Note: Descriptions are shown in the official language in which they were submitted.
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Novel Compounds
FIELD OF THE INVENTION
This invention relates to polynucleotides, (herein referred to as "BASB009
polynucleotide(s)"), polypeptides encoded by them (referred to herein as
"BASB009" or
"BASB009 polypeptide(s)"), recombinant materials and methods for their
production. In
another aspect, the invention relates to methods for using such polypeptides
and
polynucleotides, including vaccines against bacterial infections. In a further
aspect, the
invention relates to diagnostic assays for detecting infection of certain
pathogens.
BACKGROUND OF THE I1WENTION
Moraxella catarrhalis (also named Branhamella catarrhalis) is a Gram negative
bacteria
frequently isolated from the human upper respiratory tract. It is responsible
for several
pathologies the main ones being otitis media in infants and children, and
pneumonia in
elderlies. It is also responsible of sinusitis, nosocomial infections and less
frequently of
invasive diseases.
Otitis media is an important childhood disease both by the number of cases and
its potential
sequelae. More than 3.5 millions cases are recorded every year in the United
States, and it is
estimated that 80 % of the children have experienced at least one episode of
otitis before
reaching the age of 3 (Klein, JO ( 1994) Clin.Inf:Dis 19:823). Left untreated,
or becoming
chronic, this disease may lead to hearing losses that could be temporary (in
the case of fluid
accumulation in the middle ear) or permanent (if the auditive nerve is
damaged). In infants,
such hearing losses may be responsible for a delayed speech learning.
Three bacterial species are primarily isolated from the middle ear of children
with otitis
media: Streptococcus pneumoniae, non typeable Haemophilus influenzae (NTIii)
and M.
catarrhalis. They are present in 60 to 90 % of the cases. A review of recent
studies shows
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that S. pneumoniae and NTHi represent both about 30 %, and M. catarrhalis
about 15 % of
the otitis media cases (Murphy, TF (1996) Microbiol.Rev. 60:267). Other
bacteria could be
isolated from the middle ear (H, in~luenzae type B, S. pyogenes etc) but at a
much lower
frequency (2 % of the cases or less).
Epidemiological data indicate that, for the pathogens found in the middle ear,
the
colonization of the upper respiratory tract is an absolute prerequisite for
the development of
an otitis; other are however also required to Iead to the disease (Dickinson,
DP et al. (1988)
J. Infect.Dis. 158:205, Faden, HL et al. (1991) Ann.Otorhinol.Laryngol.
100:612). These are
important to trigger the migration of the bacteria into the middle ear via the
Eustachian
tubes, followed by the initiation of an inflammatory process. These factors
are unknown
todate. It has been postulated that a transient anomaly of the immune system
following a
viral infection, for example, could cause an inability to control the
colonization of the
respiratory tract (Faden, HL et al (1994) J. Infect.Dis. 169:1312). An
alternative explanation
is that the exposure to environmental factors allow a more important
colonization of some
children, who subsequently become susceptible to the development of otitis
media because
of the sustained presence of middle ear pathogens (Murphy, TF (1996)
Microbiol.Rev.
60:267).
The immune response to M. catarrhalis is poorly characterized. The analysis of
strains
isolated sequentially from the nasopharynx of babies followed from 0 to 2
years of age,
indicates that they get and eliminate frequently new strains. This indicates
that an
efficacious immune response against this bacteria is mounted by the colonized
children
(Faden, HL et al ( 1994) J. Infect.Dis. 169:1312).
In most adults tested, bactericidal antibodies have been identified (Chapman,
AJ et al.
(1985) J. Infect.Dis. 15I :878). Strains of M. catarrhalis present variations
in their capacity
to resist serum bactericidal activity: in general, isolates from diseased
individuals are more
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resistant than those who are simply colonized (Hol, C et al. {1993) Lancet
341:1281, 3ordan,
KI. et al. (1990) Am.J.Med. 88 (suppl. SA):28S). Serum resistance could
therfore be
considered as a virulence factor of the bacteria. An opsonizing activity has
been observed in
the sera of children recovering from otitis media.
The antigens targetted by these different immune responses in humans have not
been
identified, with the exception of OMP B 1, a 84 kDa protein which expression
is regulated
by iron, and that is recognized by the sera of patients with pneumonia (Sethi,
S, et al. (1995)
Infect.Imrnun. 63:1516), and of UspAl and UspA2 (Chen D. et al.(1999),
Infect.Immun.
67:1310).
A few other membrane proteins present on the surface of M. catarrhalis have
been
characterized using biochemical method, or for their potential implication in
the induction of
a protective immunity (for review, see Murphy, fF (1996) Microbiol.Rev.
60:267). In a
1 S mouse pneumonia model, the presence of antibodies raised against some of
them (UspA,
CopB) favors a faster clearance of the pulmonary infection. Another
polypeptide (OMP CD)
is highly conserved among M. catarrhalis strains, and presents homologies with
a porin of
Pseudomonas aeruginosa, which has been demonstrated efficacious against this
bacterium
in animal models.
The frequency of Moraxella catarrhalis infections has risen dramatically in
the past few
decades. This has been attributed to the emergence of multiply antibiotic
resistant strains
and an increasing population of people with weakened immune systems. It is no
longer
uncommon to isolate Moraxella catarrhalis strains that are resistant to some
or all of the
standard antibiotics. This phenomenon has created an unmet medical need and
demand for
new anti-microbial agents, vaccines, drug screening methods, and diagnostic
tests for this
organism.
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SUMMARY OF THE INVENTION
The present invention relates to BASB009, in particular BASB009 polypeptides
and
BASB009 polynucleotides, recombinant materials and methods for their
production. In
another aspect, the invention relates to methods for using such polypeptides
and
polynucleotides, including prevention and treatment of microbial diseases,
amongst others.
In a further aspect, the invention relates to diagnostic assays for detecting
diseases
associated with microbial infections and conditions associated with such
infections, such
as assays for detecting expression or activity of BASB009 polynucleotides or
polypeptides.
Various changes and modifications within the spirit and scope of the disclosed
invention
will become readily apparent to those skilled in the art from reading the
following
descriptions and from reading the other parts of the present disclosure.
DESCRIPTION OF THE INVENTION
The invention relates to BASB009 polypeptides and polynucleotides as described
in greater
detail below. In particular, the invention relates to polypeptides and
polynucleotides of
BASB009 of Moraxella catarrhalis, which is related by amino acid sequence
homology to
TIyC hemolysin protein of Serpulina hyodysenteriae. The invention relates
especially to
BASB009 having the nucleotide and amino acid sequences set out in SEQ ID
N0:1,3,5 or 7
and SEQ ID N0:2,4,6 or 8 respectively. It is understood that sequences recited
in the
Sequence Listing below as "DNA" represent an exemplification of one embodiment
of the
invention, since those of ordinary skill will recognize that such sequences
can be usefully
employed in polynucleotides in general, including ribopolynucieotides.
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Polypeptides
In one aspect of the invention there are provided polypeptides of Moraxella
catarrhalis
referred to herein as "BASB009" and "BASB009 polypeptides" as well as
biologically,
diagnostically, prophylactically, clinically or therapeutically useful
variants thereof, and
compositions comprising the same.
The present invention further provides for:
(a) an isolated polypeptide which comprises an amino acid sequence which has
at least
85% identity, preferably at least 90% identity, more preferably at least 95%
identity, most
preferably at least 97-99% or exact identity, to that of SEQ ID N0:2, 4, 6 or
8;
(b) a polypeptide encoded by an isolated polynucleotide comprising a
polynucleotide
sequence which has at least 85% identity, preferably at least 90% identity,
more
preferably at least 95% identity, even more preferably at least 97-99% or
exact identity to
1 S SEQ ID NO:1, 3, S or 7 over the entire length of SEQ ID NO:1, 3, S or 7
respectively; or
(c) a polypeptide encoded by an isolated polynucleotide comprising a
polynucleotide
sequence encoding a polypeptide which has at least 85% identity, preferably at
least 90%
identity, more preferably at least 95% identity, even more preferably at least
97-99% or
exact identity, to the amino acid sequence of SEQ ID N0:2, 4, 6 or 8.
The BASB009 polypeptides provided in SEQ ID N0:2,4,6 or 8 are the BASB009
polypeptides from Moraxella catarrhalis strains MC2931 (ATCC 43617), MC2912,
MC2913 and MC2969,.
?5 The invention also provides an immunogenic fragment of a BASB009
polypeptide, that
is, a contiguous portion of the BASB009 polypeptide which has the same or
substantially
the same immunogenic activity as the polypeptide comprising the amino acid
sequence of
SEQ ID N0:2,4,6 or 8; That is to say, the fragment (if necessary when coupled
to a
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carrier) is capable of raising an immune response which recognises the BASB009
polypeptide. Such an immunogenic fragment may include, for example, the
BASB009
polypeptide lacking an N-terminal leader sequence, and/or a transmembrane
domain
and/or a C-terminal anchor domain. In a preferred aspect the immunogenic
fragment of
BASB009 according to the invention comprises substantially all of the
extracellular
domain of a polypeptide which has at least 85% identity, preferably at least
90% identity,
more preferably at least 95% identity, most preferably at least 97-99%
identity, to that
of SEQ ID N0:2,4,6 or 8 over the entire length of SEQ ID N0:2
A fragment is a polypeptide having an amino acid sequence that is entirely the
same as part
but not all of any amino acid sequence of any polypeptide of the invention. As
with
BASB009 polypeptides, fragments may be "free-standing," or comprised within a
larger
polypeptide of which they form a part or region, most preferably as a single
continuous
region in a single larger poiypeptide.
Preferred fragments include, for example, truncation polypeptides having a
portion of an
amino acid sequence of SEQ ID N0:2,4,6 or 8 or of variants thereof, such as a
continuous
series of residues that includes an amino- and/or carboxyl-terminal amino acid
sequence.
Degradation forms of the polypeptides of the invention produced by or in a
host cell, are
also preferred. Further prefen:ed are fragments characterized by structural or
functional
attributes such as fragments that comprise alpha-helix and alpha-helix forming
regions,
beta-sheet and beta-sheet-forming regions, turn and turn-forming regions, coil
and coil-
forming regions, hydrophilic regions, hydrophobic regions, alpha amphipathic
regions, beta
amphipathic regions, flexible regions, surface-forming regions, substrate
binding region, and
high antigenic index regions.
Further prefer:ed fragments include an isolated polypeptide comprising an
amino acid
sequence having at least 15, 20, 30, 40, 50 or 100 contiguous amino acids from
the
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amino acid sequence of SEQ ID N0:2, 4, 6 or 8, or an isolated polypeptide
comprising
an amino acid sequence having at least 15, 20, 30, 40, 50 or 100 contiguous
amino
acids truncated or deleted from the amino acid sequence of SEQ ID N0:2, 4, 6
or 8.
Fragments of the polypeptides of the invention may be employed for producing
the
corresponding full-length polypeptide by peptide synthesis; therefore, these
fragments
may be employed as intermediates for producing the full-length polypeptides of
the
invention.
Particularly preferred are variants in which several, S-10, 1-5, I-3, 1-2 or 1
amino acids
are substituted, deleted, or added in any combination.
The polypeptides, or immunogenic fragments, of the invention may be in the
form of
the "mature" protein or may be a part of a larger protein such as a precursor
or a fusion
1 S protein. It is often advantageous to include an additional amino acid
sequence which
contains secretory or leader sequences, pro-sequences, sequences which aid in
purification such as multiple histidine residues, or an additional sequence
for stability
during recombinant production. Furthermore, addition of exogenous polypeptide
or
lipid tail or polynucleotide sequences to increase the immunogenic potential
of the final
molecule is also considered.
In one aspect, the invention relates to genetically engineered soluble fusion
proteins
comprising a polypeptide of the present invention, or a fragment thereof, and
various
portions of the constant regions of heavy or light chains of immunoglobulins
of various
?5 subclasses (IgG, IgM, IgA, IgE). Preferred as an immunoglobulin is the
constant part of
the heavy chain of human IgG, particularly IgGI, where fusion takes place at
the hinge
region. In a particular embodiment, the Fc part can be removed simply by
incorporation
of a cleavage sequence which can be cleaved with blood clotting factor Xa.
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Furthermore, this invention relates to processes for the preparation of these
fusion
proteins by genetic engineering, and to the use thereof for drug screening,
diagnosis and
therapy. A further aspect of the invention also relates to polynucleotides
encoding such
fusion proteins. Examples of fusion protein technology can be found in
International
Patent Application Nos. W094/29458 and W094/22914.
The proteins may be chemically conjugated, or expressed as recombinant fusion
proteins allowing increased levels to be produced in an expression system as
compared
to non-fused protein. The fusion partner may assist in providing T helper
epitopes
(immunological fusion partner), preferably T helper epitopes recognised by
humans, or
assist in expressing the protein (expression enhancer) at higher yields than
the native
recombinant protein. Preferably the fusion partner will be both an
immunological
fusion partner and expression enhancing partner.
Fusion partners include protein D from Flaemophilus influenzae and the non-
structural
protein from influenza virus, NS 1 (hemagglutinin). Another fusion partner is
the
protein known as LytA. Preferably the C terminal portion of the molecule is
used. Lyta
is derived from Streptococcus pneumoniae which synthesize an N-acetyl-L-
alanine
amidase LytA, (coded by the lytA gene { Gene, 43 ( 1986) page 265-272 } ) an
autolysin
that specifically degrades certain bonds in the peptidoglycan backbone. The C-
terminal
domain of the LytA protein is responsible for the affinity to the choline or
to some
choline analogues such as DEAE. This property has been exploited for the
development
of E.coli C-LytA expressing plasmids useful for expression of fusion proteins.
Purification of hybrid proteins containing the C-LytA fragment at its amino
terminus
has been described {Biotechnology: 10, (1992) page 795-798}. It is possible to
use the
repeat portion of the LytA molecule found in the C tezminal end starting at
residue 178,
for example residues 188 - 305.
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The present invention also includes variants of the aforementioned
polypeptides, that is
polypeptides that vary from the referents by conservative amino acid
substitutions,
whereby a residue is substituted by another with like characteristics. Typical
such
substitutions are among Ala, Val, Leu and Ile; among Ser and Thr; among the
acidic
residues Asp and Glu; among Asn and Gln; and among the basic residues Lys and
Arg; or
aromatic residues Phe and Tyr.
Polypeptides of the present invention can be prepared in any suitable manner.
Such
polypeptides include isolated naturally occurring polypeptides, recombinantly
produced
polypeptides, synthetically produced polypeptides, or polypeptides produced by
a
combination of these methods. Means for preparing such polypeptides are well
understood in the art.
It is most preferred that a polypeptide of the invention is derived from
Moraxella
catarrhalis, however, it may preferably be obtained from other organisms of
the same
taxonomic genus. A polypeptide of the invention may also be obtained, for
example, from
organisms of the same taxonomic family or order.
Polvnucleotides
It is an object of the invention to provide polynucleotides that encode
BASB009
polypeptides, particularly polynucleotides that encode the polypeptide herein
designated
BASB009.
?5 In a particularly preferred embodiment of the invention the polynucleotide
comprises a
region encoding BASB009 polypeptides comprising a sequence set out in SEQ ID
N0:1,3,5
or 7 which includes a full length gene, or a variant thereof.
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The BASB009 polynucleotides provided in SEQ ID N0:1,3,5 or 7 are the BASB009
polynucleotides from Moraxella catarrhalis strains MC2931 (ATCC 43617),
MC2912,
MC2913 and MC2969.
As a further aspect of the invention there are provided isolated nucleic acid
molecules
encoding and/or expressing BASB009 poiypeptides and polynucleotides,
particularly
Moraxella catarrhalis BASB009 polypeptides and polynucleotides, including, for
example, unprocessed RNAs, ribozyme RNAs, mRNAs, cDNAs, genomic DNAs, B-
and Z-DNAs. Further embodiments of the invention include biologically,
. diagnostically, prophylactically, clinically or therapeutically useful
polynucleotides and
polypeptides, and variants thereof, and compositions comprising the same.
Another aspect of the invention relates to isolated polynucleotides, including
at least one full
length gene, that encodes a BASB009 polypeptide having a deduced amino acid
sequence of
SEQ ID N0:2,4,6 or 8 and polynucleotides closely related thereto and variants
thereof.
In another particularly preferred embodiment of the invention there is a
BASB009
polypeptide from Moraxella catarrhalis comprising or consisting of an amino
acid
sequence of SEQ ID N0:2,4,6 or 8 or a variant thereof.
Using the information provided herein, such as a polynucleotide sequence set
out in SEQ ID
NO:1, 3, 5 or 7, a polynucleotide of the invention encoding BASB009
polypeptide may be
obtained using standard cloning and screening methods, such as those for
cloning and
sequencing chromosomal DNA fragments from bacteria using Moraxella catarrhalis
Catlin
cells as starting material, followed by obtaining a full length clone. For
example, to obtain a
polynucleotide sequence of the invention, such as a polynucleotide sequence
given in
SEQ ID NO:1, 3, 5 or 7, typically a library of clones of chromosomal DNA of
Moraxella
catarrhalis in E.coli or some other suitable host is probed with a
radiolabeled
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oligonucleotide, preferably a 17-mer or longer, derived from a partial
sequence. Clones
carrying DNA identical to that of the probe can then be distinguished using
stringent
hybridization conditions. By sequencing the individual clones thus identified
by
hybridization with sequencing primers designed from the original polypeptide
or
polynucleotide sequence it is then possible to extend the polynucleotide
sequence in both
directions to determine a full length gene sequence. Conveniently, such
sequencing is
performed, for example, using denatured double stranded DNA prepared from a
plasmid
clone. Suitable techniques are described by Maniatis, T., Fritsch, E.F. and
Sambrook et
al., MOLECULAR CLONING, A LABORATORYMANUAL, 2nd Ed.; Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, New York ( 1989). (see in particular
Screening By
Hybridization 1.90 and Sequencing Denatured Double-Stranded DNA Templates
13.70).
Direct genomic DNA sequencing may also be performed to obtain a full length
gene
sequence. Illustrative of the invention. each polynucleotide set out in SEQ ID
NO: l, 3, 5 or
7 was discovered in a DNA library derived from Moraxella catarrhalis.
Moreover, each DNA sequence set out in SEQ ID NO:1, 3, 5 or 7 contains an open
reading
frame encoding a protein having about the number of amino acid residues set
forth in SEQ
ID N0:2, 4, 6 or 8 with a deduced molecular weight that can be calculated
using amino acid
residue molecular weight values well known to those skilled in the art.
The polynucleotide of SEQ ID NO: l, between the start codon at nucleotide
number 1 and
the stop codon which begins at nucleotide number 1321 of SEQ ID NO:1, encodes
the
polypeptide of SEQ ID N0:2.
The polynucleotide of SEQ ID N0:3, between the start codon at nucleotide
number l and
the stop codon which begins at nucleotide number 1321 of SEQ ID N0:3, encodes
the
polypeptide of SEQ ID N0:4.
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The polynucleotide of SEQ ID NO:S, between the start codon at nucleotide
number 1 and
the stop codon which begins at nucleotide number 1321 of SEQ ID NO:S, encodes
the
polypeptide of SEQ ID N0:6.
The polynucleotide of SEQ ID N0:7, between the start codon at nucleotide
number l and
the stop codon which begins at nucleotide number 1321 of SEQ ID N0:7, encodes
the
polypeptide of SEQ ID N0:8.
In a further aspect, the present invention provides for an isolated
polynucleotide
comprising or consisting of:
(a) a polynucleotide sequence which has at least 85% identity, preferably at
least 90%
identity, more preferably at least 95% identity, even more preferably at least
97-99% or
exact identity to SEQ ID NO:1, 3, 5 or 7 over the entire length of SEQ ID
NO:1, 3, 5 or 7
respectively; or
(b) a polynucleotide sequence encoding a polypeptide which has at least 85%
identity,
1 ~ preferably at least 90% identity, more preferably at least 95% identity,
even more
preferably at least 97-99% or 100% exact, to the amino acid sequence of SEQ ID
N0:2,
4, 6 or 8, over the entire length of SEQ ID N0:2, 4, 6 or 8 respectively.
A polynucleotide encoding a polypeptide of the present invention, including
homologs and
?0 orthologs from species other than Moraxella catarrhalis, may be obtained by
a process
which comprises the steps of screening an appropriate library under stringent
hybridization
conditions (for example, using a temperature in the range of 45 - 65°C
and an SDS
concentration from 0.1 --1 %) with a labeled or detectable probe consisting of
or comprising
the sequence of SEQ ID NO:1, 3, 5 or 7 or a fragment thereof; and isolating a
full-length
?5 gene and/or genomic clones containing said polynucleotide sequence.
The invention provides a polynucleotide sequence identical over its entire
length to a coding
sequence (open reading frame) in SEQ ID NO:1, 3, 5 or 7. Also provided by the
invention
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is a coding sequence for a mature polypeptide or a fragment thereof, by itself
as well as a
coding sequence for a mature polypeptide or a fragment in reading frame with
another
coding sequence, such as a sequence encoding a leader or secretory sequence, a
pre-, or pro-
or prepro-protein sequence. The polynucleotide of the invention may also
contain at least
one non-coding sequence, including for example, but not limited to at least
one non-coding
5' and 3' sequence, such as the transcribed but non-translated sequences,
termination signals
(such as rho-dependent and rho-independent termination signals), ribosome
binding sites,
Kozak sequences, sequences that stabilize mRNA, introns, and polyadenylation
signals.
The polynucleotide sequence may also comprise additional coding sequence
encoding
additional amino acids. For example, a marker sequence that facilitates
purification of the
fused polypeptide can be encoded. In certain embodiments of the invention, the
marker
sequence is a hexa-histidine peptide, as provided in the pQE vector (Qiagen,
Inc.) and
described in Gentz et al., Proc. Natl. Acad Sci., USA 86: 821-824 (1989), or
an HA peptide
tag (Wilson et al., Cell 37: 767 (1984), both of which may be useful in
purifying
I 5 polypeptide sequence fused to them. Polynucleotides of the invention also
include, but are
not limited to, polynucleotides comprising a structural gene and its naturally
associated
sequences that control gene expression.
The nucleotide sequence encoding BASB009 polypeptide of SEQ ID N0:2, 4, 6 or 8
may
be identical to the polypeptide encoding sequence contained in nucleotides 1
to 1320 of
SEQ ID N0:1,3,S,or 7 respectively. Alternatively it may be a sequence, which
as a result
of the redundancy (degeneracy) of the genetic code, also encodes the
polypeptide of SEQ
ID N0:2, 4, 6 or 8.
The term "polynucleotide encoding a polypeptide" as used herein encompasses
polynucleotides that include a sequence encoding a polypeptide of the
invention,
particularly a bacterial polypeptide and more particularly a polypeptide of
the Moraxella
catarrhalis BASB009 having an amino acid sequence set out in SEQ ID N0:2, 4, 6
or 8.
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The term also encompasses polynucleotides that include a single continuous
region or
discontinuous regions encoding the polypeptide (for example, polynucleotides
intemipted
by integrated phage, an integrated insertion sequence, an integrated vector
sequence, an
integrated transposon sequence, or due to RNA editing or genomic DNA
reorganisation)
together with additional regions, that also may contain coding and/or non-
coding sequences.
The invention further relates to variants of the polynucleotides described
herein that encode
variants of a polypeptide having a deduced amino acid sequence of SEQ ID N0:2,
4, 6 or 8.
Fragments of polynucleotides of the invention may be used, for example, to
synthesize full-
length polynucleotides of the invention.
Further particularly preferred embodiments are polynucleotides encoding
BASB009
variants, that have the amino acid sequence of BASB009 polypeptide of SEQ ID
N0:2, 4, 6
or 8 in which several, a few, ~ to 10, 1 to 5, I to 3, 2, 1 or no amino acid
residues are
substituted, modified, deleted andlor added, in any combination. Especially
preferred
among these are silent substitutions, additions and deletions, that do not
alter the properties
and activities of BASB009 polypeptide.
Further preferred embodiments of the invention are polynucleotides that are at
least 85%
identical over their entire length to a polynucleotide encoding BASB009
polypeptide having
an amino acid sequence set out in SEQ ID N0:2, 4, 6 or 8, and polynucleotides
that are
complementary to such polynucleotides. Alternatively, most highly preferred
are
polynucleotides that comprise a region that is at least 90% identical over its
entire length to
a polynucleotide encoding BASB009 polypeptide and polynucleotides
complementary
thereto. In this regard, polynucleotides at least 95% identical over their
entire length to the
same are particularly preferred. Furthermore, those with at least 97% are
highly preferred
among those with at least 95%. and among these those with at least 98% and at
least 99%
are particularly highly preferred. with at least 99% being the more preferred.
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Preferred embodiments are polynucleotides encoding polypeptides that retain
substantially
the same biological function or activity as the mature polypeptide encoded by
a DNA of
SEQ ID NO:1, 3, 5 or 7.
In accordance with certain preferred embodiments of this invention there are
provided
polynucleotides that hybridize, particularly under stringent conditions, to
BASB009
polynucleotide sequences, such as those polynucleoddes in SEQ ID NO:I, 3, 5 or
7.
The invention further relates to polynucleotides that hybridize to the
polynucleotide
sequences provided herein. In this regard, the invention especially relates to
polynucleotides
that hybridize under stringent conditions to the polynucleotides described
herein. As herein
used, the terms "stringent conditions" and "stringent hybridization
conditions" mean
hybridization occurring only if there is at least 95% and preferably at least
97% identity
between the sequences. A specific example of stringent hybridization
conditions is
overnight incubation at 42°C in a solution comprising: 50% formamide,
Sx SSC (150mM
NaCI, lSznM trisodium citrate), 50 mM sodium phosphate (pH7.6), Sx Denhardt's
solution, 10% dextran sulfate, and 20 micrograms/ml of denatured, sheared
salmon sperm
DNA, followed by washing the hybridization support in O.lx SSC at about
65°C.
Hybridization and wash conditions are well known and exemplified in Sambrook,
et al.,
Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor,
N.Y.,
( 1989), particularly Chapter 11 therein. Solution hybridization may also be
used with the
polynucleotide sequences provided by the invention.
2~ The invention also provides a polynucleotide consisting of or comprising a
polynucleotide
sequence obtained by screening an appropriate library containing the complete
gene for a
polynucleotide sequence set forth in SEQ ID NO:1, 3, S or 7 under stringent
hybridization
conditions with a probe having the sequence of said polynucleotide sequence
set forth in
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SEQ ID NO:1, 3, S or 7 or a fragment thereof; and isolating said
poiynucleotide sequence.
Fragments useful for obtaining such a polynucleotide include, for example,
probes and
primers fully described elsewhere herein.
As discussed elsewhere herein regarding polynucleotide assays of the
invention, for
instance, the polynucleotides of the invention, may be used as a hybridization
probe for
RNA, cDNA and genomic DNA to isolate full-length cDNAs and genomic clones
encoding
BASB009 and to isolate cDNA and genomic clones of other genes that have a high
identity,
particularly high sequence identity, to the BASB009 gene. Such probes
generally will
I 0 comprise at least 1 S nucleotide residues or base pairs. Preferably, such
probes will have at
least 30 nucleotide residues or base pairs and may have at least 50 nucleotide
residues or
base pairs. Particularly preferred probes will have at least 20 nucleotide
residues or base
pairs and will have less than 30 nucleotide residues or base pairs.
15 A coding region of a BASB009 gene may be isolated by screening using a DNA
sequence
provided in SEQ ID NO:1, 3, 5 or 7 to synthesize an oligonucleodde probe. A
labeled
oligonucleotide having a sequence complementary to that of a gene of the
invention is then
used to screen a library of cDNA, genomic DNA or mRNA to determine which
members of
the library the probe hybridizes to.
There are several methods available and well known to those skilled in the art
to obtain
full-length DNAs, or extend short DNAs, for example those based on the method
of Rapid
Amplification of cDNA ends (RACE) (see, for example, Frohman, et al., PNAS
LISA 85:
8998-9002, 1988). Recent modifications of the technique, exemplified by the
MarathonTM
technology (Clontech Laboratories Inc.) for example, have significantly
simplified the
search for longer cDNAs. In the MarathonTM technology, cDNAs have been
prepared
from mRNA extracted from a chosen tissue and an 'adaptor' sequence ligated
onto each
end. Nucleic acid amplification (PCR) is then carried out to amplify the
"missing" 5' end
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of the DNA using a combination of gene specific and adaptor specific
oligonucleotide
primers. The PCR reaction is then repeated using "nested" primers, that is,
primers
designed to anneal within the amplified product (typically an adaptor specific
primer that
anneals further 3' in the adaptor sequence and a gene specific primer that
anneals further 5'
in the selected gene sequence). The products of this reaction can then be
anaiyzed by
DNA sequencing and a full-length DNA constructed either by joining the product
directly
to the existing DNA to give a complete sequence, or carrying out a separate
full-length
PCR using the new sequence information for the design of the 5' primer.
I 0 The polynucleotides and polypeptides of the invention may be employed, for
example, as
research reagents and materials for discovery of treatments of and diagnostics
for diseases,
particularly human diseases, as further discussed herein relating to
polynucleotide assays.
The polynucleotides of the invention that are oligonucleotides derived from a
sequence of
1 ~ SEQ ID NOS:-1,3,5 or 7 may be used in the processes herein as described,
but preferably
for PCR, to determine whether or not the polynucleotides identified herein in
whole or in
part are transcribed in bacteria in infected tissue. It is recognized that
such sequences will
also have utility in diagnosis of the stage of infection and type of infection
the pathogen
has attained.
The invention also provides polynucleotides that encode a polypeptide that is
the mature
protein plus additional amino or carboxyl-terminal amino acids, or amino acids
interior to
the mature polypeptide (when the mature form has more than one polypeptide
chain, for
instance). Such sequences may play a role in processing of a protein from
precursor to a
5 mature form, may allow protein transport, may lengthen or shorten protein
half life or may
facilitate manipulation of a protein for assay or production, among other
things. As
generally is the case in vivo, the additional amino acids may be processed
away from the
mature protein by cellular enzymes.
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For each and every polynucleotide of the invention there is provided a
polynucleotide
complementary to it. It is preferred that these complementary polynucleotides
are fully
complementary to each polynucleotide with which they are complementary.
A precursor protein, having a mature form of the polypeptide fused to one or
more
prosequences may be an inactive form of the polypeptide. When prosequences are
removed
such inactive precursors generally are activated. Some or all of the
prosequences may be
removed before activation. Generally, such precursors are called proproteins.
In addition to the standard A, G, C, T/U representations for nucleotides, the
term "N" may
also be used in describing certain polynucleotides of the invention. "N" means
that any of
the four DNA or RNA nucleotides may appear at such a designated position in
the DNA
or RNA sequence, except it is preferred that N is not a nucleic acid that when
taken in
1 S combination with adjacent nucleotide positions, when read in the correct
reading frame,
would have the effect of generating a premature termination codon in such
reading frame.
In sum, a polynucieotide of the invention may encode a mature protein, a
mature protein
plus a leader sequence (which may be referred to as a preprotein), a precursor
of a mature
protein having one or more prosequences that are not the leader sequences of a
preprotein,
or a preproprotein, which is a precursor to a proprotein, having a leader
sequence and one or
more prosequences, which generally are removed during processing steps that
produce
active and mature forms of the polypeptide.
In accordance with an aspect of the invention, there is provided the use of a
polynucleotide of the invention for therapeutic or prophylactic purposes, in
particular
genetic immunization.
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The use of a polynucleotide of the invention in genetic immunization will
preferably
employ a suitable delivery method such as direct injection of plasmid DNA into
muscles
(Wolff et al., Hum Mol Genet (1992) l: 363, Manthorpe et al., Hum. Gene Ther.
(1983) 4:
419), delivery of DNA complexed with specific protein carriers (Wu et al.,
JBiol Chem.
S (1989) 264: 16985), coprecipitation of DNA with calcium phosphate
(Benvenisty &
Reshef, PNAS USA, ( 1986) 83 : 9S S 1 ), encapsulation of DNA in various forms
of
liposomes (Kaneda et al., Science (1989) 243: 37S), particle bombardment (Tang
et al.,
Nature (1992) 3S6:1S2, Eisenbraun et al., DNA Cell Biol (1993) 12: 791) and in
vivo
infection using cloned retroviral vectors (Seeger et al., PNAS USA ( 1984) 81:
5849).
Vectors, Host Cells, Expression Systems
The invention also relates to vectors that comprise a polynucleotide or
polynucleotides of
the invention, host cells that are genetically engineered with vectors of the
invention and the
production of polypeptides of the invention by recombinant techniques. Cell-
free
translation systems can also be employed to produce such proteins using RNAs
derived
from the DNA constructs of the invention.
Recombinant polypeptides of the present invention may be prepared by processes
wel!
known in those skilled in the art from genetically engineered host cells
comprising
expression systems. Accordingly, in a further aspect, the present invention
relates to
expression systems that comprise a polynucleotide or polynucleotides of the
present
invention, to host cells which are genetically engineered with such expression
systems, and
to the production of polypeptides of the invention by recombinant techniques.
2S
For recombinant production of the polypeptides of the invention, host cells
can be
genetically engineered to incorporate expression systems or portions thereof
or
polynucleotides of the invention. Introduction of a polynucleotide into the
host cell can be
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effected by methods described in many standard laboratory manuals, such as
Davis, et al.,
BASICMETHODSINMOLECULAR BIOLOGY, (1986) and Sambrook, et al.,
MOLECULAR CLONING: A LABORATORYMANUAL, 2nd Ed., Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, N.Y. (1989), such as, calcium phosphate
transfection, DEAE-dextran mediated transfection, transvection,
microinjection, cationic
lipid-mediated transfection, electroporation, transduction, scrape loading,
ballistic
introduction and infection.
Representative examples of appropriate hosts include bacterial cells, such as
cells of
I 0 streptococci, staphylococci, enterococci, E. coli, streptomyces,
cyanobacteria, Bacillus
subtilis, Neisseria meningitides and Moraxella catarrhalis; fungal cells, such
as cells of a
yeast. Kluveromyces, Saccharomyces, a basidiomycete, Candida. albicans
andAspergillus;
insect cells such as cells of Drosophila S2 and Spodoptera Sfi3; animal cells
such as CHO,
COS, HeLa, C127, 3T3, BHK, 293, CV-1 and Bowes melanoma cells; and plant
cells, such
I 5 as cells of a gymnosperm or angiosperm.
A great variety of expression systems can be used to produce the polypeptides
of the
invention. Such vectors include. among others, chromosomal-, episomal- and
virus-derived
vectors, for example, vectors derived from bacterial plasmids, from
bacteriophage, from
20 transposons, from yeast episomes, from insertion elements, from yeast
chromosomal
elements. from. viruses such as baculoviruses, papova viruses, such as SV40,
vaccinia
viruses, adenoviruses, fowl pox viruses, pseudorabies viruses, picornaviruses,
retroviruses,
and alphaviruses and vectors derived from combinations thereof, such as those
derived from
plasmid and bacteriophage genetic elements, such as cosmids and phagemids. The
25 expression system constructs may contain control regions that regulate as
well as engender
expression. Generally, any system or vector suitable to maintain, propagate or
express
polynucleotides and/or to express a polypeptide in a host may be used for
expression in this
regard. The appropriate DNA sequence may be inserted into the expression
system by any
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of a variety of well-known and routine techniques, such as, for example, those
set forth in
Sambrook et al., MOLECULAR CLONING, A LABORATORYMANUAL, (supra).
In recombinant expression systems in eukaryotes, for secretion of a translated
protein into
the lumen of the endoplasmic reticulum, into the periplasmic space or into the
extracellular
environment, appropriate secretion signals may be incorporated into the
expressed
polypeptide. These signals may be endogenous to the polypeptide or they may be
heterologous signals.
Polypeptides of the present invention can be recovered and purified from
recombinant
cell cultures by well-known methods including ammonium sulfate or ethanol
precipitation, acid extraction, anion or cation exchange chromatography,
phosphocellulose
chromatography, hydrophobic interaction chromatography, affinity
chromatography,
hydroxylapatite chromatography and lectin chromatography. Most preferably, ion
metal
affinity chromatography (IMAC) is employed for purification. Well known
techniques
for refolding proteins may be employed to regenerate active confonmation when
the
polypeptide is denatured during intracellular synthesis, isolation and or
purification.
The expression system may also be a recombinant live microorganism, such as a
virus
or bacterium. The gene of interest can be inserted into the genome of a live
recombinant
virus or bacterium. Inoculation and in vivo infection with this live vector
will lead to in
vivo expression of the antigen and induction of immune responses. Viruses and
bacteria
used for this purpose are for instance: poxviruses (e.g; vaccinia, fowlpox,
canarypox),
alphaviruses (Sindbis virus, Sernliki Forest Virus, Venezuelian Equine
Encephalitis
Virus), adenoviruses, adeno-associated virus, picornaviruses (poliovirus,
rhinovirus),
herpesviruses (varicella zoster virus, etc), Listeria, Salmonella , Shigella,
Neisseria,
BCG. These viruses and bacteria can be virulent, or attenuated in various ways
in order
to obtain live vaccines. Such live vaccines also form part of the invention.
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Diagnostic, Prognostic, Serotypin~ and Mutation Assays
This invention is also related to the use of BASB009 polynucleotides and
polypeptides of
the invention for use as diagnostic reagents. Detection of BASB009
polynucleotides and/or
polypeptides in a eukaryote, particularly a mammal, and especially a human,
will provide a
diagnostic method for diagnosis of disease, staging of disease or response of
an infectious
organism to drugs. Eukaryotes, particularly mammals, and especially humans,
particularly
those infected or suspected to be infected with an organism comprising the
BASB009 gene
or protein, may be detected at the nucleic acid or amino acid level by a
variety of well
known techniques as well as by methods provided herein.
Polypeptides and polynucleotides for prognosis, diagnosis or other analysis
may be obtained
from a putatively infected and/or infected individual's bodily materials.
Polynucleotides
from any of these sources, particularly DNA or RNA, may be used directly for
detection or
may be amplified enzymatically by using PCR or any other amplification
technique prior to
analysis. RNA, particularly mRNA, cDNA and genomic DNA may also be used in the
same ways. Using amplification, characterization of the species and strain of
infectious or
resident organism present in an individual, may be made by an analysis of the
genotype of a
selected polynucleotide of the organism. Deletions and insertions can be
detected by a
change in size of the amplified product in comparison to a genotype of a
reference sequence
selected from a related organism, preferably a different species of the same
genus or a
different strain of the same species. Point mutations can be identified by
hybridizing
amplified DNA to labeled BASB009 polynucleotide sequences. Perfectly or
significantly
matched sequences can be distinguished from imperfectly or more significantly
mismatched
duplexes by DNase or RNase digestion, for DNA or RNA respectively, or by
detecting
differences in melting temperatures or renaturation kinetics. Polynucleotide
sequence
differences may also be detected by alterations in the electrophoretic
mobility of
polynucleotide fragments in gels as compared to a reference sequence. This may
be carried
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out with or without denaturing agents. Polynucleotide differences may also be
detected by
direct DNA or RNA sequencing. See, for example, Myers et aL, Science, 230.
1242 (1985).
Sequence changes at specific locations also may be revealed by nuclease
protection assays,
such as RNase, V 1 and S 1 protection assay or a chemical cleavage method.
See, for
example, Cotton et al., Proc. Natl. Acad. Sci., USA, 85: 4397-4401 (1985).
In another embodiment, an array of oligonucleotides probes comprising BASB009
nucleotide sequence or fragments thereof can be constructed to conduct
efficient screening
of for example, genetic mutations, serotype, taxonomic classification or
identification.
Array technology methods are well known and have general applicability and can
be used to
address a variety of questions in molecular genetics including gene
expression, genetic
linkage, and genetic variability (see, for example. Chee et al., Science, 274:
610 ( 1996)).
Thus in another aspect, the present invention relates to a diagnostic kit
which comprises:
(a) a polynucleotide of the present invention, preferably the nucleotide
sequence of SEQ
ID NO:1, 3, 5 or 7, or a fragment thereof ;
(b) a nucleotide sequence complementary to that of (a);
(c) a polypeptide of the present invention, preferably the polypeptide of SEQ
ID N0:2, 4,
6 or 8 or a fragment thereof; or
(d) an antibody to a polypeptide of the present invention, preferably to the
polypeptide of
SEQ ID NO:2, 4, 6 or 8.
It will be appreciated that in any such kit, (a), (b), {c) or (d) may comprise
a substantial
component. Such a kit will be of use in diagnosing a disease or susceptibility
to a
Disease, among others.
This invention also relates to the use of polynucleotides of the present
invention as
diagnostic reagents. Detection of a mutated form of a polynucleotide of the
invention,
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preferable, SEQ ID NO:1, 3, 5 or 7, which is associated with a disease or
pathogenicity will
provide a diagnostic tool that can add to, or define, a diagnosis of a
disease, a prognosis of a
course of disease, a determination of a stage of disease, or a susceptibility
to a disease,
which results from under-expression, over-expression or altered expression of
the
polynucieotide. Organisms, particularly infectious organisms, carrying
mutations in such
polynucleotide may be detected at the polynucleotide level by a variety of
techniques, such
as those described elsewhere herein.
Cells from an organism carrying mutations or polymorphisms (allelic
variations) in a
I 0 polynucleotide and/or polypeptide of the invention may also be detected at
the
polynucleotide or polypeptide level by a variety of techniques, to allow for
serotyping, for
example. For example, RT-PCR can be used to detect mutations in the RNA. It is
particularly preferred to use RT-PCR in conjunction with automated detection
systems, such
as, for example, GeneScan. RNA, cDNA or genomic DNA may also be used for the
same
purpose, PCR. As an example, PCR primers complementary to a polynucleotide
encoding
BASB009 polypeptide can be used to identify and analyze mutations.
The invention further provides primers with 1, 2, 3 or 4 nucleotides removed
from the 5'
and/or the 3' end. These primers may be used for, among other things,
amplifying
BASB009 DNA and/or RNA isolated from a sample derived from an individual, such
as a
bodily material. The primers may be used to amplify a polynucleotide isolated
from an
infected individual, such that the polynucleotide may then be subject to
various techniques
for elucidation of the polynucleotide sequence. In this way, mutations in the
polynucleotide
sequence may be detected and used to diagnose and/or prognose the infection or
its stage or
course, or to serotype andlor classify the infectious agent.
The invention further provides a process for diagnosing, disease, preferably
bacterial
infections, more preferably infections caused by Moraxella cararrhalis,
comprising
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determining from a sample derived from an individual, such as a bodily
material, an
increased level of expression of polynucleotide having a sequence of SEQ ID
NO:I, 3, 5
or 7. Increased or decreased expression of a BASB009 polynucleotide can be
measured
using any on of the methods well known in the art for the quantitation of
polynucleotides,
such as, for example, amplification, PCR, RT-PCR, RNase protection, Northern
blotting,
spectrometry and other hybridization methods.
In addition, a diagnostic assay in accordance with the invention for detecting
over-
expression of BASB009 polypeptide compared to normal control tissue samples
may be
used to detect the presence of an infection, for example. Assay techniques
that can be used
to determine levels of a BASB009 polypeptide, in a sample derived from a host,
such as a
bodily material, are well-known to those of skill in the art. Such assay
methods include
radioimmunoassays, competitive-binding assays, Western Blot analysis, antibody
sandwich
assays, antibody detection and ELISA assays.
l~
The polynucleotides of the invention may be used as components of
polynucleotide
arrays, preferably high density arrays or grids. These high density arrays are
particularly useful for diagnostic and prognostic purposes. For example, a set
of spots
each comprising a different gene, and further comprising a polynucleotide or
polynucieotides of the invention, may be used for probing, such as using
hybridization
or nucleic acid amplification, using a probes obtained or derived from a
bodily sample,
to determine the presence of a particular polynucleotide sequence or related
sequence in
an individual. Such a presence may indicate the presence of a pathogen,
particularly
Moraxella catarrhalis, and may be useful in diagnosing and/or prognosing
disease or a
course of disease. A grid comprising a number of variants of the
polynucleotide
sequence of SEQ ID NO:1, 3, 5 or 7 are preferred. Also preferred is a
comprising a
number of variants of a polynucleotide sequence encoding the polypeptide
sequence of
SEQ ID N0:2, 4, 6 or 8.
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Antibodies
The polypeptides and polynucleotides of the invention or variants thereof, or
cells
expressing the same can be used as immunogens to produce antibodies
immunospecific for
such polypeptides or polynucleotides respectively.
In certain preferred embodiments of the invention there are provided
antibodies against
BASB009 polypeptides or polynucleotides.
Antibodies generated against the polypeptides or polynucleotides of the
invention can be
obtained by administering the polypeptides and/or polynucleotides of the
invention, or
epitope-bearing fragments of either or both, analogues of either or both, or
cells expressing
either or both, to an animal, preferably a nonhuman, using routine protocols.
For
preparation of monoclonal antibodies, any technique known in the art that
provides
antibodies produced by continuous cell line cultures can be used. Examples
include various
techniques, such as those in Kohler, G. and Milstein, C., Nature 256: 495-497
(1975);
Kozbor et al., Immunology Todav 4: 72 (1983); Cole et al., pg. 77-96 in
MONOCLONAL
ANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inca ( 1985).
Techniques for the production of single chain antibodies (U.S. Patent No.
4,946,778) can be
adapted to produce single chain antibodies to polypeptides or polynucleotides
of this
invention. Also, transgenic mice, or other organisms or animals, such as other
mammals,
may be used to express humanized antibodies immunospecific to the polypeptides
or
polynucleotides of the invention.
Alternatively, phage display technology may be utilized to select antibody
genes with
binding activities towards a polypeptide of the invention either from
repertoires of PCR
amplified v-genes of lymphocytes from humans screened for possessing anti-
BASB009 or
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from naive libraries (McCafferty, et al., (1990), Nature 348, 552-554; Marks,
et. a1,
(1992) Biotechnology 10, 779-783). The affnity of these antibodies can also be
improved
by, for example, chain shuffling (Clackson et al., (1991) Nature 351: 628).
The above-described antibodies may be employed to isolate or to identify
clones expressing
the polypeptides or polynucleotides of the invention to purify the
polypeptides or
polynucleotides by, for example, affinity chromatography.
Thus, among others, antibodies against BASB009-polypeptide or BASB009-
polynucleotide
may be employed to treat infections, particularly bacterial infections.
Polypeptide variants include antigenically, epitopically or immunologically
equivalent
variants form a particular aspect of this invention.
Preferably, the antibody or variant thereof is modified to make it less
immunogenic in the
individual. For example, if the individual is human the antibody may most
preferably be
"humanized," where the complimentarity determining region or regions of the
hybridoma-
derived antibody has been transplanted into a human monoclonal antibody, for
example as
described in Jones et al. (1986), Nature 321, 522-525 or Tempest et al.,
(1991)
Biotechnology 9, 266-273.
Antagonists and A~onists - Assavs and Molecules
Polypeptides and polynucleotides of the invention may also be used to assess
the binding of
small molecule substrates and ligands in, for example, cells, cell-free
preparations, chemical
libraries, and natural product mixtures. These substrates and ligands may be
natural
substrates and ligands or may be structural or functional mimetics. See, e.g.,
Coligan et al.,
Current Protocols in Immunology I (2): Chapter 5 ( 1991 ).
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The screening methods may simply measure the binding of a candidate compound
to the
polypeptide or polynucleotide, or to cells or membranes bearing the
polypeptide or
polynucleotide, or a fusion protein of the polypeptide by means of a label
directly or
indirectly associated with the candidate compound. Alternatively, the
screening method
may involve competition with a labeled competitor. Further, these screening
methods
may test whether the candidate compound results in a signal generated by
activation or
inhibition of the polypeptide or polynucleotide, using detection systems
appropriate to the
cells comprising the polypeptide or polynucleotide. Inhibitors of activation
are generally
assayed in the presence of a known agonist and the effect on activation by the
agonist by
the presence of the candidate compound is observed. Constitutively active
polypeptide
and/or constitutively expressed polypeptides and polynucleotides may be
employed in
screening methods for inverse agonists or inhibitors, in the absence of an
agonist or
inhibitor, by testing whether the candidate compound results in inhibition of
activation of
1 ~ the polypeptide or polynucleotide, as the case may be. Further, the
screening methods
may simply comprise the steps of mixing a candidate compound with a solution
containing a polypeptide or polynucleotide of the present invention, to form a
mixture,
measuring BASB009 polypeptide and/or polynucleotide activity in the mixture,
and
comparing the BASB009 polypeptide and/or polynucleotide activity of the
mixture to a
standard. Fusion proteins, such as those made from Fc portion and BASB009
polypeptide, as hereinbefore described, can also be used for high-throughput
screening
assays to identify antagonists of the polypeptide of the present invention, as
well as of
phylogenetically and and/or functionally related polypeptides (see D. Bennett
et al., J Mol
Recognition, 8:52-58 (1995); and K. Johanson et al., J Biol Chem, 270(16):9459-
9471
( 1995)).
The polynucleotides, polypeptides and antibodies that bind to and/or interact
with a
polypeptide of the present invention may also be used to configure screening
methods for
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detecting the effect of added compounds on the production of mRNA and/or
polypeptide
in cells. For example, an ELISA assay may be constructed for measuring
secreted or cell
associated levels of polypeptide using monoclonal and polyclonal antibodies by
standard
methods known in the art. This can be used to discover agents which may
inhibit or
enhance the production of polypeptide (also called antagonist or agonist,
respectively)
from suitably manipulated cells or tissues.
The invention also provides a method of screening compounds to identify those
which
enhance (agonist) or block (antagonist) the action of BASB009 polypeptides or
polynucleotides, particularly those compounds that are bacteriostatic and/or
bactericidal.
The method of screening may involve high-throughput techniques. For example,
to screen
for agonists or antagonists, a synthetic reaction mix, a cellular compartment.
such as a
membrane, cell envelope or cell wall, or a preparation of any thereof
comprising BASB009
polypeptide and a labeled substrate or ligand of such polypeptide is incubated
in the absence
or the presence of a candidate molecule that may be a BASB009 agonist or
antagonist. The
ability of the candidate molecule to agonize or antagonize the BASB009
polypeptide is
reflected in decreased binding of the labeled ligand or decreased production
of product from
such substrate. Molecules that bind gratuitously, i.e., without inducing the
effects of
BASB009 polypeptide are most likely to be good antagonists. Molecules that
bind well
and, as the case may be. increase the rate of product production from
substrate, increase
signal transduction, or increase chemical channel activity are agonists.
Detection of the rate
or level of, as the case may be, production of product from substrate, signal
transduction, or
chemical channel activity may be enhanced by using a reporter system. Reporter
systems
that may be useful in this regard include but are not limited to colorimetric,
labeled substrate
converted into product, a reporter gene that is responsive to changes in
BASB009
polynucleotide or polypeptide activity, and binding assays known in the art.
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Another example of an assay for BASB009 agonists is a competitive assay that
combines
BASB009 and a potential agonist with BASB009-binding molecules, recombinant
BASB009 binding molecules, natural substrates or ligands, or substrate or
ligand mimetics,
under appropriate conditions for a competitive inhibition assay. BASB009 can
be labeled,
such as by radioactivity or a colorimetric compound, such that the number of
BASB009
molecules bound to a binding molecule or converted to product can be
determined
accurately to assess the effectiveness of the potential antagonist.
Potential antagonists include, among others, small organic molecules,
peptides, polypeptides
and antibodies that bind to a polynucleotide and/or polypeptide of the
invention and thereby
inhibit or extinguish its activity or expression. Potential antagonists also
may be small
organic molecules, a peptide, a polypeptide such as a closely related protein
or antibody that
binds the same sites on a binding molecule, such as a binding molecule,
without inducing
BASB009-induced activities, thereby preventing the action or expression of
BASB009
I ~ polypeptides and/or polynucleotides by excluding BASB009 polypeptides
and/or
polynucleotides from binding.
Potential antagonists include a small molecule that binds to and occupies the
binding site of
the polypeptide thereby preventing binding to cellular binding molecules, such
that normal
biological activity is prevented. Examples of small molecules include but are
not limited to
small organic molecules, peptides or peptide-like molecules. Other potential
antagonists
include antisense molecules (see Okano, J. Neurochem. S6: 560 (1991 );
OLIGODEOXYNUCLEOTIDES AS ANTISENSE INHIBITORS OF GENE EXPRESSION,
CRC Press, Boca Raton, FL (1988), for a description of these molecules).
Preferred
potential antagonists include compounds related to and variants of BASB009.
In a further aspect, the present invention relates to genetically engineered
soluble fusion
proteins comprising a polypeptide of the present invention, or a fragment
thereof, and
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various portions of the constant regions of heavy or light chains of
immunoglobulins of
various subclasses (IgG, IgM, IgA, IgE). Preferred as an immunoglobulin is the
constant
part of the heavy chain of human IgG, particularly IgGl, where fusion takes
place at the
hinge region. In a particular embodiment, the Fc part can be removed simply by
incorporation of a cleavage sequence which can be cleaved with blood clotting
factor Xa.
Furthermore, this invention relates to processes for the preparation of these
fusion
proteins by genetic engineering, and to the use thereof for drug screening,
diagnosis and
therapy. A further aspect of the invention also relates to polynucleotides
encoding such
fusion proteins. Examples of fusion protein technology can be found in
International
Patent Application Nos. W094/29458 and W094/22914.
Each of the polynucleotide sequences provided herein may be used in the
discovery and
development of antibacterial compounds. The encoded protein, upon expression,
can be
used as a target for the screening of antibacterial drugs. Additionally, the
polynucleotide
sequences encoding the amino terminal regions of the encoded protein or Shine-
Delgarno
or other translation facilitating sequences of the respective mRNA can be used
to
construct antisense sequences to control the expression of the coding sequence
of interest.
The invention also provides the use of the polypeptide, polynucleotide,
agonist or
antagonist of the invention to interfere with the initial physical interaction
between a
pathogen or pathogens and a eukaryotic, preferably mammalian, host responsible
for
sequelae of infection. In particular, the molecules of the invention may be
used: in the
prevention of adhesion of bacteria, in particular gram positive and/or gram
negative
bacteria, to eukaryotic, preferably mammalian, extracellular matrix proteins
on in-
dwelling devices or to extracellular matrix proteins in wounds; to block
bacterial adhesion
between eukaryotic, preferably mammalian, extracellular matrix proteins and
bacterial
BASB009 proteins that mediate tissue damage and/or; to block the normal
progression of
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pathogenesis in infections initiated other than by the implantation of in-
dwelling devices
or by other surgical techniques.
In accordance with yet another aspect of the invention, there are provided
BASB009
agonists and antagonists, preferably bacteristatic or bactericidal agonists
and antagonists.
The antagonists and agonists of the invention may be employed, for instance,
to prevent,
inhibit and/or treat diseases.
I 0 In a further aspect, the present invention relates to mimotopes of the
polypeptide of the
invention. A mimotope is a peptide sequence, sufficiently similar to the
native peptide
(sequentially or structurally), which is capable of being recognised by
antibodies which
recognise the native peptide; or is capable of raising antibodies which
recognise the
native peptide when coupled to a suitable carrier.
Peptide mimotopes may be designed for a particular purpose by addition,
deletion or
substitution of elected amino acids. Thus, the peptides may be modified for
the purposes
of ease of conjugation to a protein carrier. For example, it may be desirable
for some
chemical conjugation methods to include a terminal cysteine. In addition it
may be
desirable for peptides conjugated to a protein carrier to include a
hydrophobic terminus
distal from the conjugated terminus of the peptide, such that the free
unconjugated end
of the peptide remains associated with the surface of the carrier protein.
Thereby
presenting the peptide in a conformation which most closely resembles that of
the
peptide as found in the context of the whole native molecule. For example, the
peptides
may be altered to have an N-terminal cysteine and a C-terminal hydrophobic
amidated
tail. Alternatively, the addition or substitution of a D-stereoisomer form of
one or more
of the amino acids may be performed to create a beneficial derivative, for
example to
enhance stability of the peptide.
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Alternatively, peptide mimotopes may be identified using antibodies which are
capable
themselves of binding to the polypeptides of the present invention using
techniques such
as phage display technology (EP 0 552 267 B 1 ). This technique, generates a
large number
of peptide sequences which mimic the structure of the native peptides and are,
therefore,
capable of binding to anti-native peptide antibodies, but may not necessarily
themselves
share significant sequence homology to the native polypeptide.
Vaccines
Another aspect of the invention relates to a method for inducing an
immunological
response in an individual, particularly a mammal, preferably humans, which
comprises
inoculating the individual with BASB009 polynucleotide and/or polypeptide, or
a
fragment or variant thereof, adequate to produce antibody and/ or T cell
immune response
to protect said individual from infection, particularly bacterial infection
and most
particularly Moraxella catarrhalis infection. Also provided are methods
whereby such
immunological response slows bacterial replication. Yet another aspect of the
invention
relates to a method of inducing immunological response in an individual which
comprises
delivering to such individual a nucleic acid vector, sequence or ribozyme to
direct
expression of BASB009 polynucleotide andlor polypeptide, or a fragment or a
variant
thereof. for expressing BASB009 polynucleotide andlor polypeptide, or a
fragment or a
variant thereof in vivo in order to induce an immunological response, such as,
to produce
antibody andl or T cell immune response, including, for example, cytokine-
producing T
cells or cytotoxic T cells, to protect said individual, preferably a human,
from disease,
whether that disease is already established within the individual or not. One
example of
administering the gene is by accelerating it into the desired cells as a
coating on particles
or otherwise. Such nucleic acid vector may comprise DNA, RNA, a ribozyme, a
modified
nucleic acid, a DNA/RNA hybrid. a DNA-protein complex or an RNA-protein
complex.
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A further aspect of the invention relates to an immunological composition that
when
introduced into an individual, preferably a human, capable of having induced
within it an
immunological response, induces an immunological response in such individual
to a
BASB009 polynucleotide and/or polypeptide encoded therefrom, wherein the
composition
comprises a recombinant BASB009 polynucleotide and/or polypeptide encoded
therefrom
and/or comprises DNA and/or RNA which encodes and expresses an antigen of said
BASB009 polynucleotide, polypeptide encoded therefrom, or other polypeptide of
the
invention. The immunological response may be used therapeutically or
prophylactically
and may take the form of antibody immunity and/or cellular immunity, such as
cellular
immunity arising from CT'L or CD4+ T cells.
A BASB009 polypeptide or a fragment thereof may be fused with co-protein or
chemical
moiety which may or may not by itself produce antibodies, but which is capable
of
stabilizing the first protein and producing a fused or modified protein which
will have
antigenic andlor immunogenic properties, and preferably protective properties.
Thus
fused recombinant protein, preferably further comprises an antigenic co-
protein, such as
lipoprotein D from Haemophilus inJluenzae, Glutathione-S-transferase (GST) or
beta-
galactosidase, or any other relatively large co-protein which solubilizes the
protein and
facilitates production and purification thereof. Moreover, the co-protein may
act as an
adjuvant in the sense of providing a generalized stimulation of the immune
system of the
organism receiving the protein. The co-protein may be attached to either the
amino- or
carboxy-terminus of the first protein.
Provided by this invention are compositions, particularly vaccine
compositions, and
2~ methods comprising the polypeptides and/or polynucleotides of the invention
and
immunostimulatory DNA sequences, such as those described in Sato, Y. et al.
Science
273 : 3 52 ( 1996).
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Also, provided by this invention are methods using the described
polynucleotide or
particular fragments thereof, which have been shown to encode non-variable
regions of
bacterial cell surface proteins, in polynucleotide constructs used in such
genetic
immunization experiments in animal models of infection with Moraxella
catarrhalis.
Such experiments will be particularly useful for identifying protein epitopes
able to
provoke a prophylactic or therapeutic immune response. It is believed that
this approach
will allow for the subsequent preparation of monoclonal antibodies of
particular value,
derived from the requisite organ of the animal successfully resisting or
clearing infection,
for the development of prophylactic agents or therapeutic treatments of
bacterial infection,
particularly Moraxella catarrhalis infection, in mammals, particularly humans.
The invention also includes a vaccine fonmuiation which comprises an
immunogenic
recombinant polypeptide and/or polynucleotide of the invention together with a
suitable
carrier, such as a pharmaceutically acceptable carrier. Since the polypeptides
and
polynucleotides may be broken down in the stomach, each is preferably
administered
parenterally, including, for example, administration that is subcutaneous,
intramuscular,
intravenous, or intradermal. Formulations suitable for parenteral
administration include
aqueous and non-aqueous sterile injection solutions which may contain anti-
oxidants,
buffers, bacteriostatic compounds and solutes which render the formulation
isotonic with
the bodily fluid, preferably the blood, of the individual; and aqueous and non-
aqueous
sterile suspensions which may include suspending agents or thickening agents.
The
formulations may be presented in unit-dose or mufti-dose containers, for
example, sealed
ampoules and vials and may be stored in a freeze-dried condition requiring
only the
addition of the sterile liquid carrier immediately prior to use.
The vaccine formulation of the invention may also include adjuvant systems for
enhancing the immunogenicity of the formulation. Preferably the adjuvant
system
raises preferentially a TH 1 type of response.
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An immune response may be broadly distinguished into two extreme categories,
being a
htunoral or cell mediated immune responses (traditionally characterised by
antibody and
cellular effector mechanisms of protection respectively). These categories of
response
have been termed TH1-type responses (cell-mediated response), and TH2-type
immune
responses (humoral response).
Extreme THl-type immune responses may be characterised by the generation of
antigen
specific, haplotype restricted cytotoxic T lymphocytes, and natural killer
cell responses.
In mice TH 1-type responses are often characterised by the generation of
antibodies of
the IgG2a subtype, whilst in the human these correspond to IgGI type
antibodies. TH2-
type immune responses are characterised by the generation of a broad range of
immunoglobulin isotypes including in mice IgGl, IgA, and IgM.
It can be considered that the driving force behind the development of these
two types of
immune responses are cytokines. High levels of THI-type cytokines tend to
favour the
induction of cell mediated immune responses to the given antigen, whilst high
levels of
TH2-type cytokines tend to favour the induction of humoral immune responses to
the
antigen.
The distinction of TH1 and TH2-type immune responses is not absolute. In
reality an
individual will support an immune response which is described as being
predominantly
TH1 or predominantly TH2. However, it is often convenient to consider the
families of
cytokines in terms of that described in marine CD4 +ve T cell clones by
Mosmann and
Coffman (Mosmann, T.R. and Coffman, R.L. (1989) THI and TH2 cells: different
patterns of lymphokine secretion lead to different functional properties.
Annual Review
of Immunology, 7, p145-173). Traditionally, TH 1-type responses are associated
with
the production of the INF-y and IL-2 cytokines by T-lymphocytes. Other
cytokines
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often directly associated with the induction of TH1-type immune responses are
not
produced by T-cells, such as IL-12. In contrast, TH2- type responses are
associated with
the secretion of IL-4, IL-5, IL-6 and IL-13.
It is known that certain vaccine adjuvants are particularly suited to the
stimulation of
either TH 1 or TH2 - type cytokine responses. Traditionally the best
indicators of the
TH i :TH2 balance of the immune response after a vaccination or infection
includes
direct measurement of the production of TH1 or TH2 cytokines by T lymphocytes
in
vitro after restimulation with antigen, and/or the measurement of the
IgG1:IgG2a ratio
of antigen specific antibody responses.
Thus, a THI-type adjuvant is one which preferentially stimulates isolated T-
cell
populations to produce high levels of TH1-type cytokines when re-stimulated
with
antigen in vitro, and promotes development of both CD8+ cytotoxic T
lymphocytes and
antigen specific immunoglobulin responses associated with TH1-type isotype.
Adjuvants which are capable of preferential stimulation of the TH1 cell
response are
described in International Patent Application No. WO 94/00153 and WO 95/17209.
3 De-O-acylated monophosphoryl lipid A (3D-MPL) is one such adjuvant. This is
known from GB 2220211 (Ribi). Chemically it is a mixture of 3 De-O-acyiated
monophosphoryl lipid A with 4, 5 or 6 acylated chains and is manufactured by
Ribi
Immunochem, Montana. A preferred form of 3 De-O-acyiated monophosphoryl lipid
A is disclosed in European Patent 0 689 454 B 1 (SmithKline Beecham
Bioiogicals SA).
Preferably, the particles of 3D-MPL are small enough to be sterile filtered
through a
0.22micron membrane (European Patent number 0 689 454).
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3D-MPL will be present in the range of l Op,g - 100pg preferably 25-50p.g per
dose
wherein the antigen will typically be present in a range 2-SOUg per dose.
Another preferred adjuvant comprises QS21, an Hplc purified non-toxic fraction
derived
from the bark of Quillaja Saponaria Molina. Optionally this may be admixed
with 3
De-O-acylated monophosphoryl lipid A (3D-MPL), optionally together with an
carrier.
The method of production of QS21 is disclosed in US patent No. 5,057,540.
Non-reactogenic adjuvant formulations containing QS21 have been described
previously (WO 96/33739). Such formulations comprising QS21 and cholesterol
have
been shown to be successful TH1 stimulating adjuvants when formulated together
with
an antigen.
Further adjuvants which are preferential stimulators of TH1 cell response
include
immunomodulatory oligonucleotides, for example unmethylated CpG sequences as
disclosed in WO 96/02555.
Combinations of different TH 1 stimulating adjuvants, such as those mentioned
?0 hereinabove, are also contemplated as providing an adjuvant which is a
preferential
stimulator of TH 1 cell response. For example, QS21 can be formulated together
with
3D-MPL. The ratio of QS21 : 3D-MPL will typically be in the order of 1 : 10 to
10 : 1;
preferably 1:5 to 5 : 1 and often substantially 1 : 1. The preferred range for
optimal
synergy is 2.5 : 1 to 1 : 1 3D-MPL: QS21.
Preferably a carrier is also present in the vaccine composition according to
the
invention. The carrier may be an oil in water emulsion, or an aluminium salt,
such as
aluminium phosphate or aluminium hydroxide.
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A preferred oil-in-water emulsion comprises a metabolisible oil, such as
squalene, alpha
tocopherol and Tween 80. In a particularly preferred aspect the antigens in
the vaccine
composition according to the invention are combined with QS21 and 3D-MPL in
such
an emulsion. Additionally the oil in water emulsion may contain span 85 and/or
lecithin
and/or tricaprylin.
Typically for human administration QS21 and 3D-MPL will be present in a
vaccine in
the range of 1 p,g - 200pg, such as 10-100p,g, preferably 1 Opg - 50~tg per
dose.
Typically the oil in water will comprise from 2 to 10% squalene, from 2 to 10%
alpha
tocopherol and from 0.3 to 3% tween 80. Preferably the ratio of squalene:
alpha
tocopherol is equal to or less than 1 as this provides a more stable emulsion.
Span 85
may also be present at a level of 1 %. In some cases it may be advantageous
that the
vaccines of the present invention will further contain a stabiliser.
Non-toxic oil in water emulsions preferably contain a non-toxic oil, e.g.
squalane or
squalene, an emulsifier, e.g. Tween 80, in an aqueous carrier. The aqueous
Garner may
be, for example, phosphate buffered saline.
A particularly potent adjuvant formulation involving QS21, 3D-MPL and
tocopherol
in an oil in water emulsion is described in WO 95/17210.
The present invention also provides a polyvalent vaccine composition
comprising a
vaccine formulation of the invention in combination with other antigens, in
particular
?5 antigens useful for treating cancers, autoimmune diseases and related
conditions. Such a
polyvalent vaccine composition may include a TH-1 inducing adjuvant as
hereinbefore
described.
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While the invention has been described with reference to certain BASB009
polypeptides
and polynucleotides, it is to be understood that this covers fragments of the
naturally
occurring polypeptides and polynucleotides, and similar polypeptides and
polynucleotides
with additions, deletions or substitutions which do not substantially affect
the
immunogenic properties of the recombinant polypeptides or polynucleotides.
Compositions, kits and administration
In a further aspect of the invention there are provided compositions
comprising a BAS8009
polynucleotide and/or a BASB009 polypeptide for administration to a cell or to
a
multicellular organism.
The invention also relates to compositions comprising a polynucleotide and/or
a
polypeptides discussed herein or their agonists or antagonists. The
polypeptides and
poiynucleotides of the invention may be employed in combination with a non-
sterile or
sterile carrier or carriers for use with cells, tissues or organisms, such as
a pharmaceutical
carrier suitable for administration to an individual. Such compositions
comprise, for
instance, a media additive or a therapeutically effective amount of a
polypeptide and/or
polynucleotide of the invention and a pharmaceutically acceptable carrier or
excipient. Such
carriers may include, but are not limited to, saline, buffered saline,
dextrose, water, glycerol,
ethanol and combinations thereof. The formulation should suit the mode of
administration.
The invention further relates to diagnostic and pharmaceutical packs and kits
comprising
one or more containers filled with one or more of the ingredients of the
aforementioned
compositions of the invention.
?5 Polypeptides, polynucleotides and other compounds of the invention may be
employed
alone or in conjunction with other compounds, such as therapeutic compounds.
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The pharmaceutical compositions may be administered in any effective,
convenient manner
including, for instance, administration by topical, oral, anal, vaginal,
intravenous,
intraperitoneal, intramuscular, subcutaneous, intranasal or intradermal routes
among others.
In therapy or as a prophylactic, the active agent may be administered to an
individual as
an injectable composition, for example as a sterile aqueous dispersion,
preferably
isotonic.
In a further aspect, the present invention provides for pharmaceutical
compositions
comprising a therapeutically effective amount of a polypeptide and/or
polynucleotide, such
as the soluble form of a polypeptide and/or polynucleotide of the present
invention, agonist
or antagonist peptide or small molecule compound, in combination with a
pharmaceutically
acceptable carrier or excipient. Such carriers include, but are not limited
to, saline, buffered
saline, dextrose, water, glycerol. ethanol, and combinations thereof. The
invention further
1 S relates to pharmaceutical packs and kits comprising one yr more containers
filled with one
or more of the ingredients of the aforementioned compositions of the
invention.
Polypeptides, polynucleotides and other compounds of the present invention may
be
employed alone or in conjunction with other compounds, such as therapeutic
compounds.
The composition will be adapted to the route of administration, for instance
by a systemic or
an oral route. Preferred forms of systemic administration include injection,
typically by
intravenous injection. Other injection routes, such as subcutaneous,
intramuscular, or
intraperitoneal, can be used. Alternative means for systemic administration
include
transmucosal and transdermal administration using penetrants such as bile
salts or fusidic
2~ acids or other detergents. In addition, if a polypeptide or other compounds
of the present
invention can be formulated in an enteric or an encapsulated formulation, oral
administration may also be possible. Administration of these compounds may
also be
topical and/or localized, in the form of salves, pastes, gels, solutions,
powders and the like.
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For administration to mammals, and particularly humans, it is expected that
the daily
dosage level of the active agent will be from 0.01 mg/kg to 10 mg/kg,
typically around 1
mglkg. The physician in any event will determine the actual dosage which will
be most
suitable for an individual and will vary with the age, weight and response of
the particular
individual. The above dosages are exemplary of the average case. There can, of
course,
be individual instances where higher or lower dosage ranges are merited, and
such are
within the scope of this invention.
The dosage range required depends on the choice of peptide, the route of
administration, the
nature of the formulation, the nature of the subject's condition, and the
judgment of the
attending practitioner. Suitable dosages, however, are in the range of 0.1-100
wg/kg of
subject.
I ~ A vaccine composition is conveniently in injectable form. Conventional
adjuvants may be
employed to enhance the immune response. A suitable unit dose for vaccination
is 0.5-5
microgram/kg of antigen, and such dose is preferably administered I-3 times
and with an
interval of I-3 weeks. With the indicated dose range, no adverse toxicological
effects will
be observed with the compounds of the invention which would preclude their
administration to suitable individuals.
Wide variations in the needed dosage, however, are to be expected in view of
the variety of
compounds available and the differing efficiencies of various routes of
administration. For
example, oral administration would be expected to require higher dosages than
administration by intravenous injection. Variations in these dosage levels can
be adjusted
using standard empirical routines for optimization, as is well understood in
the art.
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Seguence Databases, Sequences in a Tangible Medium, and Algorithms
Polynucleotide and polypeptide sequences form a valuable information resource
with which
to determine their 2- and 3-dimensional structures as well as to identify
further sequences of
similar homology. These approaches are most easily facilitated by storing the
sequence in a
computer readable medium and then using the stored data in a known
macromolecular
structure program or to search a sequence database using well known searching
tools, such
as the GCG program package.
Also provided by the invention are methods for the analysis of character
sequences or
strings, particularly genetic sequences or encoded protein sequences.
Preferred methods
of sequence analysis include, for example, methods of sequence homology
analysis, such
as identity and similarity analysis, DNA, RNA and protein structure analysis,
sequence
assembly, cladistic analysis, sequence motif analysis, open reading frame
determination,
nucleic acid base calling, codon usage analysis, nucleic acid base trimming,
and
sequencing chromatogram peak analysis.
A computer based method is provided for performing homology identification.
This
method comprises the steps of: providing a first polynucleotide sequence
comprising the
sequence of a polynucleotide of the invention in a computer readable medium;
and
comparing said first polynucleotide sequence to at least one second
polynucleotide or
polypeptide sequence to identify homology.
A computer based method is also provided for performing homology
identification, said
method comprising the steps of: providing a first polypeptide sequence
comprising the
sequence of a polypeptide of the invention in a computer readable medium; and
comparing said first polypeptide sequence to at least one second
polynucleotide or
polypeptide sequence to identify homology.
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All publications and references, including but not limited to patents and
patent
applications, cited in this specification are herein incorporated by reference
in their
entirety as if each individual publication or reference were specifically and
individually
indicated to be incorporated by reference herein as being fully set forth. Any
patent
application to which this application claims priority is also incorporated by
reference
herein in its entirety in the manner described above for publications and
references.
DEFINITIONS
"Identity," as known in the art, is a relationship between two or more
polypeptide sequences
or two or more polynucleotide sequences, as the case may be, as determined by
comparing
the sequences. In the art, "identity" also means the degree of sequence
relatedness between
polypeptide or polynucleotide sequences, as the case may be, as detenmined by
the match
between strings of such sequences. "Identity" can be readily calculated by
known
1 ~ methods, including but not limited to those described in (Computational
Molecular
Biology, Lesk, A.M., ed., Oxford University Press, New York, 198$;
Biocomputing:
Informatics and Genome Projects, Smith, D.W., ed., Academic Press, New York,
1993;
Computer Analysis of Sequence Data, Part I, Griffin, A.M., and Griffin, H.G.,
eds.,
Humana Press, New Jersey, 1994; Sequence Analysis in Molecular Biology, von
Heine,
G., Academic Press, 1987; and Sequence Analysis Primer, Gribskov, M. and
Devereux, J.,
eds., M Stockton Press, New York, 1991; and Carillo, H., and Lipman, D., SIAM
J.
Applied Math., 48.~ 1073 (1988). Methods to determine identity are designed to
give the
largest match between the sequences tested. Moreover, methods to determine
identity are
codified in publicly available computer programs. Computer program methods to
?5 determine identity between two sequences include, but are not limited to,
the GAP
program in the GCG program package (Devereux, J., et al., Nucleic Acids
Research 12(1):
387 (1984)), BLASTP, BLASTN (Altschul, S.F. et al., J. Molec. Biol. 215: 403-
410
( 1990), and FASTA( Pearson and Lipman Proc. Natl. Acad. Sci. USA 85; 2444-
2448
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WO 99158562 PCT/EP99/03262
( 1988). The BLAST family of programs is publicly available from NCBI and
other
sources (BLAST Manual, Altschul, S., et al., NCBI NLM NIH Bethesda, MD 20894;
Altschul, S., et al., J. Mol. Biol. 215: 403-410 (1990). The well known Smith
Waterman
algorithm may also be used to determine identity.
Parameters for polypeptide sequence comparison include the following:
Algorithm: Needleman and Wunsch, J. Mol Biol. 48: 443-453 (I970)
Comparison matrix: BLOSSUM62 from Henikoff and Henikoff,
Proc. Natl. Acad. Sci. USA. 89:10915-10919 (1992)
Gap Penalty: 8
Gap Length Penalty: 2
A program useful with these parameters is publicly available as the "gap"
program from
Genetics Computer Group, Madison WI. The aforementioned parameters are the
default
parameters for peptide comparisons (along with no penalty for end gaps).
Parameters for polynucleotide comparison include the following:
Algorithm: Needleman and Wunsch, J. Mol Biol. 48: 443-453 ( 1970)
Comparison matrix: matches = +10, mismatch = 0
Gap Penalty: ~0
Gap Length Penalty: 3
Available as: The "gap" program from Genetics Computer Group, Madison WI.
These
are the default parameters for nucleic acid comparisons.
A preferred meaning for "identity" for polynucleotides and polypeptides, as
the case may
?5 be, are provided in (1) and (2) below.
( 1 ) Polynucleotide embodiments further include an isolated polynucleotide
comprising a polynucleotide sequence having at least a 50, 60, 70, 80, 85, 90,
95, 97 or
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100% identity to the reference sequence of SEQ ID NO:1, wherein said
polynucleotide
sequence may be identical to the reference sequence of SEQ ID NO:1 or may
include up
to a certain integer number of nucleotide alterations as compared to the
reference
sequence, wherein said alterations are selected from the group consisting of
at least one
S nucleotide deletion, substitution, including transition and transversion, or
insertion, and
wherein said alterations may occur at the S' or 3' terminal positions of the
reference
nucleotide sequence or anywhere between those terminal positions, interspersed
either
individually among the nucleotides in the reference sequence or in one or more
contiguous groups within the reference sequence, and wherein said number of
nucleotide
alterations is determined by multiplying the total number of nucleotides in
SEQ ID NO:1
by the integer defining the percent identity divided by 100 and then
subtracting that
product from said total number of nucleotides in SEQ ID NO:1, or:
nn ~ xn ' ~xn' Y)
1S
wherein nn is the number of nucleotide alterations, xn is the total number of
nucleotides
in SEQ ID NO:1, y is O.SO for SO%, 0.60 for 60%, 0.70 for 70%, 0.80 for 80%,
0.85 for
8S%, 0.90 for 90%, 0.95 for 9S%, 0.97 for 97% or 1.00 for 100%, and ~ is the
symbol for
the multiplication operator. and wherein any non-integer product of xn and y
is rounded
down to the nearest integer prior to subtracting it from xn. Alterations of a
polynucleotide
sequence encoding the polypeptide of SEQ ID N0:2 may create nonsense, missense
or
frameshift mutations in this coding sequence and thereby alter the polypeptide
encoded by
the polynucleotide following such alterations.
2S By way of example, a polynucleotide sequence of the present invention may
be identical
to the reference sequence of SEQ ID NO:1, that is it may be 100% identical, or
it may
include up to a certain integer number of nucleic acid alterations as compared
to the
reference sequence such that the percent identity is less than 100% identity.
Such
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alterations are selected from the group consisting of at least one nucleic
acid deletion,
substitution, including transition and transversion, or insertion, and wherein
said
alterations may occur at the 5' or 3' terminal positions of the reference
polynucleotide
sequence or anywhere between those terminal positions, interspersed either
individually
among the nucleic acids in the reference sequence or in one or more contiguous
groups
within the reference sequence. The number of nucleic acid alterations for a
given percent
identity is determined by multiplying the total number of nucleic acids in SEQ
ID NO:1
by the integer defining the percent identity divided by 100 and then
subtracting that
product from said total number of nucleic acids in SEQ ID NO:1, or:
nn ~ xn ' (xn' Y)
wherein nn is the number of nucleic acid alterations, xn is the total number
of nucleic
acids in SEQ ID NO:1, y is, for instance 0.70 for 70%, 0.80 for 80%, 0.85 for
85% etc.,
1 ~ is the symbol for the multiplication operator, and wherein any non-integer
product of xn
and y is rounded down to the nearest integer prior to subtracting it from xn.
(2) Polypeptide embodiments further include an isolated polypeptide comprising
a
polypeptide having at least a 50,60, 70, 80, 85, 90, 95, 97 or 100% identity
to a
polypeptide reference sequence of SEQ ID N0:2, wherein said polypeptide
sequence may
be identical to the reference sequence of SEQ ID N0:2 or may include up to a
certain
integer number of amino acid alterations as compared to the reference
sequence, wherein
said alterations are selected from the group consisting of at least one amino
acid deletion,
substitution, including conservative and non-conservative substitution, or
insertion, and
?5 wherein said alterations may occur at the amino- or carboxy-terminal
positions of the
reference polypeptide sequence or anywhere between those terminal positions,
interspersed either individually among the arriino acids in the reference
sequence or in one
or more contiguous groups within the reference sequence, and wherein said
number of
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amino acid alterations is determined by multiplying the total number of amino
acids in
SEQ ID N0:2 by the integer defining the percent identity divided by 100 and
then
subtracting that product from said total number of amino acids in SEQ ID N0:2,
or:
na ~ xa - ~xa ~ Y)
wherein na is the number of amino acid alterations, xa is the total number of
amino acids
in SEQ ID N0:2, y is 0.50 for 50%, 0.60 for 60%, 0.70 for 70%, 0.80 for 80%,
0.85 for
85%, 0.90 for 90%, 0.95 for 95%, 0.97 for 97% or 1.00 for 100%, and ~ is the
symbol for
the multiplication opexator, and wherein any non-integer product of xa and y
is rounded
down to the nearest integer prior to subtracting it from xa.
By way of example, a polypeptide sequence of the present invention may be
identical to
the reference sequence of SEQ ID N0:2, that is it may be 100% identical, or it
may
include up to a certain integer number of amino acid alterations as compared
to the
reference sequence such that the percent identity is less than 100% identity.
Such
alterations are selected from the group consisting of at least one amino acid
deletion,
substitution, including conservative and non-conservative substitution, or
insertion, and
wherein said alterations may occur at the amino- or carboxy-terminal positions
of the
reference polypeptide sequence or anywhere between those terminal positions,
interspersed either individually among the amino acids in the reference
sequence or in one
or more contiguous groups within the reference sequence. The number of amino
acid
alterations for a given % identity is determined by multiplying the total
number of amino
acids in SEQ ID N0:2 by the integer defining the percent identity divided by
100 and
3~ then subtracting that product from said total number of amino acids in SEQ
ID N0:2, or:
na ~ xa - ~xa ~ Y)
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wherein na is the number of amino acid alterations, xa is the total number of
amino acids
in SEQ ID N0:2, y is, for instance 0.70 for 70%, 0.80 for 80%, 0.85 for 85%
etc., and ~ is
the symbol for the multiplication operator, and wherein any non-integer
product of xa and
y is rounded down to the nearest integer prior to subtracting it from xa.
"Individual{s)," when used herein with reference to an organism, means a
multicellular
eukaryote, including, but not limited to a metazoan, a mammal, an ovid, a
bovid, a simian,
a primate, and a human.
"Isolated" means altered "by the hand of man" from its natural state, i.e., if
it occurs in
nature, it has been changed or removed from its original environment, or both.
For example,
a polynucleotide or a polypeptide naturally present in a living organism is
not "isolated," but
the same polynucleotide or polypeptide separated from the coexisting materials
of its natural
state is "isolated", as the term is employed herein. Moreover, a
polynucleotide or
polypeptide that is introduced into an organism by transformation, genetic
manipulation or
by any other recombinant method is "isolated" even if it is still present in
said organism,
which organism may be living or non-living.
"Polynucleotide(s)" generally refers to any polyribonucleotide or
polydeoxyribonucleotide,
which may be unmodified RNA or DNA or modified RNA or DNA including single and
double-stranded regions.
"Variant" refers to a polynucleotide or polypeptide that differs from a
reference
polynucleotide or polypeptide, but retains essential properties. A typical
variant of a
polynucleotide differs in nucleotide sequence from another, reference
polynucleotide.
Changes in the nucleotide sequence of the variant may or may not alter the
amino acid
sequence of a polypeptide encoded by the reference polynucleotide. Nucleotide
changes
may result in amino acid substitutions, additions, deletions, fusions and
truncations in
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the polypeptide encoded by the reference sequence, as discussed below. A
typical
variant of a polypeptide differs in amino acid sequence from another,
reference
polypeptide. Generally, differences are limited so that the sequences of the
reference
polypeptide and the variant are closely similar overall and, in many regions,
identical.
A variant and reference polypeptide may differ in amino acid sequence by one
or more
substitutions, additions, deletions in any combination. A substituted or
inserted amino
acid residue may or may not be one encoded by the genetic code. A variant of a
polynucleotide or polypeptide may be a naturally occurring such as an allelic
variant, or
it may be a variant that is not known to occur naturally. Non-naturally
occurring
I 0 variants of polynucleotides and polypeptides may be made by mutagenesis
techniques
or by direct synthesis.
"Disease(s)" means any disease caused by or related to infection by a
bacteria, including,
for example, otitis media in infants and children, pneumonia in elderlies,
sinusitis,
15 nosocomial infections and invasive diseases, chronic otitis media with
hearing loss, fluid
accumulation in the middle ear, auditive nerve damage, delayed speech
learning, infection
of the upper respiratory tract and inflammation of the middle ear.
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EXAMPLES:
The examples below are carried out using standard techniques, which are well
known and
routine to those of skill in the art, except where otherwise described in
detail. The examples
are illustrative, but do not limit the invention.
Example 1:
Discovery and confirmatory DNA sequencing of the BASB009 gene from
Moraxella catarrhalis strain ATCC 43617.
The BASB009 gene of SEQ ID NO:1 was first discovered in the Incyte PathoSeq
data
base containing unfinished genomic DNA sequences of the Moraxella catarrhalis
strain
ATCC 43617 (also referred to as strain Mc2931 ). The translation of the
BASB009
polynucleotide sequence, shown in SEQ ID N0:2, showed significant similarity
(27
identity in a 237 amino acids overlap) to the TIyC hemolysin protein of
Serpulina
hyodysenteriae.
The sequence of the BASB009 gene was further confirmed experimentally. For
this
purpose, genomic DNA was extracted from 10'° cells of the M.
catarrhalis cells (strain
ATCC 43617) using the QIAGEN genomic DNA extraction kit (Qiagen Gmbh), and
1 pg of this material was submitted to Polymerase Chain Reaction DNA
amplification
using primers E475777a (5'-GCC TGA GGA TAT CAT GCC AG-3') [SEQ ID N0:9]
and E475778a (5'-GTG TAT TTG ATG CCA TAC AGG-3') [SEQ ID NO:10]. This
PCR product was purified on a Biorobot 9600 (Qiagen Gmbh) apparatus and
subjected
to DNA sequencing using the Big Dye Cycle Sequencing kit (Perkin-Elmer) and an
ABI
377/PRISM DNA sequencer. DNA sequencing was performed on both strands with a
redundancy of 2 and the full-length sequence was assembled using the
SequencherTM
software (Applied Biosytems). The resulting DNA sequence turned out to be 100
identical to SEQ ID NO:1.
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Example 2:
Variability analysis of the BASB009 gene among several Moraxella catarrhalis
strains.
2A: Restriction Fragment Length Analysis (RFLP).
Genomic DNA was extracted from 16 M. catarrhalis strains (presented in table
1) as
described below. M. catarrhalis was streaked for single colonies on BHI agar
plates and
grown overnight at 37°C. Three or four single colonies were picked and
used to
inoculate a ~l.Sml BHi (Brain-heart infusion) broth seed culture which was
grown
overnight in a shaking incubator, ~300rpm, at 37°C. A SOOmI erlenmeyer
flask
containing ~150m1 of BHI broth was inoculated with the seed culture and grown
for
~12-16 hours at 37°C in a shaking incubator, 175 rpm, to generate cell
mass for DNA
isolation. Cells were collected by centrifugation in a Sorvall GSA rotor at
~2000xg for
15 minutes at room temperature. The supernatant was removed and the cell
pellet
suspended in ~S.OmI of sterile water. An equal volume of lysis buffer (200mM
NaCI,
20mM EDTA, 40mM Tris-Hcl, pH 8.0, 0.5% (w/v) SDS, 0.5% (vlv) 2-
mercaptoethanol, and 250pg/ml of proteinase K) was added and the cells
suspended by
gentle agitation and trituration. The cell suspension was then incubated ~12
hours at
50°C to lyse the bacteria and liberate chromosomal DNA. Proteinaceous
material was
precipitated by the addition of S.OmI of saturated NaCI (~6.0 M, in sterile
water) and
centrifugation at ~S,SOOxg in a Sorvall SS34 rotor at room temperature.
Chromosomal
DNA was precipitated from the cleared supernatant by the addition of two
volumes of
100% ethanol. Aggregated DNA was collected and washed using gentle agitation
in a
2~ small volume of a 70% ethanol solution. Purified chromosomal DNA was
suspended in
sterile water and allowed to dissolve/.disburse overnight at 4°C by
gentle rocking. The
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concentration of dissolved DNA was determined spectrophotometrically at 260nm
using
an extinction coe~cient of 1.0 O.D. unit ~SOpg/ml.
This material was next submitted to PCR amplification using the MC-Hlyl-BamF
(5'
AAG GGC CCA ATT ACG CAG AGG GGA TCC GAA ATT GCT TTG GCA GGT
TCA AGA AAA ATC AAA C-3') [SEQ ID NO:11] and MC-Hlyl-SaIRC (5'-AAG
GGC CCA ATT ACG CAG AGG GTC GAC TTA TTA GTC TTC GTG CTT GGG
CAG TTG CTC TAG GCG-3') [SEQ ID N0:12] oligonucleotides. The corresponding
BASB009 gene amplicons were then subjected independantly to hydrolysis using
restriction enzymes (Alul, Maelll, Msel, Nlalll, Rsal, Sau3AlJ and restriction
products
were separated by agarose or polyacrylamide gel electrophoresis using standard
molecular biology procedures as described in "Molecular Cloning, a Laboratory
Manual, Second Edition, Eds: Sambrook, Fritsch & Maniatis, Cold Spring Harbor
press
1989". The photographs of the resulting electrophoresis gels are displayed in
Figure I .
For each strain, RFLP patterns corresponding to the 6 restriction enzymes were
scored
and combined. Groups of strains sharing identical combination of RFLP patterns
were
then defined. Using this methodology, the strains tested in this study fell
into 4 genomic
groups (Group I: Mc2912; Group 2: Mc2904, Mc2905, Mc2906, Mc2907, Mc2908,
Mc2909, Mc2913, Mc2926, Mc2931; Group 3; Mc2911; Group 4: Mc2910, Mc2912).
These RFLP data support that all the Moraxella catarrhalis strains used in
this study
display limited nucleotide sequence diversity for the BASB009 gene.
2B: DNA sequencing in other strains.
Using the experimental procedure described in Example 1, the sequence of the
BASB009 gene was also determined for three additional Moraxella catarrhalis
strains.
The nucleotide sequences of the BASB009 gene of the strains Mc2912 and Mc2913
and
Mc2969 are shown in SEQ ID N0:3, 5 and 7, respectively. These nucleotide
sequences
were translated into amino acid sequences, which are shown in SEQ ID N0:4, 6
and 8,
respectively. Using the MegAlign program from the DNASTAR Lasergene package, a
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multiple alignment of the nucleotide sequences of SEQ ID NO:1, 3, 5 and 7 was
performed, and is displayed in Figure 2. A pairwise comparison of identities
is
summarized in Table 2, showing that the four BASB009 nucleotide gene sequences
are
all similar at a identity level greater than 99% . Using the same program, a
multiple
alignment of the protein sequences of SEQ ID N0:2, 4, 6 and 8 was performed,
and is
displayed in Figure 3. A pairwise comparison of identities is summarized in
Table 3,
showing that the four BASB009 protein sequences are all similar at a identity
level
greater than 99 %. Taken together, these data indicate very strong sequence
conservation of the BASB009 gene among Moraxella catarrhalis strains.
Table 1: Features of the Moraxella catarrhalis strains used in this study
Strain Isolated from:
in:
_
Mc2904 USA Tympanocentesis
Mc2905 USA Tympanocentesis
Mc2906 USA Tympanocentesis
Mc2907 USA Tympanocentesis
Mc2908 USA ACUte otitis Tympanocentesis
Mc2909 USA Tympanocentesis
Mc2910 USA Tympanocentesis
Mc2911 USA ACUte OtitlS Tympanocentesis
Mc2912 USA Acute OtltiS Tympanocentesis
Mc2913 USA Acute otitis Tympanocentesis
Mc2926 USA ATCC49143
Mc2931 USA Transtracheal aspirate
/ATCC
Mc2956 Finland Middle ear fluid
Mc2960 Finland Middle ear fluid
Mc2969 Norway Nasopharynx(Pharyngitis-
Rhinitis)
Mc2975 Norwav Nasopharynx (Rhinitis)
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Table 2: Pairwise identities of the BASB009 polynucleotide sequences ( in % )
SeqID No:3SeqID No:SSeqID No:7
SeqID No:l99.5 99.9 99.5
SeqID No:3 99.4 99.9
SeqID No:S 99.5
Table 3. Pairwise identities of the BASB009 polypeptide sequences ( in % )
SeqID No:4SeqID No:6SeqID No:8
SeqID No:299.8 100. 100.
SeqID No:4 99.8 99.8
SeqID No:6 100.
Example 3: Efficacy of BASB09 vaccine: enhancement of lung clearance of M.
catarrhalis in mice.
Recombinant BASB09 protein was expressed in E. toll as a 6xHis tag fusion
protein
and was purified by Ni2+ -loaded Hitrap affinity chromatography (Pharmacia
Biotech).
The protective capacity of the purified recombinant BASB09 protein can be
evaluated
1 ~ in a mouse model.
This mouse model is based on the analysis of the lung invasion by M.
catarrhalis
following a standard intranasal challenge to vaccinated mice.
Groups of 6 BALB/c mice (females, 6 weeks old) are immunized subcutaneously
with
100.1 of vaccine corresponding to a l Opg dose and are boosted 2 weeks later.
One week
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after the booster, the mice are challenged by instillation of 50 ~l of
bacterial suspension
(+/-10° CFU/50 ~,1) into the left nostril under anaesthesia (mice are
anaesthetised with a
combination of ketamine and xylazine anaesthetics, 0.24 mg xylazine (Rompun)
and 0.8
mg ketamine (Imalgene)/100 ~l). Mice are killed 4 hours after challenge and
the lungs
are removed aseptically and homogenized individually. The log 10 weighted mean
number of CFU/lung is determined by counting the colonies grown on Mueller-
Hinton
agar plates after plating of 20 pl of 5 serial dilutions of the homogenate.
The arithmetic
mean of the 1og10 weighted mean number of CFU/lung and the standard deviations
are
calculated for each group.
Results are analysed statistically by applying 1-way ANOVA after assuming
equality of
variance (checked by Brown and Forsythe's test) and normality (checked using
the
Shapiro-Wilk test). Differences between groups were analysed using the Dunnet
test,
Tukey's studentised range test (HSD) and Student-Newman-Keuls test.
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Deposited materials
A deposit containing a Mcraxella catarrhalis Catlin strain has been deposited
with the American
Type Culture Collection (herein "ATCC") on June 21, 1997 and assigned deposit
number 43617.
The deposit was described as Branhamella catarrhalis (Frosch and Kolle) and is
a freeze-dried, 1.5-
2.9 kb insert library constructed from M. catanrhalis isolate obtained from a
transtracheal aspirate of
a coal miner with chronic bronchitits. The deposit is described in Antimicrob.
Agents Chemother.
21: 506-508 ( 1982).
The Moraxella catarrhali.s strain deposit is referred to herein as "the
deposited strain" or as "the
DNA of the deposited strain."
The deposited strain contains a full lengthBASB009 gene.
A deposit of the vector pMC-Hlyl consisting ofMoraxella catarrhalis DNA
inserted in pQE30 has
been deposited with the American Type Culture Collection (ATCC) on February 12
1999 and
assigned deposit number 207104.
The sequence of the polynucleotides contained in the deposited strain / clone,
as well as the amino
acid sequence of any polypeptide encoded thereby, are controlling in the event
of any conflict with
any description of sequences herein.
The deposit of the deposited strains have been made under the terms of the
Budapest Treaty on the
lntemational Recognition of the Deposit of Micro-organisms for Purposes of
Patent Procedure. The
deposited strains will be irrevocably and without restriction or condition
released to the public upon
the issuance of a patent. The deposited strains are provided merely as
convenience to those of skill
in the art and are not an admission that a deposit is required for enablement,
such as that required
under 35 U.S.C. ~ 112.
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SEQUENCE LISTING
<110> SmithKline Heecham Biologicals S.A.
<120> Novel Compounds
<130> BM45317
<160> 12
<170> FastSEQ for Windows Version 3.0
<210> 1
<211> 1323
<212> DNA
<213> Bacteria
<400> 1
atgggtgttactgtgagtttgtttcaaaactttatgattattcttgtactgattttgaca60
tcgagttttttctcgatttcagaaattgctttggcaggttcaagaaaaatcaaacttaaa120
ttactggcagaatcaggcgatgaccgtgccgagaaagtcttaaaattgcaagaaaattca180
gctgatttttttgccacttcacaaattggcctaaatgctgtcgccattttgggcggttcg240
gttggtgaaagtgccttgcgtccttatttttccgaatggattggcttggtatatcaaggg300
atttggcttgacagcatcgcttttttttcgtcgtttgttttggtaacactgctatttatt360
ttatatgctgacctgattcccaaacgcattgcaatgattaatcctgagcgagtggctttg420
gtggtcatcaatccgattttatggacaattcgtgtggtcaagcccttggcatggatcatc480
aataccatcgcagatgtgacttttcggctttttaaatttgatacggctcgtgatgacagt540
atcacctttgatgatatttctgccattgttgatgctggggcagaggctggcgttttgatg600
gaacaagaacagcactttatcgaaaatgtttttgaacttgaagaacgcaccgtgccatca660
tcgatgacggctcgtgaggatgtggtatattttgcactcagtgaaagcgaggagagtatt720
cgtcaaaagattgccgattatccttattctaaatttttggtctgtaatgagcatatcgac780
caagtcatcggttatgtcgataccaaggatattttggtacgaattttaagcgaacagcca840
atttttcagctgaatgaatctaccattcgtaatgtactgattattccagatacactcact900
ttatccgagcttttggataaatttcgtgccagtaatgaaaaaatggcggtagtcattaat960
gaatatgcattggttgttgggctaattacactatcagatattatgatgactgtcatgggc1020
gattgggcagccgctgagcctgaagatttacaaatcattcgccgtgatgaaaattcatgg1080
CA 02328061 2000-11-10
WO 99/58562 PC'T/EP99/83262
ctgattgatgggattacgccgattgatgatgttaaacatgcccttgatattaatgagttt1140
cctgattgggatcactatgagacgctggcgggctttattatgtatcgcctgcgtaagatt1200
ccacgccctgcagactgggtagagcatgagggctttaaatttgaggtggtagatatcgac1260
cattataagattgaccaacttttggtaactcgcctagagcaactgcccaagcacgaagac1320
taa 1323
c210> 2
<211> 440
<212> PRT
<213> Bacteria
<400> 2
Met Gly Val Thr Val Ser Leu Phe Gln Asn Phe Met Ile Ile Leu Val
1 5 10 15
Leu Ile Leu Thr Ser Ser Phe Phe Ser Ile Ser Glu Ile Ala Leu Ala
20 25 30
Gly Ser Arg Lys Ile Lys Leu Lys Leu Leu Ala Glu Ser Gly Asp Asp
35 40 45
Arg Ala Glu Lys Val Leu Lys Leu Gln Glu Asn Ser Ala Asp Phe Phe
50 55 60
Ala Thr Ser Gln Ile Gly Leu Asn Ala Val Ala Ile Leu Gly Gly Ser
65 70 75 80
Val Gly Glu Ser Ala Leu Arg Pro Tyr Phe Ser Glu Trp Ile Gly Leu
85 90 95
Val Tyr Gln Gly Ile Trp Leu Asp Ser Ile Ala Phe Phe Ser Ser Phe
100 105 110
Val Leu Val Thr Leu Leu Phe Ile Leu Tyr Ala Asp Leu Ile Pro Lys
115 120 125
Arg Ile Ala Met Ile Asn Pro Glu Arg Val Ala Leu Val Val Ile Asn
130 135 140
Pro Ile Leu Trp Thr Ile Arg Val Val Lys Pro Leu Ala Trp Ile Ile
145 150 155 160
Asn Thr Ile Ala Asp Val Thr Phe Arg Leu Phe Lys Phe Asp Thr Ala
165 170 175
Arg Asp Asp Ser Ile Thr Phe Asp Asp Ile Ser Ala Ile Val Asp Ala
180 185 190
Gly Ala Glu Ala Gly Val Leu Met Glu Gln Glu Gln His Phe Ile Glu
195 200 205
Asn Val Phe Glu Leu Glu Glu Arg Thr Val Pro Ser Ser Met Thr Ala
2
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210 215 220
Arg Glu Asp Val Val Tyr Phe Ala Leu Ser Glu Ser Glu Glu Ser Ile
225 230 235 240
Arg Gln Lys Ile Ala Asp Tyr Pro Tyr Ser Lys Phe Leu Val Cys Asn
245 250 255
Glu His Ile Asp Gln Val Ile Gly Tyr Val Asp Thr Lys Asp Ile Leu
260 265 270
Val Arg Ile Leu Ser Glu Gln Pro Ile Phe Gln Leu Asn Glu Ser Thr
275 280 285
Ile Arg Asn Val Leu Ile Ile Pro Asp Thr Leu Thr Leu Ser Glu Leu
290 295 300
Leu Asp Lys Phe Arg Ala Ser Asn Glu Lys Met Ala Val Val Ile Asn
305 310 315 320
Glu Tyr Ala Leu Val Val Gly Leu Ile Thr Leu Ser Asp Ile Met Met
325 330 335
Thr Val Met Gly Asp Trp Ala Ala Ala Glu Pro Glu Asp Leu Gln Ile
340 345 350
Ile Arg Arg Asp Glu Asn Ser Trp Leu Ile Asp Gly Ile Thr Pro Ile
355 360 365
Asp Asp Val Lys His Ala Leu Asp Ile Asn Glu Phe Pro Asp Trp Asp
370 375 380
His Tyr Glu Thr Leu Ala Gly Phe Ile Met Tyr Arg Leu Arg Lys Ile
385 390 395 400
Pro Arg Pro Ala Asp Trp Val Glu His Glu Gly Phe Lys Phe Glu Val
405 410 415
Val Asp Ile Asp His Tyr Lys Ile Asp Gln Leu Leu Val Thr Arg Leu
420 425 430
Glu Gln Leu Pro Lys His Glu Asp
435 440
<210> 3
<211> 1323
<212> DNA
<213> Bacteria
<400> 3
atgggtgtta ctgtgagttt gtttcaaaac tttatgatta ttcttgtact gattttgaca 60
tcgagttttt tctcgatttc agaaattgct ttggcaggtt caagaaaaat caaacttaaa 120
ttactggcag aatcaggcga tgaccgtgcc gagaaagtct tgaaattgca agaaaattca 180
3
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gctgatttttttgccacttcacaaattggcctaaatgctgtcgccattttgggcggttcg240
gttggtgaaagtgccttgcgtccttattttCccgaatggattggcttggtatatcaaggg300
atttggcttgacagcatcgcttttttttcgtcgtttgttttggtaacactgctatttatt360
ttatatgctgacctgattcccaaacgcattgcaatgattaatcctgagcgagtggctttg420
gtggtcatcaatccgattttgtggacaattcgtgtggtcaagcccttggcatggattatc480
aataccatcgcagatgtgacttttcggttttttaaatttgatacggctcgtgatgacagt540
atcacctttgatgatatttctgccattgttgatgctggggcagaggctggcgttctgatg600
gaacaagaacaacattttatcgaaaatgtttttgaacttgaagaacgcaccgtgccatca660
tcgatgacggctcgtgaggatgtggtatattttgcactcagtgaaagcgaggagagtatt720
cgtcaaaagattgccgattatccttattctaaatttttggtctgtaatgagcatatcgac780
caagtcatcggttatgtcgataccaaggatattttggtacgaattttaagcgaacagcca840
atttttcagctgaatgaatctaccattcgtaatgtactgattattccagatacactcact900
ttatccgagcttttggataaatttcgtgccagtaatgaaaaaatggcggtagtcattaat960
gaatatgcattggttgttgggctaattacactatcagatattatgatgactgtcatgggc1020
gattgggcagccgctgagcctgaagatttacaaatcattcgccgtgatgaaaattcatgg1080
ctgattgatgggattacgccgattgatgatgttaaacatgcccttgatattaatgagttt1140
cctgattgggatcactatgagacgctggcgggctttattatgtatcgcctgcgtaagatt1200
ccacgccctgcagactgggtagagcatgagggctttaaatttgaggtggtagatatcgac1260
cattataagattgaccaacttttggtaactcgcctagagcaactgcccaagcacgaagac1320
taa
1323
<210> 4
<211> 440
<212> PRT
<213> Bacteria
<400> 4
Met Gly Val Thr Val Ser Leu Phe Gln Asn Phe Met Ile Ile Leu Val
1 5 10 15
Leu Ile Leu Thr Ser Ser Phe Phe Ser Ile Ser Glu Ile Ala Leu Ala
20 25 30
Gly Ser Arg Lys Ile Lys Leu Lys Leu Leu Ala Glu Ser Gly Asp Asp
35 40 45
Arg Ala Glu Lys Val Leu Lys Leu Gln Glu Asn Ser Ala Asp Phe Phe
50 55 60
Ala Thr Ser Gln Ile Gly Leu Asn Ala Val Ala Ile Leu Gly Gly Ser
65 70 75 80
Val Gly Glu Ser Ala Leu Arg Pro Tyr Phe Ser Glu Trp Ile Gly Leu
85 90 95
4
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Val Tyr Gln Gly Ile Trp Leu Asp Ser Ile Ala Phe Phe Ser Ser Phe
100 105 110
Val Leu Val Thr Leu Leu Phe Ile Leu Tyr Ala Asp Leu Ile Pro Lys
115 120 125
Arg Ile Ala Met Ile Asn Pro Glu Arg Val Ala Leu Val Val Ile Asn
130 135 140
Pro Ile Leu Trp Thr Ile Arg Val Val Lys Pro Leu Ala Trp Ile Ile
145 150 155 160
Asn Thr Ile Ala Asp Val Thr Phe Arg Phe Phe Lys Phe Asp Thr Ala
165 170 175
Arg Asp Asp Ser Ile Thr Phe Asp Asp Ile Ser Ala Ile Val Asp Ala
180 185 190
Gly Ala Glu Ala Gly Val Leu Met Glu Gln Glu Gln His Phe Ile Glu
195 200 205
Asn Val Phe Glu Leu Glu Glu Arg Thr Val Pro Ser Ser Met Thr Ala
210 215 220
Arg Glu Asp Val Val Tyr Phe Ala Leu Ser Glu Ser Glu Glu Ser Ile
225 230 235 240
Arg Gln Lys Ile Ala Asp Tyr Pro Tyr Ser Lys Phe Leu Val Cys Asn
245 250 255
Glu His Ile Asp Gln Val Ile Gly Tyr Val Asp Thr Lys Asp Ile Leu
260 265 270
Val Arg ile Leu Ser Glu Gln Pro Ile Phe Gln Leu Asn Glu Ser Thr
275 280 285
Ile Arg Asn Val Leu Ile Ile Pro Asp Thr Leu Thr Leu Ser Glu Leu
290 295 300
Leu Asp Lys Phe Arg Ala Ser Asn Glu Lys Met Ala Val Val Ile Asn
305 310 315 320
Glu Tyr Ala Leu Val Val Gly Leu Ile Thr Leu Ser Asp Ile Met Met
325 330 335
Thr Val Met Gly Asp Trp Ala Ala Ala Glu Pro Glu Asp Leu Gln Ile
340 345 350
Ile Arg Arg Asp Glu Asn Ser Trp Leu Ile Asp Gly Ile Thr Pro Ile
355 360 365
Asp Asp Val Lys His Ala Leu Asp Ile Asn Glu Phe Pro Asp Trp Asp
370 375 380
His Tyr Glu Thr Leu Ala Gly Phe Ile Met Tyr Arg Leu Arg Lys Ile
385 390 395 400
Pro Arg Pro Ala Asp Trp Val Glu His Glu Gly Phe Lys Phe Glu Val
CA 02328061 2000-11-10
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405 410 415
Val Asp Ile Asp His Tyr Lys Ile Asp Gln Leu Leu Val Thr Arg Leu
420 425 430
Glu Gln Leu Pro Lys His Glu Asp
435 440
<210> 5
<211> 1323
<212> DNA
<213> Bacteria
<400> 5
atgggtgttactgtgagtttgtttcaaaactttatgattattcttgtactgattttgaca60
tcgagttttttctcgatttcagaaattgctttggcaggttcaagaaaaatcaaacttaaa120
ttactggcagaatcaggcgatgaccgtgccgagaaagtcttaaaattgcaagaaaattca180
gctgatttttttgccacttcacaaattggcctaaatgctgtcgccattttgggcggttcg240
'
gttggtgaaagtgccttgcgtccttatttttccgaatggattggcttggtatatcaaggg300
atttggcttgacagcatcgcttttttttcgtcgtttgttttggtaacactgctatttatt360
ttatatgctgacctgattcccaaacgcattgcaatgattaatcctgagcgagtggctttg420
gtggtcatcaatccgattttatggacaattcgtgtggtcaagcccttggcatggatcatc480
aataccatcgcagatgtgacttttcggctttttaaatttgatacggctcgtgatgacagt540
atcacctttgatgatatttctgccattgttgatgctggggcagaggctggcgttttgatg600
gaacaagaacagcactttatcgaaaatgtttttgaacttgaagaacgcaccgtgccatca660
tcgatgacggctcgtgaggatgtggtatattttgcactcagtgaaagcgaggagagtatt720
cgtcaaaagattgccgattatccttattctaaatttttggtctgtaatgagcatatcgac780
caagtcatcggttatgtcgataccaaggatattttggtacgaattttaagcgaacagcca840
atttttcagctgaatgaatctaccattcgaaatgtactgattattccagatacactcact900
ttatccgagcttttggataaatttcgtgccagtaatgaaaaaatggcggtagtcattaat960
gaatatgcattggttgttgggctaattacactatcagatattatgatgactgtcatgggc1020
gattgggcagccgctgagcctgaagatttacaaatcattcgccgtgatgaaaattcatgg1080
ctgattgatgggattacgccgattgatgatgttaaacatgcccttgatattaatgagttt1140
cctgattgggatcactatgagacgctggcgggctttattatgtatcgcctgcgtaagatt1200
ccacgccctgcagactgggtagagcatgagggctttaaatttgaggtggtagatatcgac1260
cattataagattgaccaacttttggtaactcgcctagagcaactgcccaagcacgaagac1320
taa
1323
<210> 6
<211> 439
<212> PRT
6
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<213> Bacteria
<400> 6
Met Gly Val Thr Val Ser Leu Phe Gln Asn Phe Met Ile Ile Leu Val
1 5 10 15
Leu Ile Leu Thr Ser Ser Phe Phe Ser Ile Ser Glu Ile Ala Leu Ala
20 25 30
Gly Ser Arg Lys Ile Lys Leu Lys Leu Leu Ala Glu Ser Gly Asp Asp
35 40 45
Arg Ala Glu Lys Val Leu Lys Leu Gln Glu Asn Ser Ala Asp Phe Phe
50 55 60
Ala Thr Ser Gln Ile Gly Leu Asn Ala Val Ala Ile Leu Gly Gly Ser
65 70 75 80
Val Gly Glu Ser Ala Leu Arg Pro Tyr Phe Ser Glu Trp Ile Gly Leu
85 90 95
Val Tyr Gln Gly Ile Trp Leu Asp Ser Ile Ala Phe Phe Ser Ser Phe
100 105 110
Val Leu Val Thr Leu Leu Phe Ile Leu Tyr Ala Asp Leu Ile Pro Lys
115 120 125
Arg Ile Ala Met Ile Asn Pro Glu Arg Val Ala Leu Val Val Ile Asn
130 135 140
Pro Ile Leu Trp Thr Ile Arg Val Val Lys Pro Leu Ala Trp Ile Ile
145 150 155 160
Asn Thr Ile Ala Asp Val Thr Phe Arg Leu Phe Lys Phe Asp Thr Ala
165 170 175
Arg Asp Asp Ser Ile Thr Phe Asp Asp Ile Ser Ala Ile Val Asp Ala
180 185 190
Gly Ala Glu Ala Gly Val Leu Met Glu Gln Glu Gln His Phe Ile Glu
195 200 205
Asn Val Phe Glu Leu Glu Glu Arg Thr Val Pro Ser Ser Met Thr Ala
210 215 220
Arg GIu Asp Val Val Tyr Phe Ala Leu Ser Glu Ser Glu Glu Ser Ile
225 230 235 240
Arg Gln Lys Ile Ala Asp Tyr Pro Tyr Ser Lys Phe Leu Val Cys Asn
245 250 255
Glu His Ile Asp Gln Val Ile Gly Tyr Val Asp Thr Lys Asp Ile Leu
260 265 270
Val Arg Ile Leu Ser Glu Gln Ile Phe Gln Leu Asn Glu Ser Thr Ile
275 280 285
7
CA 02328061 2000-11-10
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Arg Asn Val Leu Ile Ile Pro Asp Thr Leu Thr Leu Ser Glu Leu Leu
290 295 300
Asp Lys Phe Arg Ala Ser Asn Glu Lys Met Ala Val Val Ile Asn Glu
305 310 315 320
Tyr Ala Leu Val Val Gly Leu Ile Thr Leu Ser Asp Ile Met Met Thr
325 330 335
Val Met Gly Asp Trp Ala Ala Ala Glu Pro Glu Asp Leu Gln Ile Ile
340 345 350
Arg Arg Asp Glu Asn Ser Trp Leu Ile Asp Gly Ile Thr Pro Ile Asp
355 360 365
Asp Val Lys His Ala Leu Asp Ile Asn Glu Phe Pro Asp Trp Asp His
370 375 380
Tyr Glu Thr Leu Ala Gly Phe Ile Met Tyr Arg Leu Arg Lys Ile Pro
385 390 395 400
Arg Pro Ala Asp Trp Val Glu His Glu Gly Phe Lys Phe Glu Val Val
405 410 415
Asp Ile Asp His Tyr Lys Ile Asp Gln Leu Leu Val Thr Arg Leu Glu
420 425 430
Gln Leu Pro Lys His Glu Asp
435
<210> 7
<211> 1323
<212> DNA
<213> Bacteria
<400>
7
atgggtgttactgtgagtttgtttcaaaactttatgattattcttgtactgattttgaca60
tcgagttttttctcgatttcagaaattgctttggcaggttcaagaaaaatcaaacttaaa120
ttactggcagaatcaggcgatgaccgtgccgagaaagtcttgaaattgcaagaaaattca180
gctgatttttttgccacttcacaaattggcctaaatgctgtcgccattttgggcggttcg240
gttggtgaaagtgccttgcgtccttatttttccgaatggattggcttggtatatcaaggg300
atttggcttgacagcatcgcttttttttcgtcgtttgttttggtaacactgctatttatt360
ttatatgctgacctgattcccaaacgcattgcaatgattaatcctgagcgagtggctttg420
gtggtcatcaatccgattttgtggacaattcgtgtggtcaagcccttggcatggattatc480
aataccatcgcagatgtgacttttcggctttttaaatttgatacggctcgtgatgacagt540
atcacctttgatgatatttctgccattgttgatgctggggcagaggctggcgttctgatg600
gaacaagaacaacattttatcgaaaatgtttttgaacttgaagaacgcaccgtgccatca660
tcgatgacggctcgtgaggatgtggtatattttgcactcagtgaaagcgaggagagtatt720
g
CA 02328061 2000-11-10
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cgtcaaaagattgccgattatccttattctaaatttttggtctgtaatgagcatatcgac780
caagtcatcggttatgtcgataccaaggatattttggtacgaattttaagcgaacagcca840
atttttcagctgaatgaatctaccattcgtaatgtactgattattccagatacactcact900
ttatccgagcttttggataaatttcgtgccagtaatgaaaaaatggcggtagtcattaat960
gaatatgcattggttgttgggctaattacactatcagatattatgatgactgtcatgggc1020
gattgggcagccgctgagcctgaagatttacaaatcattcgccgtgatgaaaattcatgg1080
ctgattgatgggattacgccgattgatgatgttaaacatgcccttgatattaatgagttt1140
cctgattgggatcactatgagacgctggcgggctttattatgtatcgcctgcgtaagatt1200
ccacgccctgcagactgggtagagcatgagggctttaaatttgaggtggtagatatcgac1260
cattataagattgaccaacttttggtaactcgcctagagcaactgcccaagcacgaagac1320
taa
1323
<210> 8
<211> 439
<212> PRT
<213> Bacteria
<400> 8
Met Gly Val Thr Val Ser Leu Phe Gln Asn Phe Met Ile Ile Leu Val
1 5 10 15
Leu Ile Leu Thr Ser Ser Phe Phe Ser Ile Ser Glu Ile Ala Leu Ala
20 25 30
Gly Ser Arg Lys Ile Lys Leu Lys Leu Leu Ala Glu Ser Gly Asp Asp
35 40 45
Arg Ala Glu Lys Val Leu Lys Leu Gln Glu Asn Ser Ala Asp Phe Phe
50 55 60
Ala Thr Ser Gln Ile Gly Leu Asn Ala Val Ala Ile Leu Gly Gly Ser
65 70 75 gp
Val Gly Glu Ser Ala Leu Arg Pro Tyr~Phe Ser Glu Trp Ile Gly Leu
85 90 95
Val Tyr Gln Gly Ile Trp Leu Asp Ser Ile Ala Phe Phe Ser Ser Phe
100 105 110
Val Leu Val Thr Leu Leu Phe Ile Leu Tyr Ala Asp Leu Ile Pro Lys
115 120 125
Arg Ile Ala Met Ile Asn Pro Glu Arg Val Ala Leu Val Val Ile Asn
130 135 140
Pro Ile Leu Trp Thr Ile Arg Val Val Lys Pro Leu Ala Trp Ile Ile
145 150 155 160
Asn Thr Ile Ala Asp Val Thr Phe Arg Leu Phe Lys Phe Asp Thr Ala
9
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165 170 175
Arg Asp Asp Ser Ile Thr Phe Asp Asp Ile Ser Ala Ile Val Asp Ala
180 185 190
Gly Ala Glu Ala Gly Val Leu Met Glu Gln Glu Gln His Phe Ile Glu
195 200 205
Asn Val Phe Glu Leu Glu Glu Arg Thr Val Pro Ser Ser Met Thr Ala
210 215 220
Arg Glu Asp Val Val Tyr Phe Ala Leu Ser Glu Ser Glu Glu Ser Ile
225 230 235 240
Arg Gln Lys Ile Ala Asp Tyr Pro Tyr Ser Lys Phe Leu Val Cys Asn
245 250 255
Glu His Ile Asp Gln Val Ile Gly Tyr Val Asp Thr Lys Asp Ile Leu
260 265 270
Val Arg Ile Leu Ser Glu Gln Pro Ile Phe Gln Leu Asn Glu Ser Thr
275 280 285
Ile Arg Asn Val Leu Ile Ile Pro Asp Thr Leu Thr Leu Ser Glu Leu
290 295 300
Leu Asp Lys Phe Arg Ala Ser Asn Glu Lys Met Ala Val Val Ile Asn
305 310 315 320
Glu Tyr Ala Leu Val Val Gly Leu Ile Thr Leu Ser Asp Ile Met Met
325 330 335
Thr Val Met Gly Asp Trp Ala Ala Ala Glu Pro Glu Asp Gln Ile Ile
340 345 350
Arg Arg Asp Glu Asn Ser Trp Leu Ile Asp Gly Ile Thr Pro Ile Asp
355 360 365
Asp Val Lys His Ala Leu Asp Ile Asn Glu Phe Pro Asp Trp Asp His
370 375 380
Tyr Glu Thr Leu Ala Gly Phe Ile Met Tyr Arg Leu Arg Lys Ile Pro
385 390 395 400
Arg Pro Ala Asp Trp Val Glu His Glu Gly Phe Lys Phc Glu Val Val
405 410 415
Asp Ile Asp His Tyr Lys Ile Asp Gln Leu Leu Val Thr Arg Leu Glu
420 425 430
Gln Leu Pro Lys His Glu Asp
435
<210> 9
<211> 20
<212> DNA
1
CA 02328061 2000-11-10
WO 99/58562 PCT/EP99/03262
<213> Artificial Sequence
<220>
c223> Oligonucleotide
<400> 9
gcctgaggat atcatgccag 20
<210> 10
<211> 21
<212> DNA
<213> Artificial Sequence
<220>
c223> Oligonucleotide
<400> 10
gtgtatttga tgccatacag g 21
<210> 11
<211> 61
<212> DNA
<213> Artificial Sequence
<220>
c223> Oligonucleotide
<400> 11
aagggcccaa ttacgcagag gggatccgaa attgctttgg caggttcaag aaaaatcaaa 60
c 61
<210> 12
<211> 63
<212> DNA
<213> Artificial Sequence
<220>
<223> oligonucleotide
11
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<400> 12
aagggcccaa ttacgcagag ggtcgactta ttagtcttcg tgcttgggca gttgctctag 60
gcg 63
12
CA 02328061 2000-11-10
WO 99158562 PCT/EP99103262
SEQUENCE INFORMATION
BASB009 Polynucleotide and Polypeptide Sequences
SEQ ID NO:1
Moraxella catarrhalis BASB009 polynucleotide sequence from strain MC2931
ATGGGTGTTACTGTGAGTTTGTTTCAAAACTTTATGATTATTCTTGTACTGATTTTGACA
TCGAGTTTTTTCTCGATTTCAGAAATTGCTTTGGCAGGTTCAAGAAAAATCAAACTTAAA
TTACTGGCAGAATCAGGCGATGACCGTGCCGAGAAAGTCTTAAAATTGCAAGAAAATTCA
GCTGATTTTTTTGCCACTTCACAAATTGGCCTAAATGCTGTCGCCATTTTGGGCGGTTCG
GTTGGTGAAAGTGCCTTGCGTCCTTATTTTTCCGAATGGATTGGCTTGGTATATCAAGGG
ATTTGGCTTGACAGCATCGCTTTTTTTTCGTCGTTTGTTTTGGTAACACTGCTATTTATT
TTATATGCTGACCTGATTCCCAAACGCATTGCAATGATTAATCCTGAGCGAGTGGCTTTG
GTGGTCATCAATCCGATTTTATGGACAATTCGTGTGGTCAAGCCCTTGGCATGGATCATC
AATACCATCGCAGATGTGACTTTTCGGCTTTTTAAATTTGATACGGCTCGTGATGACAGT
ATCACCTTTGATGATATTTCTGCCATTGTTGATGCTGGGGCAGAGGCTGGCGTTTTGATG
GAACAAGAACAGCACTTTATCGAAAATGTTTTTGAACTTGAAGAACGCACCGTGCCATCA
TCGATGACGGCTCGTGAGGATGTGGTATATTTTGCACTCAGTGAAAGCGAGGAGAGTATT
CGTCAAAAGATTGCCGATTATCCTTATTCTAAATTTTTGGTCTGTAATGAGCATATCGAC
CAAGTCATCGGTTATGTCGATACCAAGGATATTTTGGTACGAATTTTAAGCGAACAGCCA
ATTTTTCAGCTGAATGAATCTACCATTCGTAATGTACTGATTATTCCAGATACACTCACT
TTATCCGAGCTTTTGGATAAATTTCGTGCCAGTAATGAAAAAATGGCGGTAGTCATTAAT
GAATATGCATTGGTTGTTGGGCTAATTACACTATCAGATATTATGATGACTGTCATGGGC
GATTGGGCAGCCGCTGAGCCTGAAGATTTACAAATCATTCGCCGTGATGAAAATTCATGG
CTGATTGATGGGATTACGCCGATTGATGATGTTAAACATGCCCTTGATATTAATGAGTTT
CCTGATTGGGATCACTATGAGACGCTGGCGGGCTTTATTATGTATCGCCTGCGTAAGATT
CCACGCCCTGCAGACTGGGTAGAGCATGAGGGCT~"TAAATTTGAGGTGGTAGATATCGAC
CATTATAAGATTGACCAACTTTTGGTAACTCGCCTAGAGCAACTGCCCAAGCACGAAGAC
TAA
SEQ ID N0:2
Moraxella catarrhalis BASB009 polypeptide sequence from strain MC2931
MGVTVSLFQNFMIILVLILTSSFFSISEIALAGSRKIKLKLLAESGDDRAEKVLKLQENS
ADFFATSQIGLNAVAILGGSVGESALRPYFSEWIGLWQGIWLDSIAFFSSFVLVTLLFI
LYADLIPKRIAMINPERVALWINPILWTIRVVKPLAWIINTIADVTFRLFKFDTARDDS
ITFDDISAIVDAGAEAGVLMEQEQHFIENVFELEERTVPSSMTAREDWYFALSESEESI
RQKIADYPYSKFLVCNEHIDQVIGYVDTKDILVRILSEQPIFQLNESTIRNVLIIPDTLT
LSELLDKFRASNEKMAWINEYALWGLITLSDIMMTVMGDWAAAEPEDLQIIRRDENSW
LIDGITPIDDVKHALDINEFPDWDHYETLAGFIMYRLRKIPRPADWVEHEGFKFEWDID
HYKIDQLLVTRLEQLPKHED
SEQ ID N0:3
Moraxella catarrhalis BASB009 polynucleotide sequence from strain Mcat 2912
13
CA 02328061 2000-11-10
WO 99158562 PCT/EP99103262
ATGGGTGTTACTGTGAGTTTGTTTCAAAACTTTATGATTATTCTTGTACTGATTTTGACATCGAGTTTTT
TCTCGATTTCAGAAATTGCTTTGGCAGGTTCAAGAAAAATCAAACTTAAATTACTGGCAGAATCAGGCGA
TGACCGTGCCGAGAAAGTCTTGAAATTGCAAGAAAATTCAGCTGATTTTTTTGCCACTTCACAAATTGGC
CTAAATGCTGTCGCCATTTTGGGCGGTTCGGTTGGTGAAAGTGCCTTGCGTCCTTATTTTTCCGAATGGA
TTGGCTTGGTATATCAAGGGATTTGGCTTGACAGCATCGCTTTTTTTTCGTCGTTTGTTTTGGTAACACT
GCTATTTATTTTATATGCTGACCTGATTCCCAAACGCATTGCAATGATTAATCCTGAGCGAGTGGCTTTG
GTGGTCATCAATCCGATTTTGTGGACAATTCGTGTGGTCAAGCCCTTGGCATGGATTATCAATACCATCG
CAGATGTGACTTTTCGGTTTTTTAAATTTGATACGGCTCGTGATGACAGTATCACCTTTGATGATATTTC
TGCCATTGTTGATGCTGGGGCAGAGGCTGGCGTTCTGATGGAACAAGAACAACATTTTATCGAAAATGTT
TTTGAACTTGAAGAACGCACCGTGCCATCATCGATGACGGCTCGTGAGGATGTGGTATATTTTGCACTCA
GTGAAAGCGAGGAGAGTATTCGTCAAAAGATTGCCGATTATCCTTATTCTAAATTTTTGGTCTGTAATGA
GCATATCGACCAAGTCATCGGTTATGTCGATACCAAGGATATTTTGGTACGAATTTTAAGCGAACAGCCA
ATTTTTCAGCTGAATGAATCTACCATTCGTAATGTACTGATTATTCCAGATACACTCACTTTATCCGAGC
TTTTGGATAAATTTCGTGCCAGTAATGAAAAAATGGCGGTAGTCATTAATGAATATGCATTGGTTGTTGG
GCTAATTACACTATCAGATATTATGATGACTGTCATGGGCGATTGGGCAGCCGCTGAGCCTGAAGATTTA
CAAATCATTCGCCGTGATGAAAATTCATGGCTGATTGATGGGATTACGCCGATTGATGATGTTAAACATG
CCCTTGATATTAATGAGTTTCCTGATTGGGATCACTATGAGACGCTGGCGGGCTTTATTATGTATCGCCTGC
GTAAGATTCCACGCCCTGCAGACTGGGTAGAGCATGAGGGCTTTAAATTTGAGGTGGTAGATATCGACCATT
ATAAGATTGACCAACTTTTGGTAACTCGCCTAGAGCAACTGCCCAAGCACGAAGACTAA
SEQ ID N0:4
Moraxella catarrhalis BASB009 polypeptide sequence from strain Mcat 2912
MGVTVSLFQNFMIILVLILTSSFFSISEIALAGSRKIKLKLLAESGDDRAEKVLKLQENSADFFATSQIG
LNAVAILGGSVGESALRPYFSEWIGLWQGIWLDSIAFFSSFVLVTLLFILYADLIPKRIAMINPERVAL
WINPILWTIRVVKPLAWIINTIADVTFRFFKFDTARDDSITFDDISAIVDAGAEAGVLMEQEQHFIENV
FELEERTVPSSMTAREDVVYFALSESEESIRQKIADYPYSKFLVCNEHIDQVIGYVDTKDILVRILSEQP
IFQLNESTIRNVLIIPDTLTLSELLDKFRASNEKMAWINEYALWGLITLSDINllHTVMGDWAAAEPEDL
QIIRRDENSWLIDGITPIDDVKHALDINEFPDWDHYETLAGFIMYRLRKIPRPADWVEHEGFKFEVVDID
HYKIDQLLVTRLEQLPKHED
SEQ ID NO:S
Moraxella catarrhalis BASB009 polynucleotide sequence from strain Mcat 2913
ATGGGTGTTACTGTGAGTTTGTTTCAAAACTTTATGATTATTCTTGTACTGATTTTGAC
ATCGAGTTTTTTCTCGATTTCAGAAATTGCTTTGGCAGGTTCAAGAAAAATCAAACTTA
AATTACTGGCAGAATCAGGCGATGACCGTGCCGAGAAAGTCTTAAAATTGCAAGAAAAT
TCAGCTGATTTTTTTGCCACTTCACAAATTGGCCTAAATGCTGTCGCCATTTTGGGCGG
TTCGGTTGGTGAAAGTGCCTTGCGTCCTTATTTTTCCGAATGGATTGGCTTGGTATATC
AAGGGATTTGGCTTGACAGCATCGCTTTTTTTTCGTCGTTTGTTTTGGTAACACTGCTA
TTTATTTTATATGCTGACCTGATTCCCAAACGCATTGCAATGATTAATCCTGAGCGAGT
GGCTTTGGTGGTCATCAATCCGATTTTATGGACAATTCGTGTGGTCAAGCCCTTGGCAT
GGATCATCAATACCATCGCAGATGTGACTTTTCGGCTTTTTAAATTTGATACGGCTCGT
GATGACAGTATCACCTTTGATGATATTTCTGCCATTGTTGATGCTGGGGCAGAGGCTGG
CGTTTTGATGGAACAAGAACAGCACTTTATCGAAAATGTTTTTGAACTTGAAGAACGCA
14
CA 02328061 2000-11-10
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CCGTGCCATCATCGATGACGGCTCGTGAGGATGTGGTATATTTTGCACTCAGTGAAAGC
GAGGAGAGTATTCGTCAAAAGATTGCCGATTATCCTTATTCTAAATTTTTGGTCTGTAA
TGAGCATATCGACCAAGTCATCGGTTATGTCGATACCAAGGATATTTTGGTACGAATTT
TAAGCGAACAGCCAATTTTTCAGCTGAATGAATCTACCATTCGAAATGTACTGATTATT
CCAGATACACTCACTTTATCCGAGCTTTTGGATAAATTTCGTGCCAGTAATGAAAAAAT
GGCGGTAGTCATTAATGAATATGCATTGGTTGTTGGGCTAATTACACTATCAGATATTA
TGATGACTGTCATG,GGCGATTGGGCAGCCGCTGAGCCTGAAGATTTACAAATCATTCGC
CGTGATGAAAATTCATGGCTGATTGATGGGATTACGCCGATTGATGATGTTAAACATGC
CCTTGATATTAATGAGTTTCCTGATTGGGATCACTATGAGACGCTGGCGGGCTTTATTA
TGTATCGCCTGCGTAAGATTCCACGCCCTGCAGACTGGGTAGAGCATGAGGGCTTTAAA
TTTGAGGTGGTAGATATCGACCATTATAAGATTGACCAACTTTTGGTAACTCGCCTAGA
GCAACTGCCCAAGCACGAAGACTAA
SEQ ID N0:6
Moraxella catarrhalis BASB009 polypeptide sequence from strain Mcat 2913
MGVTVSLFQNFMIILVLILTSSFFSISEIALAGSRKIKLKLLAESGDDRAEKVLKLQENSADFFATSQIG
LNAVAILGGSVGESALRPYFSEWIGLVYQGIWLDSIAFFSSFVI~VTLLFILYADLIPKRIAMINPERVAL
WINPILWTIRWKPLAWIINTIADVTFRLFKFDTARDDSITFDDISAIVDAGAEAGVLMEQEQHFIENV
FELEERTVPSSMTAREDWYFALSESEESIRQKIADYPYSKFLVCNEHIDQVIGYVDTKDILVRILSEQI
FQLNESTIRNVLIIPDTLTLSELLDKFRASNEKMAWINEYALWGLITLSDIMMTVMGDWAAAEPEDLQ
IIRRDENSWLIDGITPIDDVKHALDINEFPDWDHYETLAGFIMYRLRKIPRPADWVEHEGFKFEVVDIDH
YKIDQLLVTRLEQLPKHED
SEQ ID NO:'7
Moraxella catarrhalis BASB009 polynucleotide sequence from strain Mcat 2969
ATGGGTGTTACTGTGAGTTTGTTTCAAAACTTTATGATTATTCTTGTACTGATTTTGAC
ATCGAGTTTTTTCTCGATTTCAGAAATTGCTTTGGCAGGTTCAAGAAAAATCAAACTTA
AATTACTGGCAGAATCAGGCGATGACCGTGCCGAGAAAGTCTTGAAATTGCAAGAAA.AT
TCAGCTGATTTTTTTGCCACTTCACAAATTGGCCTAAATGCTGTCGCCATTTTGGGCGG
TTCGGTTGGTGAAAGTGCCTTGCGTCCTTATTTTTCCGAATGGATTGGCTTGGTATATC
AAGGGATTTGGCTTGACAGCATCGCTTTTTTTTCGTCGTTTGTTTTGGTAACACTGCTA
TTTATTTTATATGCTGACCTGATTCCCAAACGCATTGCAATGATTAATCCTGAGCGAGT
GGCTTTGGTGGTCATCAATCCGATTTTGTGGACAATTCGTGTGGTCAAGCCCTTGGCAT
GGATTATCAATACCATCGCAGATGTGACTTTTCGGCTTTTTAAATTTGATACGGCTCGT
GATGACAGTATCACCTTTGATGATATTTCTGCCATTGTTGATGCTGGGGCAGAGGCTGG
CGTTCTGATGGAACAAGAACAACATTTTATCGAAAATGTTTTTGAACTTGAAGAACGCA
CCGTGCCATCATCGATGACGGCTCGTGAGGATGTGGTATATTTTGCACTCAGTGAAAGC
GAGGAGAGTATTCGTCAAAAGATTGCCGATTATCCTTATTCTAAATTTTTGGTCTGTAA
TGAGCATATCGACCAAGTCATCGGTTATGTCGATACCAAGGATATTTTGGTACGAATTT
TAAGCGAACAGCCAATTTTTCAGCTGAATGAATCTACCATTCGTAATGTACTGATTATT
CCAGATACACTCACTTTATCCGAGCTTTTGGATAAATTTCGTGCCAGTAATGAAAAP.AT
GGCGGTAGTCATTAATGAATATGCATTGGTTGTTGGGCTAATTACACTATCAGATATTA
TGATGACTGTCATGGGCGATTGGGCAGCCGCTGAGCCTGAAGATTTACAAATCATTCGC
CGTGATGAAAATTCATGGCTGATTGATGGGATTACGCCGATTGATGATGTTAAACATG
CA 02328061 2000-11-10
WO 99/58562 PCT/EP99/03262
CCCTTGATATTAATGAGTTTCCTGATTGGGATCACTATGAGACGCTGGCGGGCTTTATT
ATGTATCGCCTGCGTAAGATTCCACGCCCTGCAGACTGGGTAGAGCATGAGGGCTTTAA
ATTTGAGGTGGTAGATATCGACCATTATAAGATTGACCAACTTTTGGTAACTCGCCTAG
AGCAACTGCCCAAGCACGAAGACTAA
SEQ ID N0:8
Moraxella catarrhalis BASB009 polypeptide sequence from strain Mcat 2969
MGVTVSLFQNFMIILVLILTSSFFSISEIALAGSRKIKLKLLAESGDDRAEKVLKLQENSADFFATSQIGLN
AVAILGGSVGESALRPYFSEWIGLVYQGIWLDSIAFFSSFVLVTLLFILYADLIPKRIAMINPERVALWIN
PILWTIRWKPLAWIINTIADVTFRLFKFDTARDDSITFDDISAIVDAGAEAGVLMEQEQHFIENVFELEER
TVPSSMTAREDWYFALSESEESIRQKIADYPYSKFLVCNEHIDQVIGYVDTKDILVRILSEQPIFQLNEST
IRNVLIIPDTLTLSELLDKFRASNEKMAWINEYALWGLITLSDIMMTVMGDWAAAEPEDQIIRRDENSWL
IDGITPIDDVKHALDINEFPDWDHYETLAGFIMYRLRKIPRPADWVEHEGFKFEWDIDHYKIDQLLVTRLE
QLPKHED
S8Q ID N0:9
GCC TGA GGA TAT CAT GCC AG
SEQ ID NO:10
GTG TAT TTG ATG CCA TAC AGG
SEQ ID NO:11
AAG GGC CCA ATT ACG CAG AGG GGA TCC GAA ATT GCT TTG GCA GGT TCA AGA
AAA ATC AAA C
$EQ ID N0:12
AAG GGC CCA ATT ACG CAG AGG GTC GAC TTA TTA GTC TTC GTG CTT GGG CAG
TTG CTC TAG GCG
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