which
naturally flank the nucleic acid molecule in genomic DNA of the cell from
which the
nucleic acid is derived (e.g, a C. glutamicum cell). Moreover, an "isolated"
nucleic acid
molecule, such as a DNA molecule, can be substantially free of other cellular
material,
or culture medium when produced by recombinant techniques, or chemical
precursors or
other chemicals when chemically synthesized.
A nucleic acid molecule of the present invention, e.g., a nucleic acid
molecule
having a nucleotide sequence of an odd-numbered SEQ ID NO of the Sequence
Listing,
or a portion thereof, can be isolated using standard molecular biology
techniques and the
sequence infonization provided herein. For example, a C. glutamicum SMP DNA
can be
isolated from a C. glulamicum library using all or portion of one of the odd-
numbered
SEQ ID NO sequences of the Sequence Listing as a hybridization probe and
standard
hybridization techniques (e.g., as described in Sambrook, J., Fritsh, E. F.,
and Maniatis,
T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor
Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY,
1989).
Moreover, a nucleic acid molecule encompassing all or a portion of one of the
nucleic
acid sequences of the invention (e.g., an odd-numbered SEQ ID NO:) can be
isolated by
the polymerase chain reaction using oligonucleotide primers designed based
upon this
sequence (e.g., a nucleic acid molecule encompassing all or a portion of one
of the
nucleic acid sequences of the invention (e.g., an odd-numbered SEQ ID NO of
the
Sequence Listing) can be isolated by the polymerase chain reaction using
oligonucleotide primers designed based upon this same sequence). For example,
mRNA
can be isolated from normal endothelial cells (e.g., by the guanidinium-
thiocyanate
extraction procedure of Chirgwin el al. (1979) Biochemistry 18: 5294-5299) and
DNA
can be prepared using reverse transcriptase (e.g., Moloney MLV reverse
transcriptase,
available from Gibco/BRL, Bethesda, MD; or AMV reverse transcriptase,
available
from Seikagaku America, Inc., St. Petersburg, FL). Synthetic oligonucleotide
primers
for polymerase chain reaction amplification can be designed based upon one of
the
nucleotide sequences shown in the Sequence Listing. A nucleic acid of the
invention
can be amplified using cDNA or, alternatively, genomic DNA, as a template and
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CA 02584021 2007-04-18
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appropriate oligonucleotide primers according to standard PCR amplification
techniques. The nucleic acid so amplified can be cloned into an appropriate
vector and
characterized by DNA sequence analysis. Furthermore, oligonucleotides
corresponding
to an SMP nucleotide sequence can be prepared by standard synthetic
techniques, e.g.,
using an automated DNA synthesizer.
In a preferred embodiment, an isolated nucleic acid molecule of the invention
comprises one of the nucleotide sequences shown in the Sequence Listing. The
nucleic
acid sequences of the invention, as set forth in the Sequence Listing ,
correspond to the
Corynebacterium glutamicum SMP DNAs of the invention. This DNA comprises
sequences encoding SMP proteins (i. e., the "coding region", indicated in each
odd-
numbered SEQ ID NO: sequence in the Sequence Listing), as well as 5'
untranslated
sequences and 3' untranslated sequences, also indicated in each odd-numbered
SEQ ID
NO: in the Sequence Listing.. Alternatively, the nucleic acid molecule can
comprise
only the coding region of any of the sequences in nucleic acid sequences of
the
Sequence Listing.
For the purposes of this application, it will be understood that each of the
nucleic
acid and amino acid sequences set forth in the Sequence Listing has an
identifying RXA,
RXN, or RXS number having the designation "RXA," "RXN," or "RXS" followed by 5
digits (i.e., RXA01626, RXN00043, or RXS0735). Each of the nucleic acid
sequences
comprises up to three parts: a 5' upstream region, a coding region, and a
downstream
region. Each of these three regions is identified by the same RXA, R3~1, or
RXS
designation to eliminate confusion. The recitation "one of the odd-numbered
sequences
of the Sequence Listing", then, refers to any of the nucleic acid sequences in
the
Sequence Listing, which may also be distinguished by their differing RXA, RXN,
or
RXS designations. The coding region of each of these sequences is translated
into a
corresponding amino acid sequence, which is also set forth in the Sequence
Listing, as
an even-numbered SEQ ID NO: immediately following the corresponding nucleic
acid
sequence . For example, the coding region for RXA02735 is set forth in SEQ ID
NO:1,
while the amino acid sequence which it encodes is set forth as SEQ ID NO:2.
The
sequences of the nucleic acid molecules of the invention are identified by the
same
RXA, RXN, or RXS designations as the amino acid molecules which they encode,
such
that they can be readily correlated. For example, the amino acid sequence
designated
I,
0 1 A
CA 02584021 2007-04-18
29
RXA00042 is a translation of the coding region of the nucleotide sequence of
nucleic
acid molecule RXA00042, and the amino acid sequence designated RXN00043 is a
translation of the coding region of the nucleotide sequence of nucleic acid
molecule
RXN00043. The correspondence between the RXA, RXN and RXS nucleotide and
amino acid sequences of the invention and their assigned SEQ ID NOs is set
forth in
Table 1.
Several of the genes of the invention are "F-designated genes". An F-
designated
gene includes those genes set forth in Table 1 which have an 'F' in front of
the
RXAdesignation. For example, SEQ ID NO: 11, designated, as indicated on Table
1, as
"F RXA01312", is an F-designated gene, as are SEQ ID NOs: 29, 33, and 39
(designated on Table I as "F RXA02803", "F RXA02854", and "F RXA01365",
respectively).
In one embodiment, the nucleic acid molecules of the present invention are not
intended to include those compiled in Table 2. In the case of the dapD gene, a
sequence
for this gene was published in Wehrmann, A., et al. (1998) J. Bacteriol.
180(12): 3159-
3165. However, the sequence obtained by the inventors of the present
application is
significantly longer than the published version. It is believed that the
published version
relied on an incorrect start codon, and thus represents only a fragment of the
actual
coding region.
In another preferred embodiment, an isolated nucleic acid molecule of the
invention comprises a nucleic acid molecule which is a complement of one of
the
nucleotide sequences of the invention (e.g., a sequence of an odd-numbered SEQ
ID
NO: of the Sequence Listing), or a portion thereof. A nucleic acid molecule
which is
complementary to one of the nucleotide sequences of the invention is one which
is
sufficiently complementary to one of the nucleotide sequences shown in the
Sequence
Listing (e.g., the sequence of an odd-numbered SEQ ID NO:) such that it can
hybridize
to one of the nucleotide sequences of the invention, thereby fonning a stable
duplex.
In still another preferred embodiment, an isolated nucleic acid molecule of
the
invention comprises a nucleotide sequence which is at least about 50%, 51%,
52%, 53%,
54%, 55%, 56%, 57%, 58%, 59%, or 60%, preferably at least about 61%, 62%, 63%,
64%, 65%, 66%, 67%, 68%, 69%, or 70%, more preferably at least about 71%, 72%,
73%, 74%, 75%, 76%, 77%, 78%, 79%, or 80%, 81%, 82%, 83%, 84%, 85%, 86%,
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87%, 88%, 89%, or 90%, or 91%, 92%, 93%, 94%, and even more preferably at
least
about 95%, 96%, 97%, 98%, 99% or more homologous to a nucleotide sequence of
the
invention (e.g., a sequence of an odd-numbered SEQ ID NO: of the Sequence
Listing),
or a portion thereof. Ranges and identity values intermediate to the above-
recited
ranges, (e.g., 70-90% identical or 80-95% identical) are also intended to be
encompassed by the present invention. For example, ranges of identity values
using a
combination of any of the above values recited as upper and/or lower limits
are intended.
to be included. In an additional preferred embodiment, an isolated nucleic
acid
molecule of the invention comprises a nucleotide sequence which hybridizes,
e.g.,
hybridizes under stringent conditions, to one of the nucleotide sequences of
the
invention, or a portion thereof.
Moreover, the nucleic acid molecule of the invention can comprise only a
portion of the coding region of the sequence of one of the odd-numbered SEQ ID
NOs
of the Sequence Listing, for example a fragment which can be used as a probe
or primer
- or a fragment encoding a biologically active portion of an SMP protein. The
nucleotide
sequences detennined from the cloning of the SMP genes from C. glutamicum
allows
for the generation of probes and primers designed for use in identifying
and/or cloning
SMP homologues in other cell types and organisms, as well as SMP homologues
from
other Corynebacteria or related species. The probe/primer typically comprises
substantially purified oligonucleotide. The oligonucleotide typically
comprises a region
of nucleotide sequence that hybridizes under stringent conditions to at least
about 12,
preferably about 25, more preferably about 40, 50 or 75 consecutive
nucleotides of a
sense strand of one of the nucleotide sequences of the invention (e.g., a
sequence of one
of the odd-numbered SEQ ID NOs of the Sequence Listing), an anti-sense
sequence of
one of these sequences, or naturally occurring mutants thereof. Primers based
on a
nucleotide sequence of the invention can be used in PCR reactions to clone SMP
homologues. Probes based on the SMP nucleotide sequences can be used to detect
transcripts or genomic sequences encoding the same or homologous proteins. In
preferred embodiments, the probe further comprises a label group attached
thereto, e.g.
the label group can be a radioisotope, a fluorescent compound, an enzyme, or
an enzyme
co-factor. Such probes can be used as a part of a diagnostic test kit for
identifying cells
which misexpress an SMP protein, such as by measuring a level of an SMP-
encoding
CA 02584021 2007-04-18
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nucleic acid in a sample of cells, e.g., detecting SMP mRNA levels or
determining
whether a genomic SMP gene has been mutated or deleted.
In one embodiment, the nucleic acid molecule of the invention encodes a
protein
or portion thereof which includes an amino acid sequence which is sufficiently
homologous to an amino acid sequence of the invention (e.g., a sequence of an
even-
numbered SEQ ID NO of the Sequence Listing) such that the protein or portion
thereof
maintains the ability to perform a function involved in the metabolism of
carbon
compounds such as sugars or in the generation of energy molecules (e.g., ATP)
by
processes such as oxidative phosphorylation in Corynebacterium glutamicum. As
used
herein, the language "sufficiently homologous" refers to proteins or portions
thereof
which have amino acid sequences which include a minimum number of identical or
equivalent (e.g., an amino acid residue which has a similar side chain as an
amino acid
residue in a sequence of one of the even-numbered SEQ ID NOs of the Sequence
Listing) amino acid residues to an amino acid sequence of the invention such
that the
protein or portion thereof is able to perform a function involved in the
metabolism of
carbon compounds such as sugars or in the generation of energy molecules
(e.g., ATP)
by processes such as oxidative phosphorylation in Corynebacterium glutamicum.
Protein members of such sugar metabolic pathways or energy producing systems,
as
described herein, may play a role in the production and secretion of one or
more fine
chemicals. Examples of such activities are also described herein. Thus, "the
function of
an SMP protein" contributes either directly or indirectly to the yield,
production, and/or
efficiency of production of one or more fine chemicals. Examples of SMP
protein
activities are set forth in Table 1.
In another embodiment, the protein is at least about 50-60%, preferably at
least
about 60-70%, and more preferably at least about 70-80%, 80-90%, 90-95%, and
most
preferably at least about 96%, 97%, 98%, 99% or more homologous to an entire
amino
acid sequence of the invention(e.g., a sequence of an even-numbered SEQ ID NO:
of the
Sequence Listing).
Portions of proteins encoded by the SMP nucleic acid molecules of the
invention
are preferably biologically active portions of one of the SMP proteins. As
used herein,
the term "biologically active portion of an SMP protein" is intended to
include a portion,
e.g., a domain/motif, of an SMP protein that participates in the metabolism of
carbon
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compounds such as sugars, or in energy-generating pathways in C. glutamicum,
or has
an activity as set forth in Table 1. To determine whether an SMP protein or a
biologically active portion thereof can participate in the metabolism of
carbon
compounds or in the production of energy-rich molecules in C. glutamicum, an
assay of
enzymatic activity may be performed. Such assay methods are well known to
those of
ordinary skill in the art, as detailed in Example 8 of the Exemplification.
Additional nucleic acid fragments encoding biologically active portions of an
SMP protein can be prepared by isolating a portion of one of the amino acid
sequences
of the invention (e.g., a sequence of an even-numbered SEQ ID NO: of the
Sequence
Listing), expressing the encoded portion of the SMP protein or peptide (e.g.,
by
recombinant expression in vitro) and assessing the activity of the encoded
portion of the
SMP protein or peptide.
The invention further encompasses nucleic acid molecules that differ from one
of
the nucleotide sequences of the invention (e.g., a sequence of an odd-numbered
SEQ ID
NO: of the Sequence Listing) (and portions thereof) due to degeneracy of the
genetic
code and thus encode the same SMP protein as that encoded by the nucleotide
sequences
of the invention. In another embodiment, an isolated nucleic acid molecule of
the
invention has a nucleotide sequence encoding a protein having an amino acid
sequence
shown in the Sequence Listing (e.g., an even-numbered SEQ ID NO:). In a still
further
embodiment, the nucleic acid molecule of the invention encodes a full length
C.
glutamicum protein which is substantially homologous to an amino acid of the
invention
(encoded by an open reading frame shown in an odd-numbered SEQ ID NO: of the
Sequence Listing).
It will be understood by one of ordinary skill in the art that in one
embodiment
the sequences of the invention are not meant to include the sequences of the
prior art,
such as those Genbank sequences set forth in Tables 2 or 4 which were
available prior to
the present invention. In one embodiment, the invention includes nucleotide
and amino
acid sequences having a percent identity to a nucleotide or amino acid
sequence of the
invention which is greater than that of a sequence of the prior art (e.g., a
Genbank
sequence (or the protein encoded by such a sequence) set forth in Tables 2 or
4). For
example, the invention includes a nucleotide sequence which is greater than
and/or at
least 58% identical to the nucleotide sequence designated RXA00014 (SEQ ID
NO:41),
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CA 02584021 2007-04-18
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a nucleotide sequence which is greater than and/or at least % identical to the
nucleotide
sequence designated RJCA00195 (SEQ ID NO:399), and a nucleotide sequence which
is
greater than and/or at least 42% identical to the nucleotide sequence
designated
RXA00196 (SEQ ID NO:401). One of ordinary skill in the art would be able to
calculate the lower threshold of percent identity for any given sequence of
the invention
by examining the GAP-calculated percent identity scores set forth in Table 4
for each of
the three top hits for the given sequence, and by subtracting the highest GAP-
calculated
percent identity from 100 percent. One of ordinary skill in the art will also
appreciate
that nucleic acid and amino acid sequences having percent identities greater
than the
lower threshold so calculated (e.g., at least 50%, 51%, 52%, 53%, 54%, 55%,
56%,
57%, 58%, 59%, or 60%, preferably at least about 61%, 62%, 63%, 64%, 65%, 66%,
67%, 68%, 69%, or 70%, more preferably at least about 71%, 72%, 73%, 74%, 75%,
76%, 77%, 78%, 79%, or 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, or
90%, or 91%, 92%, 93%, 94%, and even more preferably at least about 95%, 96%,
97%,
98%, 99% or more identical) are also encompassed by the invention.
In addition to the C glutamicum SMP nucleotide sequences set forth in the
Sequence Listing as odd-numbered SEQ ID NOs, it will be appreciated by those
of
ordinary skill in the art that DNA sequence polymorphisms that lead to changes
in the
amino acid sequences of SMP proteins may exist within a population (e.g., the
C.
glutamicum population). Such genetic polymorphism in the SMP gene may exist
among
individuals within a population due to natural variation. As used herein, the
terms
"gene" and "recombinant gene" refer to nucleic acid molecules comprising an
open
reading frame encoding an SMP protein, preferably a C. glutamicum SMP protein.
Such
natural variations can typically result in 1-5% variance in the nucleotide
sequence of the
SMP gene. Any and all such nucleotide variations and resulting amino acid
polymorphisms in SMP that are the result of natural variation and that do not
alter the
functional activity of SMP proteins are intended to be within the scope of the
invention.
Nucleic acid molecules corresponding to natural variants and non-C.
glutarnicum
homologues of the C. glutamicum SMP DNA of the invention can be isolated based
on
3C- their homology to the C. glutarnicum SMP nucleic acid disclosed herein
using the C.
glutamicum DNA, or a portion thereof, as a hybridization probe according to
standard
hybridization techniques under stringent hybridization conditions.
Accordingly, in
11
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another embodiment, an isolated nucleic acid molecule of the invention is at
least 15
nucleotides in length and hybridizes under stringent conditions to the nucleic
acid
molecule comprising a nucleotide sequence of of an odd-numbered SEQ ID NO: of
the
Sequence Listing. In other embodiments, the nucleic acid is at least 30, 50,
100, 250 or
more nucleotides in length. As used herein, the term "hybridizes under
stringent
conditions" is intended to describe conditions for hybridization and washing
under
which nucleotide sequences at least 60% homologous to each other typically
remain
hybridized to each other. Preferably, the conditions are such that sequences
at least
about 65%, more preferably at least about 70%, and even more preferably at
least about
75% or more homologous to each other typically remain hybridized to each
other. Such
stringent conditions are known to those of ordinary skill in the art and can
be found in
Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-
6.3.6.
A preferred, non-limiting example of stringent hybridization conditions are
hybridization in 6X sodium chloride/sodium citrate (SSC) at about 45 C,
followed by
one or more washes in 0.2 X SSC, 0.1% SDS at 50-65 C. Preferably, an isolated
nucleic acid molecule of the invention that hybridizes under stringent
conditions to a
nucleotide sequence of the invention corresponds to a naturally-occurring
nucleic acid
molecule. As used herein, a "naturally-occurring" nucleic acid molecule refers
to an
RNA or DNA molecule having a nucleotide sequence that occurs in nature (e.g.,
encodes a natural protein). In one embodiment, the nucleic acid encodes a
natural C.
glutamicum SMP protein.
In addition to naturally-occurring variants of the SMP sequence that may exist
in
the population, one of ordinary skill in the art will further appreciate that
changes can be
introduced by mutation into a nucleotide sequence of the invention, thereby
leading to
changes in the amino acid sequence of the encoded SMP protein, without
altering the
functional ability of the SMP protein. For example, nucleotide substitutions
leading to
amino acid substitutions at "non-essential" amino acid residues can be made in
a
nucleotide sequence of the invention. A "non-essential" amino acid residue is
a residue
that can be altered from the wild-type sequence of one of the SMP proteins
(e.g., an
even-numbered SEQ ID NO: of the Sequence Listing) without altering the
activity of
said SMP protein, whereas an "essential" amino acid residue is required for
SMP protein
activity. Other amino acid residues, however, (e.g., those that are not
conserved or only
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CA 02584021 2007-04-18
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semi-conserved in the domain having SMP activity) may not be essential for
activity and
thus are likely to be amenable to alteration without altering SMP activity.
Accordingly, another aspect of the invention pertains to nucleic acid
molecules
encoding SMP proteins that contain changes in amino acid residues that are not
essential
for SMP activity. Such SMP proteins differ in amino acid sequence from a
sequence of
an even-numbered SEQ ID NO: of the Sequence Listing yet retain at least one of
the
SMP activities described herein. In one embodiment, the isolated nucleic acid
molecule
comprises a nucleotide sequence encoding a protein, wherein the protein
comprises an
amino acid sequence at least about 50% homologous to an amino acid sequence of
the
invention and is capable of participate in the metabolism of carbon compounds
such as
sugars, or in the biosynthesis of high-energy compounds in C. glutamicum, or
has one or
more activities set forth in Table 1. Preferably, the protein encoded by the
nucleic acid
molecule is at least about 50-60% homologous to the amino acid sequence of one
of the
odd-numbered SEQ ID NOs of the Sequence Listing, more preferably at least
about 60-
70% homologous to one of these sequences, even more preferably at least about
70-
80%, 80-90%, 90-95% homologous to one of these sequences, and most preferably
at
least about 96%, 97%, 98%, or 99% homologous to one of the amino acid
sequences of
the invention.
To determine the percent homology of two amino acid sequences (e.g., one of
the amino acid sequences of the invention and a mutant form thereof) or of two
nucleic
acids, the sequences are aligned for optimal comparison purposes (e.g., gaps
can be
introduced in the sequence of one protein or nucleic acid for optimal
alignment with the
other protein or nucleic acid). The amino acid residues or nucleotides at
corresponding
amino acid positions or nucleotide positions are then compared. When a
position in one
sequence (e.g., one of the amino acid sequences the invention) is occupied by
the same
amino acid residue or nucleotide as the corresponding position in the other
sequence
(e.g., a mutant form of the amino acid sequence), then the molecules are
homologous at
that position (i.e., as used herein amino acid or nucleic acid "homology" is
equivalent to
amino acid or nucleic acid "identity"). The percent homology between the two
sequences is a function of the number of identical positions shared by the
sequences
(r. e. ,% homology = # of identical positions/total # of positions x 100).
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CA 02584021 2007-04-18
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An isolated nucleic acid molecule encoding an SMP protein homologous to a
protein sequence of the invention (e.g., a sequence of an even-numbered SEQ ID
NO: of
the Sequence Listing) can be created by introducing one or more nucleotide
substitutions, additions or deletions into a nucleotide sequence of the
invention such that
one or more amino acid substitutions, additions or deletions are introduced
into the
encoded protein. Mutations can be introduced into one of the nucleotide
sequences of
the invention by standard techniques, such as site-directed mutagenesis and
PCR-
mediated mutagenesis. Preferably, conservative amino acid substitutions are
made at
one or more predicted non-essential amino acid residues. A "conservative amino
acid
substitution" is one in which the amino acid residue is replaced with an amino
acid
residue having a similar side chain. Families of amino acid residues having
similar side
chains have been defined in the art. These families include amino acids with
basic side
chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic
acid, glutamic
acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine,
serine,
threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine,
leucine,
isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched
side chains
(e.g., threonine, valine, isoleucine) and aromatic side chains (e.g.,
tyrosine,
phenylalanine, tryptophan, histidine). Thus, a predicted nonessential amino
acid residue
in an SMP protein is preferably replaced with another amino acid residue from
the same
side chain family. Alternatively, in another embodiment, mutations can be
introduced
randomly along all or part of an SMP coding sequence, such as by saturation
mutagenesis, and the resultant mutants can be screened for an SMP activity
described
herein to identify mutants that retain SMP activity. Following mutagenesis of
the
nucleotide sequence of one of the odd-numbered SEQ ID NOs of the Sequence
Listing,
the encoded protein can be expressed recombinantly and the activity of the
protein can
be determined using, for example, assays described herein (see Example 8 of
the
Exemplification).
In addition to the nucleic acid molecules encoding SMP proteins described
above, another aspect of the invention pertains to isolated nucleic acid
molecules which
are antisense thereto. An "antisense" nucleic acid comprises a nucleotide
sequence
which is complementary to a "sense" nucleic acid encoding a protein, e.g.,
complementary to the coding strand of a double-stranded DNA molecule or
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complementary to an mRNA sequence. Accordingly, an antisense nucleic acid can
hydrogen bond to a sense nucleic acid. The antisense nucleic acid can be
complementary to an entire SMP coding strand, or to only a portion thereof. In
one
embodiment, an antisense nucleic acid molecule is antisense to a "coding
region" of the
coding strand of a nucleotide sequence encoding an SMP protein. The term
"coding
region" refers to the region of the nucleotide sequence comprising codons
which are
translated into amino acid residues (e.g., the entire coding region of NO. 3
(RXA01626)
comprises nucleotides I to 345). In another embodiment, the antisense nucleic
acid
molecule is antisense to a"noncoding region" of the coding strand of a
nucleotide
sequence encoding SMP. The term "noncoding region" refers to 5' and 3'
sequences
which flank the coding region that are not translated into amino acids (i.e.,
also referred
to as 5' and 3' untranslated regions).
Given the coding strand sequences encoding SMP disclosed herein (e.g., the
sequences set forth as odd-numbered SEQ ID NOs in the Sequence Listing),
antisense
1.5 nucleic acids of the invention can be designed according to the rules of
Watson and
Crick base pairing. The antisense nucleic acid molecule can be complementary
to the
entire coding region of SMP mRNA, but more preferably is an oligonucleotide
which is
antisense to only a portion of the coding or noncoding region of SMP mRNA. For
example, the antisense oligonucleotide can be complementary to the region
surrounding
the translation start site of SMP mRNA. An antisense oligonucleotide can be,
for
example, about 5, 10, 15, 20, 25, 30, 35, 40,45 or 50 nucleotides in length.
An
antisense nucleic acid of the invention can be constructed using chemical
synthesis and
enzymatic ligation reactions using procedures known in the art. For example,
an
antisense nucleic acid (e.g., an antisense oligonucleotide) can be chemically
synthesized
using naturally occurring nucleotides or variously modified nucleotides
designed to
increase the biological stability of the molecules or to increase the physical
stability of
the duplex formed between the antisense and sense nucleic acids, e.g.,
phosphorothioate
derivatives and acridine substituted nucleotides can be used. Examples of
modified
nucleotides which can be used to generate the antisense nucleic acid include 5-
fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine,
xanthine, 4-
acetylcytosine, 5-(carboxyhydroXylmethyl) uracil, 5-carboxymethylaminomethyl-2-
thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-
I
" 1 6 .
CA 02584021 2007-04-18
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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, 5'-
methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-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. Alternatively, the
antisense
nucleic acid can be produced biologically using an expression vector into
which a
nucleic acid has been subcloned in an antisense orientation (i.e., RNA
transcribed from
the inserted nucleic acid will be of an antisense orientation to a target
nucleic acid of
interest, described further in the following subsection).
The antisense nucleic acid molecules of the invention are typically
administered
to a cell or generated in situ such that they hybridize with or bind to
cellular mRNA
andlor genomic DNA encoding an SMP protein to thereby inhibit expression of
the
protein, e.g., by inhibiting transcription and/or translation. The
hybridization can be by
conventional nucleotide complementarity to form a stable duplex, or, for
example, in the
case of an antisense nucleic acid molecule which binds to DNA duplexes,
through
specific interactions in the major groove of the double helix. The antisense
molecule can
be modified such that it specifically binds to a receptor or an antigen
expressed on a
selected cell surface, e.g., by linking the antisense nucleic acid molecule to
a peptide or
an antibody which binds to a cell surface receptor or antigen. The antisense
nucleic acid
molecule can also be delivered to cells using the vectors described herein. To
achieve
sufficient intracellular concentrations of the antisense molecules, vector
constructs in
which the antisense nucleic acid molecule is placed under the control of a
strong
prokaryotic, viral, or eukaryotic promoter are preferred.
In yet another embodiment, the antisense nucleic acid molecule of the
invention
is an a-anomeric nucleic acid molecule. An a-anomeric nucleic acid molecule
forms
specific double-stranded hybrids with complementary RNA in which, contrary to
the
usual R-units, the strands run parallel to each other (Gaultier et al. (1987)
Nucleic Acids.
Res. 15:6625-6641). The antisense nucleic acid molecule can also comprise a 2'-
o-
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methylribonucleotide (Inoue et al. (1987) Nucleic Acids Res. 15:6131-6148) or
a
chimeric RNA-DNA analogue (Inoue et al. (1987) FEBSLett. 215:327-330).
In still another embodiment, an antisense nucleic acid of the invention is a
ribozyme. Ribozymes are catalytic RNA molecules with ribonuclease activity
which are
capable of cleaving a single-stranded nucleic acid, such as an mRNA, to which
they
have a complementary region. Thus, ribozymes (e.g., hammerhead ribozymes
(described in Haselhoff and Gerlach (1988) Nature 334:585-591)) can be used to
catalytically cleave SMP mRNA transcripts to thereby inhibit translation of
SMP
mRNA. A ribozyme having specificity for an SMP-encoding nucleic acid can be
designed based upon the nucleotide sequence of an SMP cDNA disclosed herein
(i.e.,
SEQ ID NO. 3(RXA01626)). For example, a derivative of a Teirahymena L-19 IVS
RNA can be constructed in which the nucleotide sequence of the active site is
complementary to the nucleotide sequence to be cleaved in an SMP-encoding
mRNA.
See, e.g., Cech et a!. U.S. Patent No. 4,987,071 and Cech ef al. U.S. Patent
No.
5,116,742. Alternatively, SMP mRNA can be used to select a catalytic RNA
having a
specific ribonuclease activity from a pool of RNA molecules. See, e.g.,
Bartel, D. and
Szostak, J.W. (1993) Science 261:1411-1418.
Alternatively, SMP gene expression can be inhibited by targeting nucleotide
sequences complementary to the regulatory region of an SMP nucleotide sequence
(e.g.,
an SMP promoter and/or enhancers) to form triple helical structures that
prevent
transcription of an SMP gene in target cells. See generally, Helene, C. (1991)
Anticancer Drug Des. 6(6):569-84; Helene, C. et al. (1992) Ann. N. Y. Acad.
Sci. 660:27-
36; and Maher, L.J. (1992) Bioassays 14(12):807-15.
B. Recombinant Expression Vectors and Host Cells
Another aspect of the invention pertains to vectors, preferably expression
vectors, containing a nucleic acid encoding an SMP protein (or a portion
thereof). As
used herein, the term "vector" refers to a nucleic acid molecule capable of
transporting
another nucleic acid to which it has been linked. One type of vector is
a"plasmid",
which refers to a circular double stranded DNA loop into which additional DNA
segments can be ligated. Another type of vector is a viral vector, wherein
additional
DNA segments can be ligated into the viral genome. Certain vectors are capable
of
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autonomous replication in a host cell into which they are introduced (e.g.,
bacterial
vectors having a bacterial origin of replication and episomal mammalian
vectors). Other
vectors (e.g., non-episomal mammalian vectors) are integrated into the genome
of a host
cell upon introduction into the host cell, and thereby are replicated along
with the host
genome. Moreover, certain vectors are capable of directing the expression of
genes to
which they are operatively linked. Such vectors are referred to herein as
"expression
vectors". In general, expression vectors of utility in recombinant DNA
techniques are
often in the form of plasmids. In the present specification, "plasmid" and
"vector" can
be used interchangeably as the plasmid is the most commonly used form of
vector.
However, the invention is intended to include such other forms of expression
vectors,
such as viral vectors (e.g., replication defective retroviruses, adenoviruses
and adeno-
associated viruses), which serve equivalent functions.
The recombinant expression vectors of the invention comprise a nucleic acid of
the invention in a form suitable for expression of the nucleic acid in a host
cell, which
means that the recombinant expression vectors include one or more regulatory
sequences, selected on the basis of the host cells to be used for expression,
which is
operatively linked to the nucleic acid sequence to be expressed. Within a
recombinant
expression vector, "operably linked" is intended to mean that the nucleotide
sequence of
interest is linked to the regulatory sequence(s) in a manner which allows for
expression
of the nucleotide sequence (e.g., in an in vitro transcription/translation
system or in a
host cell when the vector is introduced into the host cell). The term
"regulatory
sequence" is intended to include promoters, enhancers and other expression
control
elements (e.g., polyadenylation signals). Such regulatory sequences are
described, for
example, in Goeddel; Gene Expression Technology: Methods in Enzymology 185,
:25 Academic Press, San Diego, CA (1990). Regulatory sequences include those
which
direct constitutive expression of a nucleotide sequence in many types of host
cell and
those which direct expression of the nucleotide sequence only in certain host
cells.
Preferred regulatory sequences are, for example, promoters such as cos-, tac-,
trp-, tet-,
trp-tet-, Ipp-, lac-, lpp-lac-, lacr-, T7-, T5-, T3-, gal-, trc-, ara-, SP6-,
amy, SPO2, X-PR-
:30 or k PL, which are used preferably in bacteria. Additional regulatory
sequences are, for
example, promoters from yeasts and fungi, such as ADC 1, MFa, AC, P-60, CYC 1,
GAPDH, TEF, rp28, ADH, promoters from plants such as CaMV/35S, SSU, OCS, lib4,
i 1 1. I Y 14 =..
CA 02584021 2007-04-18
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usp, STLS 1, B33, nos or ubiquitin- or phaseolin-promoters. It is also
possible to use
artificial promoters. It will be appreciated by those of ordinary skill in the
art that the
design of the expression vector can depend on such factors as the choice of
the host cell
to be transformed, the level of expression of protein desired, etc. The
expression vectors
of the invention can be introduced into host cells to thereby produce proteins
or
peptides, including fusion proteins or peptides, encoded by nucleic acids as
described
herein (e.g., SMP proteins, mutant forms of SMP proteins, fusion proteins,
etc.).
The recombinant expression vectors of the invention can be designed for
expression of SMP proteins in prokaryotic or eukaryotic cells. For example,
SMP genes
can be expressed in bacterial cells such as C. glutamicum, insect cells (using
baculovirus
expression vectors), yeast and other fungal cells (see Romanos, M.A. et al.
(1992)
"Foreign gene expression in yeast: a review", Yeast 8: 423-488; van den
Hondel,
C.A.M.J.J. et al. (1991) "Heterologous gene expression in fi lamentous fungi"
in: More
Gene Manipulations in Fungi, J.W. Bennet & L.L. Lasure, eds., p. 396-428:
Academic
Press: San Diego; and van den Hondel, C.A.M.J.J. & Punt, P.J. (1991) "Gene
transfer
systems and vector development for filamentous fungi, in: Applied Molecular
Genetics
of Fungi, Peberdy, J.F. et al., eds., p. 1-28, Cambridge University Press:
Cambridge),
algae and multicellular plant cells (see Schmidt, R. and Willmitzer, L. (1988)
High
efficiency Agrobacterium tumefaciens -mediated transformation of Arabidopsis
thaliana leaf and cotyledon explants" Plant Cell Rep: 583-586), or mammalian
cells.
Suitable host cells are discussed further in Goeddel, Gene Expression
Technology:
Methods in Enzymology 185, Academic Press, San Diego, CA (1990).
Alternatively, the
recombinant expression vector can be transcribed and translated in vitro, for
example
using T7 promoter regulatory sequences and T7 polymerase.
Expression of proteins in prokaryotes is most often carried out with vectors
containing constitutive or inducible promoters directing the expression of
either fusion
or non-fusion proteins. Fusion vectors add a number of amino acids to a
protein
encoded therein, usually to the amino terminus of the recombinant protein but
also to the
C-terminus or fused within suitable regions in the proteins. Such fusion
vectors
typically serve three purposes: 1) to increase expression of recombinant
protein; 2) to
increase the solubility of the recombinant protein; and 3) to aid in the
purification of the
recombinant protein by acting as a ligand in affinity purification. Often, in
fusion
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CA 02584021 2007-04-18
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expression vectors, a proteolytic cleavage site is introduced at the junction
of the fusion
moiety and the recombinant protein to enable separation of the recombinant
protein
from the fusion moiety subsequent to purification of the fusion protein. Such
enzymes,
and their cognate recognition sequences, include Factor Xa, thrombin and
enterokinase.
Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith,
D.B. and Johnson, K.S. (1988) Gene 67:31-40), pMAL (New England Biolabs,
Beverly,
MA) and pRIT5 (Pharmacia, Piscataway, NJ) which fuse glutathione S-transferase
(GST), maltose E binding protein, or protein A, respectively, to the target
recombinant
protein. In one embodiment, the coding sequence of the SMP protein is cloned
into a
pGEX expression vector to create a vector encoding a fusion protein
comprising, from
the N-terminus to the C-terminus, GST-thrombin cleavage site-X protein. The
fusion
protein can be purified by affinity chromatography using glutathione-agarose
resin.
Recombinant SMP protein unfused to GST can be recovered by cleavage of the
fusion
protein with thrombin.
Examples of suitable inducible non-fusion E. coli expression vectors include
pTrc (Amann et al., (1988) Gene 69:301-315), pLG338, pACYCl84, pBR322, pUC18,
pUC 19, pKC30, pRep4, pHS 1, pHS2, pPLc236, pMBL24, pLG200, pUR290, pIN-
II1113-B 1, kgtl 1, pBdCl, and pET l ld (Studier et al., Gene Expression
Technology:
Methods in Enzymology 185, Academic Press, San Diego, California (1990) 60-89;
and
Pouwels et al., eds. (1985) Cloning Vectors. Elsevier: New York IBSN 0 444
904018).
Target gene expression from the pTrc vector relies on host RNA polymerase
transcription from a hybrid trp-lac fusion promoter. Target gene expression
from the
pET I 1 d vector relies on transcription from a T7 gnl 0-lac fusion promoter
mediated by
a coexpressed viral RNA polymerase (T7 gnl). This viral polymerase is supplied
by
host strains BL21(DE3) or HMS174(DE3) from a resident X prophage harboring a
T7
gnl gene under the transcriptional control of the lacUV 5 promoter. For
transformation
of other varieties of bacteria, appropriate vectors may be selected. For
example, the
plasrnids pIJ101, pIJ364, pIJ702 and pIJ361 are known to be useful in
transforming
Streptomyces, while plasmids pUB I 10, pC 194, or pBD214 are suited for
transformation
of Bacillus species. Several plasmids of use in the transfer of genetic
information into
Corynebacterium include pHM 1519, pBLI, pSA77, or pAJ667 (Pouwels et al., eds.
(1985) Cloning Vectors. Elsevier: New York IBSN 0 444 904018).
1 1
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One strategy to maximize recombinant protein expression is to express the
protein in a host bacteria with an impaired capacity to proteolytically cleave
the
recombinant protein (Gottesman, S., Gene Expression Technology: Methods in
Enzymology 185, Academic Press, San Diego, Califomia (1990) 119-128). Another
strategy is to alter the nucleic acid sequence of the nucleic acid to be
inserted into an
expression vector so that the individual codons for each amino acid are those
preferentially utilized in the bacterium chosen for expression, such as C.
glutamicum
(Wada et al. (1992) Nucleic Acids Res. 20:2111-2118). Such alteration of
nucleic acid
sequences of the invention can be carried out by standard DNA synthesis
techniques.
In another embodiment, the SMP protein expression vector is a yeast expression
vector. Examples of vectors for expression in yeast S. cerevisiae include
pYepSecl
(Baldari, et al., (1987) Embo J. 6:229-234), 2 , pAG-1, Yep6, Yep 13,
pEMBLYe23,
pMFa (Kurjan and Herskowitz, (1982) Cell 30:933-943), pJRY88 (Schultz et al.,
(1987)
Gene 54:113-123), and pYES2 (Invitrogen Corporation, San Diego, CA). Vectors
and
methods for the construction of vectors appropriate for use in other fungi,
such as the
filamentous fungi, include those detailed in: van den Hondel, C.A.M.J.J. &
Punt, P.J.
(1991) "Gene transfer systems and vector development for filamentous fungi,
in:
Applied Molecular Genetics of Fungi, J.F. Peberdy, et al., eds., p. 1-28,
Cambridge
University Press: Cambridge, and Pouwels et al., eds. (1985) Cloning Vectors.
Elsevier:
New York (IBSN 0 444 904018).
Alternatively, the SMP proteins of the invention can be expressed in insect
cells
using baculovirus expression vectors. Baculovirus vectors available for
expression of
proteins in cultured insect cells (e.g., Sf 9 cells) include the pAc series
(Smith et al.
(1983) Mol. Cell Biol. 3:2156-2165) and the pVL series (Lucklow and Summers
(1989)
Virology 170:31-39).
In another embodiment, the SMP proteins of the invention may be expressed in
unicellular plant cells (such as algae) or in plant cells from higher plants
(e.g., the
spermatophytes, such as crop plants). Examples of plant expression vectors
include
those detailed in: Becker, D., Kemper, E., Schell, J. and Masterson, R. (1992)
"New
plant binary vectors with selectable markers located proximal to the left
border", Plant
Mol. Biol. 20: 1195-1197; and Bevan, M.W. (1984) "Binary Agrobacterium vectors
for
plant transformation", Nuc1. Acid Res. 12: 8711-8721, and include pLGV23,
pGHlac+,
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CA 02584021 2007-04-18
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pBIN19, pAK2004, and pDH51 (Pouwels et al., eds. (1985) Cloning Vectors.
Elsevier:
New York IBSN 0 444 904018). .
In yet another embodiment, a nucleic acid of the invention is expressed in
mammalian cells using a mammalian expression vector. Examples of mammalian
expression vectors include pCDM8 (Seed, B. (1987) Nature 329:840) and pMT2PC
(Kaufman et al. (1987) EMBO J. 6:187-195). When used in mammalian cells, the
expression vector's control functions are often provided by viral regulatory
elements.
For example, commonly used promoters are derived from polyoma, Adenovirus 2,
cytomegalovirus and Simian Virus 40. For other suitable expression systems for
both
prokaryotic and eukaryotic cells see chapters 16 and 17 of Sambrook, J.,
Fritsh, E. F.,
and Maaiatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring
Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor,
NY,
1989.
In another embodiment, the recombinant mammalian expression vector is
capable of directing expression of the nucleic acid preferentially in a
particular cell type
(e.g., tissue-specific regulatory elements are used to express the nucleic
acid). Tissue-
specific regulatory elements are known in the art. Non-limiting examples of
suitable
tissue-specific promoters include the albumin promoter (liver-specific;
Pinkert et al.
(1987) Genes Dev. 1:268-277), lymphoid-specific promoters (Calame and Eaton
(1988)
Adv. Immunol, 43:235-275), in particular promoters of T cell receptors (Winoto
and
Baltimore (1989) EMBOJ. 8:729-733) and immunoglobulins (Banerji et al. (1983)
Cell
33:729-740; Queen and Baltimore (1983) Cell 33:741-748), neuron-specific
promoters
(e.g., the neurofilament promoter; Byrne and Ruddle (1989) PNAS 86:5473-5477),
pancreas-specific promoters (Edlund et al. (1985) Science 230:912-916), and
mammary
gland-specific promoters (e.g., milk whey promoter; U.S. Patent No. 4,873,316
and
European Application Publication No. 264,166). Developmentally-regulated
promoters
are also encompassed, for example the murine hox promoters (Kessel and Gruss
(1990)
Science 249:374-379) and the a-fetoprotein promoter (Campes and Tilghman
(1989)
Genes Dev. 3:537-546).
31) The invention further provides a recombinant expression vector comprising
a
DNA molecule of the invention cloned into the expression vector in an
antisense
orientation. That is, the DNA molecule is operatively linked to a regulatory
sequence in
II
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a manner which allows for expression (by transcription of the DNA molecule) of
an
RNA molecule which is antisense to SMP mRNA. Regulatory sequences operatively
linked to a nucleic acid cloned in the antisense orientation can be chosen
which direct
the continuous expression of the antisense RNA molecule in a variety of cell
types, for
instance viral promoters and/.or enhancers, or regulatory sequences can be
chosen which
direct constitutive, tissue specific or cell type specific expression of
antisense RNA.
The antisense expression vector can be in the form of a recombinant plasmid,
phagemid
or attenuated virus in which antisense nucleic acids are produced under the
control of a
high efficiency regulatory region, the activity of which can be determined by
the cell
type into which the vector is introduced. For a discussion of the regulation
of gene
expression using antisense genes see Weintraub, H. et al., Antisense RNA as a
molecular tool for genetic analysis, Reviews - Trends in Genetics, Vol. 1(1)
1986.
Another aspect of the invention pertains to host cells into which a
recombinant
expression vector of the invention has been introduced. The terms "host cell"
and
"recombinant host cell" are used interchangeably herein. It is understood that
such
terms refer not only 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 or 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.
A host cell can be any prokaryotic or eukaryotic cell. For example, an SMP
protein can be expressed in bacterial cells such as C. glutamicum, insect
cells, yeast or
mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells).
Other
suitable host cells are known to one of ordinary skill in the art.
Microorganisms related
to Corynebacterium glulamicum which may be conveniently used as host cells for
the
nucleic acid and protein molecules of the invention are set forth in Table 3.
Vector DNA can be introduced into prokaryotic or eukaryotic cells via
conventional transformation or transfection techniques. As used herein, the
terms
"transformation" and "transfection", "conjugation" and "transduction" are
intended to
refer to a variety of art-recognized techniques for introducing foreign
nucleic acid (e.g.,
linear DNA or RNA (e.g., a linearized vector or a gene construct alone without
a vector)
or nucleic acid in the form of a vector (e.g., a plasmid, phage, phasmid,
phagemid,
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CA 02584021 2007-04-18
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transposon or other DNA) into a host cell, including calcium phosphate or
calcium
chloride co-precipitation, DEAE-dextran-mediated transfection, lipofection,
natural
competence, chemical-mediated transfer, or electroporation. Suitable methods
for
transforming or transfecting host cells can be found in Sambrook, el al.
(Molecular
Cloning: A Laboratory Manual. 2nd, ed, Cold Spring Harbor Laboratory, Cold
Spring
Harbor Laboratory Press, Cold Spring Harbor, NY, 1989), and other laboratory
manuals.
For stable transfection of mammalian cells, it is known that, depending upon
the
expression vector and transfection technique used, only a small fraction of
cells may
integrate the foreign DNA into their genome. In order to identify and select
these
integrants, a gene that encodes a selectable marker (e.g., resistance to
antibiotics) is
generally introduced into the host cells along with the gene of interest.
Preferred
selectable markers include those which confer resistance to drugs, such as
G418,
hygromycin and methotrexate. Nucleic acid encoding a selectable marker can be
introduced into a host cell on the same vector as that encoding an SMP protein
or can be
introduced on a separate vector. Cells stably transfected with the introduced
nucleic
acid can be identified by, for example, drug selection (e.g., cells that have
incorporated
the selectable marker gene will survive, while the other cells die).
To create a homologous recombinant microorganism, a vector is prepared which
contains at least a portion of an SMP gene into which a deletion, addition or
substitution
has been introduced to thereby alter, e.g., functionally disrupt, the SMP
gene.
Preferably, this SMP gene is a Corynebacterium glutamicum SMP gene, but it can
be a
homologue from a related bacterium or even from a manunalian, yeast, or insect
source.
In a preferred embodiment, the vector is designed such that, upon homologous
recombination, the endogenous SMP gene is functionally disrupted (i.e., no
longer
encodes a functional protein; also referred to as a "knock out" vector).
Altematively,
the vector can be designed such that, upon homologous recombination, the
endogenous
SMP gene is mutated or otherwise altered but still encodes functional protein
(e.g., the
upstream regulatory region can be altered to thereby alter the expression of
the
endogenous SMP protein). In the homologous recombination vector, the altered
portion
of the SMP gene is flanked at its 5' and 3' ends by additional nucleic acid of
the SMP
gene to allow for homologous recombination to occur between the exogenous SMP
gene
carried by the vector and an endogenous SMP gene in a microorganism. The
additional
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CA 02584021 2007-04-18
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flanking SMP nucleic acid is of sufficient length for successful homologous
recombination with the endogenous gene. Typically, several kilobases of
flanking DNA
(both at the 5' and 3' ends) are included in the vector (see e.g., Thomas,
K.R., and
Capecchi, M.R. (1987) Cell 51: 503 for a description of homologous
recombination
vectors). The vector is introduced into a microorganism (e.g., by
electroporation) and
cells in which the introduced SMP gene has homologously recombined with the
endogenous SMP gene are selected, using art-known techniques.
In another embodiment, recombinant microorganisms can be produced which
contain selected systems which allow for regulated expression of the
introduced gene.
For example, inclusion of an SMP gene on a vector placing it under control of
the lac
operon permits expression of the SMP gene only in the presence of IPTG. Such
regulatory systems are well known in the art.
In another embodiment, an endogenous SMP gene in a host cell is disrupted
(e.g., by homologous recombination or other genetic means known in the art)
such that
expression of its protein product does not occur. In another embodiment, an
endogenous
or introduced SMP gene in a host cell has been altered by one or more point
mutations,
deletions, or inversions, but still encodes a functional SMP protein. In still
another
embodiment, one or more of the regulatory regions (e.g., a promoter,
repressor, or
inducer) of an SMP gene in a microorganism has been altered (e.g., by
deletion,
truncation, inversion, or point mutation) such that the expression of the SMP
gene is
modulated. One of ordinary skill in the art will appreciate that host cells
containing
more than one of the described SMP gene and protein modifications may be
readily
produced using the methods of the invention, and are meant to be included in
the present
invention.
A host cell of the invention, such as a prokaryotic or eukaryotic host cell in
culture, can be used to produce (i.e., express) an SMP protein. Accordingly,
the
invention further provides methods for producing SMP proteins using the host
cells of
the invention. In one embodiment, the method comprises culturing the host cell
of
invention (into which a recombinant expression vector encoding an SMP protein
has
been introduced, or into which genome has been introduced a gene encoding a
wild-type
or altered SMP protein) in a suitable medium until SMP protein is produced. In
another
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CA 02584021 2007-04-18
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embodiment, the method fiuther comprises isolating SMP proteins from the
medium or
the host cell.
C. Isolated SMP Proteins
Another aspect of the invention pertains to isolated SMP proteins, and
biologically active portions thereof. An "isolated" or "purified" protein or
biologically
active portion thereof is substantially free of cellular material when
produced by
recombinant DNA techniques, or chemical precursors or other chemicals when
chemically synthesized. The language "substantially free of cellular material"
includes
preparations of SMP protein in which the protein is separated from cellular
components
of the cells in which it is naturally or recombinantly produced. In one
embodiment, the
language "substantially free of cellular material" includes preparations of
SMP protein
having less than about 30% (by dry weight) of non-SMP protein (also referred
to herein
as a "contaminating protein"), more preferably less than about 20% of non-SMP
protein,
still more preferably less than about 10% of non-SMP protein, and most
preferably less
than about 5% non-SMP protein. When the SMP protein or biologically active
portion
thereof is recombinantly produced, it is also preferably substantially free of
culture
medium, f.e., culture medium represents less than about 20%, more preferably
less than
about 10%, and most preferably less than about 5% of the volume of the protein
preparation. The language "substantially free of chemical precursors or other
chemicals" includes preparations of SMP protein in which the protein is
separated from
chemical precursors or other chemicals which are involved in the synthesis of
the
protein. In one embodiment, the language "substantially free of chemical
precursors or
other chemicals" includes preparations of SMP protein having less than about
30% (by
dry weight) of chemical precursors or non-SMP chemicals, more preferably less
than
about 20% chemical precursors or non-SMP chemicals, still more preferably less
than
about I0% ehemical precursors or non-SMP chemicals, and most preferably less
than
about 5% chemical precursors or non-SMP chemicals. In preferred embodiments,
isolated proteins or biologically active portions thereof lack contaminating
proteins from
the same organism from which the SMP protein is derived. Typically, such
proteins are
produced by recombinant expression of, for example, a C. glutamicum SMP
protein in a
microorganism such as C. glutamicum.
II
I. IIY1
CA 02584021 2007-04-18
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An isolated SMP protein or a portion thereof of the invention can participate
in
the metabolism of carbon compounds such as sugars, or in the production of
energy
compounds (e.g., by oxidative phosphorylation) utilized to drive unfavorable
metabolic
pathways, or has one or more of the activities set forth in Table 1. In
preferred
embodiments, the protein or portion thereof comprises an amino acid sequence
which is
sufficiently homologous to an amino acid sequence of the invention (e.g., a
sequence of
an even-numbered SEQ ID NO: of the Sequence Listing) such that the protein or
portion
thereof maintains the ability to perform a function involved in the metabolism
of carbon
compounds such as sugars or in the generation of energy molecules by processes
such as
oxidative phosphorylation in Corynebacterium glutamicum. The portion of the
protein
is preferably a biologically active portion as described herein. In another
preferred
embodiment, an SMP protein of the invention has an amino acid sequence set
forth as an
even-numbered SEQ ID NO: of the Sequence Listing. In yet another preferred
embodiment, the SMP protein has an amino acid sequence which is encoded by a
nucleotide sequence which hybridizes, e.g., hybridizes under stringent
conditions, to a
nucleotidg sequence of the invention (e.g., a sequence of an odd-numbered SEQ
ID NO:
of the Sequence Listing). In still another preferred embodiment, the SMP
protein has an
amino acid sequence which is encoded by a nucleotide sequence that is at least
about
50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, or 60%, preferably at least
about 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, or 70%, more preferably at
least about 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, or 80%, 81%, 82%,
83%, 84%, 85%, 86%, 87%, 88%, 89%, or 90%, or 91%, 92%, 93%, 94%, and even
more preferably at least about 95%, 96%, 97%, 98%, 99% or more homologous to
one
of the nucleic acid sequences of the invention, or a portion thereof. Ranges
and identity
values intertnediate to the above-recited values, (e.g., 70-90% identical or
80-95%
identical) are also intended to be encompassed by the present invention. For
example,
ranges of identity values using a combination of any of the above values
recited as upper
and/or lower limits are intended to be included. The preferred SMP proteins of
the
present invention also preferably possess at least one of the SMP activities
described
herein. For example, a prefen-ed SMP protein of the present invention includes
an
amino acid sequence encoded by a nucleotide sequence which hybridizes, e.g.,
hybridizes under stringent conditions, to a nucleotide sequence of the
invention, and
I.I
CA 02584021 2007-04-18
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which can perform a function involved in the metabolism of carbon compounds
such as
sugars or in the generation of energy molecules (e.g., ATP) by processes such
as
oxidative phosphorylation in Corynebacterium glutamicum, or which has one or
more of
the activities set forth in Table 1.
In other embodiments, the SMP protein is substantially homologous to an amino
acid sequence of of the invention (e.g., a sequence of an even-numbered SEQ ID
NO: of
the Sequence Listing)and retains the functional activity of the protein of one
of the
amino acid sequences of the invention yet differs in amino acid sequence due
to natural
variation or mutagenesis, as described in detail in subsection I above.
Accordingly, in
another embodiment, the SMP protein is a protein which comprises an amino acid
sequence which is at least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%,
59 /a, or 60%, preferably at least about 61%, 62%, 63%, 64%, 65%, 66%, 67%,
68%,
69%, or 70%, more preferably at least about 71%, 72%, 73%, 74%, 75%, 76%, 77%,
78%, 79%, or 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, or 90%, or
1.5 91%, 92%, 93%, 94%, and even more preferably at least about 95%, 96%, 97%,
98%,
99% or more homologous to an entire amino acid sequence of the invention and
which
has at least one of the SMP activities described herein. Ranges and identity
values
intermediate to the above-recited values, (e.g., 70-90% identical or 80-95%
identical)
are also intended to be encompassed by the present invention. For example,
ranges of
identity values using a combination of any of the above values recited as
upper and/or
lower limits are intended to be included. In another embodiment, the invention
pertains
to a full length C. glutamicum protein which is substantially homologous to an
entire
amino acid sequence of the invention.
Biologically active portions of an SMP protein include peptides comprising
amino acid sequences derived from the amino acid sequence of an SMP protein,
e.g., an
amino acid sequence of an even-numbered SEQ ID NO: of the Sequence Listing or
the
amino acid sequence of a protein homologous to an SMP protein, which include
fewer
amino acids than a full length SMP protein or the full length protein which is
homologous to an SMP protein, and exhibit at least one activity of an SMP
protein.
Typically, biologically active portions (peptides, e.g., peptides which are,
for example,
5, 10, 15, 20, 30, 35, 36, 37, 38, 39, 40, 50, 100 or more amino acids in
length) comprise
a domain or motif with at least one activity of an SMP protein. Moreover,
other
' I1
i 1 li IillYd
CA 02584021 2007-04-18
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biologically active portions, in which other regions of the protein are
deleted, can be
prepared by recombinant techniques and evaluated for one or more of the
activities
described herein. Preferably, the biologically active portions of an SMP
protein include
one or more selected domains/motifs or portions thereof having biological
activity.
SMP proteins are preferably produced by recombinant DNA techniques. For
example, a nucleic acid molecule encoding the protein is cloned into an
expression
vector (as described above), the expression vector is introduced into a host
cell (as
described above) and the SMP protein is expressed in the host cell. The SMP
protein
can then be isolated from the cells by an appropriate purification scheme
using standard
protein purification techniques. Altennative to recombinant expression, an SMP
protein,
polypeptide, or peptide can be synthesized chemically using standard peptide
synthesis
techniques. Moreover, native SMP protein can be isolated from cells (e.g.,
endothelial
cells), for example using an anti-SMP antibody, which can be produced by
standard
techniques utilizing an SMP protein or fragment thereof of this invention.
The invention also provides SMP chimeric or fusion proteins. As used herein,
an
SMP "chimeric protein" or "fusion protein" comprises an SMP polypeptide
operatively
linked to a non-SMP polypeptide. An "SMP polypeptide" refers to a polypeptide
having
an amino acid sequence corresponding to an SMP protein, whereas a "non-SMP
polypeptide" refers to a polypeptide having an amino acid sequence
corresponding to a
protein which is not substantially homologous to the SMP protein, e.g., a
protein which
is different from the SMP protein and which is derived from the same or a
different
organism. Within the fusion protein, the term "operatively linked" is intended
to
indicate that the SMP polypeptide and the non-SMP polypeptide are fused in-
frame to
each other. The non-SMP polypeptide can be fused to the N-terminus or C-
terminus of
the SMP polypeptide. For example, in one embodiment the fusion protein is a
GST-
SMP fusion protein in which the SMP sequences are fused to the C-terminus of
the GST
sequences. Such fusion proteins can facilitate the purification of recombinant
SMP
proteins. In another embodiment, the fusion protein is an SMP protein
containing a
heterologous signal sequence at its N-terminus. In certain host cells (e.g.,
mammalian
host cells), expression and/or secretion of an SMP protein can be increased
through use
of a heterologous signal sequence.
, ~.
w w
CA 02584021 2007-04-18
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Preferably, an SMP chimeric or fusion protein of the invention is produced by
standard recombinant DNA techniques. For example, DNA fragments coding for the
different polypeptide sequences are ligated together in-frame in accordance
with
conventional techniques, for example by employing blunt-ended or stagger-ended
termini for ligation, restriction enzyme digestion to provide for appropriate
termini,
filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to
avoid
undesirable joining, and enzymatic ligation. In another embodiment, the fusion
gene
can be synthesized by conventional techniques including automated DNA
synthesizers.
Alternatively, PCR amplification of gene fragments can be carried out using
anchor
primers which give rise to complementary overhangs between two consecutive
gene
fragments which can subsequently be annealed and reamplified to generate a
chimeric
gene sequence (see, for example, Current Protocols in Molecular Biology,
Ausubel et
al., eds. John Wiley & Sons: 1992). Moreover, many expression vectors are
commercially available that already encode a fusion moiety (e.g., a GST
polypeptide).
An SMP-encoding nucleic acid can be cloned into such an expression vector such
that
the fusion moiety is linked in-frame to the SMP protein.
Homologues of the SMP protein can be generated by mutagenesis, e.g., discrete
point mutation or truncation of the SMP protein. As used herein, the term
"homologue"
refers to a variant fonn of the SMP protein which acts as an agonist or
antagonist of the
activity of the SMP protein. An agonist of the SMP protein can retain
substantially the
same, or a subset, of the biological activities of the SMP protein. An
antagonist of the
SMP protein can inhibit one or more of the activities of the naturally
occurring form of
the SMP protein, by, for example, competitively binding to a downstream or
upstream
member of the sugar molecule metabolic cascade or the energy-producing pathway
which includes the SMP protein.
In an alternative embodiment, homologues of the SMP protein can be identified
by screening combinatorial libraries of mutants, e.g., truncation mutants, of
the SMP
protein for SMP protein agonist or antagonist activity. In one embodiment, a
variegated
library of SMP variants is generated by combinatorial mutagenesis at the
nucleic acid
level and is encoded by a variegated gene library. A variegated library of SMP
variants
can be produced by, for example, enzymatically ligating a mixture of synthetic
oligonucleotides into gene sequences such that a degenerate set of potential
SMP
1
CA 02584021 2007-04-18
-53-
sequences is expressible as individual polypeptides, or altematively, as a set
of larger
fusion proteins (e.g., for phage display) containing the set of SMP sequences
therein.
There are a variety of methods which can be used to produce libraries of
potential SMP
homologues from a degenerate oligonucleotide sequence. Chemical synthesis of a
degenerate gene sequence can be performed in an automatic DNA synthesizer, and
the
synthetic gene then ligated into an appropriate expression vector. Use of a
degenerate
set of genes allows for the provision, in one mixture, of all of the sequences
encoding
the desired set of potential SMP sequences. Methods for synthesizing
degenerate
oligonucleotides are known in the art (see, e.g., Narang, S.A. (1983)
Tetrahedron 39:3;
Itakura el al. (1984) Annu. Rev. Biochem. 53:323; Itakura et al. (1984)
Science
198:1056; Ike et a1. (1983) Nucleic Acid Res. 11:477.
In addition, libraries of fragments of the SMP protein coding can be used to
generate a variegated population of SMP fragments for screening and subsequent
selection of homologues of an SMP protein. In one embodiment, a library of
coding
sequence fragments can be generated by treating a double stranded PCR fragment
of an
SMP coding sequence with a nuclease under conditions wherein nicking occurs
only
about once per molecule, denaturing the double stranded DNA, renaturing the
DNA to
form double stranded DNA which can include sense/antisense pairs from
different
nicked products, removing single stranded portions from reformed duplexes by
treatment with S 1 nuclease, and ligating the resulting fragment library into
an expression
vector. By this method, an expression library can be derived which encodes N-
terminal,
C-terminal and intemal fragments of various sizes of the SMP protein.
Several techniques are known in the art for screening gene products of
combinatorial libraries made by point mutations or truncation, and for
screening cDNA
libraries for gene products having a selected property. Such techniques are
adaptable for
rapid screening of the gene libraries generated by the combinatorial
mutagenesis of SMP
homologues. The most widely used techniques, which are amenable to high
through-put
analysis, for screening large gene libraries typically include cloning the
gene library into
replicable expression vectors, transforming appropriate cells with the
resulting library of
vectors, and expressing the combinatorial genes under conditions in which
detection of a
desired activity facilitates isolation of the vector encoding the gene whose
product was
detected. Recursive ensemble mutagenesis (REM), a new technique which enhances
the
CA 02584021 2007-04-18
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frequency of functional mutants in the libraries, can be used in combination
with the
screening assays to identify SMP homologues (Arkin and Yourvan (1992) PNAS
89:7811-7815; Delgrave et al. (1993) Protein Engineering 6(3):327-331).
In another embodiment, cell based assays can be exploited to analyze a
variegated SMP library, using methods well known in the art.
D. Uses and Methods of the Invention
The nucleic acid molecules, proteins, protein homologues, fusion proteins,
primers, vectors, and host cells described herein can be used in one or more
of the
following methods: identification of C. gluramicum and related organisms;
mapping of
genomes of organisms related to C. glutamicum; identification and localization
of C.
glutamicum sequences of interest; evolutionary studies; detenmination of SMP
protein
regions required for function; modulation of an SMP protein activity;
modulation of the
metabolism of one or more sugars; modulation of high-energy molecule
production in a
cell (i.e., ATP, NADPH); and modulation of cellular production of a desired
compound,
such as a fine chemical.
The SMP nucleic acid molecules of the invention have a variety of uses. First,
they may be used to identify an organism as being Corynebacterium glutamicum
or a
close relative thereof. Also, they may be used to identify the presence of C.
glutamicum
or a relative thereof in a mixed population of microorganisms. The invention
provides
the nucleic acid sequences of a number of C. glutamicum genes; by probing the
extracted genomic DNA of a culture of a unique or mixed population of
microorganisms
under stringent conditions with a probe spanning a region of a C glutamicutn
gene
which is unique to this organism, one can ascertain whether this organism is
present.
Although Corynebacterium glulamicum itself is nonpathogenic, it is related to
pathogenic species, such as Corynebacterium diphtheriae. Corynebacterium
diphtheriae
is the causative agent of diphtheria, a rapidly developing, acute, febrile
infection which
involves both local and systemic pathology. In this disease, a local lesion
develops in
the upper respiratory tract and involves necrotic injury to epithelial cells;
the bacilli
secrete toxin which is disseminated through this lesion to distal susceptible
tissues of the
body. Degenerative changes brought about by the inhibition of protein
synthesis in
these tissues, which include heart, muscle, peripheral nerves, adrenals,
kidneys, liver and
I1
,
CA 02584021 2007-04-18
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spleen, result in the systemic pathology of the disease. Diphtheria continues
to have
high incidence in many parts of the world, including Africa, Asia, Eastern
Europe and
the independent states of the former Soviet Union. An ongoing epidemic of
diphtheria
in the latter two regions has resulted in at least 5,000 deaths since 1990.
In one embodiment, the invention provides a method of identifying the presence
or activity of Cornyebacterium diphtheriae in a subject. This method includes
detection
of one or more of the nucleic acid or amino acid sequences of the invention
(e.g., the
sequences set forth as odd-numbered or even-numbered SEQ ID NOs, respectively,
in
the Sequence Listing) in a subject, thereby detecting the presence or activity
of
Corynebacterium diphtheriae in the subject. C. glutamicum and C. diphtheriae
are
related bacteria, and many of the nucleic acid and protein molecules in C.
gluramicum
are homologous to C. diphtheriae nucleic acid and protein molecules, and can
therefore
be used to detect C. diphtheriae in a subject.
The nucleic acid and protein molecules of the invention may also serve as
markers for specific regions of the genome. This has utility not only in the
mapping of
the genome, but also for functional studies of C. glutamicum proteins. For
example, to
identify the region of the genome to which a particular C. glutamicum DNA-
binding
protein binds, the C. glutamicum genome could be digested, and the fragments
incubated
with the DNA-binding protein. Those which bind the protein may be additionally
probed
with the nucleic acid molecules of the invention, preferably with readily
detectable
labels; binding of such a nucleic acid molecule to the genome fragment enables
the
localization of the fragment to the genome map of C. glutamicum, and, when
performed
multiple times with different enzymes, facilitates a rapid determination of
the nucleic
acid sequence to which the protein binds. Further, the nucteic acid molecules
of the
invention may be sufficiently homologous to the sequences of related species
such that
these nucleic acid molecules may serve as markers for the construction of a
genomic
map in related bacteria, such as Brevibacterium lactofermentum.
The SMP nucleic acid molecules of the invention are also useful for
evolutionary
and protein structural studies. The metabolic and energy-releasing processes
in which
the molecules of the invention participate are utilized by a wide variety of
prokaryotic
and eukaryotic cells; by comparing the sequences of the nucleic acid molecules
of the
present invention to those encoding similar enzymes from other organisms, the
I
CA 02584021 2007-04-18
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evolutionary relatedness of the organisms can be assessed. Similarly, such a
comparison
permits an assessment of which regions of the sequence are conserved and which
are
not, which may aid in determining those regions of the protein which are
essential for
the functioning of the enzyme. This type of determination is of value for
protein
engineering studies and may give an indication of what the protein can
tolerate in terms
of mutagenesis without losing function.
Manipulation of the SMP nucleic acid molecules of the invention may result in
the production of SMP proteins having functional differences from the wild-
type SMP
proteins. These proteins may be improved in efficiency or activity, may be
present in
greater numbers in the cell than is usual, or may be decreased in efficiency
or activity.
The invention provides methods for screening molecules which modulate the
activity of an SMP protein, either by interacting with the protein itself or a
substrate or
binding partner of the SMP protein, or by modulating the transcription or
translation of
an SMP nucleic acid molecule of the invention. In such methods, a
microorganism
expressing one or more SMP proteins of the invention is contacted with one or
more test
compounds, and the effect of each test compound on the activity or level of
expression
of the SMP protein is assessed.
There are a number of mechanisms by which the alteration of an SMP protein of
the invention may directly affect the yield, production, and/or efficiency of
production
of a fine chemical from a C. glutamicum strain incorporating such an altered
protein.
The degradation of high-energy carbon molecules such as sugars, and the
conversion of
compounds such as NADH and FADHZ to more useful forms via oxidative
phosphorylation results in a number of compounds which themselves may be
desirable
fine chemicals, such as pyruvate, ATP, NADH, and a number of intermediate
sugar
compounds. Further, the energy molecules (such as ATP) and the reducing
equivalents
(such as NADH or NADPH) produced by these metabolic pathways are utilized in
the
cell to drive reactions which would otherwise be energetically unfavorable.
Such
unfavorable reactions include many biosynthetic pathways for fine chemicals.
By
improving the ability of the cell to utilize a particular sugar (e.g., by
manipulating the
genes encoding enzymes involved in the degradation and conversion of that
sugar into
energy for the cell), one may increase the amount of energy available to
permit
. . I .. .. .
CA 02584021 2007-04-18
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unfavorable, yet desired metabolic reactions (e.g., the biosynthesis of a
desired fine
chemical) to occur.
Further, modulation of one or more pathways involved in sugar utilization
permits optimization of the conversion of the energy contained within the
sugar
molecule to the production of one or more desired fine chemicals. For example,
by
reducing the activity of enzymes involved in, for example, gluconeogenesis,
more ATP
is available to drive desired biochemical reactions (such as fine chemical
biosyntheses)
in the cell. Also, the overall production of energy molecules from sugars may
be
modulated to ensure that the cell maximizes its energy production from each
sugar
molecule. Inefficient sugar utilization can lead to excess COZ production and
excess
energy, which may result in futile metabolic cycles. By improving the
metabolism of
sugar molecules, the cell should be able to function more efficiently, with a
need for
fewer carbon molecules. This should result in an improved fine chemical
product: sugar
molecule ratio (improved carbon yield), and permits a decrease in the amount
of sugars
that must be added to the medium in large-scale fermentor culture of such
engineered C.
gl utamicum.
The mutagenesis of one or more SMP genes of the invention may also result in
SMP proteins having altered activities which indirectly impact the production
of one or
more desired fine chemicals from C. glutamicum. For example, by increasing the
efficiency of utilization of one or more sugars (such that the conversion of
the sugar to
useful energy molecules is improved), or by increasing the efficiency of
conversion of
reducing equivalents to useful energy molecules (e.g., by improving the
efficiency of
oxidative phosphorylation, or the activity of the ATP synthase), one can
increase the
amount of these high-energy compounds available to the cell to drive normally
unfavorable metabolic processes. These processes include the construction of
cell walls,
transcription, translation, and the biosynthesis of compounds necessary for
growth and
division of the cells (e.g., nucleotides, amino acids, vitamins, lipids, etc.)
(Lengeler et at.
(1999) Biology of Prokaryotes, Thieme Verlag: Stuttgart, p. 88-109; 913-918;
875-899).
By improving the growth and multiplication of these engineered cells, it is
possible to
increase both the viability of the cells in large-scale culture, and also to
improve their
rate of division, such that a relatively larger number of cells can survive in
fermentor
culture. The yield, production, or efficiency of production may be increased,
at least
I
CA 02584021 2007-04-18
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due to the presence of a greater number of viable cells, each producing the
desired fine
chemical.
Further, many of the degradation products produced during sugar metabolism are
themselves utilized by the cell as precursors or intermediates for the
production of a
number of other useful compounds, some of which are fine chemicals. For
example,
pyruvate is converted into the amino acid alanine, and ribose-5-phosphate is
an integral
part of, for example, nucleotide molecules. The amount and efficiency of sugar
metabolism, then, has a profound effect on the availability of these
degradation products
in the cell. By increasing the ability of the cell to process sugars, either
in terms of
efficiency of existing pathways (e.g., by engineering enzymes involved in
these
pathways such that they are optimized in activity), or by increasing the
availability of
the enzymes involved in such pathways (e.g., by increasing the number of these
enzymes present in the cell), it is possible to also increase the availability
of these
degradation products in the cell, which should in turn increase the production
of many
different other desirable compounds in the cell (e.g., fine chemicals).
The aforementioned mutagenesis strategies for SMP proteins to result in
increased yields of a fine chemical from C. glulamicum are not meant to be
limiting;
variations on these strategies will be readily apparent to one of ordinary
skill in the art.
Using such strategies, and incorporating the mechanisms disclosed herein, the
nucleic
acid and protein molecules of the invention may be utilized to generate C.
gtutamicum
or related strains of bacteria expressing mutated SMP nucleic acid and protein
molecules
such that the yield, production, and/or efficiency of production of a desired
compound is
improved. This"desired compound may be any product produced by C glutamicum,
which includes the final products of biosynthesis pathways and intermediates
of
naturally-occurring metabolic pathways, as well as molecules which do not
naturally
occur in the metabolism of C. glutamicum, but which are produced by a C.
glutamicum
strain of the invention.
This invention is fiuther illustrated by the following examples which should
not
be construed as limiting.
TABLE 1: GENES IN THE APPL{CAT!nN
HMP:
Nucleic Acid Amino Atid Wentification Code Conti NT Start NT Stop Function
SEO ID NO SEQ 10 NO
1 2 RXS02735 W0074 14576 15280 8-Phosphogluconolactonase
3 4 RXA01626 GR00452 4270 3926 L-fibuloaelhoephate 4epimstase
6 RXA02245 GR00854 13639 14295 RIBULOSE-PHOSPHATE 3-EPIMERASE (EC 5.1.3.1)
7 8 RXA01015 GR00290 346 5 RIBOSE S-PHOSPHATE ISOMERASE (EC 5.3.1.6)
TCA:
NudeicAcid AminoAcid Identfication Code Conti . NT Start NT Stop Function
SEO 10 NO SEO ID NO
9 10 RXN01312 W0082 20803 18785 SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
(EC
1.3.99.1) cn
11 12 F RXA01312 43R00380 2690 1614 SUCCINATE DEHYDROGENASE FLAVOPROTEIN
SUBUNIT (EC 00
1.3.99.1) o
13 14 RXN00231 W0083 15484 14015 SUCCINATE-SEMIALDEHYDE DEHYDROGENASE (NADP+)
(EC 1.2.1.16)
16 RXA01311 GR00380 1611 865 SUCCINATE DEHYDROGENASE IRON-SULFUR PROTEIN (EC
1.3.99.1)
17 18 RXA01535 GR00427 1354 2760 FUMARATE HYORATASE PRECURSOR (EC 4.2.1.2)
19 20 RXA00517 GR00131 1407 2447 MALATE OEHYDROGENASE (EC 1,11.37) (EC
1.1.1.82)
21 22 RXA01350 GR00392 1844 2827 MALATE DEHYDROGENASE (EC 1.1.1.37)
cn o
EMB-PBttmay 00
Nudeic Amino Add Identification Code Cwuig- NT Start NT Stop Function
Aaid SEQ SEQ tD NO
IDNO
23 24 RXA02149 GR00639 17786 18754 GLUCOKINASE (EC 2.7.1.2)
26 RXA01814 GR00515 2571 910 PHOSPHOGLUCOMUTASE (EC 5.4.2.2)1
PHOSPHOMANNOMUTASE
(EC 5.4.2.8)
27 28 RXN02803 W0066 1 657 PHOSPHOGLUCOMUTASE (EC 5.4.2.2) /
PHOSPHOMANNOMUTASE
(EC 5.4.2.8)
29 30 F RXA02803 GR00784 2 400 PHOSPHOGLUCOMUTASE (EC 5.4.2.2)1
PHOSPHOMANNOMUTASE
(EC 5.4.2.8)
31 32 RXN03076 W0043 1624 35 PHOSPHOGLUCOMUTASE (EC 5.4.2.2) /
PHOSPHOMANNOMUTASE
(EC 5.4.2.8)
33 34 F RXA02654 GR1G002 1588 5 PHOSPHOGLUCOMUTASE (EC 5.4.2.2) /
PHOSPHOMANNOMUTASE
(EC 5.4.2.8)
36 RXA00511 GR00129 1 513 PHOSPHOGLUCOMUTASE (EC 5.4.2.2) / PHOSPHOMANNOMUTASE
(EC 5.4.2.8)
Table I (continued)
NudeicAcid AminoAad tEentificatbn Code Contag NT Start NT Stop Function
SEQ 10 NO SEG iD NO
37 38 RXN01365 W0091 1476 103 PHOSPHOGLUCOMUTASE (EC 5.4.2.2)1
PHOSPHOMANNOMUTASE
(EC 5.4.2.8)
39 40 F RXA01365 GR00397 897 4 PHOSPHOGLUCOMUTASE (EC 5.4.2.2) /
PHOSPHOMANNOMUTASE
(EC 5.4.2.8)
41 42 RXA00098 GR00014 6525 8144 GLUCOSE'6-PHOSPHATE ISOMERASE (GPI) (EC
5.3.1.9)
43 44 RXA01989 GR00578 1 630 GLUCOSE46-PHOSPHATE ISOMERASE A (GPI A) (EC
5.3,1.9)
45 46 RXA00340 GR00059 1549 2694 PHOSPHOGLYCERATE MUTASE (EC 5.4.2.1)
47 48 RXA02492 GR00720 2201 2917 PHOSPHOGLYCERATE MUTASE (EC 5.4.2.1)
49 50 RXA00381 GR00082 1451 846 PHOSPHOGLYCERATE MUTASE (EC 5.4.2.1)
51 52 RXA02122 GR00636 6511 5813 PHOSPHOGLYCERATE MUTASE (EC 5.4.2.1)
53 54 RXA00206 GR00032 6171 5134 6-PHOSPHOFRUCTOKINASE (EC 2.7.1.11) 0
55 56 RXA01243 GR00359 2302 3261 1-PHOSPHOFRUCTOKINASE (EC 2.7.1.56)
57 58 RXA01882 GR00538 1165 2154 1-PHOSPHOFRUCTOKINASE (EC 2.7.1.56)
59 80 RXA01702 GR00479 1397 366 FRUCTOSE-BISPHOSPHATE ALDOLASE (EC 4.1.2.13)
Lri
61 62 RXA02258 GR00854 26451 27227 TRIOSEPHOSPHATE ISOMERASE (EC 5.3.1.1) ao
63 64 RXN01225 VV0084 6382 4943 GLYCERALDEHYOE 3-PHOSPHATE OEHYDROGENASE (EC
1.2.1.12) p -
65 66 F RXA01225 GR00354 5302 6741 GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
HOMOLOG C)
67 68 RXA02256 GR00654 23934 24935 GLYCERALDEHYOE 3-PHOSPHATE DEHYDROGENASE
(EC 1.2.1.12)
69 70 RXA02257 GR00854 25155 26369 PHOSPHOGLYCERATE KINASE (EC 2.7.2.3)
71 72 RXA00235 GR00036 2365 1091 ENOLASE (EC 4.2.1.11) o
73 74 RXA01093 GR00306 1552 122 PYRUVATE KINASE (EC 2.7.1.40)
75 76 RXN02675 VV0098 72801 70945 PYRUVATE KINASE (EC 2.7.1.40)
77 78 F RXA02675 GR00754 2 364 PYRUVATE KINASE (EC 2.7.1.40)
79 80 F RXA02695 GR00755 2949 4370 PYRUVATE KINASE (EC 2.7.1.40)
8i 82 RXA00682 GR00179 5299 3401 PHOSPHOENOLPYRUVATE SYNTHASE (EC 2.7.9.2) , ~
83 84 RXA00663 GR00179 6440 5349 PHOSPHOENOLPYRUVATE SYNTHASE (EC 2.7.9.2)
85 86 RXN00635 VV0135 22708 20972 PYRUVATE DEHYDROGENASE (CYTOCHROME) (EC
1,2.2.2)
87 88 F RXA02807 GR00788 88 552 PYRUVATE DEHYDROGENASE (CYTOCHROME) (EC
1.2.2.2)
89 90 F RXA00635 GR00167 3 923 PYRUVATE DEHYDROGENASE (CYTOCHROME) (EC
1.2.2.2)
91 92 RXN03044 VV0019 1391 2221 PYRUVATE OEHYOROGENASE El COMPONENT (EC
1.2.4.1)
93 94 F RXA02852 GR00852 3 281 PYRUVATE OEHYDROGENASE El COMPONENT (EC
1.2.4.1)
95 96 F RXA00268 GR00041 125 955 PYRUVATE DEHYDROGENASE El COMPONENT (EC
1.2.4.1)
97 98 RXN03086 VV0049 2243 2650 PYRUVATE OEHYDROGENASE El COMPONENT (EC
1.2.4.1)
99 100 F RXA02887 GR10022 411 4 PYRUVATE OEHYDROGENASE El COMPONENT (EC
1.2.4.1)
101 102 RXN03043 VV0019 1 1362 PYRUVATE DEHYDROGENASE El COMPONENT (EC
1.2.4.1)
103 104 F RXA02897 GR10039 1291 5 PYRUVATE DEHYDROGENASE El COMPONENT (EC
1.2.4.1)
105 106 RXN03083 VV0047 88 1110 DIHYDROUPOAMIDE DEHYDROGENASE (EC 1.8.1.4)
107 108 F RXA02853 GR10001 89 1495 DIHYDROLIPOAMIDE DEHYDROGENASE (EC 1.8.1.4)
109 110 RXA02259 GR00654 27401 30172 PHOSPHOENOLPYRUVATE CARBOXYLASE (EC
4.1.1.31)
111 112 RXN02326 VV0047 4500 5315 PYRUVATE CARBOXYLASE (EC 6.4. 1. 1)
113 114 F RXA02326 GR00668 5338 4523 PYRUVATE CARBOXYLASE
115 116 RXN02327 VV0047 3533 4492 PYRUVATE CARBOXYLJISE (EC 8.4.1.1)
117 118 F RXA02327 GR00668 6305 5346 PYRUVATE CARBOXYLASE
119 120 RXN02328 VV0047 1842 3437 PYRUVATE CARBOXYLASE (EC 6.4.1.1)
121 122 F RXA02328 GR00668 7783 6401 PYRUVATE CARBOXYLASE (EC 6.4.1.1)
123 124 RXN01048 VV0079 12539 11316 MALBC ENZYME (EC 1.1.1.39)
Table I (continued)
Nuc'm Ac;a' Amino AciO Identilicatian Code Conk NT Start NT Stop Function
SEO ID NO SEQ ID NO
125 126 F RXA01048 GR00296 3. 290 MALIC ENIYME (EC 1.1.1.39)
127 128 F RXA00290 GR00046 4693 5655 MALIC ENZYME (EC 1.1.1.39)
129 130 RXA02694 GR00755 1879 2820 L-LACTATE DEHYDROGENASE (EC 1.1.1.27)
131 132 RXN00296 W0176 35763 38606 D-LACTATE DEHYDROGENASE (CYTOCHROME) (EC
1.1.2.4)
133 134 F RXA00296 GR00048 3 2837 D-LACTATE DEHYDROGENASE (CYTOCHROME) (EC
1.1.2.4)
135 136 RXA01901 GR00544 4158 5417 L-LACTATE DEHYDROGENASE (CYTOCHROME) (EC
1.1.2.3)
137 138 RXN01952 W0105 9954 11666 D-LACTATE DEHYDROGENASE (EC 1.1.1.28)
139 140 F RXA01952 GR00562 1 216 D-LACTATE DEHYOROGENASE (EC 1.1.1.28)
141 142 F RXA01955 GR0o562 4611 6209 D-LACTATE DEHYDROGENASE (EC 1.1.1.28)
143 144 RXA00293 GR00047 2645 1734 D-3-PHOSPHOGLYCERATE DEHYDROGENASE (EC
1.1.1.95)
145 146 RXN01130 W0157 6138 5536 D-3-PHOSPHOGLYCERATE DEHYDROGENASE (EC
1.1.1.95)
147 148 F RXA01130 GR00315 2 304 D-3-PHOSPHOGLYCERATE DEHYDROGENASE (EC
1.1.1.95)
149 150 RXN03112 W0085 509 6 D-3-PHOSPHOGLYCERATE DEHYDROGENASE (EC 1.1.1.95)
151 152 F RXA01133 GR00316 568 1116 D-3-PHOSPHOGLYCERATE DEHYDROGENASE (EC
1.1.1.95) tv
153 154 RXN00871 W0127 3127 2240 IOLB PROTEIN Ln
155 156 F RXA00871 GR00239 2344 3207 IOLB PROTEIN: D-FRUCTOSE 1,6-BISPHOSPHATE
= GLYCERONE-CC
PHOSPHATE + D- GLYCERALDEHYDE 3-PHOSPHATE. N _
157 158 RXN02829 W0354 287 559 IOLS PROTEIN
159 160 F RXA02829 0R00816 287 562 K>LS PROTEIN
161 162 RXN01468 W0019 7474 8298 NAGD PROTEIN
163 164 F RXA01468. GR00422 1250 2074 PUTATIVE N-GLYCERALDEHYDE-2-
PHOSPHOTRANSFERASE o
165 166 RXA00794 GROO211 3993 2989 GLPX PROTEIN -.3
167 168 RXN02920 W0213 6135 5224 D-3-PHOSPHOGLYCERATE DEHYDROGENASE (EC
1.1.1.95)
169 170 F RXA02379 GR00690 1390 686 0-3-PHOSPHOGLYCERATE DEHYDROGENASE (EC
1.1.1.95)
171 172 RXN02688 W0098 59053 58385 PHOSPHOGLYCERATE MUTASE (EC 5.4.2.1)
173 174 RXN03087 W0052 3216 3428 PYRUVATE CARBOXYLASE (EC 6.4.1.1) ao
175 176 RXN03186 W0377 310 519 PYRUVATE DEHYDROGENASE El COMPONENT (EC
1.2.4.1)
177 178 RXN03187 W0382 3 281 PYRUVATE DEHYDROGENASE El COMPONENT (EC 1.2.4.1)
179 180 RXN02591 W0098 14370 12541 PHOSPHOENOLPYRUVATE CARBOXYKINASE (GTP) (EC
4.1.1.32)
181 182 RXS01260 W0009 3477 2296 LIPOAMIDE DEHYDROGENASE COMPONENT (E3) OF
BRANCHED-
CHAIN ALPHA-KETO ACID DEHYDROGENASE COMPLEX (EC 1.8.1.4)
183 184 RXS01261 W0009 3703 3533 LIPOAMIDE DEHYDROGENASE COMPONENT (E3) OF
BRANCHED-
CHAIN ALPHA-KETO ACID DEHYDROGENASE COMPLEX (EC 1.8.1.4)
Glycerol metabolism
Nudeic Acid Amino Acid Identificatfon Code ConliR, NT Start NT Stop Function
SEQ ID NO SEQ ID NO
185 186 RXA02640 GR00749 1400 2926 GLYCEROL KINASE (EC 2.7.1.30)
187 188 RXN01025 W0143 5483 4488 GLYCEROL-3-PHOSPHATE DEHYDROGENASE (NAD(P)+)
(EC 1.1.1.94)
189 190 F RXA01025 GR00293 939 1853 GLYCEROL-3-PHOSPHATE DEHYDROGENASE
(NAD(P)+) (EC 1.1.1.94)
191 192 RXA01851 GR00525 3515 1830 AEROBIC GLYCEROL-3-PHOSPHATE DEHYDROGENASE
(EC 1.1.99.5)
193 194 RXA01242 GR00359 1526 2302 GLYCEROL-3-PHOSPHATE REGULON REPRESSOR
195 196 RXA02288 GR00661 992 147 GLYCEROL-3-PHOSPHATE REGULON REPRESSOR
Table I (continued)
Nucleic Acid ;mino Acid identification Code Contig NT Start NT Stop Function
SEQ ID NO SEQ ID NO
197 198 RXN01891 W0122 24949 24086 GLYCEROL-3-PHOSPHATE-BINDING PERIPLASMIC
PROTEIN
PRECURSOR
199 200 F RXA01891 GR00541 1736 918 GLYCEROL-3-PHOSPHATE-BINDING PERIPLASMIC
PROTEIN
PRECURSOR
201 202 RXA02414 GR00703 3808 3062 Uncharacterized protein involved in
glycerol metabolism (homolog of
DrosophRa rhomboid)
203 204 RXN01580 W0122 22091 22807 Gtycerophosphoryi diester phosphodiesterase
Acetate metabolism Nucleic Acid Amino Acid Identification Code Contig. NT
Start NT Stop Function
SEQ ID NO SEQ ID NO ~
205 206 RXA01436 GR00418 2547 1357 ACETATE KINASE (EC 2.7.2.1)
207 208 RXA00686 GR00179 8744 7941 ACETATE OPERON REPRESSOR
209 210 RXA00246 GR00037 4425 3391 ALCOHOL DEHYDROGENASE (EC 1.1.1.1)
211 212 RXA01571 GR00438 1360 1959 ALCOHOL DEHYDROGENASE (EC 1.1.1.1)
213 214 RXA01572 GR00438 1928 2419 ALCOHOL OEHYDROGENASE (EC 1.1.1.1) o
215 216 RXA01758 GR00498 3961 2945 ALCOHOL DEHYDROGENASE (EC 1.1.1.1) o -
217 218 RXA02539 GR00726 11676 10159 ALDEHYDE DEHYDROGENASE (EC
219 220 RXN03061 W0034 108 437 ALDEHYDE DEHYDROGENASE (EC 1.2.1.3) ~ ~ 0
221 222 RXN03150 W0155 10678 10055 ALDEHYDE DEHYDROGENASE (EC 1.2.1.3) p
223 224 RXN01340 W0033 3 860 ALDEHYDE DEHYDROGENASE (EC 1.2.1.3)
225 228 RXN01498 W0008 1598 3160 ALDEHYDE DEHYDROGENASE (EC 1.2.1.3) 00
227 228 RXN02874 W0315 15614 14163 ALDEHYDE DEHYDROGENASE (EC 1.2.1.3)
229 230 RXN00868 W0127 2230 320 ACETOLACTATE SYNTHASE LARGE SUBUNIT (EC
4.1.3.18)
231 232 RXN01143 W0077 9372 8254 ACETOLACTATE SYNTHASE LARGE SUBUNIT (EC
4.1.3.18)
233 234 RXN01146 W0264 243 935 ACETOLACTATE SYNTHASE LARGE SUBUNIT (EC
4.1.3.18)
235 236 RXN01144 W0077 8237 7722 ACETOtACTATE SYNTHASE SMALL SUBUNIT (EC
4.1.3.18)
Butanediol, diacetyl and acetoin formation
NuGeic Acid Amino Acid Identification Code Conti . NT Start NT Stop Function
SEQIDNO SEQIONO
237 238 RXA02474 GR00715 8082 7309 (S,S)-butane-2,3-diol dehydrogenase (EC
1.1.1.76)
239 240 RXA02453 GR00710 6103 5351 ACETOIN(DIACETYL) REDUCTASE (EC 1.1.1.5)
241 242 RXS01758 W0112 27383 28399 ALCOHOL DEHYDROGENASE (EC 1.1.1.1)
Table I (continued)
HMP-iCycle
Nudeic Acid Antino Acid idsntlfiaelion Code Contig NT Start NT Stop Function
SEQ ID NO SEQ ID NO
243 244 RXA02737 GR00763 3312 1771 GLUCOSE-6-PHOSPHATE i-DEHYDROGENASE (EC 11.
1.49)
245 246 RXA02738 GR00763 4499 3420 TRANSALDOLASE (EC 2.2.1.2)
247 248 RXA02739 GR00763 6769 4670 TRANSKETOLASE (EC 2.2.1.1)
249 250 RXA00965 GR00270 1232 510 6-PHOSPHOGLUCONATE DEHYDROGENASE,
DECARBOXYLATING (EC
1.1.1.44)
251 252 RXN00998 W0106 2817 1366 6-PHOSPHOGLUCONATE DEHYDROGENASE,
DECARBOXYLATING (EC
1.1.1.44)
253 254 F RXA00999 GR00283 3012 4448 6-PHOSPHOGLUCONATE DEMYDROGENASE,
DECARBOXYLATING (EC
1.1.1.44)
Nucleotide sugar conversion ~
Nudeic Acid Amino A,dd Identtfication Code Concia. NT Stan NT Function 00
SEQ ID NO SEQ ID NO
255 256 RXN02596 W0098 48784 47582 UDP-GALACTOPYRANOSE MUTASE (EC 5.4.99.9)
257 258 F RXA02596 GR00742 1 489 UDP-GALACTOPYRANOSE MUTASE (EC 5.4.99.9)
259 260 F RXA02642 GR00749 5383 5880 UDP-GALACTOPYRANOSE MUTASE (EC 5.4.99.9)
261 262 RXA02572 GR00737 2 646 UDP-GLUCOSE 6-DEHYDROGENASE (EC 1.1.1.22)
263 264 RXA02485 GR00718 2345 3445 UDP-N-ACETYLENOLPYRUVOYLGLUCOSAMINE
REDUCTASE (EC .3
1.1.1.158)
265 266 RXA01216 GR00352 2302 1202 UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE
(EC 2.7.7.23)
267 268 RXA01259 GR00367 987 130 UTP--GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
(EC 2.7.7.9)
269 270 RXA02028 GR00616 573 998 UTP-GLUCOSE-I-PHOSPHATE URIDYLYLTRANSFERASE
(EC 2.7.7.9) 00
271 272 RXA01262 GR00367 8351 7191 GDP-MANNOSE 8-DEHYDROGENASE (EC 1.1.1.132)
273 274 RXA01377 GR00400 3935 5020 MANNOSE-1-PHOSPHATE GUANYLTRANSFERASE (EC
2.7.7.13)
275 276 RXA02063 GR00626 3301 4527 GLUCOSE-I-PHOSPHATE ADENYLYLTRANSFERASE (EC
2.7.7.27)
277 278 RXN00014 VN0048 8848 9627 GLUCOSE-I-PHOSPHATE THYMIDYLYLTRANSFERASE
(EC 2.7,7.24)
279 280 F RXA00G14 GR00002 4448 5227 GLUCOSE-I-PHOSPHATE THYMIDYLYLTRANSFERASE
(EC 2.7.7.24)
281 282 RXA01570 GR00438 427 1281 GLUCOSE-I-PHOSPHATE THYMIDYLYLTRANSFERASE
(EC 2.7.7.24)
283 284 RXA02866 GR00753 7260 6493 D-RIBITOL-5-PHOSPHATE CYTIDYLYLTRANSFERASE
(EC 2.7.7.40)
285 286 RXA00825 GR00222 222 1154 DTDP-GLUCOSE 4,8-DEHYDRATASE (EC 4.2.1.46)
inositol and ribitol metabolism
Nudac Aeid Aroino Acid IAenti6ation Code Contig NT Stert NT Stop Funation
SEQ 10 NO SEQ ID NO
287 286 RXA01887 GR00539 4219 3209 MYO=INOSITOL 2-DEHYDROGENASE (EC 1.1.1.18)
Table 1 (continuedl
Nudeic Ac1d Amino Acid IdentifieaBon Code ConG NT Start NT Stop Functian
SEQ 10 140 SEQ 10 NO
289 290 RXN00013 W0048 7966 8838 MYO-INOSITOL-1(OR 4)-MONOPHOSPHATASE 1(EC
3.1_3.25)
291 292 F RXA00013 GR00002 3586 4438 MYO-INOSITOL-1(OR 4)-MONOPHOSPHATASE 1(EC
3.1.3.25)
293 294 RXA01099 GR00906 6328 5504 fNOSITOL MONOPHOSPHATE PHOSPHATASE
295 296 RXN01332 VV0273 579 4 MYO-INOSITOL 2-DEHYDROGENASE (EC 1.1.1.18)
297 296 F RXA01332 GR00388 552 4 MYO-1NOSiTOL 2-DEHYDROGENASE (EC 1.1.1_18)
299 300 RXA01632 GR00454 2338 3342 MYO-INOSITOL 2-DEHYOROCiENASE (EC 1.1.1.18)
301 302 RXA01633 GR00454 3380 4462 MYO-INOSfTOL 2-DEHYDROGENASE (EC 1.1.1.18)
303 304 RXN01406 W0278 2999 1977 MYO-INOStTOL 2-DEHYDROGENASE (EC 1.1.1.18)
305 306 RXN01630 W0050 48113 47037 MYO-{NOSITOL 2-DEHYDROGENASE (EC 1.1.1.18)
307 308 RXN00528 W0079 23406 22318 MYO-INOSITOL-1-PHOSPHATE SYNTHASE (EC
5.5.1.4)
309 310 RXN03057 W0028 7017 7688 MYO-INOSROL 2-DEHYDROGENASE (EC 1.1.1.18)
311 312 F RXA02902 GR10040 10277 10948 GLUCOSE-FRUCTOSE OXIDOREDUCTASE
PRECURSOR (EC 1.1.99.28)
313 314 RXA00251 GR00038 931 224 RIBITOL 2-DEHYDROGENASE (EC 1.1.1.56)
0
Utilization of sugars Nucleic Add Amhio Add IdentilfCation Code C2nt1R. NT
Start NT Stop Function
SEQ (D NO SEQ ID NO
315 316 RXN02654 W0090 12206 13090 GLUCOSE 1-DEHYDROGENASE (EC 1.1.1.47)
317 318 F RXA02654 GR00752 7405 8289 GLUCOSE 1-DEHYDROGENASE li (EC 1.1.1.47)
~ o -
319 320 RXN01049 W0079 9833 11114 GLUCONOKINASE (EC 2.7.1.12)
321 322 F RXA01049 fa'R00296 1502 492 GLUCONOKINASE (EC 2.7.1.12) . o
323 324 F RXA01050 GR00296 1972 1499 GLUCONOK1NASE (EC 2.7.1.12)
325 326 RXA00202 (3R00032 1216 275 D-RIBOSE-81NDING PERIPLASMIC PROTEIN
PRECURSOR
327 328 RXN00872 W0127 6557 5604 FRUCTOKINASE (EC 2.7.1.4) D
329 330 F RXA00872 GR00240 565 1086 FRUCTOKINASE (EC 2.7.1.4)
331 332 RXN00799 W0009 58477 56834 PERIPLASMIC BETA-GLUCOSIDASElBETA-
XYLOSIDASE PRECURSOR
(EC 3.2.1.21) (EC 3.2.1.37)
333 334 F RXA00799 OR00214 1 1584 PERIPLASMIC BETA-GLUCOSIDASE/BETA-XYLOSSNISE
PRECURSOR
(EC 3.2.1.21) (EC 3.2.1.37)
335 336 RXA00032 (;R00003 12028 10520 MANNITOL 2-DEHYDROGENASE (EC 1.1.1.67)
337 338 RXA02528 0R00725 6880 7854 FRUCTOSE REPRESSOR
339 340 RXN00316 W0006 7035 8180 Hypotheticai Oxidaroducxaae (EC 1.1.1.-)
341 342 F RXA00309 GR00053 316 5 GLUCOSE-FRUCTOSE OXIDOREDUCTASE PRECURSOR (EC
1.1.99.28)
343 344 RXN00310 W0006 6616 7050 GLUCOSE-FRUCTOSE OXIDOREDUCTASE PRECURSOR (EC
1.1.99.28)
345 346 F RXA00310 GR00053 735 301 GLUCOSE-FRUCTOSE OXIDOREDUCTASE PRECURSOR
(EC
1.1.99.28)
347 348 RXA00041 (3R00007 1246 5 SUCROSE-6-PHOSPHATE HYDROLASE (EC 3.2.1.26)
349 350 RXA02026 GR00815 725 6 SUCROSE-6-PHOSPHATE HYDROLASE (EC 3.2.1.26)
351 352 RXA02061 GR00626 1842 349 SUCROSE-6-PHOSPHATE HYDROLASE (EC 3.2.1.26)
Tabte 1 continued)
NudBicAcicF Amiho Acid identihcatlon Code CoMig NT StaR NT StoP Funcdon
SE4ID NO SEQIONO
353 354 RXN01369 W0124 595 1776 MANNOSE-6-PHOSPHATE ISOMERASE (EC 5.3.1.8)
355 356 F RXA01369 GR00398 3 503 MANNOSE-6-PHOSPHATE 1SOMERASE (EC 5.3.1.8)
357 356 F RXA01373 GR00399 595 1302 MANNOSE-B-PHOSPHATE ISOMERASE (EC 5.3.1.8)
359 360 RXA02611 GR00743 1 1752 1,4 ALPHA-GLUCAN BRANCHING ENZYME (EC
2.4.1.18)
361 362 RXAGU12 GR00743 1793 3985 1,4-ALPHA-GLUCAN BRANCHING ENZYME (EC
2.4.1.18)
363 364 RXN01884 W0184 1 1890 GLYCOGEN DEBRANCHQVG ENZYME (EC 2.4.1.25) (EC
3.2.1.33)
365 366 F RXA01884 GR00539 3 1475 GLYCOGEN DEBRANCHING ENZYME (@C 2.4.1.25)
(EC 3.2.1.33)
367 388 RXA01111 GR0O306 16981 17427 GLYCOGEN OPERON PROTEIN GLGX (EC 3.2.1-)
n
369 370 RXN01550 V1/0143 14749 16260 GLYCOGEN PHOSPHORYLASE (EC 2.4.1.1) y
371 372 F RXA01550 GR00431 3 1348 GLYCOGEN PHOSPHORYLASE (EC 2.4.1.1) o
373 374 RXN02100 VY0318 2 2326 GLYCOGEN PHOSPHORYLASE (EC 2.4.1.1)
375 376 F RXA02100 GR00631 3 920 GLYCOGEN PHOSPHORYLASE (EC 2.4.1.1)
377 378 F RXA02113 GR00633 2 1207 GLYCOGEN PHOSPHORYLASE (EC 2.4.1.1) 00
379 380 RXA02147 GR00639 15516 16532 ALPHAAMYLASE (EC 3.2.1.1) N
381 382 10A01478 GR00422 10517 12352 GLUCOAMYLASE 01 AND G2 PRECURSOR (EC
3.2.1.3)
383 384 RXAOi888 GR00539 4366 4923 GLUCOSE-REStSTANCE AMYLASE REGULATOR
385 386 RXN01927 W0127 50623 49244 XYLULOSE KINASE (EC 2.7.1.17)
387 388 F RXA01927 GR0G555 3 1118 XYLULOSE KtNASE (EC 2.7.1.17) o =
389 390 RXA02729 GR00762 747 4 RfBOKINASE (EC 2.7.1.15)
391 392 RXA02797 GR00778 1739 2641 RIBOKINASE (EC 2.7.1.15)
393 394 RXA02730 GR00782 1768 731 RIBOSE OPERON REPRESSOR
395 396 RXA02551 GR00729 2193 2552 B-PHOSPHO-BETA-GLUCOSlDASE (EC 3.2.1.86)
398 RXA01325 GR00385 8676 5005 DEOXYRIBOSE-PHOSPHATE ALDOLASE (EC 4.1.2.4) oa
397
399 400 RXA00195 GR00030 543 1103 1-deoxy-D-xylulose S-phosphate
reducxoisomerase (EC
401 402 R)LA00196 GR00030 1094 1708 1-d oxy-D-xyfubse 5-phoaphatf
toduct0isamerase (EC
403 404 RXN01562 W0191 1230 3137 1-0EOXYXYLULOSE-5-PHOSPHAT'E SYNTFU0.SE
405 408 F RXA01562 GR00436 2 1039 1-DEOXYXYLULOSE-5-PHOSPHATE SYNTHASE
407 408 F RXA01705 GR00480 971 1573 1-DEOXYXYLULOSE-5-PHOSPHATE SYNTHASE
409 410 RXN00879 bV'0099 8763 6646 4-ALPHA-GLUCANOTRANSFERASE (EC 2.4.1.25)
411 412 f RXA00879 GR00242 5927 3828 4-ALPHA-GLUCANOTRANSFERASE (EC 2.4.1.25),
emyiomaRase
413 414 RXN00043 W0119 3244 2081 N-ACETYLGLUCOSAMINE-8=PHOSPHATE DEACETYLASE
(EC 3.5.1_25)
415 416 F RXA00043 GR00007 3244 2081 NACETYLGLUCOSAMINE-6-PHDSPHATE
1)EACETYLASE (EC 3.5.1.25)
417 418 RXN01752 W0127 35265 33805 N-ACETYLGUICOSAMINYLTRANSFERASE (EC 2.4.1 -
)
419 420 F RXA01839 GR00520 1157 510 NACETYLGLUCOSAMtNYLTRANSFERASE (EC 2.4.1.-
)
421 422 RXA01859 GR00529 1473 547 N-ACETYLGLUCOSAMINYLTRANSFERASE (EC 2.4.1.-)
423 424 RXA00042 GR00007 2037 1279 GLUCOSAMINE-6-PHOSPHATE ISOMERASE (EC
5.3.1.10)
425 426 RXA01482 GR00422 17271 15397 GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE
AMINOTRANSFERASE
(tSOMERlZING) (EC 2.6.1.16)
427 428 RXN03179 VY0336 2 667 URONATE ISOMERASE (EC 5.3.1.12)
429 430 F RXA02672 GR10013 675 4 URONATE ISOMERASE, Ghaarccnate isomemse (EC
5.3.1.i2)
431 432 RXA103180 W0337 872 163 URONATE ISOMERASE (EC 51.1.12)
433 434 F RXA02873 GR10014 672 163 URONATE tSOMERASE, Giucwonate isotneras!
(EC 5.3.1.12)
435 436 RXA02292 GR00662 1611 2285 GALACTOStOE O,ACETYLTRANSFERASE (EC
2.3.1.18)
437 438 RXA02666 GR00753 7260 6493 D-RIBiTOL-5-PHOSPHATE CYTIOYLYLTRANSFERASE
(EC 2.7.7.40)
439 440 RXA00202 GR0G032 1216 273 0-RfBOSE-BINDING PERiPLASMK; PROTEIN
PRECURSOR
441 442 RXA02440 GR00709 5097 4258 D-RJBOSE-BINOING PERIPLASMIC PROTEIN
PRECURSOR
Table I (continued)
Nudeic Acid Amino Acid Identification Code Contig. NT Start NT Stop Function
SEQ ID NO SEQ ID NO
443 444 RXN01569 W0009 41086 42444 dTDP+DEHYDRORHAMNOSE REDUCTASE (EC
1.1.1.133)
445 446 F RXA01569 GR00438 2 427 DTDP-4-DEHYDRORHAMNOSE REDUCTASE (EC
1.1.1.133)
447 448 F RXA02055 GR00624 7122 8042 DTDP-4DEHYDRORHAMNOSE REDUCTASE (EC
1.1.1.133)
449 450 RXA00825 GR00222 222 1154 DTDP-GLUCOSE 4,6-DEHYDRATASE (EC 4.2.1.46)
451 452 RXA02054 GR00624 6103 7119 DTDP-GLUCOSE 4,6-DEHYDRATASE (EC 4.2.1.46)
453 454 RXN00427 W0112 7004 6219 dTDP-RHAMNOSYL TRANSFERASE RFBF (EC 2.-.-.-)
455 456 F RXA00427 GR00098 1591 2022 DTDP-RHAMNOSYL TRANSFERASE RFBF (EC 2.-.-
.-)
457 458 RXA00327 GR00057 10263 9880 PROTEIN ARAJ
459 460 RXA00328 GR00057 11147 10656 PROTEIN ARAJ
461 462 RXA00329 GR00057 12390 11167 PROTEIN ARAJ
463 464 RXN01554 W0135 28686 . 26545 GLUCAN ENDO-1,3-BETA-GLUCOSIDASE Al
PRECURSOR (EC 3.2.1.39)
465 466 RXN03015 W0063 289 8 UDP-GLUCOSE 6-DEHYDROGENASE (EC 1.1.1.22)
467 468 RXN03056 W0028 6258 6935 PUTATIVE HEXULOSE-B-PHOSPHATE ISOMERASE (EC
5.-.--)
469 470 RXN03030 W0009 57006 56443 PERIPLASMIC BETA-GLUCOSIDASE/BETA-
XYLOSIDASE PRECURSOR
(EC 3.2.1.21) (EC 3.2.1.37) Ln
471 472 RXN00401 W0025 12427 11489 5-DEHYDRO-4-DEOXYGLUCARATE DEHYDRATASE (EC
4.2.1.41) 00
473 474 RXN02125 W0102 23242 22442 ALDOSE REDUCTASE (EC 1.1.1.21) ro _
475 476 RXN00200 W0181 1679 5116 arabinosyl transferase subunR B(EC 2.4.2.-)
477 478 RXN01175 W0017 39688 38303 PHOSPHO-2-DEHYDRO-3-OEOXYHEPTONATE ALDOLASE
(EC 4.1.2.15)
479 480 RXN01376 W0091 5610 4750 PUTATIVE GLYCOSYL TRANSFERASE WBIF 481 482
RXN01631 W0050 47021 46143 PUTATIVE HEXULOSE-6-PHOSPHATE ISOMERASE (EC 5-.-.-)
483 484 RXN01593 W0229 13274 12408 NAGD PROTEIN CN -.3
485 486 RXN00337 W0197 20369 21418 GALACTOKINASE (EC 2.7.1.6) o =
487 488 RXS00584 W0323 5516 6640 PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
(EC 4.1.2.15)
489 490 RXS02574 BETA-HEXOSAMINIDASE A PRECURSOR (EC 3.2.1.52)
491 492 RXS03215 GLUCOSE-FRUCTOSE OXIDOREDUCTASE PRECURSOR (EC co
1.1.99.28)
493 494 F RXA01915 GR00549 1 1008 GLUCOSE-FRUCTOSE OXIDOREDUCTASE PRECURSOR
(EC
1.1.99.28)
495 496 RXS03224 CYCLOMALTODEXTRINASE (EC 3.2.1.54)
497 498 F RXA00038 GR00006 1417 260 CYCLOMALTODEXTRINASE (EC 3.2.1.54)
499 500 RXC00233 protein involved in sugar metabolism
501 502 RXC00236 Membrane Lipoprotein involved in sugar metabolism
503 504 RXC00271 Exported Protein involved in ribose metabolism
505 506 RXC00338 protein invoNed in sugar metaboiism
507 508 RXC00362 Membrane Spanning Protein involved in metaboGsm of diols
509 510 RXC00412 Amino Acid ABC Transporter ATP-Binding Protein invoNed in
sugar
metabolism
511 512 RXC00526 ABC Transporter ATP-Binding Protein invohred in sugar
metabolism
513 514 RXC01004 Membrane Spanning Protein involved in sugar metabofism
515 516 RXC01017 Cytosolic Protein involved In sugar metaboiism
517 518 RXC01021 Cytosolic Kinase involved in ms4aboVisrn of sugars and
thiamin
519 520 RXC01212 ABC Transporter ATP-Binding Protein involved in sugar
metabolism
521 522 RXC01306 Membrane Spanning Protein invoNed in sugar metabolism
523 524 RXC01366 Cytosolic Protein invotved in sugar metabolism
525 526 RXC01372 Cytosoiic Protein involved in sugar metabolism
Table 1 (continued)
Nudeic Acid Amino Acid Identification Code Contig NT Start NT Stop Function
SEQ 10 NO SEQ IO NO
527 528 RXC01659 protein Involved in sugar metabolism
529 530 RXC01663 protein Involved in sugar rrbtabolism
531 532 RXC01693 protein invoived in sugar metabolism
533 534 RXC01703 Cytosolio Protein involved in sugar metabolism
535 536 RXC02254 Membrane Associated Protein involved in sugar metabolism
537 538 RXC02255 CytosoGa Protein involved in sugar metabolism
539 540 RXC02435 protein Involved in sugar metabolism
541 542 F RXA02435 GR00709 625 268 Uncharacterized protein involved in
glycerol metaboiism (homolog of
Drosophila rhomboid)
543 S44 RXC03216 protein involved in sugar metabolism
TCA-cycle Nudeic Acid Amino Acid identification Code Conci . NT StaR NT Stop
Function
SEQ IO NO SEQ ID NO Ln
$45 ao
546 RXA02175 GR00641 10710 9418 CITRATE SYNTHASE (EC 4.1.3.7)
547 548 RXA02621 GR00746 2647 1829 CITRATE LYASE BETA CHAIN (EC 4.1.3.6)
549 550 RXN00519 W0144 5585 3372 ISOCITRATE DEHYDROGENASE (NADP) (EC 1,1,1.42)
551 552 F RXA00521 GR00133 2 1060 ISOCITRATE DEHYDROGENASE (NADP) (EC
1.1.1.42)
553 554 RXN02209 W0304 1 1671 ACONITATE HYDRATASE (EC 4.2.1.3) " N
555 556 F RXA02209 GR0o648 3 1661 ACONITATE HYDRATASE (EC 4.2.1.3)
557 55B RXN02213 W0305 1378 2151 ACONITATE HYDRATASE (EC 4.2.1.3) -.3
559 560 F RXA02213 GR00649 1330 2046 ACONITATE HYORATASE (EC 4.2.1.3)
561 562 RXA02056 GR00825 3 2870 2-OXOGLUTARATE DEHYDROGENASE El COMPONENT (EC
1.2.4.2)
563 564 RXA01745 GR00495 2 1495 DIHYDROUPOAMIDE SUCCINYLTRANSFERASE COMPONENT
(E2) OF
2-OXOGLUTARATE DEHYDROGENASE COMPLEX (EC 2.3.1.61) 00
565 566 RXA00782 GR00206 3984 3103 SUCCINYL-COA SYNTHETASE ALPHA CHAIN (EC
6.2.1.5)
587 568 RXA00783 GR00206 5280 4009 SUCCINYL-COA SYNTFIETASE BETA CHAIN (EC
6.2.1.5)
569 570 RXN01695 W0139 11307 12806 L-MALATE DEHYDROGENASE (ACCEPTOR) (EC
1.1.99.16)
571 572 F RXA01615 GR00449 8606 9546 L-MALATE DEHYDROGENASE (ACCEPTOR) (EC
1.1.99.16)
573 574 F RXA01695 GR00474 4388 4179 L-MALATE DEHYDROGENASE (ACCEPTOR) (EC
1.1.99.16)
575 576 RXA00290 GR00046 4693 5655 MAUC ENZYME (EC 1.1.1.39)
577 578 RXN01048 W0079 12539 11316 MALIC ENZYME (EC 1.1.1.39)
579 580 F RXA01048 GR00296 3 290 MALIC ENZYME (EC 1.1.1.39)
581 582 F RXA00290 GR00046 4693 5655 MAUC ENZYME (EC 1.1.1.39)
583 584 RXN03101 W0066 2 583 DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE COMPONENT
(E2) OF
2-OXOGLUTARATE DEHYDROGENASE COMPLEX (EC 2.3.1.61)
585 586 RXN02046 W0025 15056 14640 DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE
COMPONENT OF 2-
OXOGWTARATE DEHYDROGENASE COMPLEX (EC 2.3.1.61)
587 588 RXN00389 W0025 11481 9922 oxoglutarate semialdehyde dehydrogenase (EC
1.2.1-)
Table I (continued)
Glyoxylate bypass
Nudeio Acid Amino Acid Identifiaatlon Code ContlR NT Start NT Stop Function
SEQ ID NO SEQ 10 NO
589 590 RXN02399 W0176 19708 18365 ISOCITRATE LYASE (EC 4.1.3.1)
591 592 F RXA02399 GR00699 478 1773 ISOCITRATE LYASE (EC 4.1.3.1)
593 594 RXN02404 W0176 20259 22475 MALATE SYPITHASE (EC 4.1.3.2)
595 596 F RXA02404 GROO700 3798 1663 MALATE SYNTHASE (EC 4.1.3.2)
597 598 RXA01089 GR00304 3209 3958 GLYOXYLATE=INDUCED PROTEIN
599 800 RXA01886 GR00539 3203 2430 GLYOXYLATE-INDUCED PROTEIN
Methylcid ate-pathway
0
Nudeic Acid Aniino Acid Identilication Code Conti . NT Start NT Stop FunCtion
Ln
00
SEQ IO NO SEQ ID NO
600 602 RXN03117 W0092 3087 1576 2-methylisocilrate synthase (EC 5.3.3: )
601 604 F RXA00406 GR00090 978 4 2-methyllsocifrate synthase (EC 5.3.3: )
603 606 F RXA00514 GR00130 1983 1576 2-methylisocitrate synthese (EC 5.3.3.-)
605 808 RXA00S12 GR00130 621 4 2-methyldarats synthase (EC 4.1.3.31) a, o
607 610 RXA00518 GR00131 3069 2773 2-msthyldtrate synthase (EC 4.1.3.31) oo -
.3
609 612 RXA01077 GR00300 4847 6017 2-methylisocitrate synthase (EC 5.3.3.-) 1
611 614 RXN03144 W0141 2 901 2-methyNsodhate synthase (EC 5.3.3.-)
613 818 F RXA02322 GR00868 415 5 2-methyRsocitrate synthase (EC 5.3.3.-)
615 618 RXA02329 GR00869 607 5 2-methy6socitrate synthase (EC 5.3.3.-)
617 620 RXA02332 GR00671 1906 764 2-nnethyloitrate synthase (EC 4.1.3.31) D
619 622 RXN02333 W0141 901 1815 methylisocitrate lyase (EC 4.1.3.30)
621 624 F RXA02333 GR00671 2120 1902 methylisocitrote tyase (EC 4.1.3.30)
623 B'28 RXA00030 GR00003 9590 9979 LACTOYLGLUTATHIONE LYASE (EC 4.4.1.5)
INethyl-Malonyl-CoA-AAutases
Nudsic Acid Amino Asid identiflcation Code Contia NT Start NT Stop Function
SEQIDNO SEQIDNO
625 828 RXN00148 W0167 9849 12059 METHYLMALONYL-COA MUTASE ALPHA-SUBUNIT (EC
5.4.99.2)
627 830 F RXA00148 GR00023 2002 5 METHYLMALONYL-COA MUTASE ALPHA-SUBUNIT (EC
5.4.99.2)
629 832 RXA00149 GR00023 3856 2009 METHYLMALONYL-COA MUTASE BETA-SUBUNIT (EC
5.4.99.2)
Table I (continued)
Othera
Nualeie Aad Amino Acid Identi8cation Code ContiR" NT Start NT Stop FunoUon
SEQIONO SEQIDNO
631 634 RXN00317 W0197 26879 27532 PHOSPHOGLYCOLATE PHOSPHATASE (EC 3.1.3.18)
635 636 F RXA00317 GR00055 344 6 PHOSPHOGLYCOLATE PHOSPHATASE (EC 3.1.3.18)
637 638 RXA02198 GR00645 3956 3264 PHOSPHOGLYCOLATE PHOSPHATASE (EC 3.1.3.18)
639 640 RXN02461 W0124 14236 14643 PHOSPHOGLYCOLATE PHOSPHATASE (EC 3.1.3.18)
Redox Chain
Nudsie Add Amino Acid Idarkf5cation Code Conti6 NT Start NT Stop Function
SEQ 10 NO SEQ ID NO
641 642 RXN01744 W0174 2350 812 CYTOCHROME 0 UBIQUINOL OXIDASE SUBUNIT I (EC
1.10.3.-) 0Ln0
643 604 F RXA00055 GR00008 11753 11890 CYTOCHROME D UBIQUINOL OXIDASE SUBUNIT
I (EC 1.10.3.-)
645 646 F RXA01744 GR00494 2113 812 CYTOCHROME D UBIQUINOL OXIDASE SUBUNR I
(EC 1.10.3.-)
647 648 RXA00379 GR00082 212 6 CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCDA
649 650 RXA00385 GR00083 773 435 CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCDA
651 652 RXA01743 GR00494 806 6 CYTOCHROME D UBIQUINOL OXIDASE SUBUNIT II (EC
1.10.3.-) ~ = o
653 654 RXN02480 W0084 31222 29567 CYTOCHROME C OXIDASE POLYPEPTIDE I (EC
1.9.3.1) -.3
655 656 F RXA01919 GR00550 288 4 CYTOCHROME C OXIDASE SUBUNIT I (EC 1.9.3.1)
657 658 F RXA02460 GR00717 1449 601 CYTOCHROME C OXIDASE POLYPEPTIDE I (EC
1.9.3.1) 0
659 660 F RXA02481 GR00717 1945 1334 CYTOCHROME C OXIDASE POLYPEPTIOE I (EC
1.9.3.1)
661 662 RXA02140 GR00639 7339 8415 CYTOCHROME C OXIDASE POLYPEPTIDE 11(EC
1.9.3.1)
663 664 RXA02142 GR00639 9413 10063 CYTOCHROME C OXIDASE POLYPEPTIDE I (EC
1.9.3.1) D
665 688 RXA02144 GR00639 11025 12248 RIESKE IRON-SULFUR PROTEIN
667 868 RXA02740 fiR00763 7613 8542 PROBABLE CYTOCHROME C OXIDASE ASSEMBLY
FACTOR
669 670 RXA02743 GR00763 13534 12497 CYTOCHROME AA3 CONTROLLING PROTEIN
671 672 RXA01227 GR00355 1199 1519 FERREDOXIN
673 674 RXA01885 GR00532 436 122 FERREDOXIN
675 676 RXA00680 GR00179 2632 2315 FERREDOXIN VI
677 678 RX1100679 GR00179 2302 1037 FERREDOXIN-NAD(+) REDUCTASE (EC 1.18.1.3)
679 680 RXA00224 GR00032 24965 24015 ELECTRON TRANSFER FLAVOPROTEIN ALPHA-
SUBUNTT
681 682 RXA00225 GR00032 25783 24998 ELECTRON TRANSFER FLAVOPROTEIN BETA-
SUBUNIT
683 684 RXN00606 W0192 11299 9026 NADH DEHYDROGENASE I CHAIN L(EC 1.6.5.3)
685 686 F RXAD0606 GR00160 121 1869 NADH DEHYDROGENASE I CHAIN L (EC 1.6.5.3)
687 688 RXN00595 W0192 8642 7113 NADH DEHYDROGENASE I CHAIN M (EC 1.6.5.3)
689 690 F RXA00808 GR00160 2253 3017 NADH DEHYDROGENASE I CHAIN M (EC 1.6.5.3)
691 692 RXA00913 GR00249 3 2120 NADH DEHYDROGENASE I CHAIN L (EC 1.6.5.3)
693 694 RXA00909 GR00247 2552 3406 NADH DEHYDROGENASE I CHAIN L(EC 1.6.5.3)
695 696 RXA00700 GR00182 846 43 NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 2
697 698 RXN00483 W0086 44824 46287 NADH-UBIQUINONE OXIDOREDUCTASE 39 KD
SUBUNIT PRECURSOR
(EC 1.6.5.3) (EC 1.6.99.3)
Table 1 (continued)
Nudeic Acid Antino Acid identiBcation Code Conti . NT Start NT Stop Function
SEQIDNO SEQIDNO
699 700 F RXA00483 GR00119 19106 20569 NADH-UBIQUINONE OXIDOREDUCTASE 39 KD
SUBUNIT PRECURSOR
(EC 1.6.5.3) (EC 1.6.99.3)
701 702 RXA01534 GR00427 1035 547 NADH-DEPENDENT FMN OXYDOREDUCTASE
703 704 RXA00288 GR00046 2646 1636 QUINONE OXIDOREDUCTASE (EC 1.6.5.5)
705 706 RXA02741 GR00763 9585 8620 QUINONE OXIDOREDUCTASE (EC 1.6.5.5)
707 708 RXN02580 VVO101 9922 10788 NADPH-FLAVIN OXIDOREDUCTASE (EC 1.6.99.-)
709 710 F RXA02560 GR00731 6339 7160 NADPH-FLAVIN OXIDOREDUCTASE (EC 1.6.99.-)
711 712 RXA01311 GR00380 1611 885 SUCCINATE DEHYDROGENASE IRON-SULFUR PROTEIN
(EC 1.3.99.1)
713 714 RXN03014 VV0058 1273 368 NADH DEHYDROGENASE I CHAIN M (EC 1.6.5.3)
715 716 F RXA00910 GR00248 3 1259 Hydrogenase sutxmits
717 718 RXN01895 W0117 955 5 NADH DEHYDROGENASE (EC 1.6.99.3)
719 720 F RXA01895 GR00543 2 817 DEHYDROGENASE
721 722 RXA00703 GR00183 2556 271 FORMATE DEHYDROGENASE ALPHA CHAIN (EC
1.2.1.2)
723 724 RXN00705 VV0005 8111 5197 FDHD PROTEIN
725 726 F RXA00705 t3R00184 1291 407 FDHD PROTEIN
727 728 RXN00388 W0025 2081 3091 CYTOCHROME C BIOGENESIS PROTEIN CCSA cNn _
729 730 F RXA00388 GR00085 969 667 essential pmtein similar to cytochrome c 00
731 732 F RXA00386 GR00084 514 5 RESC PROTEIN, essential protein sUnilsr to
cytochrome c biogenesis ro _
protein
733 734 RXA00945 GR00259 1876 2847
putative eytochronx oxidase
735 736 RXN02556 VV0101 5602 6759 FLAVOHEMOPROTEIN I DIHYDROPTERIDINE
REDUCTASE (EC - N
1.6.99.7) ' . o
737 738 F RXA02556 GR00731 2019 3176 FLAVOHEMOPROTEIN .3
- 739 740 RXA01392 GR00408 2297 3373 GLUTATHIONE S-TRANSFERASE (EC 2.5.1.18)
741 742 RXA00800 GR00214 2031 3134 GLUTATHIONE-DEPENDENT FORMALDEHYDE
DEHYDROGENASE (EC
1.2.1.1)
743 744 RXA02143 GR00639 10138 11025 QCRC PROTEIN, rnenaquinoi:aytocfirome c
oxidoredudase 00
745 746 RXN03096 VV005e 405 4 NADH DEHYDROGENASE I CHAIN M (EC 1.6.5.3)
747 748 RXN02036 W0176 32683 33063 NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 4 (EC
1.6.5.3)
749 750 RXN02765 W0317 3552 2794 Hypotheticai Oxidorductase
751 752 RXN02206 VV0302 1784 849 HypoMroticalOxidoredudaae
753 754 RXN02554 VV0101 4633 4010 Hypothedcal Oxidoreductase (EC
ATP-Synthase
Nudeic Acid AeAno Acid Identiflcaion Code Conux. NT Start NT Stop Funotion
SEQ ID NO SEQ ID NO
755 756 RXN01204 W0121 1270 461 ATP SYNTHASE A CHAtN (EC 3.6.1.34)
757 758 F RXA01204 GR00345 394 1155 ATP SYNTHASE A CHAIN (EC 3.6.1.34)
759 760 RXA01201 GR00344 675 2315 ATP SYNTHASE ALPHA CHAIN (EC 3.6.1.34)
761 762 RXN01193 VV0175 5280 3832 ATP SYNTHASE BETA CHAIN (EC 3.6.1.34)
763 764 F RXA01193 GR00343 15 755 ATP SYNTHASE BETA CHAIN (EC 3.6.1.34)
765 766 F RXA01203 GR00344 3355 3993 ATP SYNTHASE BETA CHAIN (EC 3.6.1.34)
Table I (continued)
Nudeic Acid Amino Acid Identifiation Code Conti . NT Start NT Stot1 Function
SEQIDNO SEQIDNO
767 768 RXN02821 W0121 324 85 ATP SYNTHASE C CHAIN (EC 3.6.1.34)
769 770 F R)tl02821 GR00802 139 318 ATP SYNTHASE C CHAIN (EC 3.6.1.34)
771 772 RXA01200 GR00344 2 610 ATP SYNTHASE DELTA CHAIN (EC 3.6.1.34)
773 774 RXA01194 GR00343 770 1141 ATP SYNTHASE EPSILON CHAIN (EC 3.6.1.34)
775 776 RXA01202 GR00344 2375 3349 ATP SYNTHASE GAMMA CHAIN (EC 3.6.1.34)
777 778 RXN02434 VV0090 4923 3274 ATP-BINDING PROTEIN
Cytochrome metabolism
Nucleic Acid Amino Acid Identification Code Comi . NT Start NT Stop Function
SEQ ID NO SEO ID NO o
779 780 RXN00684 1N0005 29864 28581 CYTOCHROME P450 116 (EC 1.14: :) Ln
781 782 RXN00387 VV0025 1150 2004 Hypothetical Cytochrome c Biogenesis Protein
00
F-' =
J
V
""'
F-'
00
TABLE 2 = Excluded Genes
GenBank"' Gene Name Gene Function Reference
Accession No.
A09073 ppg Phosphoenol pyruvate carboxylase Bachmann, B. et at. "DNA fragment
coding for phosphoenolpyruvat
corboxylase, recombinant DNA canying said fragment, strains carrying the
necombinant DNA and method for producing L-aminino acids using said
strains," Patent: EP 0358940-A 3 03/21/90
A45579, Threonine dehydratase Moeckel, B. et al. "Production of L-isoleucine
by means of recombinant
A4558I, micro-organisms with deregulated threonine dehydratase," Patent: WO
A45583, 9519442-A 5 07/20/95
A45585
A45587
AB003132 murC; ftsQ; 8sZ Kobayashi, M. et al. "Cloning, sequencing, and
characterization of the ftsZ
gene from corynefonn bacteria," Biochem. Biophys. Res. Commun.,
236(2):383-388 (1997) Ln
AB015023 murC; t'isQ Wachi, M. et al. "A murC gene from Coryneform bacteria,"
Appi. tLlicrobiol. 00
Biotechnol., 51(2):223-228 (1999)
AB018530 dtsR Kimura, E. et al. "Molecular cloning of a novel gene, dtsR,
which rescues the ~
detergent sensitivity of a mutant derived frrnn Brevibmterimn
/aclojennentum," Biosci. Biotechnol. Biochem., 60(10):1565-1570 (1996)
~ o
AB018531 dtsRl ; dtsR2 N AB020624 murl D-glutamate racemase
AB023377 tkt transketolase
AB024708 g1tB; gltD Glutamine 2-oxoglutarate aminotransferase 0D
large and small subunits
AB025424 acn aconitase
AB027714 rep Replication protein
AB0277I5 rep; aad Replication protein; aminoglycoside
adenyltransferase
AF005242 argC N-acetylglutamate-5-semialdehyde
dehydrogenase
AF005635 ginA Glutamine synthetase
AF030405 hisF cyelase
AF030520 argG Argininosuccinate synthetase
AF031518 argF Ornithine carbamotytransferase
AF036932 aroD 3-dehydroquinate dehydratase
AF038548 c Pyeuvate carboxylase
Table 2 continued
AF038651 dciAE; apt; rel Dipeptide-binding protein; adenine Wehmeier, L. et
al. "The role of the Corynebacterium glutamicum rel gene in
phospboribosyltransferase; GTP (p)ppGpp metabolism," Microbiolo83; 144:1853-
1862 (1998)
pyrophosphokinase
AF041436 argR Arginine repressor
AF045998 impA Inositol monophosphate phosphatase
AF048764 argH Argininosuccinate tyase
AF049897 argC; argl; argB; N-acetylglutamylphosphate reductase;
argD; argF; argR; ornithine acetyltransferase; N-
argG; argH acerylglutamate kinase; acetylornithine
transminase; omithine
carbamoyltransferase; arginine repressor;
argininosuccinate synthase;
argininosuccinate lyase
AF050109 tnhA Enoyl-acyl carrier protein reductase
AF050166 hisG ATP phosphoribosyltransferase
L,,
AF051846 hisA Phosphoribosylformimino-5-amino-l- co
phosphoribosyl-4-imidazolecarboxamide
isomerase ~
AF052652 metA Homoserine 0-acetyltransferase Park, S. et al. "Isolation and
analysis of metA, a methionine biosynthetic gene
encoding homoserine acetyltransferase in Corynebacterium glutamicum," Mol. o
Cells.. 8(3):286-294 (1998) AF053071 aroB Dehydroquinate synthetase 0
AF060558 hisH Glutamine amidotransferase
AF086704 hisE Phosphonbosyl-ATP- co
pyrophosphohydrolase
AF114233 aroA 5-enolpyruvylshikimate 3-phosphate
synthase
AF116184 panD L-aspartate-alpha-decarboxylase precursor Dusch, N. et al.
"Expression of the Corynebacterium glutatnicum panD gene
encoding L-aspartate-alpha-decarboxylase leads to pantothenate
overproduction in Escherichia coli," Appl. Environ. Microbial., 65(4)1530-
1539(1999)
AF124518 aroD; aroE 3-dehydroquinase; shikimate
dehydrogenase
AF124600 aroC; aroK; aroB; Chorismate synthase; shikimate kinase; 3-
pepQ dehydroquinate synthase; putative
cytoplasmic peptidase
AF 145897 mhA
AF 145898 inhA
Table 2 contiaued
AJ001436 ectP Transport of ectoine, glycine betaine, Peter, H. et al.
"Corynebacterium glutamicum is equipped with four secondary
proline carriers for compatible solutes: Identification, sequencing, and
characterization
of the proline/ectoine uptake system, ProP, and the ectoine/proline/glycine
betaine carrier, EctP," J. Bacteriol., 180(22):6005-6012 (1998)
AJ004934 dapD Tetrahydrodipicolinate succinylase Wehrmann, A. et al.
"Different modes of diaminopimelate synthesis and their
(incomplete) role in cell wall integrity: A study with Corynebacterium
glutamicum," J.
Bacteriol., 180(12):3159-3165 (1998)
AJ007732 ppc; secG; amt; ocd; Phosphoenolpyruvate-carboxylase; ?; high
soxA affinity ammonium uptake protein; putative
ornithine-cyclodecarboxylase; sarcosine
oxidase
AJ010319 SsY, ginB, ginD; srp; Involved in cell division; Pil protein; Jakoby,
M. et al. "Nitrogen regulation in Corynebacterium glutamicum; C)
amtP uridylyltransferase (uridylyl-removing Isolation of genes involved in
biochemical characterization of corresponding
enzmye); signal recognition particle; low proteins," FEMSMicrobiol.,
173(2):303-310 (1999)
affinity ammonium uptake protein
AJ132968 cat Chioram henicol aceteyl transferase
AJ224946 mqo L-malate: quinone oxidoreductase Molenaar, D. et al. "Biochemical
and genetic characterization of the
membrane-associated malate dehydrogenase (acceptor) from Corynebacterium
glutamicum," Eur. J. Biochem., 254(2):395-403 (1998)
AJ238 50 ndh NADH dehydrogenase
AJ238703 porA Porin Lichtinger, T. et a."Biochemical and biophysical
characterization of the cell
wall porin of Corynebacterium glutamicum: The channel is formed by a low
molecular mass polypeptide," Biochemistry, 37(43):15024-15032 (1998)
D1742 Transposable e ement IS31831 Vertes et a"Isolation and characterization
of IS31831, a transposable element 0D
from Corynebacterium glutamicum," Mol. Microbiol., 11(4):739-746 (1994)
D84102 odhA 2-oxoglutarate ehydrogenase Usuda, Y. et al. "Molecular cloning of
the Corynebacterium glutamicum
(Brevibacterium lactofermentum AJ 12036) odhA gene encoding a novel type
of 2-oxoglutarate dehydrogenase," Microbiology, 142:3347-3354 (1996)
E01358 hdh; hk Homoserine dehydrogenase; homoserine Katsumata, R. et al.
"Production of L-thereonine and L-isoleucine," Patent: JP
kinase 1987232392-A 1 10/12/87
E01359 Upstream of the start codon of homoserine Katsumata, R. et
a."Production of L-thereonine and L-isoleucine," Patent: JP
kinase gene 1987232392-A 2 10/12/87
E01375 Tryptophan operon
E01376 trpL; trpE Leader peptide; anthranilate synthase Matsui, K. et al.
"Tryptophan operon, peptide and protein coded thereby,
utilization of tryptophan operon gene expression and production of
tryptophan," Patent: JP 1987244382-A 1 10/24/87
Table 2 continued
E01377 Promoter and operator regions of Matsui, K. et al. "Tryptophan operon,
peptide and protein coded thereby,
tryptophan operon utilization of tryptophan operon gene expression and
production of
Gyptophan." Patent: JP 1987244382-A 1 10/24/87
E03937 Biotin-synthase Hatakeyama, K. et al. "DNA fi-agment containing gene
capable of coding
biotin synthetase and its utilization," Patent: JP 1992278088-A 1 10/02/92
E04040 Diamino pelargonic acid atninotransferase Kohama, K. et al. "Gene
coding diaminopelargonic acid aminotransferase and
desthiobiotin synthetase and its utilization," Patent: JP 1992330284-A I
l l/18/92
E04041 Desthiobiotinsynthetase Kohama, K. et al. "Gene coding
diaminopelargonic acid aminotranskrase and
desthiobiotin synthetase and its utilization," Patent: JP 1992330284-A 1
11/18/92 E04307 Flavum aspartase Kurusu, Y. et al. "Gene DNA coding aspartase
and utilization thereof," Patent:
JP 1993030977-A 1 02/09/93
E04376 Isocitric acid lyase Katsumata, R. et al. " ene mantfestation
controlling DNA," Patent: JP
1993056782-A 3 03/09/93
E04377 Isocitric aeid lyase N-terminal fragment Katsumata, R. et al. "Gene
manifestation controlling DNA," Patent: JP
1993056782-A 3 03/09/93
04484 Prephenate dehydratase Sotouchi, N. et al. "Production of L-
phenylalanine by fermentatton," Patent: JP
1993076352-A 2 03/30/93
E03108 Aspartokinase Fugono, N. et al. "Gene DNA coding Aspartokinase and its
use," Patent: JP
1993184366-A 1 07/27/93
- ~ i
E05112 Dihydro-dipichorinate synthetase Hatakeyama, K. et al. "Gene DNA coding
dihydrodipicolinic acid synthetase ~
and its use," Patent: JP 1993184371-A 1 07l27/93
E05776 Diaminopimelic acid dehydrogenase Kobayashi, M. et al. "Gene DNA coding
Diaminopimelic acid dehydrogenase
and its use," Patent: JP 1993284970-A I I I/02/93
E05779 Threonine synthase Kohama, K. et al. "Gene DNA coding threonine
synthase and its use," Patent:
JP 1993284972-A 1 11/02/93
E06110 Prephenate ehydratase Kikuchi, T. et al. "Production of L-phenylalanine
by fermentation m ,
Patent: JP 1993344881-A 1 12/27/93
E0611 i Mutated Prephenate dehydratase Kikuchi, T. et al. "Production of L-
phenylalanine by fermentation method,"
Patent: JP 1993344881-A 1 12/27/93
E06146 Acetohydroxy acid synthetase Inui, M. et al. "Gene capable of coding
Acetohydroxy acid synthetase and its
use," Patent: JP 1993344893-A 1 12/27/93
E06825 Aspartokinase Sugimoto, M. et al. "Mutant aspartokinase gene," patent:
JP 1994062866-A 1
03/08/94
E06826 Mutated aspartokinase alpha subunit ugimoto, M. et al. "Mutant
aspartokinase gene," patent: JP 19940628 A 1
03/08/94
Table 2 continued
E06827 Mutated aspartokinase alpha subunit Sugimoto, M. et al. "Mutant
aspartokinase gene," patent: JP 1994062866-A 1
03/08/94
E07701 secY Honno, N. et al. "Gene DNA participating in integration of
inembraneous
protein to membrane," Patent: JP I994169780-A 1 06/21/94
E08177 Aspartokinase Sato, Y. et al. "Genetic DNA capable of coding
Aspartokinase released from
feedback inhibition and its utilization," Patent JP 1994261766-A 109/20/94
E08178, Feedback inhibition-released Aspartokinase Sato, Y. et al. "Genetic
DNA capable of coding Aspartokinase released from
E08179, feedback inhibition and its utilization," Patent: JP 1994261766-A 1
09l20/94
E08180,
E08181,
E08182
E08232 Acetohydroxy-acid isomeroreductase Inui, M. et al. "Gene DNA coding
acetohydroxy acid isomeroreductase,"
Patent: JP 1994277067-A I 10/04/94
E08234 secE Asai, Y. et al. "Gene DNA coding for translocation machinery of
protein,"
Patent: JP 1994277073-A 1 10/04/94 cn -
E08643 FT aminotransferase and desthiobiotin Hatakeyama, K. et al. "DNA
fragment having promoter function in 00
synthetase promoter region coryneform bacterium," Patent: JP 1995031476-A
102103/95
E08646 Biotin synthetase Hatakeyama, K. et al. "DNA fragment having promoter
function in
coryneform bacterium," Patent: JP 1995031476-A 1 02/03/95
E08649 Aspartase Kohama, K. et al "DNA fragment having promoter function in
coryneform ~ o
bacterium," Patent: JP 1995031478-A 1 02/03/95
E08900 Dihydrodipicolinate reductase Madori, M. et al. "DNA fragment
containing gene coding Dihydrodipicolinate
acid reductase and utilization theroof; Patent=. JP 1995075578-A 1 03/20/95
E08901 Diaminopimelic acid decarboxylase Madori, M. et al. "DNA fragment
containing gene tng Diaminopime ic acid 00
decarboxylase and utilization theraof," Patenr JP 1995075579-A I 03/20/95
E12594 Serine hydroxymethyltransferase Hatakeyama, K. et al. "Production of L-
nypophan," Patent JP 1997028391-A
1 02/04/97
E12760, transposase Moriya, M. et al. "Amplification of gene using artificial
transposon," Patent:
E12759, JP1997070291-A 03/18/97
E12758
E12764 Arginyl-tRNA synthetase; diaminopimelic Moriya, M. et al.
"Amplification of gene using artificial transposon," Patent:
acid decarboxylase JP 1997070291-A 03/18/97
E12767 Di ydrodipicolinic acid synthetase Moriya, M. et al. "Amplification of
gene using arti tc' transposon," Patent:
JP 1997070291-A 03/18/97
E12770 aspartokinase Moriya, M. et al. "Amplification of gene using artificial
transposon,' Patent:
JP 1997070291-A 03/18/97
E12773 Dihydrodipicolinic acid reductase Moriya, M. et al. "Amplification of
gene using artificial transposon," Patent:
JP1997070291-A 03/18/97
Table 2 continued
E13655 Glucose-6-phosphate dehydrogenase Hatakeyama, K. et al. "Glucose-6-
phosphate dehydrogenase and DNA capable
of coding the same," Patent: 3P 1997224661-A 1 09/02/97
L01508 IIvA Threonine dehydratase Moeckel, B. et al. "Functional and
structural analysis of the threonine
dehydratase of Corynebacterium glutamicum," J. Bacteriol., 174:8065-8072
(1992)
l.07603 EC 4.2.1.15 3-deoxy-D-arabinoheptulosonate-7- Chen, C. et al. "The
cloning and nucleotide sequence of Corynebacterium
phosphate synthase glutamicum 3-deoxy-D-arrabinoheptulosonate-7-phosphate
synthase gene,"
FEMS MicrobioL Lett., 107:223-230 (1993)
L09232 IIvB; i1vN; i1vC Acetohy roxy acid synthase large subunit; Keilhauer,
C. et al. "Isoleucine synthesis in Corynebacterium glutamicum:
Acetohydroxy acid synthase small subunit; molecular analysis of the i1vB-ilvN-
i1vC operon," J. Bacreriol., 175(17):5595-
Acetohydroxy acid isomeroreductase 5603 (1993)
L18874 PtsM Phosphoenolpyruvate sugar Fouet, A et al. "Bacillus subtilis
sucrose-specific enzyme 11 of the o
phosphotransferasc phosphotransferase system: expression in Escherichia coli
and homology to Lõ
enzymes It from enteric bacteria," PNAS USrt, 84(24):8773-8777 (1987); Lee, 00
J.K. et al. "Nucleotide sequence of the gene encoding the Corynebacterium N
glutamicum mannose enzyme 11 and analyses of the deduced protein r
sequence,"FEMSMicrobiot. Lett., 119(1-2):137-145(1994)
L27123 aceB Malate synthase Lee, H-S. et al. "Molecular characterization of
aceB, a gene encoding malate
synthase in Corynebacterium ghitamicum," J. Microbiol. Biorechnot.,
4(4):256-263 (1994) v o
L27126 Pyruvate kinase Jetten, M. S. et al. "Structural and functional
analysis of pyruvate kinase from Corynebacterium glutamicum," Appl. Environ.
Microbio%, 60(7):2501-2507 co
(1994)
L28760 aceA Isocitrate lyase
L35906 dtxr Diphtheria toxin repressor Oguiza, I.A. et al. "Molecular cloning,
DNA sequence analysis, and
characterization of the Corynebacterium diphtheriae dtxR from Brevibacterium
lactofermentum," J. Bacteriol., 177(2):465-467 (1995)
M13774 Prephenate dehy ratase Follettie, M.T. et ai. "Molecular cloning and
nucleotide sequence of the
Corynebacterium glutamicum pheA gene," J. Bacieriol., 167:695-702 (1986)
M16175 SS rRNA Pa , Y-H. et al. "Phylogenetic analysis o the coryneform
bacteria by 56
rRNA sequences," J. Baeterrol., 169:1801-1806 (1987)
M 16663 trpE Anthranilate synthase, 5' en o, K. et al. "Sttucture and function
of the trp operon control regions o
Brevibacterium lactofermentum, a glutamiaacid-producing bacterium," Gene,
52:191-200 (1987)
M16664 trpA Tryptophan synthase, 3'end Sano, K. et al. "Structure and function
of the trp operon control regions of
Brevibacterium lactofermentum, a giutarnie-acid-producing bacterium," Ge,re,
52:191-200 (1987)
Table 2 (continued
M25819 Phosphoenolpyruvate c xylase O'Regan, M. et al. "Cloning and nucleotide
sequence of the
Phosphoenolpyruvate carboxylase-coding gene of Corynebacterium
glutamicum ATCC13032," Gene, 77(2):237-251 (1989)
M85106 23S rRNA gene insertion sequence Roller, C. et al. " ram-positive
bacteria with a high DNA G+C content are
characterized by a common insertion within their 23S rRNA genes," J. Gen.
Microbiol., 138:1167-1175 (1992)
M85107, 23S rRNA gene insertion sequence Roller, C. et al. "Gram-positive
bacteria with a high DNA G+C content are
M85108 characterized by a common insertion within their 23S rRNA genes," J.
Gen.
Microbiol., 138:1167-1175 (1992)
M89931 aec ; bm ; yhbw Beta C-S lyase; branched-chain amino acid Rossol, 1. et
al. "The Corynebacterium glutamicum aecD gene encodes a C-S
uptake carrier; hypothetical protein yhbw lyase with alpha, beta-elimination
activity that degrades aminoethylcysteine,"
J. Bacteriol.. 174(9):2968-2977 (1992); Tauch, A. et al. "Isoleucine uptake in
Corynebacterium glutamicum ATCC 13032 is directed by the brnQ gene
product," Arch. Microbiol., 169(4):303-312 (1998)
S59299 trp Leader gene (promoter) Herry, D.M. et al. "Cloning of the trp gene
cluster from a ttyptophan- Ln
hyperproducing strain of Corynebacterium glutamicum: identification of a 00
mutation in the trp leader sequence,"App/. Environ. Microbiol., 59(3):791-799
r =
(1993) F-'
U11545 trpD Anthranilate phosphoribosyltransferase O'Gara, I.P. and Dunican,
L.K. (1994) Complete nucleotide sequence of the
Corynebacterium glutamicum ATCC 21850 tpD gene." Thesis, Microbiology ~ o
Department, University College Galway, Ireland.
U13922 cgllM; eglIR; clgllR Putative type 1l 5-cytosoine Schafer, A. et al.
"Cloning and characterization of a DNA region encoding a
methyltransferase; putative type 11 stress-sensitive restriction system from
Corynebacterium glutamicum ATCC
restriction endonuclease; putative rype I or 13032 and analysis of its role in
intergeneric conjugation with Escherichia 00
type IIl restriction endonuclease coli," J. Bacteriol., 176(23):7309-7319
(1994); Schafer, A. et al. "The
Corynebacterium glutamicum cgIIM gene encoding a 5-cytosine in an McrBC-
deficient Escherichia eoli strain," Gertp, 203(2):95-101 (1997)
U 14965 recA
U31224 ppx Ankri, S. et al. "Mutations in the Corynebacterium
glutamicumproline
biosynthetic pathway: A natural bypass of the proA step," J. Bacteriol.,
178(15):4412-4419 (1996)
U31225 proC L-proline: NADP+ 5-oxidoreductase Ankri, S. et al. "Mutations in
the Corynebacterium glutamicumproline
biosynthetic pathway: A natural bypass of the proA step," J. Bacteriol.,
178(15):4412-4419 (1996)
U31230 obg; proB; unkdh ?;gamma glutamyl kinase;similar to D- Ankri, S. et al.
"Mutations in the Cotynebacterium glutamicumproline
isomer specific 2-hydroxyacid biosynthetic pathway: A natural bypass of the
proA step," J. Bacteriol.,
dehydrogenases 178(15):4412-4419 (1996)
Table 2 (continued
U31281 bioB Biotin synthase Serebriiskii, I.G., "Two new members of the bio B
superfamily: Cloning,
sequencing and expression of bio B genes of Methylobacillus flagellatum and
Corynebacterium glutamicum," Gene, 175:15-22 (1996)
U35023 thtR; accBC Thiosulfate sulfurtransferase; acyl CoA Jager, W. et al. "A
Corynebacterium glutamicum gene encoding a two-domain
carboxylase protein similar to biotin carboxylases and biotin-carboxyl-carrier
proteins,"
Arch. Microbiol., 166(2);76-82 (1996)
U43535 cmr Multidrug resistance protein Jager, W. et al. "A Corynebacterium
glutamicum gene con erring multidrug
resistance in the heterologous host Escherichia coli," J. Bacteriol.,
179(7):2449-2451 (1997)
U43536 c1pB Heat shock ATP-binding protein
U53587 aphA-3 3'S"-aminoglycoside phosphotransferase
U89648 Corynebacterium glutamicum unidentified
sequence involved in histidine biosynthesis, N
partial sequence L,
X04960 trpA; trpB; trpC; trpD; Tryptophan operon Matsui, K. et al. "Complete
nucleotide and deduced amino acid sequences of 00
trpE; trpG; trpL the Brevibacterium lactofermentum tryptophan operon," Nucleic
Acids Res.,
14(24):t0113-10114(1986) F'
=
X07563 lys A DAP decarboxylase (meso-diaminopimelate Yeh, P. et al. "Nucleic
sequence of the lysA gene of Corynebacterium
decarboxylase, EC 4.1.1.20) glutamicum and possible mechanisms for modulation
of its expression," Mol. o
Gen. Genel., 212(I):112-119 (1988) v i =
X14234 EC 4.1.1.31 Phosphoenolpyruvate carboxylase Eikmanns, B.J. et al. "The
Phosphoenolpyruvate carboxylase gene of
Corynebacterium glutamicum: Molecular cloning, nucleotide sequence, and
expression," MoL Gen. Genet., 218(2):330-339 (1989); Lepiniec, L. et al.
"Sorghum Phosphoenolpyruvate carboxylase gene family: structure, function
and molecular evolution," Plant. Afol. Biol., 21 (3):487-502 (1993)
X 17313 fda Fructose-bisphosphate aldolase Von der Osten, C.H. et al.
"Molecular cloning, nucleotide sequence and fine-
structural analysis of the Corynebacterium glutamicum fda gene: structural
comparison of C. glutamicum fructose-1, 6-biphosphate akiolase to class I and
class 11 aldolases," Mol. Microbiol.,
X53993 dapA L-2, 3-dihydrodipicolinate synthetase (EC Bonnassie, S. et al.
"Nucleic sequence of the dapA gene from
4.2.1.52) Corynebacterium glutamicum," Nucleic Acids Res., 18(21):6421 (1990)
X54223 AttB-related site Cianciotto, N. et at. "DNA sequence homology between
att B-related sites of
Corynebacterium diphtheriae, Corynebacterium ulcerans, Corynebacterium
glutamicum , and the attP site of lambdacorynephage," FEMS. Microbiol,
Lett., 66:299-302 (1990)
X54740 argS; IysA Arginyl-tRNA synthetase; Diaminopimelate Marcel, T. et al.
"Nucleotide sequence and organization of the upstream region
decarboxylase of the Corynebacterium glutamicum lysA gene," Mol. Microbiol.,
4(1 1):1819-
1830(1990)
Table 2 'continued
X55994 trpL; trpE Putative leader peptide; anthranilate Heery, D.M. et al.
"Nucleotide sequence of tfte Corynebacterium glutamicum
synthase component I trpE gene," Nucleic Acids Res., 18(23):7138 (1990)
X56037 thrC Threonine synthase Han, K.S. et al. "'Tbe molecular structure of
the Corynebactenum glutamtcum
threonine synthase gene," Mol. Microbiol., 4(10):1693-1702 (1990)
X56075 attB-related site Attachment site Cianciotto, N. et al. "DNA sequence
homology between att B-related sites of
Corynebacterium diphtheriae, Corynebacterium ulcerans, Corynebacterium
glutamicum , and the attP site of lambdacorynephage," FEMS. Microbiol,
Lett., 66:299-302 (1990)
X57226 lysC-alpha; lysC-beta; Aspartokinase-alpha subunit; Kalinowski, J. et
al. "Genetic and biochemical analysis of the Aspartokinase
asd Aspartokinase-beta subunit; aspartate beta from Corynebacterium
glutamicum," Mol. MicrobioL, 5(5):1197-1204 (1991);
semialdehyde dehydrogenase Kalinowski, J. et al. "Aspartokinase genes lysC
alpha and lysC beta overlap
and are adjacent to the aspertate beta-semialdehyde dehydrogenase gene asd in
Corynebacterium glutamicum," MoL Gen. Genet., 224(3):317-324 (1990)
X59403 gap;pgk; tpi Glyceraldehyde-3-phosphate; Eikmanns, B.J.
"Iderttification, sequence analysis, and expression of a
phosphoglycerate kinase; triosephosphate Corynebacterium glutamicum gene
cluster encoding the three glycolytic
isomerase enzymes glyceraldehyde-3 -phosphate dehydrogenase, 3-
phosphoglycerate
kinase, and triosephosphate isomeras," J. Bacteriol., 174(19):6076-6086
(1992) X59404 gdh Glutamate dehydrogenase Bormann, E.R. et al. "Molecular
analysis of the Corynebacterium glutamicum gdh gene encoding glutamate
dehydrogenase," Mol. Microbiol., 6(3):317-326
(1992)
X60312 lysl L-lysine permease Seep-Feldhaus, A.H. et al. "Molecular analysis
of the Corynebacterium
glutamicum lysl gene involved in lysine uptake," Mol. Microbiol., 5(12):2995-
. r
3005 (1991) D
X66078 copt Psi protein Joliff, G. et al. "Cloning and nucleotide sequence of
the espl gene encoding
PSI, one of the two major secreted proteins of Corynebacterium glutamicum:
The deduced N-terminal region of PSI is similar to the Mycobacterium antigen
85 complex," Mol. Microbiol., 6(16):2349-2362 (1992)
X66112 glt Citrate synthase Eikmanns, B.J. et aL "Cloning sequence, expression
and transcriptional
analysis of the Corynebacterium glutamicum gltA gene encoding citrate
synthase," Microbiol., 140:1817-1828 (1994)
X67737 dapB Dihydrodipicolinate reductase
X69103 csp2 Surface layer protein PS2 Peyret, J.L. et al. "Characterization of
the cspB gene encoding PS2, an ordered
surface-layer protein in Corynebacteriurn glutamicum," MoL Microbiol.,
9(1):97-109 (1993)
X69104 IS3 related insertion element Bonamy, C. et al. "Identification of IS
1206, a Corynebacterium glutamicum
IS3-related insertion sequence and phylogenctic analysis," Mol. Microbial.,
14(3):571-581 (1994)
Table 2 continued
X70959 IeuA Isopropylmalate synthase Patek, M. et al. "Leucine synthesis in
Corynebacterium glutamicum: enzyme
activities, structure of leuA, and effect of IeuA inactivation on lysine
synthesis," Appt. Environ. Microbiol., 60(1):133-140 (1994)
X71489 icd lsocitrate dehydrogenase (NADP+) Eikmanns, B.J. et al. "Cloning
sequence analysis, expression, and inactivation
of the Corynebacterium glutamicum icd gene encoding isocitrate
dehydrogenase and biochemical characterization of the enzyme," J. Bacteriol.,
177(3):774-782 (1995)
X72855 GDHA Glutamate dehydrogenase (NADP+)
X75083, mtrA 5-methyftryptophan resistance Heery, D.M. et al. "A sequence from
a tryptophan-hyperproducing strain of
X70584 Corynebacterium glutamicum encoding resistance to 5-methyltryptophan,"
Biochem. Biophys. Res. Com+nwi., 201(3):1255-1262 (1994)
X75085 recA Fitzpatrick, R. et al. "Construction and characterization of recA
mutant strains
of Corynebacterium glutamicum and Brevibacterium lactofermentum," Appl.
Microbiol. Biotechnol., 42(4):575-580 (1994) o
X75504 aceA; thiX Partial lsocitrate lyase; 7 Reinscheid, D.J. et al.
"Characterization of the isocitrate lyase gene from c.i, -
Corynebacterium glutamicum and biochemical analysis of the enzyme," J. co
Bacteriol., 176( i 2):34743483 (1994) r =
X76875 ATPase beta-subunit Ludwig, W. et al. "Phylogenetic relationships of
bacteria based on comparative
sequence analysis of elongation factor Tu and ATP-synthase beta-subunit
genes," Antonie Van Leeuwrnhoek, 64:285-305 (1993) ~ o=
X77034 tuf Elongation factor Tu Ludwig, W. et al. "Phylogenetic relationships
of bacteria based on comparative ;-' - .3
sequence analysis of elongation factor Tu and ATP-synthase beta-subunit
genes," Anionie Van Leeuwnhoeh 64:285-305 (1993)
X77384 recA BiHman-Jacobe, H. "Nucleotide sequence of a recA gene from D
Corynebacterium glutamicum," DNA Se ., 4(6):403-404 (1994)
X78491 aceB Malate synthase Reinscheid, D.J. et al. "Malate synthase from
Corynebacterium glutamicum
pta-ack operon encoding phosphotransacetylase: sequence analysis,"
Microbiology, 140:3099-3108 (1994)
X80629 16S rDNA 16S ribosomal RNA Rainey, F.A. et al. "Phylogenetic analysis
of the genera Rhodococcus and
Norcardia and evidence for the evolutionary origin of the genus Norcardia
from within the radiation of Rhodococcus species," Microbiol., 141:523-528
(1995)
X81191 gluA; gluB; gluC; Glutamate uptake system Kronemeyer, W. et al.
"Structure of the gIuABCD cluster encoding the
gluD glutamate uptake system of Corynebacterium glutamicum," J. BacterioL,
177(5):1152-1158 (1995)
X81379 dapE Succinyldiarninopimelate desuccinylase Wehrmann, A. et al.
"Analysis of different DNA fragments of
Corynebacterium glutamicum complementing dapE of Escherichia coli,"
Microbiology, 40:3349-56 (1994)
Table 2 "continued
X82061 16S rDNA 16S ribosomal RNA Ruimy, R. et al. "Phylogeny of the genus
Corynebacterium deduced from
analyses of small-subunit ribosomal DNA sequences," Int. J. Syst. Bacterioi.,
45(4):740-746 (1995)
X82928 asd; lysC Aspartate-semialdehyde dehydrogenase; ? Serebrijski, I. et
al. "Multicopy suppression by asd gene and osmotic stress-
dependent canplementation by heterologous proA in proA mutants," J.
Bacteriol.. I77(24):7255-7260 (1995)
X82929 proA Gamma-glutamyl phosphate reductase Serebrijski,1. et al.
"Multicopy suppression by asd gene and osmotic stress-
dependent complementation by heterologous proA in proA mutants," J.
Bacieriol., 177(24):7255-7260 (1995)
X84257 16S rDNA 16S ribosomal RNA Pascual, C. et al. "Phylogenetic analysis of
the genus Corynebacterium based
on 16S rRNA gene sequences," int. J. S,yst. Bacteriol., 45(4):724-728 (1995)
X8S965 aroP; dapE Aromatic amino acid petmease; ? Wehrmann et al. "Functional
analysis of sequences adjacent to dapE of C.
glutamicum proline reveals the presence of aroP, which encodes the aromatic
amino acid transporter," J. Bacteriol., 177(20):5991-5993 (1995)
X86157 argB; argC; argD; Acetylglutamate kinase; N-acetyl-gamma- Sakanyan, V.
et al. "Genes and enzymes of the acetyl cycle of arginine ci, _
argF; argJ glutamyl-phosphate reductase; biosynthesis in Corynebacterium
glutamicum: enzyme evolution in the early 00
acetylomithine aminotransferase; ornithine steps of the arginine pathway,"
Microbiology, 142:99-108 (1996) r =
carbamoyltransferase; glutamate N-
acetyhransferase
X89084 pta; ackA Phosphate acety sferase; acetate kinase Reinscheid, D.J. et
al. "Cloning, sequence analysis, expression and inactivation ~ o
of the Corynebacterium glutamicum pta-ack operon encoding
phosphotransacetylase and acetate kinase," Microbiolo , 145:503-513 (1999)
X89850 attB Attachment site Le Marrec, C. et al. "Genetic characterization of
site-specific integration
functions of phi AAU2 infecting "Arthrobacter aureus C70," J. Bacteriol., 00
178(7):1996-2004 (1996)
X90356 Promoter fragment Fl Patek, M. et al. "Promoters from Corynebacterium
glutamicum: cloning,
molecular analysis and search for a consensus motif," Microbiolog);
142:1297-1309 (1996)
X90357 Promoter fragment F2 Patek, M. et al. "Promoters from Corynebacterium
glutamicum: cloning,
molecular analysis and search for a consensus motif," Microbiology,
142:1297-1309 (1996)
X90358 Promoter fragment F10 Patek, M. et al. "Promoters from Corynebacterium
glutamicum: cloning,
molecular analysis and search for a consensus motif," Microbiology,
142:1297-1309 (1996)
X90359 Promoter fragment F 13 Patek, M. et al. "Promoters from Corynebacterium
glutamicum: cloning,
molecular analysis and search for a consensus motif," Microbiology,
142:1297-1309 (1996)
Table 2 continued
X90360 Promoter fragment F22 Patek, M. et al. "Promoters from Corynebacterium
glutamicum: cloning,
molecular analysis and search for a consensus motif," Microbiology;
142:1297-1309(1996)
X90361 Promoter fragment F34 Patek, M. et al. "Promoters from Corynebacterium
glutamicum: cloning,
molecular analysis and search for a consensus motif," Microbiology,
142:1297-1309 (1996)
X90362 Promoter fragment F37 Patek, M. et al. "Promoters from C. glutamicum:
cloning, molecular analysis
and search for a consensus motif," Microbfology 142:1297-1309 (1996)
X90363 Promoter gment F45 Patek, M. et al. "Promoters from Corynebacterium
glutamicum: cloning,
molecular analysis and search for a consensus motif," Microbiology,
142:1297-1309 (1996)
X90364 Promoter fragment F64 Patek, M. et al. "Promoters from Corynebacterium
glutamicum: cloning,
molecular analysis and search for a consensus motif," Microbiology,
142:1297-1309(1996)
X90365 Promoter fragment F75 Patek, M. et al. "Promoters from Corynebacterium
glutamicum: cloning, o"'o
molecular analysis and search for a consensus motif," Microbiology,
142:1297-1309(1996) N
X90366 Promoter fiagment PF IOI Patek, M. et al. "Promoters from
Corynebacterium glutaJtticum: cloning,
molecular analysis and search for a consensus motif," Microbiology,
142:1297-1309 (1996)
00 -.3
X90367 Promoter fragment PF 104 Patek, M. et al. "Promoters rom
Corynebacterium utamicum: cloning,
molecular analysis and search for a consensus motif," Microbiology,
142:1297-1309(1996)
X90368 Promoter fragment PF 109 Patek, M. et a."Promoters from Corynebacterium
glutamicum: cloning, 00
molecular analysis and search for a consensus motif," Microbiology,
142:1297-1309(1996)
X93513 amt Ammonium transport system Siewe, R.M. et al. "Functional and
genetic characterization of the (methyl)
ammonium uptake carrier of Corynebacterium ghn'amicum," J. Biol. Chem.,
271(10):5398-5403(1996)
X93514 betP Glycine betaine transport system Peter, H. et al. "Isolation,
characterization, and expression of the
Corynebacterium glutamicum betP gene, encoding the transport system for the
compatible solute glycine betaine," J. Bacteriol., 178(17):5229-5234 (1996)
X95649 o 4 Patek, M. et al. "Idend cation and transcriptional analysis of the
dap6-ORF'2-
dapA-ORF4 operon of Corynebacterium glutamicum, encoding two enzymes
involved in L-Iysine synthesis," BiotechnoL Lett., 19:1113-1117 (1997)
X96471 lysE; lysG Lysine exporter protein; Lysine export Vrljic, M. et al_ "A
new type of transporter with a new type of cellular
regulator protein function: L-lysine export from Corynebacterium glutamicum,"
MoL
Microbiol., 22(5):815-826 (1996)
Table 2 (coattinued)
X96580 panB; panC; xylB 3-methyl-2-oxobutanoate Sahm, H. et al. "D-
pantothenate synthesis in Corynebactaium glutam~cum and
hydroxymethyltransferase; pantoate-beta- use of panBC and genes encoding L-
valine synthesis for D-pantothenate
alanine ligase; xylulokinase overproduction," Appl. Environ Microbiol..
65(5):1973-1979 (1999)
X96962 Insertion sequence 1S1207 and transposase
X99289 Elongation factor P Ramos, A. et al. "Cloning, sequencing and
expression of the gene encoding
elongation factor P in the amitto-acid producer Brevibacteriutn
lactofettnentum
(Corynebacterium glutamicum ATCC 13869)," Gene, 198:217-222 (1997)
Y00140 thrB Homoserine kinase Mateos, L.M. et al. "Nucleotide sequence of the
homoserine kinase (thrB) gene
of the Brevibacterium lactofermentum," Nucleic Acids Res., 15(9):3922 (1987)
Y00151 ddh Meso-diaminopimelate D-dehydrogenase Is ino, S. et al. "Nucleotide
sequence of the meso-diaminopimelate D- <,,
(EC 1.4.1.16) dehydrogenase gene from Corynebacterium glutamicum," Nuclele
Acids Res., 00
I5(9):3917 (1987) o
Y00476 thrA Homoserine dehydrogenase Mateos, L.M. et al. "Nucleotide sequence
of the homoserine dehydrogenase N
(thrA) gene of the Brevibacterium lactofermentum," Nucleic Acids Res.,
15(24):10598 (1987)
Y00546 hom; thrB Homoserine dehydrogenase; homoserine Peoples, O.P. et al.
"Nuc otide sequence and fine structural analysis of the , .3
kinase Corynebacterium glutamicum hom-thrB operon," Mol. Microbiol., 2(l):63-
72 00
(1988)
Y08964 murC; ivD; fksZ
UPD-N-acetylmuramate-alanine ligase; Honrubia, M.P. et al. "Identification,
characterization, and chromosomal oo
division initiation protein or cell division organization of the ftsZ gene
from Brevibacterium lactofermentum," Mol. Gen.
protein; cell division protein Genei., 259(l):97-104 (1998)
Y09163 putP High affinity proline transport system Peter, H. et al. "Isolation
of the putP gene of Corynebacterium
glutamicumproline and characterization of a low-affinity uptake system for
compatible solutes," Arch. MicrobioL, 168(2):143-151(1997)
Y09548 pyc Pyruvate carboxylase Peters-Wendisch, P.G. et al. "Pyruvate
carboxylase from Corynebacterium
glutamicum: characterization, expression and inactivation of the pyc gene,"
Microbiology, 144:915-927 (1998)
Y09578 leuB 3-isopropylmalate dehydrogenase Patek, M. et al. "Analysis of the
leuB gene from Corynebacterium
glutamicum," App1. Microbiol. Blolecirnol., 50(1):42-47 (1998)
Y 12472 Attachment site bacteriophage Phi- 16 Moreau, S. et al. "Site-specific
integration of corynephage Phi- 1The
construction of an integration vector," Microbiol., 145:539-548 (1999)
Y12537 proP Proline/ectoine uptake system protein Peter, H. et al.
"Corynebacterium glutamicum is equipped with four secondary
carriers for compatible solutes: Identification, sequencing, and
characterization
of the prolinelectoine uptake system, ProP, and the ectoine/prolinelglycine
betaine carrier, EctP," J. BacterioL, 180(22):6005-6012 (1998)
Table 2 'continued
Y13221 g1nA Glutamine synthetase I Jakoby, M. et al. "Isolation of Coryne
erium glutamicum g1nA gene
encoding glutamine synthetase I," FEMS Microbiol. Lett., 15 1):81-88 (1997)
Y16642 Ipd Dihydrolipoamide dehydrogenase
Y18059 Attachment site Corynep age 304L Moreau, S. et al. "Analysis of the
integration functions of φ304L: An
integrase module among coryne hages," Yirology, 255(1):150-159 (1999)
Z21501 argS; lysA Arginyl-tRNA synthetase; diaminopimelate Oguiza, J.A. et al.
"A gene encoding arginyl-tRNA synthetase ts located m e
decarboxylase (partial) upstream region of the lysA gene in Brevibacterium
tactofermentum:
Regulation of argS-lysA cluster expression by arginine," J.
BacterioL,175(22):7356-7362 (1993)
Z21502 dapA; dapB Dihydrodipicolinate synthase; Pisabarro, A. et al. "A
cluster of three genes (dapA, orfl, and dapB) of
dihydrodipicolinate reductase Brevibacterium lactoferrnentum encodes
dt7tydrodipicolinate reductase, and a
third polypeptide of unknown function," J. Bacreriol., 175(9):2743-2749
(1993) . cn
Z29563 thrC Threonine synthase Malumbres. M. et al. "Anaiysts and expression
of the t1uC gene of the encoded co
threonine synthase," APPI. Environ. Mkrobiol, 60(7)2209-2219 (1994)
Z46753 16S rDNA Gene for 16S ribosomat RNA H
Z49822 sigA SigA sigma factor Oguiza, J.A. et al "Mukiple sigma factor genes
in Brevibacterium
lactofermentum: Characterization of sigA and sigB," J. Bacteriol., 178(2):550-
553 (1996)
Z49823 galE; dtxR Catalytic activity UDP-galactose 4- Oguiza, J.A. et al "The
galE gene encoding the UDP-galactose 4-epimerase of
00 p =
epimerase; diphtheria toxin regulatory Brevibacterium Iactofermentum is
coupled transcriptionally to the dmdR
protein gene," Gene, 177:103-107 (1996) C0
Z49824 SigB ?; SigB sigma factor Ogutza, J.A. et af "Multiple sigma factor
genes in Bnevibactertum
iactofenmentum: Characterization of sigA and sigB," J. Bacteriol., 178(2):550-
553 (1996)
Z66534 Ttansposase Correia, A. et al. "Cloning and characterization of an (S-
like element present in
the genome of Brevibacterium lactoferrnentum ATCC 13869," Gene,
170(1):91-94 (1996)
A sequence for this gene was published in the indicated reference. However,
the sequence obtained by the inventors of the present application is
significantly longer than
the published version. It is believed that the published version retied on an
incorrect start codon, and thus represents only a fragment of the actual
coding region.
I II IfIIN1 =
CA 02584021 2007-04-18
-86-
TABLE 3: Corynebacterium and Brevibacterium Strains Which May be Used in
the Practice of the Invention
., : _. ::. , - -
- A
Brevibactertum ammoniagenes 21054
Brevibacterium ammoniagenes 19350
Brevibacterium ammoniagenes 19351
Brevibacterium ammoniagenes 19352
Brevibacterium ammoniagenes 19353
Brevibacterium ammoniagenes 19354
8revibacterium ammoniagenes 19355
Brevibacterium ammoniagenes 19356
Brevibacterium ammoniagenes 21055
Brevibacterium ammoniagenes 21077
Brevibacterium ammoniagenes 21553
Brevibacterium ammoniagenes 21580
Brevibacterium ammoniagenes 39101
Brevibacterium butanicum 21196
Brevibacterium divaricatum 21792 P928
Brevibacterium flavum 21474
Brevibacterium flavum 21129
Brevibacterium flavum 21518
Brevibacterium flavum B11474
Brevibacterium flavum B 11472
Brevibacterium flavum 21127
Brevibacterium flavum 21128
Brevibacterium flavum 21427
Brevibacterium flavum 21475
Brevibacterium flavum 21517
Brevibacterium flavum 21528
Brevibacterium flavum 21529
Brevibacterium flavum B 11477
Brevibacterium flavum B 11478
Brevibacterium flavum 21127
Brevibacterium flavum B11474
Brevibacterium healii 15527
Brevibacterium ketoglutamicum 21004
Brevibacterium ketoglutamicum 21089
Brevibacterium ketosoreductum 21914
Brevibacterium lactofermentum 70
Brevibacterium lactofermentum 74
Brevibacterium lactofermentum 77
Brevibacterium lactofermentum 21798
Brevibacterium lact.ofermentum 21799
Brevibacterium lactofermentum 21800
Brevibacurium acto ennentum 21801
Brevibacterium lactofermentum B11470
Brevibacterium lactofermentum B11471
. ..
CA 02584021 2007-04-18
-87-
aeaus < :=: : . speek~ : -. . ,+TGC. FERM rrRRL. cECr . c[W css ; CM _Ustviz
Brevibacterium lactofermentum 21086
Brevibacterium lactofermentum 21420
Brevibacterium Iactofetmentum 21086
Brevibacterium lactofermentum 31269
8revibactenum linens 9174
Brevibacterium linens 19391
Brevibacterium Iinens 8377
Brevibacterium paratffmolyticum 11160
Brevibactertum spec. 717.73
Brevibacterium Spec. 717.73
Brevibacterium spec. 14604
Brevibacterium spec. 21860
Brevibacterium spec. 21864
Brevibacterium spec. 21865
Brevibacterium Spec. 21866
Brevibacterium spec. 19240
Corynebacterium acetoacidophilum 21476
Corynebacterium acetoacidophilum 13870
Corynebacterium acetoglutamicum B11473
Corynebacterium acetoglutamicum B 11475
Corynebacterium acetoglutamicum 15806
Corynebacterium aceloglutamicum 21491
Corynebacterium acetoglutamicum 31270
Corynebacterium acetophilum B3671
Corynebacterium ammoniagenes 6872 2399
Corynebacterium ammoniagenes 15511
Corynebacterium fujiokense 21496
Corynebacterium glutamicum 14067
Corynebacterium glutamicum 39137
Corynebacterium glutamicum 21254
Corynebacterium glutamicum 21255
Corynebacterium glutamicum 31830
Carynebacterium glutamicum 13032
Corynebacterium glutamicum 14305
Coryne cterium glutamicum 15455
Corynebactertum glutamicum 13058
Corynebacterium glutamicum 13059
Corynebacterium glutamicum 13060
Corynebacterium glutamicum 21492
Corynebacterium glutamicum 21513
Corynebacterium glutamicum 21526
Corynebacterium glutamicum 21543
Corynebacterium glutamicum 13287
Corynebacterium glutamicum 21851
Coryne acterium glutamicum 21253
Coryne cterium g utamtcum 21514
Corynebacterium g utamicum 21516
Corynebacterium glutamicum 21299
I. ,.
1 I, Ix
CA 02584021 2007-04-18
-88-
p
Corynebacterium glutainicum 21300
Corynebacterium glutamicum 39684
Corynebacterium glutamicum 21488
Corynebacterium glutamicum 21649
Corynebacterium glutamicum 21650
Corynebacterium glutamicum 19223
Corynebacterium glutainicum 13869
Corynebacterium glutamicum 21157
Corynebacterium glutamicum 21158
Corynebacterium glutamicum 21159
Corynebacterium glutamicum 21355
Corynebacterium glutamicum 31808
Corynebacterium glutainicum 21674
Corynebacterium glutamicum 21562
Corynebacterium glutamicum 21563
Coryne acterium glutamicum 21564
Corynebacterium glutamicum 21565
Corynebacterium glutamicum 21566
Corynebacterium glutam icum 21567
Corynebacterium glutamicum 21568
Corynebacterium glutamicum 21569
Corynebacterium glutamicum 21570
Corynebacterium glutamicum 21571
Corynebacterium glutamicum 21572
Corynebacterium glutamicum 21573
Corynebacterium glutamicum 21579
Corynebacterium glutamicum 19049
Corynebacterium glutamicum 19050
Corynebacterium glutamicum 19051
Corynebacterium glutainicum
19052
Corynebacterium glutainicum 19053
Corynebacterium glutamicum 19054
Corynebacterium glutainicum 19055
Corynebacterium glutainicum 19056
Corynebacterium glutamicum 19057
Corynebacterium glutamicum 19058
Corynebacterium glutamicum 19059
Corynebacterium glutainicum 19060
Corynebacterium glutamicum 19185
Coryne acterium g utamicum 13286
Corynebacterium glutamicum 21515
Corynebacterium glutamicum 21527
Corynebacterium glutamicum 21544
Corynebacterium glutamicum 21492
Corynebacterium glutamicum B8183
Corynebacterium glutamicum B8182
Corynebacterium glutamicum B12416
Corynebacterium glutamicum B12417
CA 02584021 2007-04-18
-89-
. .. .._... .. . .; .. _. _.
;:.-.
. .
- :. r.
en . : :., s C
.. .:... ~.,...,... ..._.... _. , ~. _.~: _ .:_.
Corynebacterium glutamicum B12418
Corynebacterium glutamicum B11476
Corynebacterium glutamicum 21608
Corynebacterium lilium P973
C"ebacterium nitrilophilus 21419 11594
Corynebacterium spec. P4445
Corynebacterium spec. P4446
Corynebacterium spec. 31088
Corynebacterium spec. 31089
Corynebacterium spec. 31090
Corynebacterium spec. 31090
Corynebacterium spec. 31090
Corynebacterium spec. 15954 20145
Corynebacterium spec. 21857
Corynebacterium spec. 21862
Corynebacterium spec. 21863
ATCC: American Type Culture Collection, Rockville, MD, USA
FERM: Fermentation Research Institute, Chiba, Japan
NRRL: ARS Culture Collection, Northern Regional Research Laboratory, Peoria,
IL, USA
CECT: Coleccion Espanola de Cultivos Tipo, Valencia, Spain
NCIMB: National Collection of Industrial and Marine Bacteria Ltd., Aberdeen,
UK
CBS: Centraalbureau voor Schimmelcultures, Baam, NL
NCTC: National Collection of Type Cultures, London, UK
DSMZ: Deutsche Sammiung von Mikroorganismen und Zellkulturen, Braunschweig,
Germany
For reference see Sugawara, H. et al. (1993) World directory of collections of
cultures of
microorganisms: Bacteria, fungi and yeasts (4i edn), World federation for
culture collections world
data center on microorganisms, Saimata, Japen.
i. ...
Table 4: Alignment Results
ID ar kan c ~',onbenk Hk Lonoth Accession Nafie of Genbank Hit 8ource of
Genbank Hit X homoloav Date of
Ir .1 c!!i'2 00006
rxa00013 996 G43_GSS4:AQ713475 581 AQ713475 HS 5402 BZ_A12_T7A RPCI-11 Human
Male BAC Library Homo sapiens Homo sapiens 37,148 13-Jul-99
genomic done Plate=978 Cot=24 Row=B, genomic sunrey sequence.
GB_HTG3AC007420 130583 AC007420 Drosophila melanogaster chnxnosome 2 clone
BACRO7M10 (0630) RPCI-98 Drosophiia nrelanogaster 34,568 20.Sep-99
07.M.10 map 24A-240 strain y; cn bw sp, - SEQUENCING IN PROGRESS
"', 83 unordered pieces.
GB HTG3AC007420 130583 AC007420 Drosophila melanogaster chromosome 2 clone
BACR07M10 (13630) RPCI-98 Drosophila melanogaster 34,568 20Sep-99
07.M.10 map 24A-24D strain y; cn bw sp. "' SEQUENCING IN
PROGRESS ', 83 unordered pieces.
nui00014 903 GB_BAI:MTCY3A2 25830 Z83867 Mycobacterium tuberculosis H37Rv
complete genonie; segment 1361162. Mycobacterium 58,140 17-Jun-98
hrberpdosis
GB_BAI:MLCB1779 43254 Z98271 M cobacterium b rae cosmid B1779. M cobaeterium
Y P Y leprae 57,589 B,Aug-97
GB_BAI:SAPURCLUS 9120 X92429 S.alboniger napH, pur7, pur10, pur6, pur4, pur5
and pur3 genes. Streptomyces anulatus 55,667 28-Feb-96
rxa00030 513 GB EST21:C89713 767 C89713 C89713 Dictyostelium discoideum SS
(H.Urushihara) DictyosteNum discoideum Dictyostelium discoideum 45,283 20-Apr-
98
cDNA clone SSG229, mRNA sequence. omo
GB_EST28:Ai497294 484 A1497294 ib83g03.y1 Zebrafth WashU MPIMG EST Danio rerio
cDNA 5' similar to Danio rerio 42.991 11-MAR-1999 0
SW:AFP4_MYOOC P80961 ANTIFREEZE PROTEIN LS-12. ;, mRNA
sequence. p
GB_EST21:C92167 637 C92167 C92167 Dictyostelium discoideum SS (H.Urushihara)
Dictyostelium diseoideum Didyostelium discoideum 44,444 12-Jul-99 0
cONA clone SSD179, mRNA sequence.
.3
nca00032 1632 GB BA2:AF010496 189370 AF010496 Rhodobacter capsulatus strain
$81003, partial genome, Rhodobacter capsulatus 39,689 12-MAY-1998
GB_BA2:AF018073 9810 AF018073 Rhodobacter sphaeroides operon regulator (smoC),
periplasmic sorbitol-binding Rhodobacter sphaeroides 48.045 22-OCT-1997 . N
protein (smoE), sorbitoUmannitot transport inner membrane protein (smoF), D
sorbitol/mannitol trensport inner membrane protein (smoG), sorbitoVmannW
transport ATP-binding transport protein (smoK), sorbitol dehydrogenase
(smoS), mannitol dehydrogenase (mtlK), and periplasmic mannitol-binding
protein (smoM) genes, complete cds.
GB_BA2:AF045245 5930 AF045245 Klebsiella pneumoniae D=arabinRol transporter
(dalT), D-arabinitol kinase Klebsiella pneumoniae 38,514 16-Jul-98
(dalK), D-arabinitol dehydrogenase (da1D), and repressor (da1R) genes,
complete cds.
nca00041 1342 EM_PAT:E11760 6911 E11760 Base sequenee of sucrase gene.
Corynebacterium 99,031 08-0CT-1997
giutamicum (Rel. 52,
GB_PAT:126124 6911 126124 C~~)
Sequence 4 from patent US 5556776. Unknown. 99,031 07-OCT-1996
GB INI:LMFL5883 31934 AL117384 Leishmania major Friedlin chromosome 23 cosmid
L5883, complete sequenoe. Leishmania major 43,663 21-OCT-1999
rxa00042 882 EM PAT:E11760 6911 E11760 Base sequence of sucrase gene,
Corynebacterium 94.767 08-OCT-1997
glutamiarm (Ref. 52,
Created)
GB_PAT:126124 6911 126124 Sequenoe 4 from patent US 5556776. Unknown. 94.767
07-OCT-1996
= r
Table 4 (continued)
Gt3_INI:CEU33051 4899 U33051 i.aenorhabditis elegans sur-2 mRNA, complete cds.
Caenorhabditis elegans 40,276 23-Jan-96
nca00043 1287 GB PAT:126124 6911 126124 Sequence 4 from patent US 5556776.
Unknown. 97,591 07-OCT-1996
EM PAT:E11760 6911 E11760 Base sequence of sucrase gene. Corynebacterium
97,591 08-OCT-1997
glutamicum (Rel. 52,
Created)
G8_PR3:AC005174 39769 AC005174 Homo sapiens clone UVYGC:g1564a012 from 7p1415,
complete sequence. Homo sapiens 35,879 24-Jun-98
rxa00098 1743 GB_BAI:MSU88433 1928 U88433 Mycobacterium smegmatis
phosphoglucose isomerase gene, complete cds. Myoobacterium smegmatis 62,658 19-
Apr-97
GB BA1:SC5A7 40337 AL031107 Streptomyces coeHcolor cosmid W. Streptomyces
coetioobr 37,638 27-Jul-98
G8 BAI:MTCYtOD7 39800 Z79700 Mycobacterium tuberculosis H37Rv complete genome;
segment 44/162. Mycobacterium 36,784 17-Jun-98
tuberculosis
rxa00148 2334 GB BAI:MTCY277 38300 Z79701 Mycobacterium tuberculosis H37Rv
complete genome; segment 651162. Mycobacterium 67,457 17-Jun-98
tuberculosis GB_BAI:MSGY456 37316 AD000001 Mycobacterium tuberculosis sequence
from clone y456. Mycobacterium 40,883 03-DEC-1996
tuberculosis GB_BAI:MSGY175 18106 AD000015 Mycobacterium tuberculosis sequence
from clone y175. Mycobacterium 67,457 10-DEC-1996
tuberculosis
rxa00149 1971 GB_BAI:MSGY456 37316 At7000001 Mycobacterium tuberculosis
sequence from clone y456. Myoobacterium 35,883 03-DEC-1996
tuberculosis
m ~ -
GB BAI:MSGY175 18106 AD000015 Myaobacterium tuberculosis sequence from clone
y175. Ntyeobacterium 51,001 10-OEC-1996
tuberculosis
GB_BAI:MTCY277 38300 Z79701 Mycobacteriurn tuberculosis H37Rv eomplete genome;
segment 65/162. Mycobacterium 51.001 17-Jun-98 -.3
tuberculosis nca00195 684 GB_BAI:MTCY274 39991 Z74024 Myoobacterium
tuberculosis H37Rv complete genome; segment 126/162. Mycobacterium 35,735
194un-98
tuberculosis 00
GB BAI:MSGB1529CS 36985 L78824 Mycobacterium leprae casmid B1529 DNA sequence.
Mycobacterium leprae 57,014 15-Jun-96
G8 BAI:MTCY274 39991 Z74024 Mycobacterium tuberculosis H37Rv complete genome;
segment 126/162. Mycobacterium 41,892 19-Jun-98
tuberculosis
rxa00196 738 GB BAI:MTCY274 39991 Z74024 Mycobacterium tuberculosis H37Rv
complete genome; segment 1261162. Mycobacterium 41,841 19-Jun-98
tuberculosis
GB_BAI:MTCY274 39991 Z74024 Mycobacterium tuberculosis H37Rv complete genome:
segment 126/162. Myoobacterium 36,599 19-Jun-98
tuberculosis
GB_RO:RATCBRQ 10752 M55532 Rat carbohydrate binding receptor gene, complete
cds. Rattus norvegicus 36,212 27-Apr-93
rxa00202 1065 GB EST11 AA253618 313 AA253618 mw95c10.r1 Soares mouse NML Mus
musculus cDNA clone IMAGE:678450 5', Mus musculus 38,816 13-MAR-1997
mRNA sequence.
GB_EST26AI390284 490 A1390284 mw96a03.y1 Soares mouse NML Mus musculus cDNA
clone IMAGE:678508 5' Mus muscusus 42,239 2-Feb-99
similar to TR:009171 009171 BETAINE-HOMOCYSTEINE
METHYLTRANSFERASE;, mRNA sequence.
GB EST26A1390280 467 A1390280 mw95c10.y1 Soares mouse NML Mus musculus cDNA
clone IMAGE:678450 Mus musculus 37,307 2-Feb-99
5', mRNA sequence.
nca00206 1161 GB BAI:MLCB637 44882 Z99263 Myoobacterium leprae cosmid B637.
Mycobacterium leprae 58,312 17-Sep-97
GB_BAI:MTV012 70287 AL021287 Myoobacterium tuberculosis H37Rv complete genome;
segment 132/162. Mycobacterium 36,632 23-Jun-99
tuberculosis
Table 4 (continued)
GB_BAi:SC6E10 23990 AL109661 Streptomyces coeiicolor cosmid 6E10. Stn!ptomyoes
coe4ookx 38,616 5-Aug-99
A3(2)
rxa00224 1074 GB BAI:BJU32230 1769 U32230 Bradyrhizobium japonicum eiectron
transfer flavoprotein small subunit (etfS) nd Bradyrhizobium japonicum 48,038
25-AAAY-1996
large subunit (etfL) genes, complete cds.
GB_BAI:PDEETFAB 2440 L14864 Paracoccus denRrificans electron transfer
flavoprotein alpha and beta subunit Parawccus denitrificans 48.351 27-OCT-1993
genes, cwmplete cds's.
GB IiTG3AC009689 177954 AC009689 Homo sapiens chromosome 4 clone 104 F 7 map
4, LOW-PASS SEQUENCE Homo sapiens 38,756 28-Aug-99
SAMPLING.
nca00225 909 GB RO:AF060178 2057 AF060178 Mus musculus heparan sulfate 2-
sutfotransferase (Hs2st) mRNA, compiete cds. Mus nwsculus 39,506 18-Jun-98
GB GSS11AQ325043 734 AQ325043 mgxb0020J01r CUGI Rice Blast BAC Ubrary
Magnaporthe grisea genomic Magnaporthe grisea 38,333 8-Jan-99
cione mgxb0020J01 r, genomic survey sequence.
GB EST31:AI676413 551 AI676413 etmEST0167 EtH1 Eimeria tenella cDNA clone
etmc074 5', mRNA sequence. Elrneria tenella 35,542 19-MAY-1999 0
rxa00235 1398 GB BAI:MTCY10G2 38970 Z92539 Myeobacterium tuberadosis H37Rv
compkte genome; segrnent 47/162. M
ycobacterium 65.759 17-Jun-98 cn
tuberculosis ao
GB 8A2AF061753 3721 AF061753 Nitrosomonas europaea CTP synthase (pyrG) gene,
partial cds; and enolase Nitrosomonas europaea 58,941 31-Aug-98 (eno) gene,
complete ods.
GB BA2:AF086791 37867 AF086791 Zymonwnas mobiiis strain ZM4 clone 67E10
carbamoylphosphate s thetase Zymomonas
yn ymonwnas mobr7a 61,239 4-Nov-98
small subunit (carA), carbamoyiphosphate synthetase large subunit (carB), N o
transcription elongation factor (greA), enoiase (eno), pyruvate dehydrogenase
-.3
alpha subunR (pdhA), pyruvate dehydrogenase beta subunit (pdhB),
ribonuckase H (mh), homoserine kinase homolog, alcohol dehydrogenase II
(adhB), and excinuclease ABC subunit A (uvrA) genes, compiete cds;
and unknown genes. ro
rxa00246 1158 GB t3A2:AF012550 2690 AF012550 Acinetobacter ep. BD413 ComP
(comP) gene, complete cAs. Acinetobat3er sp. BD413 53,726 27-Sep-99
GB_PAT:E03856 1506 E03856 gDNA encoding aieohoi dehydrogenase. BaciNus 51,686
29-Sep-97
stearothermophifus
GB_BA1:13ACADHT 1688 D90421 B.stearothermophilus adhT gene for alcohol
dehydrogenase. Baciiius 51,602 7-Feb-99
stearothermophiius
rxa00251 831 GB_BAI:MTCY20G9 37218 Z77162 Mycobacterium tuberculosis H37Rv
eompiete genome; segment 25/162. Myoobacterium 42,875 17-Jun-98
tubercuklsis
GB_BA1:M1Y004 69350 AL009198 Mycobacterium tuberculosis H37Rv complete genome;
segment 144/162. Mycobacterium 40,380 18-Jun-98
tuberculosis
GB_BAI:MTV004 69350 AL009198 Mycobacterium tuberculosis H37Rv complete genoms;
segment 144/162. Myeobaderhmt 41,789 18-Jun-98
tubercuk-sis
rxa00288 1134 GB BA2J1F050114 1038 AF050114 Pseudomonas sp. W7 aiginate lyase
gene, complete ods. Pseudomonas sp. W7 49,898 03-MAR-1999
GB GSS3:B16984 469 B16984 344A14.TVC CIT978SKA1 Homo sapiens genomic clone A-
344A14, genomic Homo sapiens 39.355 4-JunAB
sunreY sequenae.
GB IN2:AF144549 7887 AF144549 Aedes albopictus nbosomal protein L34 (rp134)
gene, complete cds. Aedes aibopictus 36,509 3-Jun-99
rxa00293 1035 GB EST1:T28483 313 T28483 E5T48182 Human Kidney Homo sapiens
cDNA 3' end similar to flavin- Homo sapiens 42,997 6-Sep-95
containing monooxygenase 1(HT:1956), mRNA sequence.
Table 4(continued)
Q8 PR1:tiUMFMOI 2134 M84082 Human Ravin-containir,g monooxygenase (FM01) mRNA,
complete cds. Homo sapiens 37,915 8-Nov-94
G8 EST32=.AI734238 512 A1734238 zb73c05.y5 Soares_fetal Iung NbHL19W Homo
sapiens eDNA clone Homo sapiens 41,502 14-Jun-99
IMAGE:309224 5' simiiar to gb:M64082 DIMETHYLANIUNE
MONOOXYGENASE (HUMAN);, mRNA sequence.
nca00ZN 2967 G8_MTG6:AC011069 168266 AC011069 Drosophiia melanogaster
chromosome X clone BACR11H20 (0881) RPCI-98 Drosophila melanogaster 33,890 02-
DEC-1999
11,H.20 map 12B-12C strain y; cn bw sp, "' SEQUENCING IN PROGRESS
, 92 unordered pieces.
GB EST15:AA531468 414 AA531468 nj63d12.s1 NCI CGAP Pr10 Homo sapiens cDNA done
IMAGE:997175, Homo sapiens 40,821 20-Aug-97
mRNA sequence.
GB_HTG6'AC011069 168266 AC011069 Orosophiia melanogaster chromosome X clone
8ACR11H20 (D881) RPCI-98 Drosophiia melanogaster 30,963 02-DEC-1999
11.H.20 map 12B-12C strain y; cn bw sp, "' SEQUENCING IN PROGRESS
"=, 92 unorderod pieces.
nuo00310 558 GB Vt:VMVY16780 186986 Y16780 varioia minor virus complete
genome. varioia minor virus 35,883 2-Sep-99 GB VI:VARCG 186103 L22579 Varioia
major virus (strain Bangladesh-1975) complete genome. Varlosa major virus
34,664 124an-95
GB_VI:VVCGAA 185578 X69198 Variola vinis DNA compfete genome. Variola vinis
36,000 13-DEC-1996
nra00317 777 G8 HTG3AC009571 159648 AC009571 Homo sapiens chromosome 4 done 57
A 22 map 4, - SEQUENCING IN Homo sapiens 36,988 29-Sep-99 0Ln0
PROGRESS =", 8 unordered pieces. o
GB_HTG3AC009571 159648 AC009571 Homo sapiens chromosome 4 clone 57 A_22 map 4,
"' SEQUENCING IN Homo sapiens 36,988 29-Sep-99 PROGRESS =", 8 unordered
pieces.
GB PR3:AC005697 174503 AC005W7 Homo sapiens chnxnosome 17, done hRPK.138 P 22,
comptete sequence. Homo sapiens 36,340 09-OCT-1998 w
rxa00327 507 GB BA1:LCATPASEB 1514 X64542 L.casei gene for ATPase beta-
subunit. Lactobaciuus oasei 34,664 11-DEC=1992
GB_BAI:LCATPASEB 1514 X64542 L.casei gene for ATPase beta-subunh.
t.actobacidus casei 39.308 11-DEC-1992
rxa00328 615 GB_BA1:S7YPUTPE 1887 L01138 Sainaneila (S2980) proiine permease
(putP) gene, 5' end. Salmonena sp. 39,623 09-MAY-1996
00
GB_BAI:STYPUTPF 1887 L01139 Saknonella (S2983) proline permease (putP) gene,
5' end. Satmonetla sp. 39,623 09-1MAY-1996
GB_8A1:SlYPUTPI 1889 L01142 Saknonella (S3015) proline pennease (putP) gene,
5' end. Salmoneiia sp. 42,906 09-MAY-1996
nca00329 1347 GB PR3AC004691 141990 AC004691 Homo sapiens PAC clone 0J0740D02
from 7p14-p15, complete sequence. Homo sapiens 38,142 16-MAY-1998
GB Pt4=.AC004916 129014 AC004916 Momo sapiens done DJ0891L14, complete
sequence. Homo sapiens 38,549 17-Jul-99
GB_PR3AC004891 141990 AC004691 Homo sapiens PAC clone DJ0740D02 from 7p14-p15,
complete sequence. Homo sapiens 35,865 16-MAY-1998
rxalX1340 1269 G8 BAI:MTCY427 38110 Z70692 Mycobadsrium tuberculosis H37Rv
complete genome: segment 99/162. Mycobadernum 38,940 24-Jun-99
tuberouiosis
GB_GSS12AQ412290 238 AQ412290 RPCI-11-195H2.TV RPCI-11 Homo sapiens genornic
clone RPCI-11-195H2, Homo sapiens 36,555 23-MAR-1999
genomic survey sequence.
GB PL2AF112871 2394 AF112871 Astasia longa smaa subunit n'bosomat RNA gene,
compbte sequence. Astasia bnga 36,465 28Jun-99
rxa00379 307 GB HTGI:CEY56A3 224746 AL022280 Caenorhabditis e(egans chromosome
III clone Y56A3, ""' SEQUENCING IN Caenorhabditis esegans 35,179 6Sep-99
PROGRESS "', in unordered pieces.
GB tiTG1:CEY56A3 224746 AL022280 Caenorhabditis eiegans chromosome III done
Y56A3, ~= SEQUENCING IN Caenorhabditis etegans 35,179 6-Sep-99
PROGRESS "', in unoniered pieces.
=,,
Table 4 (continued)
GB_PR2:HS134419 86897 AL034555 Human DNA sequence irom clone 134019 on
chromosome tp36.11-36.33. Homo sapiens 40,604 23-Nov-99
complete sequence.
nnr00381 729 GB_GSS4AQ730532 416 AQ730532 HS_2149_A1 C06_T7C CIT Approved
Human Genomic Sperm Library D Homo sapiens 35,766 15=JuM99
Homo sapiens genomic clone Piale~2149 Co1=i 1 Row=E, genomic survey
sequence.
GB EST23AI120939 561 A1120939 ub74f05.r1 Soares mouse mammary gland NMLMG Mus
musculus cDNA clone Mus musculus 41,113 2-Sep-98
IMAGE:1383489 5' sirnilar to gb:J04046 CALMOOULIN (HUMAN); gb:M19381
Mouse caimodulin (MOUSE);, mRNA sequence.
GB EST23AI120939 561 A1120939 ub74t05.r1 Soares mouse manunary gland NMLMG Mus
musculus cONA done Mus musculus 41,113 2-Sep-98
IMAGE:1383489 5' similar to gb:J04046 CALMODUUN (HUMAN); gb:M19381
Mouse caimoduiin (MOUSE);, mRNA sequence.
nca00385 362 GB EST'32:AI726450 565 A1726450 BNL.GHi5857 Six-day Cotton fiber
Gossypium hinwtum cDNA 5' simiiar to Gossypium hirsutum 41,152 11-Jun-99
(AF015913) Skb1Hs (Homo sapiens), mRNA sequence.
GB GSS4:AQ740856 768 AQ74085e HS 2274 A2 A07 T7C CIT Approved Human Genomic
Sperm Library 0 Homo sapiens 41,360 16-Jut=99
Homo sapiens genomic done Piates2274 Col=14 Row=A, genamic survey vi
sequenc.e. D
.r.
GB PRI:HSPAIP 1587 X91809 H.sapiens mRNA for GAIP protein. Homo sapiens 36,792
29-MAR-1996 N
r
rxa00388 1134 GB_BAI:MTY25D1G 40838 Z95558 Mycobacterium tubercutosis H37Rv
oompiete genome: segment 281162. Myeobaeterium 51,852 17-Jun-98
A o
tuberculosis
GB_BAI:MSGY224 40051 AD000004 Mycobacterium tubercuiosis sequenoe from clone
y224. Mycobacterium 51,852 03-OEC=1996
tubetx:ulosis o ~
GB_HTGI:AP000471 72466 AP000471 Homo sapiens chromosome 21 clone B230SH15 map
21q22.3, Homo sapiens 36,875 13-Sep-99
SEQUENCING IN PROGRESS "', in unordered pieoes_
nca00427 909 GB_BAI:MSGY126 37164 AD000012 Myoobacterium tuberculosis sequence
from done y126. Myeobaderium 60,022 10-0EC=1996 0
tuberpuktsia
GB_8A1:MTY13012 37085 Z80343 Myeobaceedum tubencutosis H37Rv complete genome;
segment 156/162. Mycobacterium 60,022 17-Jun-98
tubercuiosis
GB_HT(31:CEY48C3 270193 Z92855 Caenorbabditis elegans chromosome Ii done
Y48C3. '- SEQUENCING IN Caenorhabd'dis elegans 28,013 29-MAY-1999
PROGRESS "', in unordered pieces.
rxa00483 1587 GB_PR2:HSAF001550 173882 AF001550 Homo sapiens chranosome 16 BAC
clone CIT987SK-334D11 complete Homo sapiens 38,226 22-Aug-97
sequence.
GB_BAI:LLCPJYW565 12828 Y12736 Ladococcus iadis cremoris plasmid pJW565 DNA,
abliM, abiiR genes and Lactocoaus iadis subap. 37,492 01-MAR-1999
orD(. cromoris
GB_HTG2AC006754 206217 AC008754 Caenorhabditis elegans done Y40Bi0, ="
SEQUENCING IN PROGRESS '==, Caenorhabditis elegans 36,648 23-Feb-99
unordered pieces.
rxa00511 615 GB PR3:HSE127C11 38423 Z74581 Human DNA sequenee from cosmid
E127C11 on chromosome 22q11.2-qter Homo sapiens 39,831 23-Nov-99
contains STS.
GI3 PR3:HSE127C11 38423 Z74581 Numan DNA sequence from cosmid E127C11 on
chromosome 22q11.2-qter Homo sapiens 36,409 23-Nov-99
contains STS.
nca00512 718 GB_BAI:MTCY22G8 22550 Z95585 Mycobaderium tuberculosis H37Rv
complete genome; segment 49l162. Mycobacterium 56,232 17Jun-98
tuberculosis
Table 4 (continued)
Gi3LsA1:MSGL TA 1776 X50313 M.smegmatis giw gene for citrate synthase.
Mycobacterium smegmat's 56,143 20-Sep-91
GB_BA2:ECU73857 128824 U73857 Escherichia coii chromosome minutes 6-8.
Escherichia coli 48,563 14-Jul-99
rxa00517 1164 GB FfTG2AC006911 298804 AC008911 Caenorhabditis etegans done
Y94H6x, "' SEQUENCING IN PROGRESS Caenorhabditiss etegans 37,889 24-Feb-99
15 unordered pieces.
GB_HTG2AC006911 298804 AC006911 Caenorhabditis elegans cione Y94H6x, "'
SEQUENCING IN PROGRESS Ceenorhabditis ekgans 37,889 24-Feb-99
15 unordered pieces.
GB EST29A1602158 481 A1602158 UI-R-ABO-vy-a-01-0-Ui.s2 UI-R-ABO Rattus
nonregicus cDNA clone UI-R-AB0- Rattus nonegicus 40,833 21-Apr-99
vy-,a-01-0-U13', mRNA sequence.
nca00518 320 GB_BA2:ECU73857 128824 U73857 Escherichia coG chromosome minutes
6-8. Escherichia coli 49,688 14JuM99
GB BA2:S1'U51879 8371 U51879 Saimonella typhirtwrium propionate cataboiism
operon: RpoN activator protein Salmone8a typhimurium 50,313 5-Aug-99
homolog (prpR), carboxyphosphonoenolpyruvate phosphonemutase homolog
(prpB), citrate synthase homoiog (prpC), prpO and prpE genes,
cernplete cds.
GB_BA2AE000140 12498 AE000140 Escherichia coli K-12 MG1655 section 30 of 400
of the complete genome. Escherichia coli 49,688 12-Nov-98
rxa00606 2378 GB_EST32AU068253 376 AU068253 AU068253 Rice callus Oryza sativa
cDNA clone C12658_9A, mRNA sequence. Oryza sativa 41,333 7-Jun-99 ~
GB_EST13:AA363046 329 AA363046 EST72922 Ovary II Homo sapiens cDNA 5' end,
mRNA sequence. Homo sapiens 34,347 21-Apr-97
GB_EST32AU068253 378 AU068253 AU068253 Rice callus Oryza sativa cDNA clone
C12658 9A, mRNA sequence. Oryza sativa 41,899 7.iun-99
C71 N
rxa00635 1860 GB_BAI:PAORFI 1440 X13378 Pseudomonas amyloderamosa DNA for ORF
1. Pseudomonas 53,912 14-Jul-95
amyloderamosa - 1 .3
GB BA1:PAORFI 1440 X13378 Pseudomonas amyloderamosa DNA for ORF 1. Pseudomonas
54,422 14-Jul-95 anYlodetamosa
r
_ 00
nca00679 1389 GB_PL2:AC010871 80381 AC010871 Arabidopsis thaliana chromosome
Ili BAC T16011 genomic sequence, Aratiidopsis thaliana 38,244 13-Nov-99
compleDa sequence.
GB_PL1AT81KBGEN 81493 X98130 A.thaliana 81kb genomic sequence. Arabidopsis
thaliana 36,091 12-MAR-1997
GB_PL2AC010871 80381 AC010871 Arabidopsis thaiiana chromosome 111 BAC T16011
genomic sequenee, Arabidopsis thalians 37,135 13-Nov-99
camplete sequence.
nca00680 441 GB_PR3:AC004058 38400 AC004058 Homo sapiens chromosome 4 clone
B241P19 map 4q25, complete sequence. Homo sapiens 36,165 30-Sep-98
GB_PL1 AT81 KBGEN 81493 X98130 A.thaliana 81kb genomic sequence. Arabidopsis
thafiana 38,732 12-MAR-1997
GB PL1 AB026648 43481 A8026648 Arabidopsis thaliana genomic DNA, chromosome 3,
Pt clone: MW 15, compieteArabidopeis thaliana 38,732 07-MAY-1999
sequence.
rxa00682 2022 GB_HTG3:AC010325 197110 AC010325 Homo sapiens chromosome 19
clone CITB-E1 2568A17, - SEQUENCING IN Homo sapiens 37,976 15-Sep-99
PROGRESS "-, 40 unordered pieoes.
GB HTG3:AC010325 197110 AC010325 Homo sapiens chromosorne 19 clone CITB-E1
2568A17, ~= SEQUENCING IN Homo sapiens 37,976 15.Sep-99
PROGRESS "', 40 unordered pieces.
GB PR4:AC008179 181745 AC008179 Homo sapiens clone NH0576F01, complete
sequence. Homo sapiens 37,143 28-Sep-99
=.s
Table 4 (continued)
sxao0683 1215 GB_BJ12:AE000896 10707 AE000$96 Methanobacterium
themtoautotrophicum frorn bases 1189349 to 1200055 Mathanobacterium 38,429 15-
Nov-97
(sect;on 102 of 148) of the complete genome, thermoautotrophiwm
GB_INI:DMBR7A4 212734 AL109630 Drosaphila mctanogaster done BACR7A4.
Drosophila metanogaster 36.454 30-Jul-99
GB EST35:AV163010 273 AV163010 AV163010 Mus musaAus head C57BU8J 13-day embryo
Mus rnusculus cDNA Mus musoulus 41,758 SJut-99
done 3110006J22, mRNA se4uence,
rxa00686 927 GB HTG2:HSDJ137K2 190223 AL049820 Homo sapiens chromosome 6 done
RP1-137K2 map q25.1-25.3. "' Homo saPiens 38,031 03-DEC-1999
SEQUENCiNG IN PROGRESS "', In unordered pieces.
GB_HTG2:HSDJ137K2 190223 AL049820 Hcmo sapiens chromosome 6 clone RPI-137K2
map q25.1-25.3, "' Homo sapiens 38,039 03-DEC-1999
SEQUENCING IN PROGRESS "', in unordered pieces.
GB EST12A,4284399 431 AA284399 zs57b04.ri NCL CG+4P_GCB1 Horno sapiens dJNA
clone IMAGE:701551 5', Homo sapiens 39,205 14-Aug-97
mRNA sequence.
rxatp700 927 GB EST34Ai785570 454 A1785570 uj44d03.x1 Sugano mouse liver mUa
Mus musculus cDNA done Mus musculus 41,943 2-Jul-99
IMAGE:1922789 3' similar to gb:228407 60S RIBOSOMAL PROTEtN L8
(HUMAN);, mRNA sequence.
Ln
GB EST25A1256147 684 AI256147 ui95e12.x1 Sugano mouse liver miia Mus musculus
cDNA clone Mus nwaculus 40,791 12-Nov-98 ro
1MAGE:1890190 3' simitar to gb:Z28407 60S RIBOSOMAL PROTEIN LB N
(HUMAN);. mRNA sequence.
GB 8A1:CARCGI2 2079 X14979 C. aurantlacus reaction oenter genes 1 and 2.
Chkxofiexus aurantiacus 37,721 23-Apr-91
rxs00703 2409 GB_BAI:SCTH2 42655 AL109732 Streptomyoes coe6cdor cosmid 7H2.
Streptomyoes coelicolor 56,646 2-Aug-99 ~ o0
A3(2) os a
GB_BAI:MTCY274 39991 Z74024 Mycobacterium tuberculosis H37Rv compkte genome:
segment 1261162. Mycobacteclum 37,389 19-Jun-98
tuberrwosis
GB_BA2:REU60056 2520 U60056 Ratstonia eutropha formate dehydrogenase-t4Ce
protein (cbb8c) gene, compiete Raistonia eutropha 51.087 16-OCT-1996 ~
ods.
rxa00705 1038 GB GSS15:AQ604477 605 A0604477 HS 2116 Bt GOt MR CIT Approved
Human Genomk: Sperm Library D Homo Homa sapiens 39,617 10-Jun-99
sapiens genomic done Plate=2118 Cot=13 RownN, genomic survey sequence.
GS ESTI1:AA224340 443 AA224340 zr14e07.s1 Stratagene hNT neuron (#937233) Homo
sapiens cONA clone Homo sapiens 35,129 11-MAR 1998
IMAGE:648804 3', mRNA sequence.
G$ EST5:N80648 291 N30648 yw77b02.s1 Soares_plaoenta 8to9weeks 2NbHP8to9W Homo
sapiens cONA Homm sapiens 43,986 5-Jan-96
dene IMAGE:258219 3', mRNA sequence.
rxa00782 1005 GB_BAI:MTCY1007 39800 Z79700 Mycobaderium tuberculosis H37Rv
complete genome; segment 44/162. Mycobaatertum 63.327 17-Jun-98
tuberoutosis
GB_t3A1:MLCL373 37304 AL035500 Mycobacterium bprae cosmid L373. Myoobacterium
leprae 62,300 27-Aug-99
G8_BA2AF128399 2842 AF128399 Pssudomonas aenigtnosa suceinyt.CoA synthetsse
beta subunh (sucC) and Pseudomonas aerugawsa 53,698 25-MAR-12f99
sucanyl-CoA synthetase alpha subunit (suc(3) genes, complete ods.
rxo00783 1395 GB_HTG2AC008158 118792 AC008158 Homo sapiens chromosome 17 clone
hRPK.42 F 20 map 17, Homo sapiens 35,135 28,hd-99
SEQUENCING IN PROGRESS "', 14 unoMered pieces.
GB HTCi2AC008158 118792 AC008158 Homo sapiens choamosome 17 clone hRPK.42_F_20
map 17, Homo sapiens 35,135 28-Jul-99
SEQUENCING IN PROGRESS "=, 14 unordered pieces.
GB_PR3:AC005017 137178 AC005017 Horno sapiens SAC done G8214N13 from 7p14-p15,
complete sequenoe. Homo sapiens 35,864 B,Aug-98
rxa00794 1128 GB_BAI:MTV017 67200 AL021897 Mycobacterium tuberculosis H37Rv
complete genome: segment 48/162. Mycobacterfum 40,331 24-Jun-99
tuberculosis
Table 4 (continued)
GB BAI:MLCB1222 347i4 AL049491 Mycobacterium leprae oosmid 81222.
Mycobacterium leprae 61,170 27-Aug-99
GB PR2:HS151 B14 128942 Z82188 Human DNA sequence from clone 151814 on
chromosome 22 Contains Homo sapiens 37,455 16-Jun-99
SOMATOSTATIN RECEPTOR TYPE 3 (SS3R) gene,pseudogene similar to
ribosomal protein L39.RAC2 (RAS-RELATED C3 BOTUUNUM TOXIN
SUBSTRATE 2 (P21-RAC2)) gene ESTs, STSs, GSSs and CpG islands,
complete sequence,
rxa00799 1767 GB_Pt2:AF016327 616 AF016327 Hordeum vulgare Barperml (perml)
mRNA, partial cds. Hordeum vulgare 41,311 01-OCT-1997
GB_HTG2:HSDJ319M7 128208 AL079341 Homo sapiens chromosome 6 clone RP1-319M7
map p21.1-21.3, "' Homo sapiens 36,845 30-Nov-99
SEQUENCING IN PROGRESS "', in unordered pieces.
GB_HTG2:HSDJ319M7 128208 AL079341 Homo sapiens cMomosome 6 clone RP1-319M7 map
p21.1-21.3, "' Homo sapiens 36,845 30-Nov-99
SEQUENCING IN PROGRESS "', in unordered pieces.
rxa00800 1227 GB BA1:M7Y022 13025 AL021925 Mycobacterium tuberculosis H37Rv
complete genome: segment 1001162. tr{yoobscterium 63,101 17Jun-98
tuberculosie
GB_BA1:AB019513 4417 A8019513 Streptomyces coelicolor genes for alcohol
dehydrogenase and ABC Streptomyces coelWor 41,312 13-Nov-98
transporter, complete cds.
GB_PL1:SCSFAARP 7008 X68020 S.cerevisiae SFA and ARP genes. Saccharomyces
Cerovisiae 36,288 29-Nov-94 Ln
ro
nca00825 1066 GB_BAI:MTY15C10 33050 Z95436 Mycobacterium tuberculosis H37Rv
complete genome; segment 154l162. Mycobacterium 39,980 17-Jun-98
tuberculosia to
4
GB_BAI:MLCB2548 38916 AL023093 Mycobscterium Ieprae cosmid 82548. Myoobaderium
leprae 39,435 27-Aug-99 ~
GB 8A2:AF169031 1141 AF169031 Xanthomonas oryzae pv. oryzae putative sugar
nudeotide Xanthomonas oryzae pv. 46,232 14-Sep-99
epimeraseldehydratase gene, paRial cds. oryzse
rxa00871
0
rxa00t172 1077 GB IN1:CEF23H12 35564 Z74472 Caenorhabditis elegans cosmid
F23H12, complete sequence. Caenorhabditis elegans 34,502 08-OCT-1999 oo
GB_HTG2:AC007263 167390 AC007263 Homo sapiens chromosome 14 done BAC 79J20 map
14q31, "' Homo sapiens 35,714 24aNAY-1999
SEQUENCING IN PROGRESS "', 5 ordered pieces.
GB_HTG2AC007263 167390 AC007263 Homo sapiens chromosome 14 done BAC 79J20 map
14q31, = Homo sapiens 35,714 24-MAY-1999
SEQUENCING IN PROGRESS "', 5 ordered pieces.
nca00879 2241 GB BAI:MTV049 40360 AL022021 Mycobacterium tuberculosis H37Rv
complete genome; segment 811162. Myaobscterium 36,981 19-Jun-98
tuberculosis
GB_PL2:CDU236897 1827 AJ236897 Candida dubliniensis ACT1 gene, exons 1-2.
Candida dubYniensis 38,716 1-3ep-99
GB PLI:CAACTIA 3206 X16377 Candids albicans actl gene for adin. Candids
albicans 36,610 10,Apr-93
nca00909 955 GB_BA2:AF010496 189370 AF010496 Rfiodobader capsulatus stmin
S81003, partial genome. Rhodobader capsulatus 51,586 12-MAY-1998
GB BA1_RMPHA 7888 X93358 Rhizobium meliloti pha[A,B,C,D,E,F,G] genes.
Sinorhizobium meliloN 48,367 12-MAR-1999
GB EST76:C23528 317 C23528 C23528 Japanese flounder spleen Paraiichthys
olivaceus cDNA done HB5(2), ParaNchthys olivaoeus 41,640 28-Sep-99
mRNA sequenoe.
rxa00913 2118 GB_HTG2:AC007734 188267 AC007734 Homo sapiens chromosome 18
clone hRPK44 O_1 map 18, Homo sapiens 34,457 5-Jun-99
SEQUENCING IN PROGRESS =", 18 unordered pieces.
Table 4 (continued)
GB HTG2:AC007734 188267 AC007734 Homo sapiens chror.3osome 18 cbne hRPK.44_O_1
map 18, Homo sapiens 34,457 5-Jun-99
SEQUENCING IN PROGRESS "', 18 unoniered pieces.
GB_EST18AA709478 406 AA709478 vv34a05.r1 Stratagene mouse heart (11937316) Mus
musculus d)NA done Mus musculus 42,065 24-DEG1997
IMAGE:1224272 5', mRNA sequence.
rxa00945 1095 GB_HTG4AC010351 220710 AC010351 Homo sapiens chromosome 5 clone
CITB-H1 202286, "" SEQUENCING IN Homo sapiens 36.448 31-OCT-1999
PROGRESS "', 68 unordered pieces.
G8_HTG4:AC010351 220710 AC010351 Homo sapiens chromosome 5 clone CITB-H7
202286, "' SEQUENCING IN Homo sapiens 36.448 31-OCT-1999
PROGRESS "', 68 unordered pieces.
G8_BAI:MTCY05A6 38631 Z96072 Mycobacterium tuberculosis H37Rv complete genome;
segment 120/162. Mycobaderium 36,218 17-Jun-98
tubercutosis
nca00965
nca00999 1575 GB PAT:E13660 1916 E13660 gDNA encoding 6-phosphogluconate
dehydrogenase. Corynebacterium 98,349 24-Jun-98
glutamicum
GB_BAI:MTCY359 36021 Z83859 Mycobacterium tuberculosis H37Rv complete genome;
segment 84/162. Mycobacterium 38.520 17-Jun-98
tuberculosis Ln
GB_BAI:MLCB1788 39228 AL008609 Mycobaderium leprae cosmid 81788. Mycobacterium
leprae 64,355 27,Aug-99 00
nca01015 442 GB_BAI:MTV008 63033 AL021246 Mycobacterium tuberculosis H37Rv
complete genorne; segment 108/162. Mycobacterium 39,860 17-Jun-98 to
tuberculosis Qa
GB_BA1:MTV008 63033 AL021246 Mycobacterium tuberculosis H37Rv complete genome:
segment 108/162. Myeobacterium 39,120 17-Jun-98
tuberculosis o
-.3
nca01025 1119 GB BA1:SC7A1 32039 AL034447 Streptomyces coeucobr cosmid 7AI.
Streptomyces coelicolor 55,287 15-DEC-1998
GB_BAI:MSGB1723CS 36477 1-78825 Mycobaderium Ieprae cosmid 01723 DNA sequence.
Mycobaaerium leprae 56,847 15-Jun-96 GB BAI:MLCB637 44882 Z99263 Myeobaderium
teprae cosmid 8637. Mycobacterium leprae 56.676 17-Sep-97
nca01048 1347 GB_BA2:AF017444 3067 AF017444 Sinorhizobium melitoti NAOP-
dependent malic enzyme (tme) gene, complete Sinorhizobium meliloti 53,660 2-
Nov-97
qda.
GB_BAI:BSUB0013 218470 Z99116 BaciNus subtilis complete genome (section 13 of
21): from 2395261 to Bacillus subtiks 37,255 26-Nov-97
2613730.
GB_VI:HSV2HG52 154746 Z86099 Herpes simplex virus type 2 (strain HG52),
complete genome. human herpesvirus 2 38,081 04-DEC-1998
rxa01049 1605 GB_HTG2AC002518 131855 AC002518 Homo sapiens chromosome X clone
bWlXD20, =" SEQUENCING IN Homo sapiens 35,647 2-Sep-97
PROGRESS "', 11 unordered pieces.
GB_H7G2:AC002518 131855 AC002518 Homo sapiens chromosome X done bWXD20, "'
SEQUENCING IN Homo sapiens 35,647 2-Sep-97
PROGRESS "', 11 unordered pieces.
GB_HTG2:AC002518 131855 AC002518 Homo sapiens chromosome X done bWXD20, "'
SEQUENCING IN Homo sapiens 26,180 2-Sep-97
PROGRESS "', 11 unordered pieces.
nca01077 1494 GB PR3:HSDJ653C5 85237 AL049743 Human DNA sequence from done
653C5 on chromosome 1p21.3-22.3 Homo sapiens 36,462 23-Nov-99
Contains CA repeat(D1S435), STSs and GSSs, complete sequence.
GB_BAI:ECU29579 72221 U29579 Escherichia coli K-12 genome; approximately 61 to
62 minutes. Escherichia coli 41.808 1-Jul-95
GB_8A1:ECU29579 72221 U29579 Escherichia coli K-12 genome; approximately 61 to
62 minutes. Esdlerichia coli 36,130 1-Jul-95
nca01089 873 G8_GSS6:A0044021 387 AQ044021 CIT-HSP-2318C18.TR CIT-HSP Homo
sapiens genomic clone 2318C18, Homo sapiens 36,528 14-Jul-98
genomic survey sequence.
Table 4 (continued)
GB GSS6-.AQ042907 392 AQ042907 CIT-HSP-2318D17.TR CIT-HSP Homo sapiens genomic
done 23181117, Homo sapiens 35,969 14Ju1-98
genomic survey sequenee.
GB_GSS6A0044021 387 AQ044021 CiT-HSP-2318C18.TR CIT-HSP Homo sapiens genomic
done 2318C18, Homo sapiens 44,545 14-Ju1-98
genomic survey sequence.
nca01093 1554 GB BAI:CORPYKI 2795 L27126 Corynebacterium pyruvate kinase gene,
complete cds. Corynebacterium 100,000 07-DEC-1994
gkAamicum
GB BAI:MTCY01B2 35938 Z95554 Mycobacterium tuberculosis H37Rv eompktegenome;
segment 721162. My<obacterium 63,771 17-Jun-98
tuberculosis
GB_BA1:M1U65430 1439 U65430 Mycobaoterium intraceltulare pyruvate kinase
(pykF) gene, complete ods. Mycobaderium 67,061 23-DEC-1996
intraoellulare
rxa01099 948 GB BA2:AF045998 780 AF045998 Corynebacterium glutamicum inositol
monophosphate phosphatase (impA) Corynebacterium 99,615 19-Feb-98
gene, complete cds. glutamicum
GB_BA2:AF051846 738 AF051646 Corynebacteriwn glutamicum
phosphoribosylformimino-5-amino-l- CorynebaeMrium 100,000 12-MAR-1998
phosphoribosyl-4- imidazokx.arboxamide isomerase (hisA) gene, complete
gkttamicum
ods.
GB_GSS1:FR0005503 619 Z89313 F.rubripes GSS sequence, done 079B16aE6, genomic
survey sequence. Fugu rubripes 37,785 01-MAR-1997
Ln
nca01111 541 GBpR3AC0W063 177014 AC004063 Homo sapiens chromosome 4 clone
B3218, complete sequence. Homo sapiens 35,835 10-Jul-98 P.
GB,FR3:HS1178121 62268 AL109852 Human DNA sequenoe from done RP5-1178121 on
cluomosome X, oomplete Homo sapiens 37,873 01-DEC-1999 W
to
sequence. F, -
GB HTG3:AC009301 163369 AC009301 Homo sapiens clone NH0062F14, "' SEQUENCING
IN PROGRESS = , 5 Hamo sapiens 37.240 13-Aug-99
unordered pieces.
nca01130 687 GB HTG3:AC009444 164587 AC009444 Homo sapiens done 1 O 3, "'
SEQUENCING IN PROGRESS 8 Homo sapiens 38,416 22-Aug-99 - .3
unordered pieces. o
GB HTG3:AC009444 164587 AC009444 Horno sapiens done 1 O 3, "' SEQUENCING IN
PROGRESS 8 Homo sapiens 38,416 22-Aug-99 unordered pieces.
GB IN1:0#AC66A1 34127 AL031227 Ckosophila rrretanogaster oosmid 66A1.
Drosophila melanogaster 38,416 05-OCT 1988 ao
nu-01193 1572 GB BAI:CGASUI9 1452 X76875 C.glutamicum (ASO 19) ATPase beta-
subunit gene. Corynebac,tertum 99.931 27-OCT-1994
glutamicum
EM_PAT:E09834 1452 E09634 Brevibacterlum flavum UncO gene whose gene product
is involved in Corynebadxrlum 99,242 07-OCT-1997
glutamicum (Rel. 52,
Created)
GB 8A1:MLU15186 36241 U75186 Mycobacterium leprae cosmid L471. Mycobacterium
Ieprae 39,153 09-MAR-1995
nca01194 495 EM_PAT:E09634 1452 E09634 Brevibacterium flavum UncD gene whose
gene product is invotved in Coryneba<xerium 100,000 07-OCT-1997
glutamicum (Rel. 52,
Creabed)
GB BAI:CGASOI9 1452 X76875 C.glutamicum (ASO 19) ATPase beta-subunit gene.
Corynebacbarium 100,000 27-OCT-1994
glutamkum
GB VI:HEPCRE48 414 X60570 Hepatitis C genomic RNA for putative envelope
protein (RE48 ts0late). Hepatitis C virus 36,769 5-Apr-92
rxa01200
Table 4 (continued)
rxa01201 1764 GB_BA1:SlATPSYNA 8560 Z22606 S.Iividans i protein and ATP
synthase genes. Streptomyces lividans 66,269 01-MAY-1995
GB BAI:MTCY373 35516 Z73419 tUyeobacterium tuberculosis H37Rv complete
genonte; segtllent 57/162. Mycobacterium 65,437 17-Jun-98
tuberculosis
GB BAI:MLU15186 36241 U15186 Mycobacterium leprae cosmid L471. Myoobacterium
laprae 39.302 09-MAR-1995
rxa01202 1098 GB BAI:SLATPSYNA 8560 Z22606 S.lividans i protein and ATP
synthase genes. Streptomyces lividans 57,087 01-MAY-1995
GB_BAI:SLATPSYNA 8560 Z22606 S.lividans i protein and ATP synthase genes.
Streptomyces lividans 38,298 01-MAY-1995
GB BA1:MCSQSSHC 5538 Y09978 M.capsulatus orfx, orty, orfz, sqs and shc genes.
Methylococcus capsulatus 37,626 26-MAY-1998
rxa01204 933 GB_PL1 AP000423 154478 AP000423 Arabidopsis thaliana chloroplast
genomic DNA, complete sequence, Chbroplast Arabidopsis 38,395 15-Sep-99
strain:C0lumbia. thaliana
GB_HTG6:AC009762 164070 AC009762 Homo sapiens done RP11-114116, "' SEQUENCING
IN PROGRESS 39 Homo sapiens 35,459 04-DEC-1999
unordered pieces. r v
GB HTG6AC009762 164070 AC009762 Homo sapiens clone RP11-114118, "= SEQUENCING
IN PROGRESS 39 Homo sapiens 36,117 04-DEC-1999
unordered pieces.
rxa01216 1124 GB BA1:MTCY10G2 38970 Z92539 Mycobacterium tubercuiosis H37Rv
complete genome; segment 47/162. Mycobaderium 39,064 17-Jun-98 noi =
tuberculosis
GB BA2:AF017435 4301 AF017435 Methylobacterium extorquens methanol oxidation
genes, gimU-like gene, Methylobaoterium 42,671 10-MAR-1998
, o
- partiat ads, and orfl2, ortt1, orfR genes, complete cds. extorquens
GB_BAI:CCRFLBOBA 4424 M69228 C.cresoentus ttagellar gene promoter region.
Caulobaater cresoentus 41,054 26Apr-93 -.3
rxa01225 1563 GB BAZAF058302 25306 AF058302 Streptomyces roseofulvus
frenolicin biosynthetic gene cluster, complete Streptomyoes roaeofuivus 36,205
2-Jun-98 sequenoe.
GB_HTG3AC007301 165741 AC007301 Drosophila melanogaster chromosome 2 clone
BACR04B09 (D576) RPCI-98 Drosophiia melanogaster 39,922 17-Aug-99 00
04.8.9 map 43E12-44F1 strain y; cn bw sp, ' SEQUENCING IN PROGRESS
-, 150 unordered pieces.
GB_HTG3:AC007301 165741 AC007301 Drosophila melanogaster chromosome 2 cbne
BACR04809 (D576) RPCI-98 Drosophiia melanogaster 39,922 17,Aug-99
04.8.9 map 43E12-44F1 strain y; cn bw sp, "= SEQUENCING IN PROGRESS
"', 150 unordered pieces.
nui01227 444 GB BAI:SERFDXA 3869 M61119 Saccharopolyspora erythraea ferredoxin
(fdxA) gene, corriplete ods. Saccharopolyspora 64,908 13-MAR-1996
eryfhraea
GB_BAI:MTV005 37840 AL010186 Mycobacterium tuberculosis H37Rv complete genome;
segment 51/162. Mycobacterium 62,838 17-Jun-98
tuberculosis
GB BAI:MSGY348 40056 AD000020 Mycobacter9um tuberculosis sequence from clone
y348. Myoobaderium 61,712 10-DEC-1996
tuberculosis
rxa01242 900 GB_PR3AC005697 174503 AC005697 Homo sapiens chromosome 17, clone
hRPK.138 P 22, complete sequenee. Homo sapiens 35,373 09-OCT-1998
GB_HTG3:AC010722 160723 AC010722 Homo sapiens done NH0122L09, "' SEQUENCING IN
PROGRESS 2 Homo sapiens 39,863 25-Sep-99
unordered pieces.
GB_HTG3:AC010722 160723 AC010722 Homo sapiens done NH0122L09, "' SEQUENCING IN
PROGRESS 2 Homo sapiens 39,863 25-Sep-99
unordered pieces.
Table 4 (continued)
nca01243 1083 GB GSS10:AQ255057 583 AQ255057 mgxb0008N01r CUGI Rice Blast BAC
Library Magnaporthe grisea genomic Magnaporthe grisea 38,722 23-OCT-1998
clone mgxb0008N01 r, genomic survey sequence.
GB_IN1:CEK05D4 19000 Z92804 Caenorhabditis elegans cosmid K0504, complete
sequence. Caenorhabditis elegans 35,448 23-Nov-98
GB_INI:CEK05D4 19000 Z92804 Caenorhabditis elegans cosmid K05D4, complete
sequence. Caenorhabditis elegans 35,694 23-Nov-98
rxa01259 981 GB BAI:CGLPD 1800 Y16642 Corynebacterium glutamicum lpd gene,
comptete CDS. Corynebacterium 100,000 1-Feb-99
glutamicaun
GB HTG4:AC010567 143287 AC010567 Drosophila melanogaster chromosome 3LI69C1
clone RPCI98-11 N6, Drosophila melanogaster 37,178 16-OCT-1999
SEQUENCING IN PROGRESS "', 70 unordered pieces.
GB HTG4AC010567 143287 AC010567 Drosophila melanogaster chromosome 3L/69C1
clone RPCI98-11 N6, Drosophila melanogaster 37,178 16-OCT-1999
"=SEQUENCING IN PROGRESS "", 70 unordered pieces.
rxa01262 1284 GB BA2AF172324 14263 AF172324 Escherichia coli GaIF (galF) gene,
partial cds; 0-antigen repeat unit transporter Escherichia coli 59,719 29-OCT-
1999
Wzx (wzx), WbnA (wbnA), 0-antigen polymerase Wzy (wzy), WbnB (wbnB),
WbnC (wbnC),1NbnD (wbnD), WbnE (wbnE), UDP-Glc-4-epimerase GalE
(galE), 6-phosphogluconate dehydrogenase Gnd (gnd), UDP-GIc-6-
dehydrogenase Ugd (ugd), and WbnF (wbnF) genes, complete cds; and chain
length determinant Wzz (wzz) gene, partial cds.
GB BA2:ECU78086 4759 U78086 Escherichia colf hypothetical uridine-5'-
diphosphoglucose dehydrogenase (ugd) Escherichia coli 59,735 5-Nov-97
and 0-chain length regulator (wzz) genes, complete ads.
GB BA1:D90841 20226 D90841 E.coli genomic DNA, Kohara clone #351(45.1-45.5
min.). Escherichia coli 37,904 21-MAR-1997 -~ N
o
rxa01311 870 GB_PR3AC004103 144368 AC004103 Homo sapiens Xp22 BAC GS-619J3
(Genome Systems Human BAC library) Homo sapiens 37,340 18-Apr-98
complete sequence.
-.3
GB HTG3:AC007383 215529 AC007383 Homo sapiens clone NH0310K15, "= SEQUENCING
IN PROGRESS ==', 4 Homo sapiens 36,385 25-Sep-99
unordered pieces. r.
GB HTG3AC007383 215529 AC007383 Homo sapiens done NH0310K15, "" SEQUENCING IN
PROGRESS =", 4 Homo sapiens 36,385 25-Sep-99
unordered pieces. D
nca01312 2142 GB BA2:AE000487 13889 AE000487 Escherichia coli K-12 MG1655
section 377 of 400 of the complete genome. Escherichia coii 39,494 12-Nov-98
GB_BAI:MTV016 53662 AL021841 Mycobacterium tuberculosis H37Rv complete genome;
segment 143/162. Mycobacterium 46,252 23-Jun-99
tuberculosis
GB BAt:U00022 36411 U00022 Mycobacterium Ieprae cosmid L308. Mycobacterium
leprae 46,368 01-MAR-1994
nca01325 795 GB HTG4AC009245 215767 AC009245 Homo sapiens chromosome 7, "='
SEQUENCING IN PROGRESS 24 Hamo sapiens 36,016 2-Nov-99
unordered pieces.
GB HTG4AC009245 215767 AC009245 Homo sapiens chromosome 7, "' SEQUENCING IN
PROGRESS 24 Homo sapiens 36,016 2-Nov-99
unordered pieces.
GB HTG4AC009245 215767 AC009245 Homo sapiens chromosome 7, '"' SEQUENCING IN
PROGRESS "=, 24 Homo sapiens 39,618 2-Nov-99
unordered pieces.
rxa01332 576 GB_HTG6AC007186 225851 AC007186 Drosophila melanogaster
chromosome 2 done BACR03D06 (D569) RPCI-98 Drosophila melanogaster 35,366 07-
DEC-1999
03.D.6 map 32A-32A strain y; cn bw sp, "' SEQUENCING IN PROGRESS"',
91 unordered pieces.
GB_HTG6AC007147 202291 AC007147 Drosophila melanogaster chromosome 2 clone
BACR19N18 (0572) RPCI-98 Drosophila melanogaster 35,366 07-DEC-1999
19.N.18 map 32A-32A strain y; cn bw sp, "" SEQUENCING IN PROGRESS
"', 22 unordered pieces.
Table 4 (continued)
GB_HTG3AC010207 207890 AC010207 Homo sapiens clone RPCI11-375120, "'
SEQUENCING IN PROGRESS =", 25Homo sapiens 34,821 16Sep-99
unordered pieces.
rxa01350 1107 GB_BA2AF109682 990 AF109682 Aquaspiriltum arcticum malate
dehydrogenase (MDH) gene, complete cds. Aquaspin7lum arcticum 58,487 19-OCT-
1999
GBJiTG2AC006759 103725 AC006759 Caenorhabditis elegans clone Y40G12, "'
SEQUENCING IN PROGRESS"', Caenorhabditls elegans 37,963 25-Feb-99
8 unordered pieces.
GB_HTG2AC006759 103725 AC006759 Caenorhabditis elegans clone Y40G12, "'
SEQUENCING IN PROGRESS"', Caenorhabditis elegans 37,963 25-Feb-99
8 unordered pieces.
rxa01365 1497 GB_BAI:MTY20811 36330 Z95121 Mycobacterium tuberculosis H37Rv
complete genome; segment 139/162_ Mycobacterium 38.011 17-Jun-98
tuberculosis
GB_BAI:XANXANAB 3410 M83231 Xanthomonas campastris phosphoglucomutase and
phosphomannomutase Xanthomonas campestris 47,726 26-Apr-93
(xanA) and phosphomannose isomerase and GDP-mannose
pyrophosphorylase (xanB) genes, complete ods.
GB_GSSI0:AQ194038 697 AQ194038 RPC111-47D24.TJ RPCI-11 Homo sapiens genomic
clone RPCI-11-47D24, Homo sapiens 36,599 20-Apr-99
genomic survey seyuence.
rxa01369 1305 GB_BAI:MTY20B11 36330 Z95121 Mycobacterium tuberculosis H37Rv
complete genome; segment 139/162. Mycobacterium 36,940 17-Jun-98
0
tuberculosis Ln
GB_GSS3:810037 974 810037 T27A19-T7 TAMU Arabidopsis thaGana genomic clone
T27A19, genomic Arabidopsis thaliana 35,284 14-MAY-1997 00
survey sequence. o
GB_GSS3:B09549 1097 B09549 T21A19-T7.1 TAMU Arabidopsis thaliana genomic clone
T21A19, genomic Arabidopsis thaliana 38,324 14-MAY-1997
survey sequence. w . N
rxa01377 1209 GB_BAI:MTCY71 42729 Z92771 Mycobacterium tuberculosis H37Rv
compfete genome; segment 141l162. Myeobacterium 39,778 10-Feb-99 00
tuberculosis -.3
GB_HTG5:AC007547 262181 AC007547 Homo sapiens clone RP1 1-252018, WORKING
DRAFT SEQUENCE, 121 Homo sapiens 32,658 16-Nov-99
unordered pieces.
GB_HTG5AC007547 262181 AC007547 Hona sapiens clone RP11-252018, WORKING DRAFT
SEQUENCE, 121 Homo sapiens 38,395 16-Nov-99
N
unordered pieces. D
rxa01392 1200 GB_BA2AF072709 8366 AF072709 Streptomyces lividans ampliflable
element AUD4: putathre Streptomyces lividans 55,221 8,lut-98
transcriptional regusator, putative fefredoxin, putative cytochrome P450
oxidoroductase, and putative oxidonsductase genes, complete ods; and
unknown genes.
GB_BAI:CGLYSEG 2374 X96471 C.glutamicum lysE and IysG genes. Corynebacterium
100,000 24-Feb-97
glutamicum
GB PR4 AC005906 185952 AC005906 Homo sapiens 12p13.3 BAC RPCIt 1-429A20
(Roswell Park Cancer Homo sapiens 36,756 30-Jan-99
Institute Human BAC Library) oomplete sequence.
rxa01436 1314 GB_BAI:CGPTAACKA 3657 X89084 C.glutamicum pta gene and ackA
gene. Corynebacterium 100,000 23-MAR-1999
glutamicum
GB BA1:D90861 14839 D90861 E.coN genornic DNA, Kohara dona e405(52.0-52.3
min.). Escherichia coN 53,041 29-MAY-1997
GB_PAT:E02087 1200 E02087 DNA encoding acetate kinase protein form Escherichia
coli. Escherichia coli 54,461 29-Sep-97
rxa01468 948 GB GSSI:HPU60627 280 U60627 HeGcobacter pylori feoB-like DNA
sequence, genomic sunrey sequence. Helicobacter pylori 39,286 9-Apr-97
GB EST31A1701691 349 A1701691 we81e04.x1 Soares_NFL T GBC S1 Homo sapiens cDNA
done Homo sapiens 39,412 3-Jun-99
IMAGE:2347494 3' similar to gb:L19686_ma1 MACROPHAGE MIGRATION
INHIBITORY FACTOR (HUMAN);, mRNA sequence.
Table 4(continued)
G4_EST15:AA460256 389 AA480258 ne31114.s1 NCI CGAP_Co3 Homo sapiens cDNA done
IMAGE:898975 3' Homo sapiens 39,574 14-Aug-97
similar to gb:L19686_rnat MACROPHAGE MIGRATION INHIBITORY
FACTOR (HUMAN);, mRNA sequence.
rxa01478 1959 G8 BA1:SCI51 40745 AL109848 Streptomyces coeNaolor cosmid 151.
Streptomyces coelioolor 54,141 16-Aug-99
A3(2)
GB BAI:SCE36 12581 AL049763 Streptomyces coeiicolor cosmid E36. Streptomyces
coelksolor 38,126 05-MAY-1999
GB_BA1:CGU43535 2531 U43535 Corynebacterium glutamicum multidrug resistance
protein (cmr) gene, Corynebactedum 41,852 9-Apr-97
cpnViste cds. glutamicum
nca01482 1998 GB_BA1:SC6G4 41055 AL031317 Streptomyces coelicolor cosmid 6G4.
Streptomyces coe6color 62,149 20,Aug-98
GB BA1:U00020 36947 U00020 Mycobacter9um lepree cosmid 8229. Mycobacterium
leprae 38,303 01-MAR-1994
G8_BAI:MTCY77 22255 Z95389 Mycobacterium tuberculosis H37Rv complete genome;
segment 146/162. Mycobacterium 38,179 18-Jun-98
tuberculosis rxa01534 0
N
U9
W
nca01535 1530 GB BAI:MLCB1222 34714 AL049491 Myoobacterium leprae cosmid
81222. Mycobacterium leprae 66,208 27-Aug-99 GB_BAI:MTV017 67200 AL021897
Mycobacterium tuberculosis H37Rv complete genome; segment 48/162.
Mycobacterium 38,553 24-Jun-99
tuberculosis
W N
GB_BAI:PAU72494 4368 U72494 Pseudomonas aeruginoss fumarese (fumC) and Mn
superoxide dismutase Pseudomonas aeruginoss 52,690 23-OCT-1996 (sodA) genes,
complete cds. o
rxa01550 1635 GB_BA1:D90907 132419 D90907 Synechocystis sp. PCC6803 complete
genome, 9/27, 1056467-1188885. Synechocystis sp. 56,487 7-Feb-99 .3
GB-IN2:AF073177 9534 AF073177 Drosophila melanogaster gycogen phasphorylase
(GlyP) gene, eompiete cds. Drosophila mdangpaster 55,100 1.lu1-99
GB IN2AF073179 3159 AF073179 Orosophila melanogaster glycogen phosphorylase
(Gip1) mRNA, complete ods. Drosophia melanogaster 56,708 27-Apr-99 00
rxa01562
nca01569 1482 G8_BA1:D78182 7836 D78182 Streptococcus mutans DNA for dTDP-
rhamnose synthesis pathway, complete Streptococcus mutans 44,050 5-Feb-99
ads.
GB_BA2AF079139 4342 AF079139 Streptomyces venezuelae pikCb operon, complete
sequence. Streptomyces venezuelae 38,587 28-0CT-1998
GB_BA2:AF087022 1470 AF087022 Strnptomyces venezuelae cytochnxne P450
monooxygenase (picK) gene, Streptomyces venezuelae 38,621 15-OCT-1996
complete cds.
rxa01570 978 GB_BAI:MTCY63 38900 Z96800 Mycobacterium tuberculosis H37Rv
eomplete genome; segnient 16/162. Mycobacterium 59,035 17-Jun-98
tuberculosis
GB_BA2:AF097519 4594 AF097519 Kiebsiella pneumoniae dTDP-D-glucose 4,6
dehydratase (rrnlB), glucose-l- KlebsieNa pneumoniae 59,714 4-Nov-98
phosphate thymidylyl translerase (rmiA), dTDP-"eto-L-rhamnose reductase
(rmlD), dTOP-4-keto-6-deoxy-D-glucose 3,"pimerase (rmlC), and rhamnosyl
transfersse (wbbL) genes, complete cds.
Table 4 (continued)
GB BA2:NGOCPSPS 8905 L09189 Neisseria meningitidis dTOP-D-glucese 4,6-
dehydratasa (rtbB), gtucose-l- Neisseda meningitkiis 58,384 30=Jul-96
phosphate thymidyl transferase (rfbA) and rfbC genes, compbte cds and UPD-
gkicose-4-epinrerase (galE) pseudogene.
nca01571 723 GB BA1 AB011413 12070 AB011413 Streptomyces griseus genes for
Orf2, O0, 064, 005, AfsA, Orfa, partial and Streptomyces griseus 57,500 7-Aug-
98
complete cds-
GB BA1:AB011413 12070 AB011413 Streptomyces griseus genes for Orf2, Orf3,
Orf4, Orf5, AfsA, OAB, partial and Streptomyoes griseus 35,655 7-Aug-98
complete cds.
rxa01572 615 GB BA1:AB011413 12070 AB011413 Streptomyces griseus genes for
Orf2, Orf3, Orf4, Orf5, AfsA, OrfB, partial and Streptomyces griseus 57,843 7-
Aug-98
complete cds.
GB_BA1:AB011413 12070 AB011413 Streptomyces griseus genes for Orf2, Orf3, 064,
065, AfsA, OrfB, partial and Streptomyces griseus 38,119 7-Aug-98
complete cds.
rxa01606 2799 GB_VI:CFU72240 4783 U72240 Choristoneura fumiierana nuclear
polyhedrosis virus ETM protein homolog, 79 Choristoneura fimw"Ferana 37,115 29-
Jan-99 kDa protein homolog, 15 kOa protein homolog and GTA protein homolog
nucleopolyhedrovirus
genas, complete cds.
GB_GSSI0:AQ213248 406 A0213248 HS_3249 81 A02_MR CIT Approved Human Genomic
Spertn LUbrary 0 Homo Horno sapiens 34,559 18-Sep-98 Lõ
sapiens genomic clone Plat"3249 Col=3 Row=B, genomic survey seQuence. 00
GB_GSSSAQ070145 285 A0070145 HS_3027 61 H02 MR CIT Approved Human Genomic
Sperm Library D Homo Homo sapiens 40,351 S4Aug 98
sapiens genomlc done Plate=3027 Col=3 Row=P, genomic survey sequence.
nca01626 468 GB_PR4:AF152510 2490 AF152510 Homo sapiens protocadhenn gamma A3
short form protein (PCDH-gamma-A3) Homo sapiens 34.298 14-Jul-99 .3
variable region sequenoe, cmplete cds.
GB_PR4:Af152'323 4605 AF152323 Hon1o sapiens protocadhedn gamma A3 (PCDH-gamma-
A3) mRNA, complete Homo sapiens 34.298 22-Jul-99 cds. ~
GB_PR4:AF152509 2712 AF152S09 Horno sapiens PCOH-gamma-A3 gene, aberrantly
spliced, mRNA sequenoe. Homo sapiens 34.298 14-Jul-99
rxa01632 1128 GB_HTG4AC006590 127171 AC006590 Drosophila rnelanogaster
chromosome 2 clone BACR13NO2 (D543) RPCI-98 Drosophiia melanogaster 33,812 19-
OCT-1999
13.N.2 map 36E-36E strain y; cn bw sp, =" SEQUENCING IN PROGRESS=",
101 unordered pieces.
GB_HTG4AC006590 127171 AC006590 Drosophila melanogaster chromosome 2 clone
BACR13N02 (D543) RPCI-98 Drosophila melanogaster 33,812 19-OCT-1999
13.N.2 map 36E-36E strain y; cn bw sp, =" SEQUENCING IN PROGRESS="',
101 unordered pieces.
GB_GSS8:B99182 415 B99182 CIT-HSP-2280113.TR CIT-HSP Homo sapiens genomic
clone 2280113, Homo sapiens 36,111 26-Jun-98
genomic survey sequence.
nur01633 1206 GB_BAI:BSUB0009 208780 Z99112 BaciAus subtilis complete genome
(section 9 of 21): fram 1598421 to 1807200. Badltus subtilia 36,591 26-Nov-97
GB_BA1:BSUB0009 208780 Z99112 BacHlus subtilis complete genome (section 9 of
21): from 1598421 to 1807200. BaciNus subtilis 34,941 26-Nov-97
c38_HTG2:AC006247 174368 AC006247 Drosophila melanogaster chromosome 2 clone
BACR48I10 (0505) RPCI-98 Drosophila rnetanogaster 37,037 2-Aug-99
48.1.10 map 49E6-49F8 strain y; cn bw sp, "' SEQUENCING IN PROGRESS
"', 17 urwniered pieoes.
Table 4 (continued)
rxa01695 1623 G8_BAI:CGA224946 2405 AJ224946 Corynebacterium gtutamicum DNA
for L-Malate:quinone oxidoreductase. Corynebaderium 100,000 11-Aug-98
glutamicum
GB BAI:MTCY24A1 20270 Z95207 Mycobacterium tuberculosis H37Rv complete genome:
segment 124/162. Mycobaderium 38,826 17-Jun-98
tuberculosis
C,B INI:DMU15974 2994 U15974 Drosophila melanogaster kinesin-like protein
(ktp68d) mRNA, comptete cds. Drosophila metanogaster 36,783 18.Jut-95
rxa01702 1155 GB_BAI:CGFDA 3371 X17313 Corynebaderium glutamicum fda gene for
fructose-bisphosphate aktolase (EC Corynebaderium 99,913 12-Sep-93
4.1.2.13). glutamicum
GB BAI:MTY13E10 35019 Z95324 Mycobacterium tuberculosis H37Rv complete genome;
segment 181162. Mycobacterium 38,786 17-Jun-98
tuberculosis
GB_BAI:MLC84 36310 AL023514 Mycobacterium leprae cosmid 64. Mycobac6erium
leprae 38,238 27,Aug-99
nca01743 901 GB (NZ:CELC27H5 35840 U14635 Caenorhabdifs elegans cosmid C27H5.
Caerarhabd9is etegans 35,334 13-Jul-95
GB EST24A1167112 579 A1167112 xylem.est.878 Poplar xylem Lambda ZAPII library
Populus balsamifera subsp. Populus baisanYderm 39,222 03-DEC-1998
trichocarpa oDNA V. mRNA sequence. subsp. trichoearpa
GB GSS9/1Q102635 347 A0102635 HS_3048_81 F08 MF CIT Approved Human Genomic
Sperm Ubrary D Homo Homo sapiens 40,653 27-Aug-98
sapiens genomic ebne Plate=3048 Cot=15 Row=L, genomic survey sequence.
nca01744 1662 GB BAI:MTCY0182 35938 Z95554 Mycobacterium tuberculosis H37Rv
complete genome; segment 72/162. Mycobacterium 36,650 17-Jun-98 cLno
tuberculosis o -
GB GSSI:AF009226 665 AF009226 Mycobacterium tuberculosis cytochrome D oxidase
subunit I (appC) gene, Mycobacterium 63,438 31-Jul-97 O N
partiat sequence, genomic survey sequence. tubercubsis
GB BAI:SCD78 36224 AL034355 Streptomyces o0ebootor coamid D78. Streptomyoes
ooeliootor 53,088 26-Nov-98 0
rxa01745 836 GB_BA1:MTCY190 34150 Z70283 Mycobacterium tuberculosis H37Rv
complete genome; segment 98/162. Mycobacterium 62,081 17-Jun-98
tuberculosis GB BAI:MLC822 40281 Z98741 Mycobacterium leprae cosmid B22.
Mycobaderium leprae 61,364 22-Aug-97
GB BA2:AE0o0175 15067 AE000175 Escherichia coil K-12 MG1655 section 65 of 400
of the eompiete genome. Esdteridhia eoli 52,323 12-Nov-98
rxa01758 1140 GB PR3:HS57G9 113872 Z95116 Human DNA sequence from BAC 57G9 on
chromosome 22q12.1 Contains Homo sapiens 39,209 23-Nov-99 00
ESTs, CA repeat, GSS.
GB PL2:YSCH9666 39057 U10397 Saccharomyces oerevisiae chromosome VIII cosmid
9666. Saccharomyces cerevisiae 40,021 S-Sep-97
GB PL2:YSCH9986 41664 U00027 Saeeharomyces cerevisiae chromosome VIII cosmid
9986. Saccharomyces eerevisiae 34,375 29-Aug-97
rxa01814 1785 GB BA1:A8CCELB 2058 L24077 Aostobader xylinum phosphoglucomutase
(eeIB) gene, complete cds. Acetobacter xytkws 62,173 21-Sep-94
GB_BAI:MTCY2207 31859 Z83866 Mycobacterium tuberculosis H37Rv complete genome;
segment 1331162. Mycobacterium 39,749 17-Jun-98
tubercuiosis
GB BAI:MTCY22D7 31859 Z83866 Mycobacterium tuberculosis H37Rv complete genome;
segment 133/162. Mycobacterium 40,034 17-Jun-98
tubercubais
rxa01651 1809 GB GSS9:AQ142579 529 AQ142579 HS 2222_B1 H03_MR CIT Approved
Human Genomic Sperm Ubrary D Homo Homo sapiens 38,068 24-Sep-98
sapiens genomic done Plate-2222 Cot=5 RowaP, genomic survey sequenoe.
GB IN2AC005889 108924 AC005889 Drosophila melanogaster, chromosome 2L, region
30A3- 30A6, P1 clones Drosophila melanogaster 36,557 30-OCT-1998
DS06958 and DS03097, complete sequence.
GB GSS1AG008814 637 AG008814 Homo sapiens genomic DNA, 21q region, done:
813787BB68, genomic survey Homo sapiens 35,316 7-Feb-99
sequence.
Table 4 (continued)
rxa011859 i050 GB BA2:AF183408 63626 AF183408 Microcystis seruginosa DNA
polymerase III beta subunit (dnaN) gene, partial Microcystls aeruginosa 36,364
03-OCT-1999
cds; micnocystin synthetase gene duster, complete sequenoe; Umal (umal),
Uma2 (uma2), Uma3 (uma3), Urna4 (uma4), and Uma5 (uma5) genes,
compbte cds; and Uma6 (uma6) gene, partial ods.
GB_HTG5:AC008031 158889 AC008031 Trypanosoma brucei chromosome 11 done RPCI93-
25N14, ' SEQUENCING Trypanosoma bruoei 35,334 15-Nov-99
IN PROGRESS '~, 2 unordered pieces.
GB_BA2:AF183408 63626 AF183408 Miaocystis aeruginosa DNA polyrnerase III beta
subunit (dnaN) gene, part7al Microcystis aeruginosa 36,529 03-0CT-1999
ods; microcystin synthetase gene cluster, complete sequence; Uma1 (umal),
Uma2 (uma2), Uma3 (uma3), Uma4 (uma4), and UmaS (uma5) genes,
complete als; and UmaS (uma6) gene, partial cds.
nca01865 438 GB_BAI:SERFOXA 3669 M61119 Saccharopolyspora erythraes ternedoxin
(fdxA) gene, complete cds. Saccharopolyspora 59,862 13-MAR-1996
erythraea
GB_BAI:MTV005 37840 AL010186 Mycobacterium tuberculosis H37Rv complete genome;
segment 511162. Mycobaderium 61,949 17-Jun-98
tuberculosis
GB_BAI:MSGY348 40056 AD000020 Mycobacterium tuberculosis sequence from clone
y348. Mycobacterium 59,908 10-DEC-1996
tubercuWsts N
rxa01882 1113 GB PRI:HUMADRA2C 1491 J03853 Human kidney alpha-2-adrenergic
receptor mRNA, complete cds. Homo sapiens 36,899 27-Apr-93 0Ln0
GB PR4:HSU72848 4850 U72648 Homo sapiens alpha2-C4-adrenergk: receptor gene,
complete ods. Homo sapiens 36,899 23-Nov-98
GB GSS3:B42200 387 B42200 HS-1055-B1,A03-MR.abi CIT Human Genomic Sperm
Library C Homo sapiens Homo sapiens 34,805 18-OCT-1997 ~ N =
genomic done Plate=CT 777 Co1=5 Row=B, genomic survey sequence. C)
rxa01884 1913 GB BAI:MTCY48 35377 Z74020 Mycobacterium tubercubsis H37Rv
compiete genome: segment 69/162. Mycobadedum 37,892 17-Jun-98
tuberculosis
GB BA1:SC0001206 9184 AJ001206 Streptomyces coeliookx A3(2), glycogen
metabolism cluster 11. Stroptomyoes eoelicolor 40,413 29-MAR-1999
GB_8A1:090908 122349 090908 Synechocystis sp. PCC6803 complete genome, 10127,
1188886-1311234. Synechocystis sp. 47,792 7-Feb-99 ro
rxa01886 897 GB GSS9AQ116291 572 AQ116291 RPCI1149P6.TK.1 RPCI-11 Homo sapiens
genomic clone RPCI-11-49P6, Honw sapiens 43,231 20-Apr-99
genomic survey sequenae.
GB BA2:AE001721 17632 AE001721 Themiotoga maritima section 33 of 136 of the
compkle genome. Thematoga marilima 39,306 2.lun-99
GB ESTIB:AA5ti7090 596 AA567090 GM01044.5prime GM Drosophla melanogaster ovary
BlueScript Drosophila Drosophila melanogaster 42,807 28-Nov-98
melanogaster cONA clone GM01044 5prime, mRNA sequenee,
rxa01887 1134 GB_HTG6:AC008147 303147 AC008147 Homo sapiens clone RP3-405J10,
"' SEQUENCING IN PROGRESS 102 Homo sapiens 36,417 03-DEC-1999 '
unordered pieoes.
GB HTG6:AC008147 303147 AC008147 Homo sapiens clone RP3-405J10, ' SEQUENCING
IN PROGRESS 102 Homo sapiens 37,867 03-DEC-1999
unordered pieces.
G0_13A2:ALVU143431 26953 AJ243431 Adnetobacter Maffii wzc, wzb, wza, weeA,
weeB, woeC, wzx, wzy, weeD, Acinetobaeter hroffii 39,640 01-OCT-1999
weeE, weeF, weeG, weeH, weel, vreeJ, weeK, galU, ugd, pgi, galE, pgm
(partia[) and mip (partial) genes (emulsan biosynthetic gene duster), strain
RAG1.
rxa01888 658 GB_HTG2:AC008197 125235 AC006197 Drosophila melanogaster
chromosome 3 clone BACR02L12 (D753) RPCI-98 Drosophila melanogaster 32,969 2-
Aug-99
02.L.12 map 94B-94C strain y; cn bw sp, "' SEQUENCING IN PROGRESS"',
113 unordered pieoes.
Table 4 (continued)
GB_HTG2AC008197 125235 AC008197 Drosophila melanogaster chromosome 3 clone
BACR02L72 (0753) RPCI-98 Drosophila meianogaster 32,969 2-Aug-99
02.L.12 map 94B-94C strain y; cn bw sp, "' SEQUENCING IN PROGRESS
' 113 unordered pieces.
GB EST36AI881527 598 A1881527 606070C09.y1 606 - Ear t'issue cONA library from
Schmidt lab Zea mays cDNA,Zea mays 43,617 21Ju499
mRNA sequence.
nca01891 887 GB VI:HIV232971 621 AJ232971 Human immunodeficiency virus type 1
subtype C nef gene, patient MP83. Human immunodeficiency 40,040 05-MAR-1999
virus type 1
GB_PL1 AFCHSE 6158 Y09542 A.fumigatus chsE gene. Aspergillus fumigatus 37,844
1-Apr-97
GB_PR3:AF064858 193387 AF064858 Homo sapiens chromosome 21q22.3 BAC 28F9,
complete sequence. Homo sapiens 37,136 2-Jun-98
rxa01895 1051 GB_BA1:CGL238250 1593 AJ238250 Corynebacterium glutamicum ndh
gene. Corynebacterium 100,000 24-Apr-99
glutamicum
GB BA2AF038423 1376 AF038423 Mycobacterium smegmatis NADH dehydrogenase (ndh)
gene, complete cds. Mycobacterium smegmatis 65,254 05-MAY-1998
C)
GB_BA1:MTCY359 36021 Z83859 Mycobactenum tuberculosis H37Rv complete genome;
segment 84/162. Mycobaderium 40,058 17-Jun-98 tuberculosis
nra01901 1383 GB_BA1:MSGB38COS 37114 L01095 M. lepree genomic DNA sequence,
cosmid B38 bfr gene, compiete cds. Mycobacterium leprae 59,551 6-Sep-94 cn
GB_BAI:SCE63 37200 AL035640 Streptomyces coelicolor cosmid E63. Streptomyces
coelicolor 39,468 17-MAR-1999 co
0
N
GB_PR3:AF093117 147216 AF093117 Homo sapiens chromosome 7qtelo BAC E3,
complete sequence. Homo saplens 39,291 02-OCT-1998
rxa01927 1503 GB_BAI:CGPAN 2164 X96580 C.giutamicum panB, panC & xylB genes.
Corynebacterium 38,384 11-MAY-1999 v N
glutamicum GB_BAI:ASXYLA 1905 X59466 Arthrobacter Sp. N.R.R.L. B3728 xylA gene
for D-xylose(D-glucose) isomerase. Arthrobacter sp. 56,283 04-MAY-1992 -.3
-- i
GB_HTG3:AC009500 176060 AC009500 Homo sapiens clone NH0511A20, "' SEQUENCING
IN PROGRESS "', 6 Homo sapiens 37,593 24-Aug-99
unordered pieces.
nra01952 1836 GB_BA2:AE000739 13335 AE000739 Aquifex aeolicus section 71 of
109 of the complete genome. Aquifex aeolic:us 36,309 25-MAR-1998
GB EST28:AI519629 612 A1519629 LD39282.5prime LD Drosophila melanogaster
embryo pOT2 Drosophila Drosophila melanogaster 41,941 16-MAR-1999
melanogaster cDNA clone LD39282 5prime, mRNA sequence.
GB_EST21:AA949396 767 AA949396 LD28277.5prime LD Drosophila melanogaster
embryo pOT2 Drosophila Drosophila melanogaster 39,855 25-Nov-98
melanogaster cDNA clone LD28277 5prime, mRNA sequence.
nra01989 630 GB_BAI:BSPGIA 1822 X16639 Bacillus stearothermophiius pgiA gene
for phosphoglucoisomerase isoenzyme Bacillus 66,292 20-Apr-95
A (EC 5.3.1.9). stearothermophiius
GB_BA1:BSUB0017 217420 Z99120 BaciNus subtilis complete genome (section 17 of
21): from 3197001 to Bacillus subtilis 37,255 26-Nov-97
3414420.
GB_BA2AF132127 8452 AF132127 Streptococcus mutans sorbitol
phosphoenolpyruvate:sugar phosphotransferase Streptocoa;us mutans 63,607 28-
Sep-99
operon, compbte sequence and unknown gene.
rxa02026 720 GB_BA1:SXSCRBA 3161 X67744 S.xyiosus scrB and scrR genes.
Staphylococcus xylosus 67,778 28-Nov-96
GB_BAI:BSUB0020 212150 Z99123 Bacillus subtiiis complete genome (sedion 20 of
21): from 3798401 to BaciAus subtilis 35,574 26-Nov-97
4010550.
GB_BAI:BSGENR 97015 X73124 B.subtilis genomic region (325 to 333). Bacillus
subtiiis 51,826 2-Nov-93
nca02028 526 GB_BAI:MTCI237 27030 Z94752 Mycobacterium tuberculosis H37Rv
complete genome; segment 46/162. Mycobacterium 54,476 17-Jun-98
tuberculosis
Table 4 (continued)
Gc PL2:SCE9537 66030 U18778 Saccharomyces oerevisiae chromosome V cosmids
9537, 9581, 9495, 9867, Saecharomyces cerevisiae 36,100 1-Aug-97
and lambda done 5898.
GB GSS13:AQ501177 767 A0501177 V26G9 mTn-3xHAAacZ Insertion Library
Saccharomyces cerevisiae genomic 5',Saccharomyces cerevisiae 32,039 29-Apr-99
genomic survey sequence.
nca02054 1140 GB BAI:MLCB1222 34714 AL049491 Mycobacterium leprae cosmid
81222. Mycobaderium leprae 61.896 27-Aug-99
GB_BA1:MTY13E12 43401 Z95390 Mycobaderium tuberculosis H37Rv complete genome:
segment 147/162. Mycobacterium 59,964 17-Jun-98
tubercutosis
GB_BA1:MTU43540 3453 U43540 Mycobacterium tuberculosis rfbA, rhamnose
biosynthesis protein (rfbA), and Mycobacterium 59,659 14-Aug-97
rmlC genes, complete cds. tuberculosis
nca02056 2891 GB PAT:E14601 4394 E14601 Brevibacterium ladofennentum gene for
alpha-ketoglutaric acid Corynebaderium 98,928 284u699
dehydrogenase. glutamicum
GB BA1:D84102 4394 084102 Corynebacterium glutamicum DNA for 2-oxoglutarate
dehydrogenase, complete Corynebacterium 98,928 6-Feb-99
cds. glutamicum
GB_BAI:MTV006 22440 AL021006 Mycobacterium tuberculosis H37Rv complete genome;
segment 54/162. Mycobacterium 39,265 18-Jun-98
tuberculosis
nca02061 1617 GB_HTG7AC005883 211682 AC005883 Homo sapiens chromosome 17 clone
RP11-958E11 map 17, Homo sapiens 37,453 08-DEC-1999 ~
SEQUENCING IN PROGRESS "=, 2 ordered pieces.
GB PL2:ATAC003033 84254 AC003033 Arabidopsis thatiana chromosome II BAC T21L14
genomic sequence, complete Arabidopsis thaliana 37,711 19-OEC-1997
sequence.
GB PL2ATAC002334 75050 AC002334 Arabidopsis thaliana chromosome II SAC F25118
genomic sequence, complete Arabidopsis thaliana 37,711 04MAR-1998
sequence.
nca02063 1350 GB BAI:SCGLGC 1518 X89733 S.coeGcobr DNA for glgC gene.
Streptomyces coelicolor 56,972 12-Jul-99 ~
GB GSS4AQ687350 786 AQ687350 nbxb0074H11r CUGI Rice SAC Library Oryza sativa
genomic clone Oryza sativa 40,696 1-Jul-99 ~
nbxb0074H11r, genomic survey sequence.
GB EST38AYY028530 444 AW028530 wv27f10.x1 NCI CGAP_Kid11 Homo sapiens cDNA
done IMAGE:2530795 3' Homo sapiens 36.795 27-OCT-1999 00
similar to WP:T03G11.6 CE04874 ;, mRNA sequence.
nca02100 2348 GB_BAI:MSGY151 37036 A0000018 Mycobacterium tuberculosis
sequence from clone y151. Mycobacterium 40,156 10-DEC-1996
tuberculosis
GB BAI:MTCY130 32514 Z73902 Mycobacterium tuberculosis H37Rv complete genome;
segment 59/162. Mycobacterium 55,218 17-Jun-98
tuberculosis
GB BA1:SC0001205 9589 AJ001205 Streptomyces coelicolorA3(2) glycogen
metabolism dusterl. Streptomyoes ooelicolor 38,475 29-MAR-1999
nxa02122 822 GB_BA1:D90858 13548 D90858 E.coli genomic DNA, Kohara done
#401(51.3-51.6 min.). Escherichia coh 38,586 29-MAY-1997
GB EST37AI948595 469 A1948595 wq07d12.x1 NCI CGAP Kid12 Homo sapiens cDNA done
IMAGE:2470583 3', Homo sapiens 37,259 6-Sep-99
mRNA sequence.
GB_HTG3AC010387 220665 AC010387 Homo sapiens chromosome 5 done CITB-H1_2074D8,
"' SEQUENCING IN Homo sapiens 38,868 15-Sep-99
PROGRESS "', 77 unordered pieces.
nca02140 1200 GB_BAI:MSGB7551CS 36548 L78813 Mycobacterium leprae cosmid B1551
DNA sequence. Mycobacterium leprae 51,399 15-Jun-96
GB BAI:MSGB1554CS 36548 L78814 Mycobacterium leprae cosmid B1554 DNA sequence.
Mycobacterium leprae 51,399 15-Jun-96
GB RO:AF093099 2482 AF093099 Mus musculus transcription factor TBLYM (Tblym)
mRNA, complete cds. Mus musculus 36,683 01-OCT-1999
rxa02142 774 GB_BAI:MTCY190 . 34150 Z70283 Mycobacterium tuberculosis H37Rv
complete genome; segment 98/162. Mycobacterium 57,292 17-Jun-98
tuberculosis
Table 4 (continued)
GB i3A1:SM10 36734 AL049497 Streptomyces coelicolor cosmid 6G10. Streptomyces
coelioolor 35,058 24MAR-1999
GB BA1A8016787 5550 AB016787 Pseudomonas putida genes for cytochrome o
ubiquinol oxidase A-E and 2 Pseudomonas putida 47,403 5-Aug-99
ORFs, complete cds.
rxa02143 1011 GB BAI:MTCY190 34150 Z70283 Mycobacterium tuberculosis H37Rv
complete genome; segment 98/162. Mycobacterium 57.317 17-Jun-98
tuberculosis
CiB i3A1:MSGB1551CS 36548 L78813 Myoobaaerium bprae cosmid 51551 DNA sequence.
MycobaeEerium leprae 38,159 15-Jun-96
GB BAI:MSGB1551CS 36548 L78814 MyCobacterium leprae cosmid 81554 DNA sequence.
Mycobacterium tepm 38,159 15.1un-98
nca02144 1347 GB 8A1:MTCY190 34150 Z70283 Mycobacterium tuberculosis H37Rv
complete genome; segment 98/162. Mycobaccertum 55,530 17Jun-98
tuberc,ubsis
GB HTG3AC011500 0 300851 AC011500 Homo sapiens chromosome 19 done CIT978SK8
60E11, "' SEQUENCING Homo sapiens 39,659 18-Feb-00
IN PROGRESS "', 246 unordered pieces.
GB HTG3AC011500 0 300851 AC011500 Homo sapiens chromosonie 19 done CIT978SKB
80E11, "" SEQUENCING Homo sapiens 39,659 18-Feb-00
IN PROGRESS -. 246 unordered pieces.
rxa02147 1140 G8
_EST28A1492095 485 A1492095 tg07a01.x1 NCI CGAP CLL1 Homo sapiens cDNA clone
IMAGE:2108040 3', Honw sapiens 39,798 30-MAR-1999 rnRNA sequenaa.
GB_ESTI0:AA157467 376 AA157467 zo50e01.r1 Stratagene endothelial cell 937223
Homo sapiens cONA cbne Homo sapiens 36,436 11-DEC-1996
IMAGE:590328 5', mRNA sequence. aLno
GB_ESTI0:AA157467 376 AA157467 zo50e01.r1 Stratagene endothetial cell 937223
Homo sapiens aDNA clone Homo sapiens 36,436 11-DEC-1996
IMAGE:590328 6, mRNA sequenoe. 00.
nca02149 1092 GB_PR3:HSBK277P6 61698 AL117347 Human DNA sequence from ctone
277P6 on chromosome 1 q25.3-31.2, Homo sapiens 36,872 23-Now99
compiete sequence.
GB BA2:EMB065R075 360 AF116423 Rhizobium etli mutant M8045 RosR-
transatptionaly reputated sequence. Rhizobium edi 43,175 08-0EC-1999
-.3
GB EST34:A1789323 574 A1789323 ukb3p05.y1 Sugano mouse kidney mkia Mus
musculus eDNA clone Mus muscuius 39,715 2-Jul-99
IMAGE:1972760 5' simiiar to WP:K11 H12.8 CE12160 ;, mRNA sequence.
nca02175 1416 GB_BA1:CGGLTG 3013 X66112 C.glutamicum gft gene for citrate
synthase and ORF. Corynebacterium 100,000 17-Feb-95
glutsmicum D
G8_8A1:MTCY31 37630 Z73101 Myoobaderium tuberculosis H37Rv complete genome;
segment 41/162. Mycobacterium 64,331 17Jun-98
tube-eubsis
GBBAI:MLC857 38029 Z99494 Mycobacterium lepm cosmid 857. Mycobacterium ieprae
62,491 10-Feb-99
nca02196 816 GB_RO:RATDAPRP 2819 M76426 Rattus norvegicus dipeptidyi
aminopeptidase-related protein (dpp6) mRNA, Rattus norvegicus 38,791 31-MAY-
1995
ConyNete cds.
GB GSS8AQ012162 763 A0012162 127PB037070197 Cosmid library of chromosome 11
Rhodobacter sphaeroides Rhodobacter sphaeroides 40,044 4-Jun-98
genomic clone 127PB037070197, genomic survey sequence.
GB RO:RATDAPRP 2819 M76426 Rattus norvegicus dipeptidyt aminopeptidase-related
protein (dpp6) mRNA, Ratb+s nonrogicus 37,312 31-MAY-1995
complete cds.
nca02209 1694 GB BA1:A8025424 2995 A8025424 Corynebacterium glutamicum gene
for aconitase, paniel cds. Corynebacterium 99.173 3-Apr-99
glutamicurn
GS BA2:AF'002133 15437 AF002133 Mycobacterium avium strain GIR70
transcriptional regulator (mav81) gene, Mycobacterium avium 40,219 28~-1998
paAqi cds, aconitase (acn), lnvasin 1(invl), lnvasin 2 (inv2), transcriptlonal
regulator (moxR), ketoaayl-reductase (fabG), enoyl-neduetase (inhA) and
terrochelatase (mav272) genes, complete ods.
Table 4 (continued)
Gk13Ai:MTV007 32806 AL021184 Mycobacterium tuberculosis H37Rv complete genome;
segment 64l162. Mycobacterium 38,253 17-Jun-98
tuberculosis
nta02213 874 GB BA7 AB025424 2995 A8025424 Corynebacterium glutamicum gene for
aconitase, partial ods. Corynebacterium 99,096 3-Apr-99
glutamicum
Gt3 BAI:MTV007 32806 AL021184 Mycobacterium tuberculosis H37Rv complete
genome; segment 64l162. Mycobaderium 34,937 17-Jun-98
tuberculosis
GB BA2AF002133 15437 AF002133 Mycobacterium avium stVain GIRIO transcriptional
regulator (mav81) gene. Mycobacterium avium 36,885 2641AAR-1998
partial cds, aconitase (acn), invasin 1(invl), invasin 2 (inv2),
transcriptional
regulator (moxR), ketoacyl-reductase (fabG), enoyl-reductase (inhA) and
ferrochelatase (mav272) genes, complete cds.
nca02245 780 GB f3A2:RCU23145 5960 U23145 Rhodobacter capsulatus Calvin cyde
carbon dioxide fixation operon: fructose- Rhodobacter capsulatus 48,701 28-OCT-
1997
1,6-/sedoheptulose-1,7-bisphosphate aklolase (cbbA) gene, partial ads, Fonn It
ribulose-1,5-bisphosphate carboxylase/oxygenase (cbbM) gene,
complete ods, and Calvin cycle operon: pentose-5-phosphate-3-epimerase
(cbbE), phosphoglycolate phosphatase (cbbZ), and cbbY genes, complete cds.
cn
GS t3A1:ECU82664 139818 U82664 Esdierichia coh minutes 9 to 11 genomic
sequence. Escherichia coli 39,119 11Jan-97
GB HTG2:AC007922 158858 AC007922 Homo sapiens chromosome 18 done hRPK.178 F 10
map 18, Homo sapiens 33,118 26-Jun-99
SEQUENCING IN PROGRESS "', 11 unordered pieoes.
nca02256 1125 GB BAI:CGGAPPGK 3804 X59403 C.glutamicum gap, pgk and tpi genes
for gtyceraldehyde-3-phosphate, Corynebacterium 99,289 05-OCT-1992 o N
phosphoglycerate kinase and triosephosphate isomerase. gkrtamicum
GB BA1:SCC54 30753 AL035591 Streptomyces coelicolor cosmid C54. Streptomyces
coelicolor 36,951 11Jun-99 G9_t3A1:MTCY493 40790 Z95844 Mycobacterium
tuberculosis H37Rv complete genome; segment 631162. Mycobacterium 64,196 19-
Jun-98 0 =
tuber culosis
rxa02257 1338 Gf3 BAI:CGGAPPGK 3804 X59403 C.glutarnicum gap, pgk and tpi
genes for gtyceraldehyde-3-phosphate, Corynebacterium 98,873 05-OCT-1992
phosphogtycerate kinase and triosephosphate isomerase. gkitamicum
GB BAI:MTCY493 40790 Z95844 Mycobacterium tuberculosis H37Rv complete genome;
segment 63/162. Myaobacterium 61,273 19-Jun-98
tuberwlosis
GB BA2:MAU82749 2530 U82749 Mycobaderium avium gtyceraldehyde-3-phosphate
dehydrogenase homolog Mycobaderium avium 61,772 6-Jan-98
(gapdh) gene, complete cds; and phosphogtycerate kinase gene, partial cds.
rxa02258 900 GB_BAI:CGGAPPGK 3804 X59403 C.glutamicum gap, pgk and tpi genes
for gyceraidehyde-3-phosphate, Corynebacterium . 99,667 05-OCT-1992
phosphoglycerate kinase and triosephosphate isomerase. glutamicum
GB BAI:CORPEPC 4885 M25819 C.glutamicum phosphoenolpyruvate carboxylase gene,
complete cds. Corynebacterium 100,000 15-DEC-1995
glutamicum
G8 PAT:A09073 4885 A09073 C.glutamicum ppg gene for phosphoenol pyruvate
carboxytase. Corynebaderium 100,000 25-Aug-93
gkrtamicum
rxa02259 2895 G8_BAI:CORPEPC 4885 M25819 C.glutamicum phosphoenolpyruvate
carboxylase gene, complete cds. Corynebacterium 100,000 15-DEC-1995
glutamicum
GB PAT:A09073 4885 A09073 C.glutamicum ppg gene for phosphoenol pyruvate
carboxylase. Corynebaderium 100,000 25-Aug-93
gkitamicum
GB 13A1:CGPPC 3292 X14234 Corynebaderium glutamicum phosphoenolpyruvate
carboxylase gene (EC Corynebaderitxn 99,827 12-Sep-93
4.1.1.31). glutamicum
Table 4 (continued)
:xa0:28E 969 Gg PR3:HSDJ94E24 243145 AL0503i7 Human DNA sequence from done RPI-
94E24 on diromosome 20q12, Homo sapiens 36,039 03-DEC-1999
complete sequence.
GB HTG3:AC010091 159526 AC010091 Homo sapiens done NH0293A01, "" SEQUENCING IN
PROGRESS 4 Homo sapiens 35,331 11Sep-99
unordered pieoes.
G8_HTG3:AC010091 159526 AC010091 Homo sapiens done NH0295A01, =" SEQUENCING IN
PROGRESS 4 Homo sapiens 35,331 11-Sep-99
unordered pieces.
rxa02292 798 G4_BA2:AF125164 26443 AF125164 Bacteroides fragilis 638R
polysaccharide 8(PS 82) biosynthesis locus, Bacteroides fragiBs 39,747 01-DEC-
1999
oomplete sequence; and unknown genes.
GB_GSS5AQ744695 827 AQ744695 HS_5505 A2_C06_SP6 RPCI-1 1 Human Male BAC
Library Homo sapiens Homo sapiens 39,185 16-Jul-99
genomic done Plate=1081 Co1=12 Row=E, genomic survey sequence.
GB_EST14:AA381925 309 AA381925 EST95058 Activated T-cells I Homo sapiens cDNA
5' end, mRNA sequence. Homo sapiens 35,922 21-Apr-97
rxa02322 511 GB_BA1:MTCY22G8 22550 Z95585 Mycobacterium tuberculosis H37Rv
complete genome; segment 49/162. Mycobacterium 57,677 17-Jun-98
tuberwbsis
GB BAI:MTCY22G8 22550 Z95585 Mycobacterium tuberculosis H37Rv complete genome;
segment 491182. Mycobacterium 37,143 17-Jun-98
tuberoulosis
0
nca02326 939 GB_BAI:CGPYC 3728 Y09548 Corynebacterium giutamicum pyc gene.
Corynebaderium 100,000 08a111AY-19~ "'
ao
gtutamicum
GB_BA2AF038548 3637 AF038548 Corynebacterium glutamicum pyruvate carboxylase
(pyc) gene, complete cds. Corynebacterium 100,000 24-DEC-1997 giutamicum
GB_BAI:MTCY349 43523 Z83018 Mycobacterium tuberculosis H37Rv complete genome;
segment 131/162. Mycobaderium 37,363 17-Jun-98
tuberoubsis o =
rxa02327 1083 GB_BAI:CGPYC 3728 Y09548 Corynebacteriurn glutamicum pyc gene.
Corynebacterium 99,259 08-MAY-1998 - .3
ghftmicum
GB_BA2:AF038548 3637 AF038548 Corynebaderium glutamicum pyruvate carboxylase
(pyc) gene, compiete eds. Corynebaderium 99,259 24-DEC-1997
glutamiuxn co
GB 8A1:MTCY349 43523 Z.83018 Mycobacterium tuberculosis H37Rv complete genome;
segment 131/162. Myeobaderium 41,317 17Jun-98
tubercubsis
rxa02328 1719 GB 8A1:CGPYC 3728 Y09548 Co-ynebacterium glutamicum pyc gene.
Carynebaderium 100,000 08aMAY-1998
glutamicum
GB BA2:AF038548 3637 AF038548 Corynebacterium giutamicum pyruvate carboxyfasa
(pyc) gene, oornpiete ads. Corynebacterium 100,000 24-DEC-1997
glutamicutn
GB_PL2AF097728 3916 AF097728 Aspergilius terreus pyruvate carboxylase (Pyc)
mRNA, complete cds. Asperyittus terreus 52,248 29-OCT-1998
nuK12332 1266 GB BAI:MSGLTA 1776 X60513 M.smegmatis getA gene for dtrate
synthase. Mycobacterium smegmatis 58,460 20Sep-91
GB_BA2:ABU85944 1334 U85944 Antarctic bacterium DS2-3R citrate synthase (cisy)
gene, complete cds. Antardic baderium OS2- 57,154 23-Sep-97
3R
GB_BA2 AE000175 15067 AE000175 Esdwrichia eoii K-12 MG1655 section 65 of 400
of the complete genome. Esdarichia coli 38,164 12-Nov-98
nca02333 1038 GB_BAI:MSGLTA 1776 X60513 M.amegmatis gitA gene for citrate
symhase. Mycobaderium smegmatis 58,929 20-Sep-91
GB PR4:HUAC002299 171681 AC002299 Homo sapiens Chromosome 16 BAC done CIT987-
SKA-113A6 -complete Homo sapiens 33,070 23-Nov-99
genomic sequence, compiete sequence.
Table 4 (continued)
GB=HTG2AC007889 127840 AC007889 Drosophile melanogaster cl-irornos4n-ie 3
cione BACR48E12 (D695) RPCi-98 Drosophita melanogester 34,897 2-Aug-99
48.E.12 map 87A-87B strain y; cn bw sp, "= SEQUENCING IN PROGRESS"',
86 unordered pieces.
nra02399 1467 GB BA1:CGACEA 2427 X75504 C.glutamicum aceA gene and thiX genes
(partial). Corynebacterium 100,000 9Sep-94
gkrtamicum
GB_BAI:CORACEA 1905 L28760 Corynebaderium glutamicum isodtrate lyase (aceA)
gene. Corynebacterium 100,000 10-Feb-95
glutamacum
GB PAT:113693 2135 113693 Sequence 3 from patent US 5439822. Unkrwwn_ 99,795
26-Sep-95
nca02404 2340 GB_8A1:CGACEB 3024 X78491 C.glutamicum (ATCC 13032) ace8 gene.
Corynebaderium 99,914 13-Jan-95
glutamicum
GB BAI:CORACEB 2725 L27123 Corynebaderium glutamicum malate synthase (aceB)
gene, complete cds. Corynebacterium 99,786 8-Jun-95
giutamicum
GB BA1:PFFC2 5588 Y11998 P.fluorescens FC2.1, FC2.2, FC2.3c, FC2.4 and FC2.5c
open reading frames. Pseudomonas fluorescens 63,539 11Jul-97
nca02414 870 GB PR4AC007102 176258 AC007102 Homo sapiens chromosome 4 clone
C0162P16 map 4p16, complete sequence. Homo sapiens 35,069 2=Jun-99
GB HTG3 AC011214 183414 AC011214 Homo sapiens clone
5_C_3, LOW-PASS SEQUENCE SAMPLING. Homo sapiens 36,885 03-0CT-1999 "'
00
GB HTG3AC011214 163414 AC011214 Homo sapiens clone 5_C 3, LOW-PASS SEQUENCE
SAMPLING. Homo sapiens 36,885 03-OCT-1999
nra02435 681 GB 8A2AF101055 7457 AF101055 Clostridium acetobutyficum atp
operon, complete sequence. Clostridium acetobutylicum 39,605 03-MAR-1999
GB OM:RABPKA 4441 J03247 Rabbit PhosPhoMase kinase (alpha suUunit) mRNA,
complete cds. OrYdola us cuniculus 36,061 27-Apr-93 9
GB OM:RABPLASfSM 4458 M64656 Oryctolagus cunicutus phosphorylase kinase alpha
subunit mRNA, complete Oryctolagus cunicutas 36,000 22-Jun-98 eds.
rza02440 963 GB_EST14:AA417723 374 AA417723 zv01bt2.s1 NCI CGAP_GCB1 Honw
sapiens eDNA done IMAGE:746207 3' Homo sapiens 38,770 16-OCT 1997
simflar to contains Alu ropetitive element;contains element Lt repetitive
element :, mRNA sequenoe. 00
GB ESTII:AA215428 303 AA215428 zr95a07.s1 NCI CGAP_GCB1 Homo sapiens cDNA
clone IMAGE:683412 3' Homo sapiens 39,934 13-Aug-97
similar to contains Alu repetitive eiemant;, mRNA sequence.
06_BAI:MTCY77 22255 Z95389 Mycobacterium tuberculosis H37Rv complete genorne;
segment 146/162. Mycobacterium 38,889 18-Jun-98
tuberrarlosis
nra02453 876 GB_EST14:AA426336 375 AA428336 zv53g02.s1 Soaros_testis_NHT Homo
sapiens cDNA ctone IMAGE:757394 3', Homo sapiens 38,043 16-OCT-1997
mRNA sequence.
GBBAI:STMAACC8 1353 M55426 S.fradiae aminoglycoside acetyitransferase (aacC8)
gene, complete cds. Streptomyoes fradiae 37,097 05-MAY-1993
GB PR3AC004500 77538 AC004500 Homo sapiens chromosome 5, P1 Gone 1076B9 (LBNL
H14), complete Homo sapiens 33,256 30-MAR-1998
sequence.
rxa02474 897 G4_13A1:A8009078 2686 AB009078 Brevibaderium saccharolyticum gene
for L-2.3-butanediol dehydrogenase, Brevibacterium 96,990 13-Feb-99
complete cds. socchwokfmm
GB aM:BTU71200 877 U71200 Bos taurus acetoin reductase mRNA, complete cds. Bos
taurus 51,859 8-Oct-97
GB EST2:F12685 287 F12685 HSC3DA031 normalized infant brain cDNA Homo sapiens
cONA done c- Homo sapiens 41,509 14-Mar-95
3da03, mRNA sequence
nca02480 1779 GB BAI:MTV012 70287 AL021287 Mycobacterium tuberculosis H37Rv
complete genome; segment 1321162. Mycobacterium 36,737 23-Jun-99
tuberculosis
Table 4 (continued)
GB BA1:SC6G10 36734 AL049497 Streptomyces coeiicoior cosmid 6G10. Streptomyoes
coeiicolor 35,511 24-MAR-1999
GB_BA1 AP000060 347800 AP000060 Aeropyrum pemix genomic DNA, section W.
Aeropynrm pemix 48,014 22-Jun-99
nca02485
rxa02492 840 G8_BAI:STMPGM 921 M83661 Streptomycxs coelicolor phosphogiycerate
mutase (PGM) gene, complete cds. Streptomyoes coeiicolor 65,672 26-Apr-93
GB_BAI:MTCY2009 37218 Z77162 Mycobacterium tuberculosis H37Rv complete genome;
segment 25/162. Mycobacterium 61,436 17-Jun-98
tuberculosis
GB_BA1:U00018 42991 U00018 Mycobacterium kprae cosmid 82168. Mycobacterium
bprae 37,893 01-MAR-1994
rxa02528 1098 GB_PR2:HS161N10 56075 AL008707 Human DNA sequenoe from PAC
161N10 on chromosome Xq25. Contains Homo sapiens 37,051 23-Nov-99
EST.
GB_HTG2AC008235 136017 AC008235 Drosophila meianogaster chromosome 3 done
BACR15B19 (D995) RPCI-98 Drosophila meianogaster 36,822 2,Aug-99
15.8.19 map 94F-95A strain y; on twv sp, '=' SEQUENCMIG IN PROGRESS 0Ln0
===, 125 unordered pieces.
GB HTG2AC008235 136017 AC008235 Drosophila melanogaster chromosome 3 clone
BACR15B19 (D995) RPCI-98 Drosophiia melanogaster 36,822 2-Aug-99
15.8.19 map 94F-95A strain y; cn bw sp, "' SEQUENCING IN PROGRESS"', ~
125 unordered pieces. W o
rxa02539 1641 GB BA2:RSU17129 17425 U17129 Rhodococcus erythropolis ThcA
(thcA) gene, complete cds; and unknown Rhodococcus erythrapoas 66,117 16titui-
99
genes.
GB 8A1:MiV038 16094 AL021933 Mycobacterium tuberculosis H37Rv complete genome;
segment 24/162. Mycobacterium 65,174 17-Jun-98 tuberculosis GB BA2:AF088264
3152 AF068264 Pseudomonas aeruginosa quinoprotein ethanol dehydrogenaae
(exaA)gene, Pseudomonas aeruginosa 65,448 1844AAR-1999 ro
partiai eds; cytochrome c550 precursor (exaB), NAD+ dependerd acetaldehyde
dehydrogenase (exaC), and pyrroioquino6ne quinone synthesis A (pqqA)
genes, complete cds; and pyrroloquinoline quinone synthesis B(pqqB) gene,
partial cds.
nca02551 483 GB BAI:BACHYPTP 17057 D29985 8aciiius subtiiis wapA and ort genes
for waN-associated protein and Bacilus subtifis 53,602 7-Feb-89
hypothetical proteins.
G8_8A1:BACHU7WAP1428954 D31856 BadYus subtilis genome containing the hut and
wapA ioci. BaoiNus subtiNs 53,602 7-Feb-99
GB BAI:BSGBGLUC 4290 Z34526 B.subtiiis (Marburg 168) genes for beta-glucoside
pennease and beta- Bacillus subtiiis 53.602 3JuM
giucosidase.
rxa02556 1281 GB_HTG3AC008128 335761 AC008128 Homo sapiens. ="' SEQUENCING IN
PROGRESS 106 unordered pieces. Homo sapiens 34,022 22,Aug-99
GB HTG3AC006128 335761 AC008128 Homo sapiens, SEQUENCING IN PROGRESS 106
unordered pieces. Homo sapiens 34,022 22-Aug-99
GB_PL2AC005292 99053 AC005292 Genomic sequence for Arabidopsis thaliana BAC
F26F24, complete sequence. Arabidopsis thaliana 33,858 16,Apr-99
nca02560 990 GB INI:CEF07A11 35692 Z66511 Caenorhabdkis ek3gans cosmid FO7A11,
complete sequence. Caenorhabditls elegans 36,420 24ep-99
GB EST32A1731605 566 A1731605 BNLGHi10201 Six-day Cotton fiber Gossypium
hirsutum cDNA 5' simiiar to Gossypium hirsutum 38,095 11Jun-99
(AC004684) hypothebcai protein (Arabidopsis thaiiana), mRNA sequence.
GB_iN1:CEF07A11 35692 Z66511 Caenorhabditis eiegans cosmid F07A11, complete
sequence. Caenorhabditis eftans 33,707 2-Sep-99
Table 4 {continued)
rxa025'72 888 GB_B-v1:MTCY63 38900 286600 Mycobacterium tuberculosis H37Rv
complete genome; segment 16/162. Mycobacteriusn 61,677 17-Jun-98
tuben:ulosis
GB BAI:MTCY63 38900 298800 Mycobacteriurn tuberculosis H37Rv complete genome;
segment 16/162. Mycabacterium 37,170 17-Jun-98
tuberculosis
GB HTGI:HS24H01 46989 AL121832 Homo sapiens chromosome 21 done LLNLc116H0124
map 21q21, Homo sapiens 19,820 29-Sep-99
SEQUENCING IN PROGRESS "', in unordered pieces.
nca02596 1326 GB_BAI:MTV026 23740 AL022076 Mycobacterium tuberculosis H37Rv
complete genome; segment 157/162. Mycobacterium 36.957 24-Jun-99
tubercutosis
GB_BA2:AF026540 1778 AF026540 Mycobactenum tuberculosis UDPyalaetopyranose
mutase (glf) gene, comptete Myoobaeterium 67,627 30-0CT-1998
ods. tuberculosis
GB_8A2:MTU96128 1200 U96128 Mycobacterium tuberculosis UDP-galactopyranose
mutese (glf) gene, complete Mycobacterium 70,417 25-MAR-1998
cds. tubetculosis
nca0Z611 1775 GB BAI:MTCY130 32514 273902 Mycobaderium tuberculosis H37Rv
complete genome; segment 59/162. Mycobacterium 38,532 174un-98
tuberculosis
GB_BA1:MSGY151 37036 AD000018 Mycobacterium tubercuiosis sequence from elone
y151. Myeobacterium 60,575 10-DEC-1996
tubenculosis Ln
GB BA1:UO0014 36470 U00014 Mycobacterium k3prae cosmid 81549. Mycobacterium
leprae 57,486 29-Sep-94 00
rxa02612 2316 GB_BAI:MTCY130 32514 Z73902 Mycobacterium tubercuiosis H37Rv
complete genome; segment 59/162. Mycobacterium 38.018 17-Jun-98 tuberculosis
G8 8A1:MSGY151 37036 11DOOW18 Mycobacterium tuberculosis sequence from clone
y151. Mycobacterium 58,510 10-DEC-1996
tuberculosis o
GB BAI:STMt3LGEN 2557 L11647 Streptomyces aureofaciens glycogen branching
enzyrne (gl9B) gene, convieta Stroptomyaes 57.1b3 25-NIAY-1995 " -.3
cds. aureofaciens
rxa02621 942 GB_BA1:CGL133719 1839 AJ133719 Corynebacterium glutamicum yjcc
gene, amtR gene and dtE gene, partial. Corynebacterium 36,858 12-Aug-99
gtutamicum 00
GB_INI:CEM106 39973 Z46935 Caenorhabditis elegans cosmid M106, oomplete
sequenoe. Caenorhabdfis elegans 37,608 2Sep-99
GB_EST29:AI547662 377 A1547662 UI-R-C3-sz-h-03-0-Ul.s1 UI-R-C3 Rattus
norvegicus cDNA done UI-R-C3-sz-h- Rattus nonregiprs 50,667 3-Jul-99
03-0-UI 3', mRNA sequence.
rtta02640 1650 G8 8A1:MTV025 121125 AL022121 Mycobacterium tuberculosis H37Rv
compbte genorne; segment 155/162. Myeobacterium 39,187 24-Jun-99
tuberculosis
GB_BAI:PAU49666 4495 U49666 Pseudomonas aeruginosa (orfX), gycerol dfdfuslon
facilitator (glpF), glycerol Pseudomonas aeruginosa 59,273 18-MAY-1997
kinase (glpK), and Gip repressor (g1pR) genes, complete ods, and (orfK) gene,
partial Cds_
GB_BA1:AB015974 1641 AB015974 Pseudomonas tolaasii glpK gene for glycerol
kinase, complete cds. Pseudomonas tolaasii 58,339 28,Aug-99
rxa02654 1008 GB_EST6:N65787 512 N65787 20827 Lambda-PRL2 Arabidopsis thaliana
cDNA done 232B7T7, mRNA Arabidopsis thaliana 39,637 54an-98
sequence.
G8 PL2:T17H3 65839 AC005916 Arabidopsis thaliana chromosome 1 BAC T17H3
sequence, complete Arabidopsis thaliana 33,735 5-Aug-99
seQuence.
GB RO:IIMNU58105 88871 U58105 Mus muscuius Btk kxus, alpha-D-gatactosidase
A(Ags), riboaomal protein Mus rtwsculus 35,431 13-Feb J7
(L44L), and Bruton's tyrosine kinase (8tk) genes, complete cds.
nca02666 891 GB_PR3AC004643 43411 AC004643 Homo sapiens chromosome 16, cosmid
done 363E3 (LANL), complete Homo sapiens 38,851 01-MAY-1998
sequenoe.
Table 4 (condnued)
G3_PR3:AC004643 43411 AC004643 Homo sapiens chromosome 16, cosmid olone 363E3
(LANL), complete Homo sapiens 41,599 01-MAY-1998
sequence.
GB_BAZAF049897 9196 AF049897 Corynebacterium glutamicum N-
acetylglutamylphosphate reductase (argC), Corynebacterium 40,413 1-Ju1-98
omithine acetyltransterase (argJ), N-acetylglutamade kinase (argB), glutamicum
acetylomithine transaminase (argD), omithine caibamoyRransterase (argF),
arginine repressor (argR), argininosuocinate synthase (argG), and
argirnnosucc7nate yase (argH) genes, complete cds.
rxa02675 1980 GB BAI:PDENQOURF 10425 L02354 Paraooccus denitrificans NADH
dehydrogenase (URF4), (NQ08), (NQ09), Paracoccus denitriflcans 40,735 20-MAY-
1993
(URF5), (URF6), (NQ010), (NOO11), (NQ012), (NQ013), and (NQ014)
genes, complete cds's; biotin (acetyl-CoA carboxyq ligase (birA) gene,
complete
ods.
GB BAI:MTCY339 42881 Z77163 Myoobacterium tuberculosis H37Rv complete genome;
segment 101/162. Mycobacterium 36,471 17 Jun-98
tuberculosis
GB BAI:MXADEVRS 2452 L19029 Myxococcus xanthus devR and devS genes, complete
ads's. Myxococcus xanthus 38,477 27-Jan-94 nca02694 1065 GB BAI:BACLDH 1147
M19394 B.cakioyticus lactate dehydrogenase (LDH) gene, complete cds. Bacillus
aakio"qus 57,371 26,Apr-93
GB_BA1:BACLDHL 1361 M14788 B.stearothernaphilus Ict gene encoding L-lactate
dehydrogenase, complete Bacillus 57,277 28-Apr-93 Ln
cds. stearethemqphilus 00
GB_PATR06664 1350 A06664 B.stearothemwphilus Ict gene. BaciUus 57,277 29-Jul-
93
stearothermophilus
rxa02729 844 GB ESTI5:AA494626 121 AA494626 ta09d04.r1 Zebrafish ICRF=tis
Danio rario cDNA clone 11A22 5' simisar to Danio rerio 50,746 27.1un-97
CA
TR:431171183 G1171163 G1T-MISMATCH BINDING PROTEIN. ;, mRNA
sequence.
-.3
GB_EST15:AA494626 121 AA494626 fa09d04.r1 2;ebra6sh ICRFzfls Danio rerlo cDNA
done 11A22 5' similar to Danio rerio 36,364 27-Jun-97
TR:G1171163 G1171163 G/T-MISMATCH BINDING PROTEIN. ;, mRNA
sequence. ro
rxa02730 1161 GB_EST19:AA758660 233 AA758660 ah67dO6.s1 Soares testis NHT Homo
sapiens cDNA clone 1320683 3', mRNA Homo sapiens 37,059 29-DEC-1998
sequence.
GB_EST15:AA494626 121 AA494626 fa09d04.r1 Zebrafish ICRFzfls Danio rer9o cONA
done 11A22 5' similar to Danio rerio 42,149 27-Jun-97
TR:G1171163 01171163 G/TaMISMATCH BINDING PROTEIN. ;, mRNA
sequence.
GB_PR4:AC006285 150172 AC006285 Homo sapiens, oorrkplete sequence. Homo
sapiens 37,655 15=Nov-99
rxa02737 1665 GB PAT:E13655 2260 E13655 gDNA enaoding gluaose-6-phosphate
dehydrogenase. Corynebacterium 99,580 24-Jun-98
glutamicum
GB_BAI:MTCY493 40790 295844 Mycobacterium tuberculosis H37Rv complete genome;
segment 63/162. Mycobacterium 38,363 19Jun-98
tuberWlosis
GB_BA1:SC5A7 40337 AL031107 Stnoptomyees aoelicolor cosmid W. Stneptomyoes
eoelieotor 39,444 27-Jut-98
rxa02738 1203 GB PAT:E13655 2260 E13655 gDNA encoding glucose-6-phosphate
dehydrogenase. Corynebacterium 98,226 24-Jun-98
glutamicum
GB BAI:SCC22 22115 AL096639 Streptomyces coeticolor cosmid C22. Streptomyces
coelicolor 60,399 12-Jul-99
GB_BA1:SC5A7 40337 AL031107 Streptomyces coelieolor cosmid W. Streptomycea
ooelicolor 36,426 27Ju1-98
rxa02739 2223 GB BA1 A8023377 2572 A8023377 Corynebacterium glutamiwm tkt gene
for transketolase, complete cds. Corynebacterium 99,640 20-Feb-99
glutarrticum
Table 4 (continued)
~B BAi:MLCL'3S 36224 Z98125 Mycobacterium ieprae cosmid L536. Mycobaderium
leprae 61,573 04-DEC-1998
GB BA1:U00013 35881 U00013 Mycobacterium leprae cosmid 81496. Mycobaderium
leprae 61,573 01-MAR-1994
rxa02740 1053 GB HTG2AC0l>6247 174368 AC006247 Drosophila melanogaster
chromosome 2 clone BACR48i10 (D505) RPCI-98 Drosophila nielanogaster 37.105 2-
Aug-99
48110 map 49E6-49F8 strain y; cn bw sp, "'= SEQUENCING IN PROGRESS
-" 17 unordered pieces.
GB_HTG2AC006247 174368 AC006247 Drosophila melanogaster chromosome 2 clone
BACR48110 (0505) RPCI-98 Drosophila melanogaster 37,105 2-Aug-99
48.1.10 map 49E6-49F8 strain y; cn bw sp, "' SEQUENCING IN PROGRESS
"', 17 unordered pieces.
GB HTG3AC007150 121474 AC007150 Drosophila melanogaster chromosome 2 clone
BACR16P13 (D597) RPCI-98 Drosophila melarwgaster 38,728 20-Sep-99
16.P.13 map 49E-49F strain y; cn bw sp, "" SEQUENCING IN PROGRESS'=',
87 unordered pieces. -
rxa02741 1089 GB_HTG2AC004951 129429 AC004951 Homo sapiens clone DJ1022114,
'=' SEQUENCING IN PROGRESS "'=, 14 Homo sapiens 33,116 12-Jun-98
unoniered pieces.
GB HTG2:AC004951 129429 AC004951 Homo sapiens done DJ1022114, SEQUENCING IN
PROGRESS 14 Homo sapiens 33,116 12-Jun-98 N
unordered pieces. Ln
GB IN1:AB006546 931 AB006546 Ephydatia fluviatilis mRNA for G protein a
subunit 4, partial cds. Ephydatia flwiatilis 36,379 23-Jun-99 D
rxa02743 1161 GB BAI:MLCL536 36224 Z99125 Mycobacterium leprae cosmid L536.
Mycobaderium bprae 48,401 04-DEC-1998
GB BA1:U00013 35881 U00013 Mycobacterium leprae cosmid 81496. MYcobacterium
leprae 48,401 01-MAR-1994 L N
GB HTG2AC007401 83657 AC007401 Homo sapiens done NH0501007, "' SEQUENCING IN
PROGRESS '=', 3 Homo sapiens 37,128 26-Jun-99
unordered pieces. .3
rxa02797 1026 GB BAI:CGBETPGEN 2339 X93514 C.glutamicum betP gene.
Corynebacterium 38,889 8-Sep-97 0
glutamicum
GB GSS9AQ148714 405 AQ148714 HS 3136 At A03_MR CIT Approved Human Genomic
Sperm Library D Homo Homo sapiens 34,321 08-OCT-1998
sapiens genomic ctone Plate=3136 Co1=5 Row=A, genomic survey sequence. ro
GB BAI:BFU64514 3837 U64514 Bacillus firmus dppABC operon, dipeptide
transporter protein dppA gene, BaciBus firmus 38,072 1-Feb-97
partial cds, and dipeptide transporter proteins dppB and dppC genes, complete
cds.
rxa02803 680 GB BA1:U00020 36947 U00020 Mycobaderium ieprae cosmid B229.
Mycobacterium leprae 34,462 01-MAR-1994
GB 8A2:PSU85643 4032 U85643 Pseudomonas syringae pv. syringae putative
dihydropteroate synthase gene, Pseudomonas syringae pv. 50,445 9-Apr-97
partial cds, regulatory protein MrsA (mrsA), triose phosphate isomerase
(tpiA), syringae
transport protein SecG (secG), tRNA-Leu, tRNA-Met, and 15 kDa
protein genes, complete cds.
GB BA1:SC6G4 41055 AL031317 Streptomyces coelicolor cosmid 6G4. Streptomyces
coelicolor 59,314 20,Aug-98
rxa02821 363 GB H7G2AC008105 91421 AC008105 Homo sapiens chromosome 17 clone
2020_K_17 map 17, "' SEQUENCING Homo sapiens 37,607 22-Jul-99
IN PROGRESS "', 12 unordered pieces.
GB HTG2AC008105 91421 AC008105 Homo aapiens chromosome 17 clone 2020_K_17 map
17, =" SEQUENCING Homo sapiens 37,607 22-Jul-99
IN PROGRESS "', 12 unordered pieoes.
GB EST33AV117143 222 AV117143 AV117143 Mus musculus C57BU6J 10-day embryo Mus
musculus cDNA done Mus musculus 40,157 30-Jun-99
2610200J 17, mRNA sequence.
Table 4 (corrtinued)
nca02829 373 GkHTGI:HSU9G8 48735 AL008714 Hoeno sapiens chromcso:ne X clor.e
LLOXNC01-9~.a8, = SEQUENCING IN Homo sapiens 41,595 23-Nov-99
PROGRESS "', in unordered pieces.
GB_HTGI:HSU9G8 48735 AL008714 Homo sapiens chromosome X clone LLOXNC01-9G8, "'
SEQUENCING IN Homo sapiens 41,595 23-Nov-99
PROGRESS'"=, in unordered pieces.
GB PR3:HSU8585 39550 Z69724 Human DNA sequence from cosmid U85B5, between
markers DXS366 and Homo sapiens 41,595 23-Nov-99
DXS87 on chromosome X.
nca03216 1141 GB HTG3=AC0G8184 151720 AC008184 Drosophila melanogaster
chromosome 2 done BACR04005 (D540) RPCI-98 Drosophila metartogaster 39,600
2,Aug-99
04Ø5 map 36E5-36F2 strain y; cn bw sp, ""' SEQUENCING IN PROGRESS
"', 27 unordered pieces.
G8 F-ST15:AA477537 411 AA477537 zu36g12.r1 Soares ovary tumor NbHOT Homo
sapiens eDNA clone Homo sapiens 37,260 9-Nov-97
IAMGE:740134 5' simi{ar to contains Alu repetitive element;contains element
HGR repetitive element ;, mRNA sequence.
G8_EST26A1339662 412 A1330662 fa91d08.y1 zebrafish fin dayl regeneration Danio
rerio cDNA 5, mRNA Danio rerio 37,805 28-DEC-1998
sequence.
rxs03215 1038 GBBA1:SC3F9 19830 AL023862 Streptomyces coelicolor cosmid 3F9.
Streptomyces coeRcolor 48,657 10-Feb-99
A3(2)
GB_8A1:SLLINC 36270 X79146 S.lincolnensis (78-1 i Lincom cin udion ) y prod
genes. Streptomyoes I"mcoMensis 39,430 15-FMY-1996 Ln
00
GB HTG5:AC009660 204320 AC009660 Homo sapiens chromosome 15 clone RP11-424J10
map 15, =" SEQUENCING Homo sapiens 35,151 04-DEC-1999 ~ p=
IN PROGRESS "'-, 41 unordered pieces. .~ N
ncs03224 1288 GB_PR3:AC004076 41322 AC004078 Homo sapiens chromosome 19,
ceamid R30217, complete sequence. Horno sapiens 37,788 29-Jan-98
G8_PL2:SPAC826 23193 AL110469 S.pombe chromosome I cosmid c926.
Schizosaccharomyces 38,474 2-Sep-99 ' o =
pomDe
.3
GB BAZ:AE001081 11473 AE001081 Archaeoglobus fulgidus section 26 of 172 of the
complete genome. Archaeoglobus futpidus 35,871 15-DEC-1997
N
00
I I I l I I I
l
CA 02584021 2007-04-18
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Exemplifii cation
Example 1: Preparation of total genomic DNA of Corynebacterium glutamicum
ATCC 13032
A culture of Corynebacterium gluramicum (ATCC 13032) was grown ovemight
at 30 C with vigorous shaking in BHI medium (Difco). The cells were harvested
by
centrifugation, the supernatant was discarded and the cells were resuspended
in 5 ml
buffer-I (5% of the original volume of the culture - all indicated volumes
have been
calculated for 100 ml of culture volume). Composition of buffer-I: 140.34 g/1
sucrose,
2.46 g/l MgSO, x 7H2O, 10 ml/l KH2PO4 solution (100 g/1, adjusted to pH 6.7
with
KOH), 50 mUl M12 concentrate (10 g/1(NH,)2S0., I g/l NaCI, 2 g/l MgSO, x 7H=O,
0.2 g/l CaCl2, 0.5 g/l yeast extract (Difco), 10 ml/1 trace-elements-mix (200
mg/i FeSO.
x HZO, 10 mg/1 ZnSO4 x 7 HZO, 3 mg/1 MnClZ x 4 H20, 30 mg/1 H3BO3 20 mg/1
CoC12 x
6 H2O, I mg/1 NiCI2 x 6 H2O, 3 mg/i Na1MoO4 x 2 H2O, 500 mg/1 complexing agent
(EDTA or critic acid), 100 ml/1 vitamins-mix (0.2 mg/1 biotin, 0.2 mg/1 folic
acid, 20
mg/l p-amino benzoic acid, 20 mg/l riboflavin, 40 mg/1 ca-panthothenate, 140
mg/I
nicotinic acid, 40 mg/1 pyridoxole hydrochloride, 200 mg/1 myo-inositol).
Lysozyme
was added to the suspension to a final concentration of 2.5 mg/ml. After an
approximately 4 h incubation at 37 C, the cell wall was degraded and the
resulting
protoplasts are harvested by centrifugation. The pellet was washed once with 5
ml
buffer-I and once with 5 ml TE-buffer (10 mM Tris-HCI,1 mM EDTA, pH 8). The
pellet was resuspended in 4 ml TE-buffer and 0.5 ml SDS solution (10%) and 0.5
ml
NaCI solution (5 M) are added. After adding of proteinase K to a final
concentration of
200 g/ml, the suspension is incubated for ca.18 h at 37 C. The DNA was
purified by
extraction with phenol, phenol-chloroform-isoamylalcohol and chloroform-
isoamylalcohol using standard procedures. Then, the DNA was precipitated by
adding
1/50 volume of 3 M sodium acetate and 2 volumes of ethanol, followed by a 30
min
incubation at -20 C and a 30 min centrifugation at 12,000 rpm in a high speed
centrifuge
using a SS34 rotor (Sorvall). The DNA was dissolved in I ml TE-buffer
containing 20
g/ml RNaseA and dialysed at 4 C against 1000 ml TE-buffer for at least 3
hours.
During this time, the buffer was exchanged 3 times. To aliquots of 0.4 ml of
the
dialysed DNA solution, 0.4 ml of 2 M LiCI and 0.8 ml of ethanol are added.
After a 30
CA 02584021 2007-04-18
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min incubation at -20 C, the DNA was collected by centrifugation (13,000 rpm,
Biofuge
Fresco, Heraeus, Hanau, Germany). The DNA pellet was dissolved in TE-buffer.
DNA
prepared by this procedure could be used for all purposes, including southern
blotting or
construction of genomic libraries.
Example 2: Construction of genomic libraries in Escherichla coli of
Corynebacteriurri
Klutamicum ATCC13032.
Using DNA prepared as described in Example 1, cosmid and plasmid libraries
were
constructed according to known and well established methods (see e.g.,
Sambrook, J. et al.
(1989) "Molecular Cloning : A Laboratory Manual", Cold Spring Harbor
Laboratory Press,
or Ausubel, F.M. et al. (1994) "Current Protocols in Molecular Biology", John
Wiley &
Sons.)
Any plasmid or cosmid could be used. Of particular use were the plasmids
pBR322
(Sutcliffe, J.G. (1979) Proc. Natl. Acad. Sci. USA, 75:3737-3741); pACYC 177
(Change &
Cohen (1978) J. Bacteriol 134:1141-1156), plasmids of the pBS series (pBSSK+,
pBSSK- and
others; Stratagene, LaJolla, USA), or cosmids as SuperCos 1(Stratagene,
LaJolla, USA) or
Lorist6 (Gibson, T.J., Rosenthal A. and Waterson, R.H. (1987) Gene 53:283-286.
Gene libraries
specifically for use in C. glutamicum may be constructed using plasmid pSL 109
(Lee, H.-S. and
A. J. Sinskey (1994)J. Microbiol. Biotechnol. 4: 256-263).
Example 3: DNA Sequencing and Computational Functional Analysis
Genomic libraries as described in Example 2 were used for DNA sequencing
according to standard methods, in particular by the chain termination method
using
AB1377 sequencing machines (see e.g., Fleischman, R.D. et al. (1995) "Whole-
genome
Random Sequencing and Assembly of Haemophilus lnfluenzae Rd., Science, 269:496-
512). Sequencing primers with the following nucleotide sequences were used: 5'-
GGAAACAGTATGACCATG-3' (SEQ ID NO:783) or 5'-GTAAAACGACGGCCAGT-3' (SEQ ID
NO:784).
Example 4: In vivo Mutagenesis
In vivo mutagenesis of Corynebacterium glutamicum can be performed by passage
of
plasmid (or other vector) DNA through E. coli or other microorganisms (e.g.
Bacillus spp. or
yeasts such as Saccharomyces cerevisiae) which are impaired in their
capabilities to maintain
I M 1 M I
CA 02584021 2007-04-18
- 120 -
the integrity of their genetic infonnation. Typical mutator strains have
mutations in the genes
for the DNA repair system (e.g., mutHLS, mutD, mutT, etc.; for reference, see
Rupp, W.D.
(1996) DNA repair mechanisms, in: Escherichia coli and Salmonella, p. 2277-
2294, ASM:
Washington.) Such strains are well known to those of ordinary skill in the
art. The use of such
strains is illustrated, for example, in Greener, A. and Callahan, M. (1994)
Strategies 7: 32-34.
Example 5: DNA Transfer Between Escherichia coli and Corynebacterium
glutamicum
Several Corynebacterium and Brevibacterium species contain endogenous
plasmids (as e.g., pHM 1519 or pBL 1) which replicate autonomously (for review
see, e.g.,
Martin, J.F. et al. (1987) Biotechnology, 5:137-146). Shuttle vectors for
Escherichia coli
atid Corynebacterium glutamicum can be readily constructed by using standard
vectors for
E. coli (Sambrook, J. et al. (1989), "Molecular Cloning: A Laboratory Manual",
Cold
Spring Harbor Laboratory Press or Ausubel, F.M. et al. (1994) "Current
Protocols in
Molecular Biology", John Wiley & Sons) to which a origin or replication for
and a
suitable marker from Corynebacterium glutamicum is added. Such origins of
replication
are preferably taken from endogenous plasmids isolated from Corynebacterium
and
Br-evibacterium species. Of particular use as transformation markers for these
species are
genes for kanamycin resistance (such as those derived from the Tn5 or Tn903
transposons) or chloramphenicol (Winnacker, E.L. (1987) "From Genes to Clones -
Introduction to Gene Technology, VCH, Weinheim). There are numerous examples
in the
literature of the construction of a wide variety of shuttle vectors which
replicate in both E.
coll and C. glulamicum, and which can be used for several purposes, including
gene over-
expression (for reference, see e.g., Yoshihama, M. et al. (1985) J. Bacteriol.
162:591-597,
Martin J.F. et al. (1987) Biotechnology, 5:137-146 and Eikmanns, B.J. et al.
(1991) Gene,
102:93-98).
Using standard methods, it is possible to. clone a gene of interest into one
of the
shu{tle vectors described above and to introduce such a hybrid vectors into
strains of
Corynebacterium glutamicum. Transformation of C. glutamicum can be achieved by
protoplast transfonmation (Kastsumata, R. et al. (1984) J. Bacteriol. 1 59306-
3 1 1),
electroporation (Liebi, E. et al. (1989) FEMS Microbiol. Letters, 53:399-303)
and in cases
where special vectors are used, also by conjugation (as described e.g. in
Schdfer, A et al.
I I i I N 114
CA 02584021 2007-04-18
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(1990) J. Bacteriol. 172:1663-1666). It is also possible to transfer the
shuttle vectors for
C. glutamicum to E. coli by preparing plasmid DNA from C. glutamicum (using
standard
methods well-known in the art) and transforming it into E. coli. This
transformation step
can be performed using standard methods, but it is advantageous to use an Mcr-
deficient
E. coli strain, such as NM522 (Gough & Murray (1983) J. Mol. Biol. 166:1-19).
Genes may be overexpressed in C. glutamfcum strains using plasmids which
comprise pCGI (U.S. Patent No. 4,617,267) or fragments thereof, and optionally
the
gene for kanamycin resistance from TN903 (Grindley, N.D. and Joyce, C.M.
(1980)
Proc. Natl. Acad. Sci. USA 77(12): 7176-7180). In addition, genes may be
overexpressed in C. glutamicum strains using plasmid pSL 109 (Lee, H.-S. and
A. J.
Sinskey (1994) J. Microbiol. Biotechnol. 4: 256-263).
Aside from the use of replicative plasmids, gene overexpression can also be
achieved by integration into the genome. Genomic integration in C. glutamicum
or other
Corynebacterium or Brevibacterium species may be accomplished by well-known
methods, such as homologous recombination with genomic region(s), restriction
endonuclease mediated integration (REMI) (see, e.g., DE Patent 19823834), or
through
the use of transposons. It is also possible to modulate the activity of a gene
of interest by
modifying the regulatory regions (e.g., a promoter, a repressor, and/or an
enhancer) by
sequence modification, insertion, or deletion using site-directed methods
(such as
homologous recombination) or methods based on random events (such as
transposon
mutagenesis or REMI). Nucleic acid sequences which function as transcriptional
terminators may also be inserted 3' to the coding region of one or more genes
of the
invention; such terminators are well-known in the art and are described, for
example, in
Winnacker, E.L. (1987) From Genes to Clones - Introduction to Gene Technology.
VCH:
Weinheim.
Example 6: Assessment of the Expression of the Mutant Protein
Observations of the activity of a mutated protein in a transformed host cell
rely on
the fact that the mutant protein is expressed in a similar fashion and in a
similar quantity
to that of the wild-type protein. A useful method to ascertain the level of
transcription of
the mutant gene (an indicator of the amount of mRNA available for translation
to the gene
product) is to perform a Northern blot (for reference see, for example,
Ausubel et al.
i.
I If~N.
CA 02584021 2007-04-18
-122-
(1988) Current Protocols in Molecular Biology, Wiley: New York), in which a
primer
designed to bind to the gene of interest is labeled with a detectable tag
(usually radioactive
or chemiluminescent), such that when the total RNA of a culture of the
organism is
extracted, run on gel, transferred to a stable matrix and incubated with this
probe, the
binding and quantity of binding of the probe indicates the presence and also
the quantity
of mRNA for this gene. This information is evidence of the degree of
transcription of the
mutant gene. Total cellular RNA can be prepared from
Corynebacterium'glutamicum by
several methods, all well-known in the art, such as that described in Bormann,
E.R. et al.
(1992) Mol. Microbiol. 6: 317-326.
To assess the presence or relative quantity of protein translated from this
mRNA,
standard techniques, such as a Western blot, may be employed (see, for
example, Ausubel
et al. (1988) Current Protocols in Molecular Biology, Wiley: New York). In
this process,
total cellular proteins are extracted, separated by gel electrophoresis,
transferred to a
matrix such as nitrocellulose, and incubated with a probe, such as an
antibody, which
specifically binds to the desired protein. This probe is generally tagged with
a
chemiluminescent or colorimetric label which may be readily detected. The
presence and
quantity of label observed indicates the presence and quantity of the desired
mutant
protein present in the cell.
Example 7: Growth of Genetically Modified Corynebacterium glutamicum - Media
and Culture Conditions
Genetically modified Corynebacteria are cultured in synthetic or natural
growth
media. A number of different growth media for Corynebacteria are both well-
known and
readily available (Lieb et al. (1989) Appl. Microbiol. Biotechnol., 32:205-
210; von der
Osten et al. (1998) Biotechnology Letters, 11:11-16; Patent DE 4,120,867;
Liebl (1992)
"The Genus Corynebacterium, in: The Procaryotes, Volume II, Balows, A. et al.,
eds.
Springer-Verlag). These media consist of one or more carbon sources, nitrogen
sources,
inorganic salts, vitamins and trace elements. Preferred carbon sources are
sugars, such as
mono-, di-, or polysaccharides. For example, glucose, fructose, mannose,
galactose,
ribose, sorbose, ribulose, lactose, maltose, sucrose, raffinose, starch or
cellulose serve as
very good carbon sources. It is also possible to supply sugar to the media via
complex
compounds such as molasses or other by-products from sugar refinement. It can
also be
I I ... 1 Y 1111
CA 02584021 2007-04-18
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advantageous to supply mixtures of different carbon sources. Other possible
carbon
sources are alcohols and organic acids, such as methanol, ethanol, acetic acid
or lactic
acid. Nitrogen sources are usually organic or inorganic nitrogen compounds, or
materials
which contain these compounds. Exemplary nitrogen sources include ammonia gas
or
ammonia salts, such as NH.CI or (NH.)2SO4, NH.OH, nitrates, urea, amino acids
or
complex nitrogen sources like corn steep liquor, soy bean flour, soy bean
protein, yeast
extract, meat extract and others.
Inorganic salt compounds which may be included in the media include the
chloride-, phosphorous- or sulfate- salts of calcium, magnesium, sodium,
cobalt,
molybdenum, potassium, manganese, zinc, copper and iron. Chelating compounds
can be
added to the medium to keep the metal ions in solution. Particularly useful
chelating
compounds include dihydroxyphenols, like catechol or protocatechuate, or
organic acids,
such as citric acid. It is typical for the media to also contain other growth
factors, such as
vitamins or growth promoters, examples of which include biotin, riboflavin,
thiamin, folic
acid, nicotinic acid, pantothenate and pyridoxin. Growth factors and salts
frequently
originate from complex media components such as yeast extract, molasses, corn
steep
liquor and others. The exact composition of the media compounds depends
strongly on
the immediate experiment and is individually decided for each specific case.
Information
about media optimization is available in the textbook "Applied Microbiol.
Physiology, A
Practical Approach (eds. P.M. Rhodes, P.F. Stanbury, IRL Press (1997) pp. 53-
73, ISBN 0
19 963577 3). It is also possible to select growth media from commercial
suppliers, like
standard 1(Merck) or BHI (grain heart infusion, DIFCO) or others.
All medium components are sterilized, either by heat (20 minutes at 1.5 bar
and
121 C) or by sterile filtration. The components can either be sterilized
together or, if
necessary, separately. All media components can be present at the beginning of
growth,
or they can optionally be added continuously or batchwise.
Culture conditions are defined separately for each experiment. The temperature
should be in a range between 15 C and 45'C. The temperature can be kept
constant or can
be altered during the experiment. The pH of the medium should be in the range
of 5 to
8.5, preferably around 7.0, and can be maintained by the addition of buffers
to the media.
An exemplary buffer for this purpose is a potassium phosphate buffer.
Synthetic buffers
such as MOPS, HEPES, ACES and others can alternatively or simultaneously be
used. It
i
I N II
CA 02584021 2007-04-18
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is also possible to maintain a constant culture pH through the addition of
NaOH or
NH,OH during growth. If complex medium components such as yeast extract are
utilized,
the necessity for additional buffers may be reduced, due to the fact that many
complex
compounds have high buffer capacities. If a fermentor is utilized for
culturing the micro-
organisms, the pH can also be controlled using gaseous ammonia.
The incubation time is usually in a range from several hours to several days.
This
time is selected in order to permit the maximal amount of product to
accumulate in the
broth. The disclosed growth experiments can be carried out in a variety of
vessels, such as
microtiter plates, glass tubes, glass flasks or glass or metal fermentors of
different sizes.
For screening a large number of clones, the microorganisms should be cultured
in
microtiter plates, glass tubes or shake flasks, either with or without
baffles. Preferably
100 ml shake flasks are used, filled with 10% (by volume) of the required
growth
medium. The flasks should be shaken on a rotary shaker (amplitude 25 mm) using
a
speed-range of 100 - 300 rpm. Evaporation losses can be diminished by the
maintenance
of a humid atmosphere; alternatively, a mathematical correction for
evaporation losses
should be performed.
If genetically modified clones are tested, an unmodified control clone or a
control
clone containing the basic plasmid without any insert should also be tested.
The medium
is inoculated to an OD6oo of 0.5 - 1.5 using cells grown on agar plates, such
as CM plates
(10 g/1 glucose, 2,5 g/1 NaCI, 2 g/1 urea, 10 g/1 polypeptone, 5 g/l yeast
extract, 5 g/1 meat
extract, 22 g/1 NaCI, 2 g/1 urea, 10 g/I polypeptone, 5 g/I yeast extract, 5
g/1 meat extract,
22 g/l agar, pH 6.8 with 2M NaOH) that had been incubated at 30 C. Inoculation
of the
media is accomplished by either introduction of a saline suspension of C.
glutamicum cells
from CM plates or addition of a liquid preculture of this bacterium.
Example 8 - In vitro Analysis of the Function of Mutant Proteins
The determination of activities and kinetic parameters of enzymes is well
established in the art. Experiments to determine the activity of any given
altered
enzyme must be tailored to the specific activity of the wild-type enzyme,
which is well
within the ability of one of ordinary skill in the art. Overviews about
enzymes in
general, as well as specific details concerning structure, kinetics,
principles, methods,
applications and examples for the determination of many enzyme activities may
be
CA 02584021 2007-04-18
-125-
found, for example, in the following references: Dixon, M., and Webb, E.C.,
(1979)
Enzymes. Longmans: London; Fersht, (1985) Enzyme Structure and Mechanism.
Freeman: New York; Walsh, (1979) Enzymatic Reaction Mechanisms. Freeman: San
Francisco; Price, N.C., Stevens, L. (1982) Fundamentals of Enzymology. Oxford
Univ.
:5 Press: Oxford; Boyer, P.D., ed. (1983) The Enzymes, 3d ed. Academic Press:
New
York; Bisswanger, H., (1994) Enzymkinetik, 2"d ed. VCH: Weinheim (ISBN
3527300325); Bergmeyer, I-i.U., Bergmeyer, J., Gra13l, M., eds. (1983-1986)
Methods of
Enzymatic Analysis, 3'd ed., vol. I-XII, Verlag Chemie: Weinheim; and
Ullmann's
Encyclopedia of Industrial Chemistry (1987) vol. A9, "Enzymes". VCH: Weinheim,
p.
352-363.
The activity of proteins which bind to DNA can be measured by severai well-
established methods, such as DNA band-shift assays (also called gel
retardation assays).
The effect of such proteins on the expression of other molecules can be
measured using
reporter gene assays (such as that described in Kolmar, H. et al. (1995) EMBO
J. 14:
3895-3904 and references cited therein). Reporter gene test systems are well
known and
established for applications in both pro- and eukaryotic cells, using enzymes
such as
beta-galactosidase, green fluorescent protein, and several others.
The determination of activity of membrane-transport proteins can be perfon-ned
according to techniques such as those described in Gennis, R.B. (1989) "Pores,
Channels and Transporters", in Biomembranes, Molecular Structure and Function,
Springer: Heidelberg, p. 85-137; 199-234; and 270-322.
Example 9: Analysis of Impact of Mutant Protein on the Production of the
Desired
Product
The effect of the genetic modification in C. glutamicum on production of a
desired compound (such as an amino acid) can be assessed by growing the
modified
microorganism under suitable conditions (such as those described above) and
analyzing
the medium and/or the cellular component for increased production of the
desired
product (i.e., an amino acid). Such analysis techniques are well known to one
of
ordinary skill in the art, and include spectroscopy, thin layer
chromatography, staining
methods of various kinds, enzymatic and microbiological methods, and
analytical
chromatography such as high performance liquid chromatography (see, for
example,
N 14
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Ullman, Encyclopedia of Industrial Chemistry, vol. A2, p. 89-90 and p. 443-
613, VCH:
Weinheim (1985); Fallon, A. et al., (1987) "Applications of HPLC in
Biochemistry" in:
Laboratory Techniques in Biochemistry and Molecular Biology, vol. 17; Rehm et
al.
(1993) Biotechnology, vol. 3, Chapter III: "Product recovery and
purification", page
469-714, VCH: Weinheim; Belter, P.A. et al. (1988) Bioseparations: downstream
processing for biotechnology, John Wiley and Sons; Kennedy, J.F. and Cabral,
J.M.S.
(1992) Recovery processes for biological materials, John Wiley and Sons;
Shaeiwitz,
J.A. and Henry, J.D. (1988) Biochemical separations, in: Ulmann's Encyclopedia
of
Industrial Chemistry, vol. B3, Chapter 11, page 1-27, VCH: Weinheim; and
Dechow,
F.J. (1989) Separation and purification techniques in biotechnology, Noyes
Publications.) =
In addition to the measurement of the final product of fermentation, it
is.also
possible to analyze other components of the metabolic pathways utilized for
the
production of the desired compound, such as intermediates and side-products,
to
determine the overall efficiency of production of the compound. Analysis
methods
include measurements of nutrient levels in the medium (e.g., sugars,
hydrocarbons,
nitrogen sources, phosphate, and other ions), measurements of biomass
composition and
growth, analysis of the production of common metabolites of biosynthetic
pathways, and
measurement of gasses produced during fermentation. Standard methods for these
measurements are outlined in Applied Microbial Physiology, A Practical
Approach,
P.M. Rhodes and P.F. Stanbury, eds., IRL Press, p. 103-129; 131-163; and 165-
192
(ISBN: 0199635773) and references cited therein.
Example 10: Purification of the Desired Product from C. glutamicum Culture
Recovery of the desired product from the C. glutamicum cells or supematant of
the above-described culture can be performed by various methods well known in
the art.
If the desired product is not secreted from the cells, the cells can be
harvested from the
culture by low-speed centrifugation, the cells can be lysed by standard
techniques, such
as mechanical force or sonication. The cellular debris is removed by
centrifugation, and
the supematant fraction containing the soluble proteins is retained for
further
purification of the desired compound. If the product is secreted from the C.
glutamicum
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cells, then the cells are removed from the culture by low-speed
centrifugation, and the
supernate fraction is retained for further purification.
The supematant fraction from either purification method is subjected to
chromatography with a suitable resin, in which the desired molecule is either
retained on
a chromatography resin while many of the impurities in the sample are not, or
where the
impurities are retained by the resin while the sample is not. Such
chromatography steps
may be repeated as necessary, using the same or different chromatography
resins. One
of ordinary skill in the art would be well-versed in the selection of
appropriate
chromatography resins and in their most efficacious application for a
particular molecule
to be purified. The purified product may be concentrated by filtration or
ultrafiltration,
and stored at a temperature at which the stability of the product is
maximized.
There are a wide array of purification methods known to the art and the
preceding method of purification is not meant to be limiting. Such
purification
techniques are described, for example, in Bailey, J.E. & Ollis, D.F.
Biochemical
Engineering Fundamentals, McGraw-Hill: New York (1986).
The identity and purity of the isolated compounds may be assessed by
techniques
standard in the art. These include high-performance liquid chromatography
(HPLC),
spectroscopic methods, staining methods, thin layer chromatography, NIRS,
enzymatic
assay, or microbiologically. Such analysis methods are reviewed in: Patek et
al. (1994)
Appl. Environ. Microbiol. 60: 133-140; Malakhova el al. (1996) Biotekhnologiya
11: 27-
32; and Schmidt et al. (1998) Bioprocess Engineer. 19: 67-70. Ulmann's
Encyclopedia
of Industrial Chemistry, (1996) vol. A27, VCH: Weinheim, p. 89-90, p. 521-540,
p. 540-
547, p. 559-566, 575-581 and p. 581-587; Michal, G. (1999) Biochemical
Pathways: An
Atlas of Biochemistry and Molecular Biology, John Wiley and Sons; Fallon, A.
et al.
(1987) Applications of HPLC in Biochemistry in: Laboratory Techniques in
Biochemistry and Molecular Biology, vol. 17.
Example 11: Analysis of the Gene Sequences of the Invention
The comparison of sequences and determination of percent homology between
two sequences are art-known techniques, and can be accomplished using a
mathematical
algorithm, such as the algorithm of Karlin and Altschul (1990) Proc. Natl.
Acad Sci.
USA 87:2264-68, modified as in Karlin and Altschul (1993) Proc. Natl. Acad.
Sci. USA
I',
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90:5873-77. Such an algorithm is incorporated into the NBLAST and XBLAST
programs (version 2.0) of Altschul, et al. (1990) J. Mol. Biol. 215:403-10.
BLAST
nucleotide searches can be performed with the NBLAST program, score = 100,
wordlength = 12 to obtain nucleotide sequences homologous to SMP nucleic acid
molecules of the invention. BLAST protein searches can be performed with the
XBLAST program, score = 50, wordlength = 3 to obtain amino acid sequences
homologous to SMP protein molecules of the invention. To obtain gapped
alignments
for comparison purposes, Gapped BLAST can be utilized as described in Altschul
et al.,
(1997) Nucleic Acids Res. 25(17):3389-3402. When utilizing BLAST and Gapped
BLAST programs, one of ordinary skill in the art will know how to optimize the
parameters of the program (e.g., XBLAST and NBLAST) for the specific sequence
being analyzed.
Another example of a mathematical algorithm utilized for the comparison of
sequences is the algorithm of Meyers and Miller ((1988) Comput. Appl. Biosci,
4: 11-
17). Such an algorithm is incorporated into the ALIGN program (version 2.0)
which is
part of the GCG sequence alignment software package. When utilizing the ALIGN
program for comparing amino acid sequences, a PAM 120 weight residue table, a
gap
length penalty of 12, and a gap penalty of 4 can be used. Additional
algorithms for
sequence analysis are known in the art, and include ADVANCE and ADAM.
described
in Torelli and Robotti (1994) Comput. Appl. Biosci. 10:3-5; and FASTA,
described in
Pearson and Lipman (1988) P.N.A.S. 85:2444-8.
The percent homology between two amino acid sequences can also be
accomplished using the GAP program in the GCG software package (available at
http://www.gcg.com), using either a Blosum 62 matrix or a PAM250 matrix, and a
gap
weight of 12, 10, 8, 6, or 4 and a length weight of 2; 3, or 4. The percent
homology
between two nucleic acid sequences can be accomplished using the GAP program
in the
GCG software package, using standard parameters, such as a gap weight of 50
and a
length weight of 3.
A comparative analysis of the gene sequences of the invention with those
present
in Genbank has been performed using techniques known in the art (see, e.g.,
Bexevanis
and Ouellette, eds. (1998) Bioinformatics: A Practical Guide to the Analysis
of Genes
and Proteins. John Wiley and Sons: New York). The gene sequences of the
invention
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were compared to genes present in Genbank in a three-step process. In a first
step, a
BLASTN analysis (e.g., a local alignment analysis) was performed for each of
the
sequences of the invention against the nucleotide sequences present in
Genbank, and the
top 500 hits were retained for further analysis. A subsequent FASTA search
(e.g., a
combined local and global alignment analysis, in which limited regions of the
sequences
are aligned) was performed on these 500 hits. Each gene sequence of the
invention was
subsequently globally aligned to each of the top three FASTA hits, using the
GAP
program in the GCG software package (using standard parameters). In order to
obtain
correct results, the length of the sequences extracted from Genbank were
adjusted to the
length of the query sequences by methods well-known in the art. The results of
this
analysis are set forth in Table 4. The resulting data is identical to that
which would have
been obtained had a GAP (global) analysis alone been performed on each of the
genes of
the invention in comparison with each of the references in Genbank, but
required
significantly reduced computational time as compared to such a database-wide
GAP
(global) analysis. Sequences of the invention for which no alignments above
the cutoff
values were obtained are indicated on Table 4 by the absence of alignment
information.
It will further be understood by one of ordinary skill in the art that the GAP
alignment
homology percentages set forth in Table 4 under the heading "% homology (GAP)"
are
listed in the European numerical format, wherein a',' represents a decimal
point. For
example, a value of "40,345" in this column represents "40.345%".
Example 12: Construction and Operation of DNA Microarrays
The sequences of the invention may additionally be used in the construction
and
application of DNA microarrays (the design, methodology, and uses of DNA
arrays are
well known in the art, and are described, for example, in Schena, M. el al.
(1995)
Science 270: 467-470; Wodicka, L. et al. (1997) Nature Biotechnology 15: 1359-
1367;
DeSaizieu, A. et al. (1998) Nature Biotechnology 16: 45-48; and DeRisi, J.L.
et al.
(1997) Science 278: 680-686).
DNA microarrays are solid or flexible supports consisting of nitrocellulose,
nylon, glass, silicone, or other materials. Nucleic acid molecules may be
attached to the
surface in an ordered manner. After appropriate labeling, other nucleic acids
or nucleic
acid mixtures can be hybridized to the immobilized nucleic acid molecules, and
the label
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may be used to monitor and measure the individual signal intensities of the
hybridized
molecules at defined regions. This methodology allows the simultaneous
quantification
of the relative or absolute amount of all or selected nucleic acids in the
applied nucleic
acid sample or mixture. DNA microarrays, therefore, permit an analysis of the
:i expression of multiple (as many as 6800 or more) nucleic acids in parallel
(see, e.g.,
Schena, M. (1996) BioEssays 18(5): 427-431).
The sequences of the invention may be used to design oligonucleotide primers
which are able to amplify defined regions of one or more C. glutamicum genes
by a
nucleic acid amplification reaction such as the polymerase chain reaction. The
choice
and design of the 5' or 3' oligonucleotide primers or of appropriate linkers
allows the
covalent attachment of the resulting PCR products to the surface of a support
medium
described above (and also described, for example, Schena, M. el at. (1995)
Science 270:
467-470).
Nucleic acid microarrays may also be constructed by in situ oligonucleotide
synthesis as described by Wodicka, L. et al. (1997) Nature Biotechnology 15:
1359-
1367. By photolithographic methods, precisely defined regions of the matrix
are
exposed to light. Protective groups which are photolabile are thereby
activated and
undergo nucleotide addition, whereas regions that are masked from light do not
undergo
any modification. Subsequent cycles of protection and light activation permit
the
synthesis of different oligonucleotides at defined positions. Small, defined
regions of
the genes of the invention may be synthesized on microarrays by solid phase
oligonucleotide synthesis.
The nucleic acid molecules of the invention present in a sample or mixture of
nucleotides may be hybridized to the microarrays. These nucleic acid molecules
can be
labeled according to standard methods. In brief, nucleic acid molecules (e.g.,
mRNA
molecules or DNA molecules) are labeled by the incorporation of isotopically
or
fluorescently labeled nucleotides, e.g., during reverse transcription or DNA
synthesis.
Hybridization of labeled nucleic acids to microarrays is described (e.g., in
Schena, M. et
al. (1995) supra; Wodicka, L. et al. (1997), supra; and DeSaizieu A. et al.
(1998),
supra). The detection and quantification of the hybridized molecule are
tailored to the
specific incorporated label. Radioactive labels can be detected, for example,
as
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described in Schena, M. et al. (1995) supra) and fluorescent labels may be
detected, for
example, by the method of Shalon et al. (1996) Genome Research 6: 639-645).
The application of the sequences of the invention to DNA microarray
technology, as described above, permits comparative analyses of different
strains of C.
glutamicum or other Corynebacteria. For example, studies of inter-strain
variations
based on individual transcript profiles and the identification of genes that
are important
for specific and/or desired strain properties such as pathogenicity,
productivity and
stress tolerance are facilitated by nucleic acid array methodologies. Also,
comparisons
of the profile of expression of genes of the invention during the course of a
fermentation
reaction are possible using nucleic acid array technology.
Example 13: Analysis of the Dynamics of Cellular Protein Populations
(Proteomics)
The genes, compositions, and methods of the invention may be applied to study
the interactions and dynamics of populations of proteins, termed 'proteomics'.
Protein
populations of interest include, but are not limited to, the total protein
population of C.
glutamicum (e.g., in comparison with the protein populations of other
organisms), those
proteins which are active under specific environmental or metabolic conditions
(e.g.,
during fermentation, at high or low temperature, or at high or low pH), or
those proteins
which are active during specific phases of growth and development.
Protein populations can be analyzed by various well-known techniques, such as
gel electrophoresis. Cellular proteins may be obtained, for example, by lysis
or
extraction, and may be separated from one another using a variety of
electrophoretic
techniques. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-
PAGE)
separates proteins largely on the basis of their molecular weight. Isoelectric
focusing
polyacrylamide gel electrophoresis (IEF-PAGE) separates proteins by their
isoelectric
point (which reflects not only the amino acid sequence but also
posttranslational
modifications of the protein). Another, more preferred method of protein
analysis is the
consecutive combination of both IEF-PAGE and SDS-PAGE, known as 2-D-gel
electrophoresis (described, for example, in Hermann et al. (1998)
Electrophoresis 19:
3217-3221; Fountoulakis el al. (1998) Electrophoresis 19: 1193-1202; Langen et
al.
(1997) Electrophoresis 18: 1184-1192; Antelmann et al. (1997) Electrophoresis
18:
li I+IIN+
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1451-1463). Other separation techniques may also be utilized for protein
separation,
such as capillary gel electrophoresis; such techniques are well known in the
art.
Proteins separated by these methodologies can be visualized by standard
techniques, such as by staining or labeling. Suitable stains are known in the
art, and
include Coomassie Brilliant Blue, silver stain, or fluorescent dyes such as
Sypro Ruby
(Molecular Probes). The inclusion of radioactively labeled amino acids or
other protein
precursors (e.g., 35S-methionine, 35S-cysteine, "C-labelled amino acids,'SN-
amino
acids,15N03 ort5NH4+ or 13C-labelled amino acids) in the medium of C.
glutamicum
permits the labeling of proteins from these cells prior to their separation.
Similarly,
fluorescent labels may be employed. These labeled proteins can be extracted,
isolated
and separated according to the previously described techniques.
Proteins visualized by these techniques can be further analyzed by measuring
the
amount of dye or label used. The amount of a given protein can be determined
quantitatively using, for example, optical methods and can be compared to the
amount
of other proteins in the same gel or in other gels. Comparisons of proteins on
gels can
be made, for example, by optical comparison, by spectroscopy, by image
scanning and
analysis of gels, or through the use of photographic films and screens. Such
techniques
are well-known in the art.
To determine the identity of any given protein, direct sequencing or other
standard techniques may be employed. For example, N- and/or C-terminal amino
acid
sequencing (such as Edman degradation) may be used, as may mass spectrometry
(in
particular MALDI or ESI techniques (see, e.g., Langen et al. (1997)
Electrophoresis 18:
1184-1192)). The protein sequences provided herein can be used for the
identification
of C. glutarnicum proteins by these techniques.
The information obtained by these methods can be used to compare pattems of
protein presence, activity, or modification between different samples from
various
biological conditions (e.g., different organisms, time points of fermentation,
media
conditions, or different biotopes, among others). Data obtained from such
experiments
alone, or in combination with other techniques, can be used for various
applications,
such as to compare the behavior of various organisms in a given (e.g.,
metabolic)
situation, to increase the productivity of strains which produce fine
chemicals or to
increase the efficiency of the production of fine chemicals.
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Equivalents
Those of ordinary skill in the art will recognize, or will be able to
ascertain using
no more than routine experimentation, many equivalents to the specific
embodiments of
the invention described herein. Such equivalents are intended to be
encompassed by the
following claims.
, .. I ,
