RATC

Abstract: The invention provides ratC polypeptides and polynucleotides encoding ratC polypeptides and methods for producing such polypeptides by recombinant techniques. Also provided are methods for utilizing ratC polypeptides to screen for antibacterial compounds.

Description: ratC FIELD OF THE INVENTION This invention relates to newly identified polynucleotides and polypeptides. and their production and uses, as well as their vanants, agonists and antagonists, and their uses In particular, the invention relates to polynucleotides and polypeptides of the ratC family, as well as their vanants. hereinafter referred to as "ratC," "ratC polynucleotιde(s)," and "ratC ρolypeptιde(s)" as the case may be BACKGROUND OF THE INVENTION The Streptococci make up a medically important genera of microbes known to cause several types of disease in humans, including, for example, otitis media, conjunctivitis, pneumonia, bacteremia, meningitis, sinusitis, pleural empyema and endocarditis, and most particularly meningitis, such as for example infection of cerebrospmal fluid Since its isolation more than 100 years ago, Streptococcus pneumomae has been one of the more intensively studied microbes For example, much of our early understanding that DNA is. in fact, the genetic matenal was predicated on the work of Griffith and of Avery. Macleod and McCarty using this microbe Despite the vast amount of research with Streptococcus pneumomae. many questions concerning the virulence of this microbe remain It is particularly preferred to employ Streptococcal genes and gene products as targets for the development of antibiotics. The frequency of Streptococcus pneumomae infections has nsen 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 Streptococcus pneumomae strains which 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 Moreover, the drug discovery process is currently undergoing a fundamental revolution as it embraces "functional genomics," that is. high throughput genome- or gene-based biology This approach is rapidly superseding earlier approaches based on "positional cloning" and other methods Functional genomics relies heavily on the various tools of bioinformatics to identify gene sequences of potential interest from the many molecular biology databases now available as well as from other sources There is a continuing and significant need to identify and charactenze further genes and other polynucleotides sequences and their related polypeptides. as targets for drug discovery Clearly, there exists a need for polynucleotides and polypeptides. such as the ratC embodiments of the invention, that have a present benefit of. among other things, being useful to screen compounds for antimicrobial activity Such factors are also useful to determine their role in pathogenesis of infection, dysfunction and disease There is also a need for identification and characterization of such factors and their antagonists and agonists to find ways to prevent, ameliorate or correct such infection, dysfunction and disease SUMMARY OF THE INVENTION The present invention relates to ratC, in particular ratC polypeptides and ratC polynucleotides. recombinant matenals and methods for their production In another aspect, the invention relates to methods for using such polypeptides and polynucleotides. including treatment of microbial diseases, amongst others In a further aspect, the invention relates to methods for identifying agonists and antagonists using the materials provided by the invention, and for treating microbial infections and conditions associated with such infections with the identified agonist or antagonist compounds In a still 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 ratC expression or activity Vaπous changes and modifications within the spint and scope of the disclosed invention will become readily apparent to those skilled in the art from reading the following descnptions and from reading the other parts of the present disclosure DESCRIPTION OF THE INVENTION The invention relates to ratC polypeptides and polynucleotides as descnbed in greater detail below In particular, the invention relates to polypeptides and polynucleotides of a ratC of Streptococcus pneumomae. which is related by amino acid sequence homology to GatC polypeptide The invention relates especially to ratC having the nucleotide and amino acid sequences set out in Table 1 as SEQ ID NO 1 and SEQ ID NO 2 respectively Note that sequences recited in the Sequence Listing below as "DNA " represent an exemplification of the invention, since those of ordinary skill will recognize that such sequences can be usefully employed in polynucleotides in general, including πbopolynucleotides TABLE 1 ratC Polynucleotide and Polypeptide Sequences (A) Streptococcus pneumomae ratC polynucleotide sequence [SEQ ID NO 1] 5 ' - atgaaaattacgcaagaagaggtaacacacgttgccaatctttcaaaattaagattctctgaaaaagaaac tgctgcctt tgcgaccaccttgtctaagattgttgacatggttgaattgctgggcgaagttgacacaactggtgtcgcac ctactacga ctatggctgaccgcaagactgtactccgccctgatgtggccgaagaaggaacagaccgtgatcgcttgttt aaaaacgta cctgaacaagacaactactatatcaaggtgccagctatcctagacgatggaggagatgcctaa-3 ' (B) Streptococcus pneumomae ratC polypeptide sequence deduced from a polynucleotide sequence m this table [SEQ ID NO 2] NH 2 - MKITQEEVTHVANLSKLRFSEKETAAFATTLSKIVDMVEL GEVDTTGVAPTTTMADRKTVLRPDVAEEGT DRDRLFKNV PEQDNYYIKVPAILDDGGDA-COOH Deposited materials A deposit containing a Streptococcus pneumomae 0100993 strain has been deposited with the National Collections of Industrial and Marine Bactena Ltd (herein "NCIMB"). 23 St Machar Dnve. Aberdeen AB2 IRY, Scotland on 11 Apnl 1996 and assigned deposit number 40794 The deposit was descnbed as Streptococcus pneumomae 0100993 on deposit On 17 Apnl 1996, a Streptococcus pneumoniae 0100993 DNA library in E coli was similarly deposited with the NCIMB and assigned deposit number 40800 The Streptococcus pneumomae strain deposit is referred to herein as "the deposited strain" or as "the DNA of the deposited strain " The deposited strain contains a full length ratC gene The sequence of the polynucleotides contained in the deposited strain, as well as the amino acid sequence of any polypeptide encoded thereby. are controlling in the event of any conflict with anv descnption of sequences herein The deposit of the deposited strain has been made under the terms of the Budapest Treaty on the International Recognition of the Deposit of Micro-organisms for Purposes of Patent Procedure The deposited strain will be irrevocably and without restnction or condition released to the public upon the issuance of a patent The deposited strain is provided merely as convemence to those of skill in the art and is not an admission that a deposit is required for enablement, such as that required under 35 U S C §112 A license may be required to make, use or sell the deposited strain, and compounds denved therefrom, and no such license is hereby granted In one aspect of the invention there is provided an isolated nucleic acid molecule encoding a mature polypeptide expressible by the Streptococcus pneumomae 0100993 strain, which polypeptide is contained in the deposited strain Further provided by the invention are ratC polynucleotide sequences in the deposited strain, such as DNA and RNA. and amino acid sequences encoded thereby Also provided by the invention are ratC polypeptide and polynucleotide sequences isolated from the deposited strain Polypeptides ratC polypeptide of the mvention is substantially phylogenetically related to other proteins of the ratC family In one aspect of the mvention there are provided polypeptides of Streptococcus pneumomae referred to herein as "ratC" and "ratC polypeptides" as well as biologically diagnosticall) . prophylactically. clinically or therapeutically useful vanants thereof, and compositions compnsing the same Among the particularly preferred embodiments of the invention are vanants of ratC polypeptide encoded by naturally occurring alleles of the ratC gene The present mvention further provides for an isolated polypeptide which (a) comprises or consists of an ammo acid sequence which has at least 70% identity, preferably at least 80% identity, more preferably at least 90% identity, yet more preferably at least 95% identity, most preferably at least 97-99% or exact identity, to that of SEQ ID NO 2 over the entire length of SEQ ID NO 2, (b) a polypeptide encoded by an isolated polynucleotide comprising or consisting of a polynucleotide sequence which has at least 70% identity, preferably at least 80% identity . more preferably at least 90% identity, yet more preferably at least 95% identity, even more preferably at least 97-99% or exact identity to SEQ ID NO 1 over the entire length of SEQ ID NO 1, (c) a polypeptide encoded by an isolated polynucleotide comprising or consisting of a polynucleotide sequence encoding a polypeptide which has at least 70% identity, preferably at least 80% identity . more preferably at least 90% identity, yet more preferably at least 95% identity, even more preferably at least 97-99% or exact identity, to the amino acid sequence of SEQ ID NO 2. over the entire length of SEQ ID NO 2 The polypeptides of the mvention include a polypeptide of Table 1 [SEQ ID NO 2] (in particular the mature polypeptide) as well as polypeptides and fragments, particularly those which have the biological activity of ratC. and also those winch have at least 70% identity to a polypeptide of Table 1 [SEQ ID NO 1 ]or the relevant portion, preferably at least 80% identity to a polypeptide of Table 1 [SEQ ID NO 2and more preferably at least 90% identity to a polypeptide of Table 1 [SEQ ID NO 2] and still more preferably at least 95% identity to a polypeptide of Table 1 [SEQ ID NO 2] and also include portions of such polypeptides with such portion of the polypeptide generally containing at least 30 ammo acids and more preferably at least 50 ammo acids The mvention also includes a polypeptide consisting of or compnsing a polypepttde of the formula X-(Rι) m -(R 2 )-(R 3 ) n -Y wherein, at the ammo tenmnus. X is hydrogen, a metal or any other moiety descnbed herein for modified polypeptides. and at the carboxyl terminus. Y is hydrogen, a metal or any other moiety descnbed herem for modified polypeptides. R] and R3 are any ammo acid residue or modified a o acid residue, m is an mteger between 1 and 1000 or zero, n is an mteger between 1 and 1000 or zero, and R 2 is an ammo acid sequence of the mvention, particularly an ammo acid sequence selected from Table 1 or modified forms thereof In the formula above, R 2 is onented so that its amino terminal ammo acid residue is at the left, covalently bound to R\ and its carboxy terminal am o acid residue is at the nght. covalently bound to R3 Any stretch of ammo acid residues denoted by either Ri or R3. where m and/or n is greater than 1. may be either a heteropolymer or a homopolymer, preferably a heteropolymer Other preferred embodiments of the mvention are provided where m is an mteger between 1 and 50. 100 or 500. and n is an mteger between 1 and 50. 100. or 500 It is most preferred that a polypeptide of the mvention is denved from Streptococcus pneumomae, however, it may preferably be obtained from other organisms of the same taxonomic genus A polypeptide of the mvention may also be obtamed, for example, from organisms of the same taxonomic family or order A fragment is a vanant polypeptide having an ammo acid sequence that is entirely the same as part but not all of any ammo acid sequence of any polypeptide of the mvention As with ratC polypeptides, fragments may be "free-standing." or compnsed within a larger polypeptide of which they form a part or region, most preferably as a single continuous region in a smgle larger polypeptide Preferred fragments include, for example, truncation polypeptides having a portion of an ammo acid sequence of Table 1 [SEQ ID NO 2], or of vanants thereof, such as a contmuous senes of residues that mcludes an ammo- and/or carboxyl-terminal ammo acid sequence Degradation forms of the polypeptides of the mvention produced by or m a host cell, particularly a Streptococcus pneumomae, are also preferred Further preferred are fragments characterized by structural or functional attributes such as fragments that compnse alpha-helix and alpha-helix forming regions, beta-sheet and beta-sheet- forming regions, turn and turn-forming regions, coil and coil-forming regions, hydrophi c regions, hydrophobic regions, alpha amphipathic regions, beta amphipathic regions, flexible regions, surface- forming regions, substrate binding region, and high antigemc index regions Further preferred 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 amino acid sequence of SEQ ID NO:2, or an isolated polypeptide comprising an amino acid sequence having at least 15, 20, 30, 40, 50 or 100 contiguous ammo acids truncated or deleted from the ammo acid sequence of SEQ ID NO:2. Also preferred are biologically active fragments which are those fragments that mediate activities of ratC. including those with a similar activity or an improved activity, or with a decreased undesirable activity Also included are those fragments that are antigemc or lmmunogemc m an animal, especially in a human Particularly preferred are fragments compnsing receptors or domains of enzymes that confer a function essential for viability of Streptococcus pneumomae or the ability to initiate, or maintain cause Disease in an individual, particularl a human Fragments of the polypeptides of the mvention may be employed for producing the corresponding full-length polypeptide by peptide synthesis, therefore, these vanants may be employed as intermediates for producing the full-length polypeptides of the mvention In addition to the standard single and triple letter representations for ammo acids, the term "X" or "Xaa" may also be used in describing certain polypeptides of the invention "X" and "Xaa" mean that any of the twenty naturally occurring ammo acids may appear at such a designated position in the polypeptide sequence Polynucleotides It is an object of the invention to provide polynucleotides that encode ratC polypeptides, particularly polynucleotides that encode the polypeptide herein designated ratC In a particularly prefened embodiment of the mvention the polynucleotide compnses a region encoding ratC polypeptides compnsing a sequence set out in Table 1 [SEQ ID NO 1] which mcludes a full length gene, or a variant thereof The Applicants believe that this full lengtli gene is essential to the growth and/or survival of an organism which possesses it. such as Streptococcus pneumomae As a further aspect of the mvention there are provided isolated nucleic acid molecules encoding and/or expressing ratC polypeptides and polynucleotides, particularly Streptococcus pneumomae ratC polypeptides and polynucleotides. including, for example, unprocessed RNAs. nbozyme RNAs. mRNAs. cDNAs. genomic D As, B- and Z-DNAs Further embodiments of the mvention mclude biologically, diagnostically. prophylactically. clinically or therapeutically useful polynucleotides and polypeptides. and vanants thereof, and compositions compnsmg the same Another aspect of the mvention relates to isolated polynucleotides, including at least one full length gene, that encodes a ratC polypeptide having a deduced ammo acid sequence of Table 1 [SEQ ID NO 2] and polynucleotides closely related thereto and vanants thereof In another particularly preferred embodiment of the invention there is a ratC polypeptide from Streptococcus pneumomae comprising or consisting of an amino acid sequence of Table 1 [SEQ ID NO 2], or a variant thereof Using the mformation provided herein, such as a polynucleotide sequence set out in Table 1 [SEQ ID NO 1], a polynucleotide of the mvention encoding ratC polypeptide may be obtamed using standard cloning and screening methods, such as those for cloning and sequencmg chromosomal DNA fragments from bactena usmg Streptococcus pneumomae 0100993 cells as starting matenal, followed by obtainmg a full length clone For example, to obtain a polynucleotide sequence of the invention, such as a polynucleotide sequence given in Table 1 [SEQ ID NO 1], typically a library of clones of chromosomal DNA of Streptococcus pneumomae 0100993 in E coli or some other suitable host is probed with a radiolabeled 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 m 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 LABORATORY MANUAL, 2nd Ed , Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York (1989) (see m 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 mvention. each polynucleotide set out m Table 1 [SEQ ID NO 1] was discovered in a DNA library denved from Streptococcus pneumomae 0100993 Moreover, each DNA sequence set out in Table 1 [SEQ ID NO 1] contains an open reading frame encoding a protem having about the number of ammo acid residues set forth Table 1 [SEQ ID NO 2] with a deduced molecular weight that can be calculated usmg ammo acid residue molecular weight values well known to those skilled in the art The polynucleotide of SEQ ID NO 1, between nucleotide number 1 and the stop codon which begins at nucleotide number 301 of SEQ ID NO 1, encodes the polypeptide of SEQ ID NO 2 In a further aspect, the present mvention provides for an isolated polynucleotide comprising or consisting of (a) a polynucleotide sequence which has at least 70% identity, preferably at least 80% identity, more preferably at least 90% identity, yet more preferably at least 95% identity, even more preferably at least 97-99% or exact identity to SEQ ID NO 1 over the entire length of SEQ ID NO 1, (b) a polynucleotide sequence encoding a polypeptide which has at least 70% identity, preferably at least 80% identity, more preferably at least 90% identity, yet more preferably at least 95% identity, even more preferably at least 97-99% or 100% exact, to the am o acid sequence of SEQ ID NO 2, over the entire length of SEQ ID NO 2 A polynucleotide encoding a polypeptide of the present mvention, including homologs and orthologs from species other than Streptococcus pneumomae. may be obtamed by a process which compnses the steps of screening an appropnate library under stringent hybndization conditions with a labeled or detectable probe consisting of or compnsmg the sequence of SEQ ID NO 1 or a fragment thereof, and isolating a full-length gene and/or genomic clones containing said polynucleotide sequence The mvention provides a polynucleotide sequence identical over its entire length to a cod g sequence (open readmg frame) m Table 1 [SEQ ID NO 1] Also provided by the mvention is a codmg sequence for a mature polypeptide or a fragment thereof, by itself as well as a codmg sequence for a mature polypeptide or a fragment in readmg frame with another codmg sequence, such as a sequence encoding a leader or secretory sequence, a pre-, or pro- or prepro-protein sequence The polynucleotide of the mvention 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 transcnbed but non-translated sequences, termination signals (such as rho-dependent and rho-independent termination signals). nbosome bmd g sites. Kozak sequences, sequences that stabilize mRNA, mtrons, and polyadenylation signals The polynucleotide sequence may also compnse additional codmg sequence encoding additional ammo acids For example, a marker sequence that facilitates punfication of the fused polypeptide can be encoded In certain embodiments of the mvention. the marker sequence is a hexa-histidine peptide. as provided m the pQE vector (Qiagen, Inc ) and descnbed in Gentz et al , Proc Nail 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 m punfying polypeptide sequence fused to them Polynucleotides of the mvention also mclude. but are not limited to. polynucleotides compnsmg a structural gene and its naturally associated sequences that control gene expression A prefened embodiment of the mvention is a polynucleotide of consisting of or compnsmg nucleotide 1 to the nucleotide immediately upstream of or including nucleotide 301 set forth m SEQ ID NO 1 of Table 1, both of which encode the ratC polypeptide The mvention also mcludes a polynucleotide consisting of or compnsmg a polynucleotide of the formula X-(R 1 ) m -(R 2 )-(R 3 ) n -Y wherein, at the 5' end of the molecule. X is hydrogen, a metal or a modified nucleotide residue, or together with Y defines a covalent bond, and at the 3' end of the molecule. Y is hydrogen, a metal, or a modified nucleotide residue, or together with X defines the covalent bond, each occurrence of Ri and R3 is independently any nucleic acid residue or modified nucleic acid residue, m is an integer between 1 and 3000 or zero , n is an integer between 1 and 3000 or zero, and R 2 is a nucleic acid sequence or modified nucleic acid sequence of the mvention, particularly a nucleic acid sequence selected from Table 1 or a modified nucleic acid sequence thereof In the polynucleotide formula above, R 2 is oriented so that its 5' end nucleic acid residue is at the left, bound to R j and its 3' end nucleic acid residue is at the nght. bound to R3 Any stretch of nucleic acid residues denoted by either R j and/or R 2 . where m and/or n is greater than 1. may be either a heteropolymer or a homopolymer. preferably a heteropolymer Where, in a preferred embodiment. X and Y together define a covalent bond, the polynucleotide of the above formula is a closed, circular polynucleotide. which can be a double-stranded polynucleotide wherein the formula shows a first strand to which the second strand is complementary In another preferred embodiment m and/or n is an integer between 1 and 1000. Other prefened embodiments of the invention are provided where m is an mteger between 1 and 50. 100 or 500. and n is an mteger between 1 and 50. 100. or 500 It is most preferred that a polynucleotide of the mvention is denved from Streptococcus pneumomae. however, it may preferably be obtamed from other orgamsms of the same taxonomic genus A polynucleotide of the mvention may also be obtamed. for example, from orgamsms of the same taxonomic family or order The term "polynucleotide encoding a polypeptide" as used herem encompasses polynucleotides that mclude a sequence encoding a polypeptide of the mvention. particularly a bactenal polypeptide and more particularly a polypeptide of the Streptococcus pneumomae ratC havmg an ammo acid sequence set out in Table 1 [SEQ ID NO 2] The term also encompasses polynucleotides that mclude a s gle continuous region or discontinuous regions encoding the polypeptide (for example, polynucleotides interrupted by mtegrated phage. an integrated insertion sequence, an integrated vector sequence, an integrated transposon sequence or due to RNA editing or genomic DNA reorganization) together with additional regions, that also mav contain codmg and/or non-coding sequences The mvention further relates to vanants of the polynucleotides descnbed herem that encode vanants of a polypeptide having a deduced ammo acid sequence of Table 1 [SEQ ID NO 2] Fragments of a polynucleotides of the mvention may be used, for example, to synthesize full-length polynucleotides of the mvention Further particularly prefened embodiments are polynucleotides encoding ratC vanants, that have the am o acid sequence of ratC polypeptide of Table 1 [SEQ ID NO 2] m which several, a few, 5 to 10. 1 to 5 1 to 3. 2. 1 or no ammo acid residues are substituted, modified, deleted and/or added, m any combination Especially prefened among these are silent substitutions, additions and deletions, that do not alter the properties and activities of ratC polypeptide Further prefened embodiments of the mvention are polynucleotides that are at least 70% identical over their entire length to a polynucleotide encoding ratC polypeptide having an ammo acid sequence set out in Table 1 [SEQ ID NO 2]. and polynucleotides that are complementary to such polynucleotides Alternatively, most highly prefened are polynucleotides that compnse a region that is at least 80% identical over its entire length to a polynucleotide encoding ratC polypeptide and polynucleotides complementary thereto In this regard, polynucleotides at least 90% identical over their entire length to the same are particularly prefened and among these particularly prefened polynucleotides those with at least 95% are especially prefened Furthermore, tliose with at least 97% are highly prefened among those with at least 95% and among these tliose with at least 98% and at least 99% are particularly highly prefened, with at least 99% being the more prefened Prefened embodiments are polynucleotides encoding polypeptides that retain substantially the same biological function or activity as the mature polypeptide encoded by a DNA of Table 1 [SEQ ID NO l] In accordance with certain prefened embodiments of this mvention there are provided polynucleotides that hybndize. particularly under stnngent conditions, to ratC polynucleotide sequences, such as those polynucleotides in Table 1 The mvention further relates to polynucleotides that hybndize to the polynucleotide sequences provided herem h tins regard, the mvention especially relates to polynucleotides that hybndize under stnngent conditions to the polynucleotides descnbed herem As herem used, the terms "stnngent conditions" and "stnngent hybndization conditions" mean hybndization 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 5x SSC (150mM NaCl. 15mM tnsodium citrate). 50 mM sodium phosphate (pH7 6), 5x 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 yvell knoyvn 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 The invention also provides a polynucleotide consisting of or comprising a polynucleotide sequence obtained by screening an appropnate library containing the complete gene for a polynucleotide sequence set forth m SEQ ID NO 1 under stringent hybridization conditions with a probe having the sequence of said polynucleotide sequence set forth m SEQ ID NO 1 or a fragment thereof, and isolating said polynucleotide sequence Fragments useful for obtaining such a polynucleotide include, for example, probes and primers fully described elsewhere herem As discussed elsewhere herem regarding polynucleotide assays of the mvention, for instance, the polynucleotides of the mvention, may be used as a hybndization probe for RNA, cDNA and genomic DNA to isolate full-length cDNAs and genomic clones encoding ratC and to isolate cDNA and genomic clones of other genes that have a high identity, particularly high sequence identity, to the ratC gene Such probes generally will compnse at least 15 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 prefened probes will have at least 20 nucleotide residues or base pairs and will have lee than 30 nucleotide residues or base pairs A codmg region of a ratC gene may be isolated by screening usmg a DNA sequence provided in Table 1 [SEQ ID NO 1J to synthesize an oligonucleotide probe A labeled oligonucleotide havmg a sequence complementary to that of a gene of the mvention is then used to screen a librar of cDNA, genomic DNA or mRNA to determine which members of the library the probe hybndizes 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 tliose based on the method of Rapid Amplification of cDNA ends (RACE) (see. for example. Frohman, et al , PNAS USA 85 8998- 9002. 1988) Recent modifications of the technique, exemplified by the Marathon™ technology (Clontech Laboratories Inc ) for example, have significantly simplified the search for longer cDNAs In the Marathon™ 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 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 pnmer that anneals further 5' in the selected gene sequence) The products of this reaction can then be analyzed 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 The polynucleotides and polypeptides of the mvention may be employed, for example, as research reagents and matenals for discovery of treatments of and diagnostics for diseases, particularly human diseases, as further discussed herem relating to polynucleotide assays The polynucleotides of the invention that are ohgonucleotides derived from a sequence of Table 1 [SEQ ID NOS 1 or 2] may be used in the processes herein as descnbed. but preferably for PCR. to determine whether or not the polynucleotides identified herem in whole or in part are transcribed in bacteria m 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 mvention also provides polynucleotides that encode a polypeptide that is the mature protem plus additional ammo or carboxyl-terminal ammo acids, or amino acids mtenor to the mature polypeptide (when the mature form has more than one polypeptide chain for instance) Such sequences may play a role in processmg of a protem from precursor to a mature form, may allow protem transport, may lengthen or shorten protem half-life or may facilitate mampulation of a protem for assay or production, among other things As generally is the case in vivo, the additional ammo acids may be processed away from the mature protem by cellular enzymes For each and every polynucleotide of the invention there is provided a polynucleotide complementary to it It is prefened that these complementary polynucleotides are fully complementary to each polynucleotide with which they are complementary A precursor protem, 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 proprotems In addition to the standard A. G. C. T/U representations for nucieotides. the term "N" may also be used in describing certain polynucleotides of the invention "N" means that any of the four DNA or RNA nucieotides may appear at such a designated position m the DNA or RNA sequence, except it is preferred that N is not a nucleic acid that when taken in combination with adjacent nucleotide positions, when read in the correct reading frame, would have the effect of generating a premature termination codon m such reading frame In sum, a polynucleotide of the mvention may encode a mature protem. a mature protem plus a leader sequence (which may be refened to as a preprotem). a precursor of a mature protein havmg one or more prosequences that are not the leader sequences of a preprotem. or a preproprotein. which is a precursor to a proprotein. havmg a leader sequence and one or more prosequences. which generally are removed during processmg steps that produce active and mature forms of the polypeptide Vectors, Host Cells, Expression Systems The mvention also relates to vectors that compnse a polynucleotide or polynucleotides of the mvention. host cells that are genetically engmeered with vectors of the mvention and the production of polypeptides of the mvention by recombinant techniques Cell-free translation systems can also be employed to produce such proteins usmg RNAs denved from the DNA constructs of the mvention Recombinant polypeptides of the present mvention may be prepared by processes well known in those skilled m the art from genetically engineered host cells compnsmg expression systems Accordingly, in a further aspect, the present mvention relates to expression systems which compnse a polynucleotide or polynucleotides of the present mvention. to host cells which are genetically engmeered with such expression systems, and to the production of polypeptides of the invention by recombinant techniques For recombinant production of the polypeptides of the invention, host cells can be genetically engmeered to incorporate expression systems or portions thereof or polynucleotides of the mvention Introduction of a polynucleotide mto the host cell can be effected by methods descnbed m many standard laboratory manuals, such as Davis, et al . BASIC METHODS IN MOLECULAR BIOLOGY. (1986) and Sambrook. et al . MOLECULAR CLONING A LABORATORY MANUAL. 2nd Ed . Cold Spring Harbor Laboratory Press. Cold Spring Harbor, N Y (1989). such as, calcium phosphate transfection, DEAE-dextran mediated transfection. transvection. micromjection. catiomc hpid-mediated transfection. electroporation. transduction, scrape loading, ballistic mtroduction and infection Representative examples of appropnate hosts mclude bactenal cells, such as cells of streptococci, staphylococci, enterococci E coli. streptomyces. cyanobactena. Bacillus sukhhs. and Streptococcus pneumomae. fungal cells, such as cells of a yeast. Kluveromyces, Saccharomyces, a basidiomycete. Candida albicans and Aspergilliis. insect cells such as cells of Drosophύa S2 and Spodoptera Sf9. animal cells such as CHO. COS. HeLa. C127. 3T3, BHK. 293. CV-1 and Bowes melanoma cells, and plant cells, such as cells of a gymnosperm or angiosperm A great vanety of expression systems can be used to produce the polypeptides of the mvention Such vectors mclude. among others, chromosomal-, episomal- and virus-denved vectors, for example, vectors denved from bactenal plasmids. from bactenophage. from 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 and retroviruses. and vectors denved from combinations thereof, such as those denved from plasmid and bactenophage genetic elements, such as cosmids and phagemids The 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 m a host may be used for expression m tins regard The appropnate DNA sequence may be inserted mto the expression system by any of a vanety of well-known and routme techniques, such as, for example, those set forth m Sambrook et al , MOLECULAR CLONING. A LABORATORY MANUAL, (supra) In recombinant expression systems m eukaryotes. for secretion of a translated protem mto the lumen of the endoplasmic reticulum, mto the penplasmic space or mto the extracellular environment, appropnate secretion signals may be incorporated mto the expressed polypeptide These signals may be endogenous to the polypeptide or they may be heterologous signals Polypeptides of the mvention can be recovered and punfied from recombinant cell cultures by well-known methods including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography. phosphocellulose chromatograph) . hydrophobic mteraction chromatography. affinity chromatography. hydroxylapatite chromatography. and lectm chromatography Most preferably, high performance liquid chromatography is employed for punfication Well known techniques for refolding protem may be employed to regenerate active conformation when the polypeptide is denatured during isolation and or punfication Diagnostic, Prognostic, Serotyping and Mutation Assays This mvention is also related to the use of ratC polynucleotides and polypeptides of the mvention for use as diagnostic reagents Detection of ratC polynucleotides and/or polypeptides m 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 mfectious organism to drugs Eukaryotes. particularly mammals, and especially humans, particularly those infected or suspected to be infected with an organism compnsmg the ratC gene or protem. may be detected at the nucleic acid or ammo acid level by a vanety of well known techniques as well as by methods provided herem Polypeptides and polynucleotides for prognosis, diagnosis or other analysis may be obtamed from a putatively mfected and/or infected individual's bodily matenals Polynucleotides from any of these sources, particularly DNA or RNA. may be used directly for detection or may be amplified enzymatically by usmg PCR or any other amplification technique pnor to analysis RNA. particularly mRNA. cDNA and genomic DNA may also be used m the same ways Usmg amplification, charactenzation of the species and stram of infectious or resident organism present m 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 m size of the amplified product m companson to a genotype of a reference sequence selected from a related organism, preferably a different species of the same genus or a different stram of the same species Pomt mutations can be identified by hybndizmg amplified DNA to labeled ratC 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 m meltmg temperatures or renaturation kinetics Polynucleotide sequence differences may also be detected by alterations m the electrophoretic mobility of polynucleotide fragments m gels as compared to a reference sequence This may be earned 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. VI and S I protection assay or a chemical cleavage method See. for example. Cotton et al . Proc Natl Acad Set , USA. 85 4397-4401 (1985) In another embodiment, an anay of ohgonucleotides probes compnsmg ratC 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 vanety of questions m molecular genetics mcludmg gene expression, genetic linkage, and genetic vanability (see. for example. Chee et al , Science, 274 610 (1996)) Thus in another aspect, the present invention relates to a diagnostic kit which compnses (a) a polynucleotide of the present invention, preferably the nucleotide sequence of SEQ ID NO 1 , 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 NO 2 or a fragment thereof or (d) an antibody to a poly peptide of the present invention, preferably to the polypeptide of SEQ ID NO 2 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 mvention also relates to the use of polynucleotides of the present mvention as diagnostic reagents Detection of a mutated form of a polynucleotide of the mvention, preferable, SEQ ID NO 1, 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 polynucleotide Orgamsms, particularly infectious orgamsms. carrying mutations in such polynucleotide may be detected at the polynucleotide level by a vanety of techniques, such as those descnbed elsewhere herem The nucleotide sequences of the present mvention are also valuable for organism chromosome identification The sequence is specifically targeted to, and can hybndize with, a particular location on an organism's chromosome, particularly to a Streptococcus pneumomae chromosome The mappmg of relevant sequences to chromosomes according to the present mvention may be an important step m conelating those sequences with pathogenic potential and/or an ecological niche of an organism and/or drug resistance of an organism, as vvell as the essentiality of the gene to the organism Once a sequence has been mapped to a precise chromosomal location, the physical position of the sequence on the chromosome can be conelated with genetic map data Such data may be found on-lme in a sequence database The relationship between genes and diseases that have been mapped to the same chromosomal region are then identified through known genetic methods for example, through linkage analysis (coinhentance of physically adjacent genes) or matmg studies, such as by con)ugatιon The differences in a poly nucleotide and/or polypeptide sequence between organisms possessing a first phenotype and organisms possessing a different, second different phenotype can also be determined If a mutation is observed in some or all organisms possessing the first phenotype but not in any organisms possessing the second phenotype. then the mutation is likely to be the causative agent of the first phenotype Cells from an organism carrying mutations or polymorphisms (alle c vanations) in a polynucleotide and/or polypeptide of the mvention may also be detected at the polynucleotide or polypeptide level by a vanety of techmques. to allow for serotypmg. for example For example, RT- PCR can be used to detect mutations the RNA It is particularly prefened 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 ratC polypeptide can be used to identify and analyze mutations Examples of representative pnmers are shown below m Table 2 Table 2 Primers for amplification of ratC polynucleotides SEQ ID NO PRIMER SEQUENCE 3 5 ' -atgaaaattacgcaagaaga-3 ' 4 5 ' -ttaggcatctcctccatcgt-3 ' The mvention also includes pnmers of the formula X-(R 1 ) m -(R 2 )-(R 3 ) n -Y wherem, at the 5' end of the molecule, X is hydrogen, a metal or a modified nucleotide residue, and at the 3' end of the molecule, Y is hydrogen, a metal or a modified nucleotide residue, R\ and R3 are any nucleic acid residue or modified nucleotide residue, m is an mteger between 1 and 20 or zero , n is an mteger between 1 and 20 or zero, and R is a pnmer sequence of the mvention, particularly a primer sequence selected from Table 2 In the polynucleotide formula above R 2 is onented so that its 5' end nucleotide residue is at the left, bound to R\ and its 3' end nucleotide residue is at the nght, bound to R3 Any stretch of nucleic acid residues denoted by either R group \yhere m and/or n is greater than 1, may be either a heteropolymer or a homopolymer. preferably a heteropolymer bemg complementary to a region of a polynucleotide of Table 1 In a prefened embodiment m and/or n is an mteger between 1 and 10. The mvention further provides these pnmers with 1 2 3 or 4 nucieotides removed from the 5' and/or the 3' end These pnmers may be used for. among other thmgs. amplifying ratC DNA and/or RNA isolated from a sample denved from an individual, such as a bodily matenal The pnmers may be used to amplify a polynucleotide isolated from an infected individual, such that the polynucleotide may then be subject to vanous techmques for elucidation of the polynucleotide sequence In this way. mutations m the polynucleotide sequence may be detected and used to diagnose and/or prognose the infection or its stage or course, or to serotype and/or classify the infectious agent The mvention further provides a process for diagnosing, disease, preferably bactenal infections, more preferably infections caused by Streptococcus pneumomae, comprising determining from a sample derived from an individual, such as a bodily material, an increased level of expression of polynucleotide having a sequence of Table 1 [SEQ ID NO 1] Increased or decreased expression of a ratC 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 m accordance with the mvention for detectmg over- expression of ratC polypeptide compared to normal control tissue samples may be used to detect the presence of an infection, for example Assay techmques that can be used to determine levels of a ratC polypeptide, m a sample denved from a host, such as a bodily matenal. are well-known to those of skill m the art Such assay methods mclude radioimmunoassays. competitive-binding assays, Western Blot analysis, antibody sandwich assays, antibody detection and ELISA assays Differential Expression The polynucleotides and polynucleotides of the mvention may be used as reagents for differential screening methods There are many differential screening and differential display methods known in the art in which the polynucleotides and polypeptides of the mvention may be used For example, the differential display technique is described by Chuang et al , J Bactenol 175 2026- 2036 (1993) This method identifies those genes which are expressed m an organism by identifying mRNA present using randomly-primed RT-PCR By comparing pre-infection and post infection profiles, genes up and down regulated during infection can be identified and the RT-PCR product sequenced and matched to ORF "unknowns " In Vivo Expression Technology (IVET) is described by Camilh et al , Proc Nat'l Acacl Scv USA 91 2634-2638 (1994) IVET identifies genes up-regulated during infection when compared to laboratory cultivation, implying an important role in infection ORFs identified by this technique are implied to have a significant role m infection establishment and/or maintenance In this technique random chromosomal fragments of target organism are cloned upstream of a promoter-less recombmase gene in a plasmid vector This construct is introduced into the target organism which carries an antibiotic resistance gene flanked by resolvase sites Growth m the presence of the antibiotic removes from the population those fragments cloned into the plasmid vector capable of supporting transcription of the recombmase gene and therefore have caused loss of antibiotic resistance The resistant pool is introduced into a host and at various times after infection bacteria may be recovered and assessed for the presence of antibiotic resistance The chromosomal fragment carried by each antibiotic sensitive bacterium should carry a promoter or portion of a gene normally upregulated during infection Sequencing upstream of the recombmase gene allows identification of the up regulated gene RT-PCR may also be used to analyze gene expression patterns For RT PCR using the polynucleotides of the invention, messenger RNA is isolated from bacterial infected tissue, e g . 48 hour murine lung infections, and the amount of each mRNA species assessed by reverse transcription of the RNA sample primed with random hexanucleotides followed by PCR with gene specific primer pairs The determination of the presence and amount of a particular mRNA species by quantification of the resultant PCR product provides information on the bacterial genes which are transcribed in the infected tissue Analysis of gene transcription can be carried out at different times of infection to gain a detailed knowledge of gene regulation in bactenal pathogenesis allowing for a clearer understanding of which gene products represent targets for screens for antibactenals Because of the gene specific nature of the PCR pnmers employed it should be understood that the bacterial mRNA preparation need not be free of mammalian RNA This allows the investigator to carry out a simple and quick RNA preparation from infected tissue to obtain bacterial mRNA species which are very short lived in the bacterium (m the order of 2 mmute halflives) Optimally the bacterial mRNA is prepared from infected munne lung tissue by mechanical disruption in the presence of TRIzole (GIBCO-BRL) for very short periods of time, subsequent processing according to the manufacturers of TRIzole reagent and DNAase treatment to remove contaminating DNA Preferably the process is optimized by finding those conditions which give a maximum amount of Streptococcus pneumomae 16S πbosomal RNA as detected by probing Northerns with a suitably labeled sequence specific oligonucleotide probe Typically a 5' dye labeled primer is used in each PCR primer pair in a PCR reaction which is terminated optimally between 8 and 25 cycles The PCR products are separated on 6% polyacrylamide gels with detection and quantification using GeneScanner (manufactured by ABI) Gridding and Polynucleotide Subtraction Methods have been described for obtaining information about gene expression and identity using so called "high density DNA arrays" or grids See, e g , M Chee et al . Science. 274 610-614 (1996) and other references cited therein Such gridding assays have been employed to identify certain novel gene sequences, referred to as Expressed Sequence Tags (EST) (Adams et a . Science, 252 1651-1656 (1991)) A variety of techniques have also been described for identifying particular gene sequences on the basis of their gene products For example, see International Patent Application No WO91/07087. published May 30. 1991 In addition, methods have been described for the amplification of desired sequences For example. see International Patent Application No W091/17271, published November 14. 1991 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 polynucleotides 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 Streptococcus pneumomae. and may be useful in diagnosing and/or prognosing disease or a course of disease A grid comprising a number of vanants of the polynucleotide sequence of SEQ ID NO 1 are preferred Also preferred is a comprising a number of variants of a polynucleotide sequence encoding the polypeptide sequence of SEQ ID NO 2 Antibodies The polypeptides and polynucleotides of the mvention or vanants thereof, or cells expressmg the same can be used as immunogens to produce antibodies immunospecific for such polypeptides or polynucleotides respectively In certain prefened embodiments of the mvention there are provided antibodies against ratC polypeptides or polynucleotides Antibodies generated against the polypeptides or polynucleotides of the mvention can be obtamed by admmistenng the polypeptides and/or polynucleotides of the mvention. or eprtope-beaπng fragments of either or both, analogues of either or botli, or cells expressmg either or botli, to an animal, preferably a nonhuman. usmg routine protocols For preparation of monoclonal antibodies, anv technique known m the art that provides antibodies produced bv contmuous cell lme cultures can be used Examples mclude vanous techmques. such as those m Kohler G and Milstem. C . Nature 256 495-497 (1975). Kozbor et al , Immunology Today 4 72 (1983) Cole et al . pg 77-96 in MONOCLONAL ANTIBODIES AND CANCER THERAPY. Alan R Liss, Inc ( 1985) Techmques for the production of smgle chain antibodies (U S Patent No 4,946,778) can be adapted to produce smgle cha antibodies to polypeptides or polynucleotides of this mvention Also, transgenic mice, or other orgamsms such as other mammals, may be used to express humanized antibodies immunospecific to the polypeptides or polynucleotides of the mvention 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-ratC or from naive hbranes (McCafferty. et al . (1990). Nature 348. 552-554. Marks, et al . (1992) Biotechnology 10. 779- 783) The affinity of these antibodies can also be improved by. for example, chain shuffling (Clackson et al , (1991) Nature 352 628) The above-descnbed antibodies may be employed to isolate or to identify clones expressmg the polypeptides or polynucleotides of the mvention to punfy the polypeptides or polynucleotides by, for example, affinity chromatography Thus, among others, antibodies against ratC -polypeptide or ratC-polynucleotide may be employed to treat infections, particularly bactenal infections Polypeptide variants include antigemcally, epitopically or immunologically equivalent variants form a particular aspect of this invention A polypeptide or polynucleotide of the invention, such as an antigemcally or immunologically equivalent derivative or a fusion protein of the polypeptide is used as an antigen to immunize a mouse or other animal such as a rat or chicken The fusion protein may provide stability to the polypeptide The antigen may be associated, for example by conjugation, with an immunogenic carrier protein for example bovine serum albumin, keyhole limpet haemocyamn or tetanus toxoid Alternatively, a multiple antigemc polypeptide comprising multiple copies of the polypeptide. or an antigemcally or immunologically equivalent polypeptide thereof may be sufficiently antigemc to improve lmmunogenicity so as to obviate the use of a carrier Preferably, the antibody or variant thereof is modified to make it less immunogenic m the individual For example, if the individual is human the antibody may most preferably be "humanized." where the comphmentarity determining region or regions of the hybπdoma-deπved antibody has been transplanted mto a human monoclonal antibody , for example as described m Jones et al (1986). Nature 321. 522-525 or Tempest et al , (1991) Biotechnology 9, 266-273 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 Among the particularly prefened embodiments of the mvention are naturally occurring allelic vanants of ratC polynucleotides and polypeptides encoded thereby 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) 1 363, Manthorpe et al . Hum Gene I her (1983) 4 419). delivery of DNA complexed with specific protem carriers (Wu et al . J Biol Chem (1989) 264 16985). coprecipitation of DNA with calcium phosphate (Benvemsty & Reshef, PNAS USA. (1986) 83 9551), encapsulation of DNA in various forms of hposomes (Kaneda et al Science (1989) 243 375). particle bombardment (Tang et al , Nature (1992) 356 152. Eisenbraun et al , DNA Cell Biol (1993) 12 791) and in vivo infection using cloned retroviral vectors (Seeger et al . PNAS USA (\9U) 5849) Antagonists and Agonists - Assays and Molecules Polypeptides and polynucleotides of the mvention may also be used to assess the bmdmg of small molecule substrates and ligands m. for example, cells, cell-free preparations, chemical libranes. and natural product mixtures These substrates and ligands may be natural substrates and ligands or may be structural or functional mimetics See, e g . Co gan et al . Current Protocols in Immunology 1(2) Chapter 5 (1991) Polypeptides and polynucleotides of the present mvention are responsible for many biological functions, mcludmg many disease states, in particular the Diseases herembefore mentioned It is therefore desirable to devise screening methods to identify compounds which stimulate or which inhibit the function of the polypeptide or polynucleotide Accordingly, m a further aspect, the present mvention provides for a method of screening compounds to identify those which stimulate or winch inhibit the function of a polypeptide or polynucleotide of the mvention. as well as related polypeptides and polynucleotides In general, agomsts or antagomsts may be employed for therapeutic and prophylactic purposes for such Diseases as herembefore mentioned Compounds may be identified from a vanety of sources, for example, cells, cell-free preparations, chemical libranes. and natural product mixtures Such agomsts. antagomsts or inhibitors so-identified may be natural or modified substrates, ligands, receptors, enzymes, etc . as the case may be. of ratC polypeptides and polynucleotides. or may be structural or functional mimetics thereof (see Cohgan et al . Current Protocols in Immunology 1(2) Chapter 5 (1991)) 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 protem 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 m 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, m the absence of an agonist or inhibitor, by testing whether the candidate compound results in inhibition of activation of 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 ratC polypeptide and/or polynucleotide activity in the mixture, and comparing the ratC polypeptide and/or polynucleotide activity of the mixture to a standard Fusion proteins, such as those made from Fc portion and ratC 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 ith a polypeptide of the present invention may also be used to configure screening methods for 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 mvention also provides a method of screening compounds to identify those which enhance (agonist) or block (antagonist) the action of ratC polypeptides or polynucleotides, particularly those compounds that are bactenstatic and/or bactencidal The method of screening may mvolve high- throughput techmques For example, to screen for agomsts or antagomsts. a synthetic reaction mix. a cellular compartment, such as a membrane, cell envelope or cell wall, or a preparation of any thereof, compnsmg ratC polypeptide and a labeled substrate or ligand of such polypeptide is mcubated m the absence or the presence of a candidate molecule that may be a ratC agomst or antagonist The ability of the candidate molecule to agomze or antagonize the ratC polypeptide is reflected m decreased bmdmg of the labeled ligand or decreased production of product from such substrate Molecules that bmd gratuitously, . e . without mducmg the effects of ratC polypeptide are most likely to be good antagomsts Molecules that bmd well and. as the case may be. mcrease the rate of product production from substrate, mcrease signal transduction. or mcrease chemical channel activity are agomsts 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 usmg a reporter system Reporter systems that may be useful m this regard mclude but are not limited to colonmetnc. labeled substrate converted mto product, a reporter gene that is responsive to changes m ratC polynucleotide or polypeptide activity, and bmdmg assays known m the art Polypeptides of the invention may be used to identify membrane bound or soluble receptors, if any. for such polypeptide. through standard receptor binding techniques known in the art These techniques include, but are not limited to. ligand binding and crosshnking assays in which the polypeptide is labeled with a radioactive isotope (for instance. l-^I). chemically modified (for instance, biotmylated). or fused to a peptide sequence suitable for detection or purification, and mcubated with a source of the putative receptor (e g , cells, cell membranes, cell supernatants, tissue extracts, bodily materials) Other methods include biophysical techniques such as surface plasmon resonance and spectroscopy These screemng methods may also be used to identify agonists and antagonists of the polypeptide which compete with the binding of the polypeptide to its receptor(s), if any Standard methods for conducting such assays are well understood in the art The fluorescence polarization value for a fluorescently-tagged molecule depends on the rotational correlation time or tumbling rate Protein complexes, such as formed by ratC polypeptide associating with another ratC polypeptide or other polypeptide. labeled to comprise a fluorescently-labeled molecule will have higher polarization values than a fluorescently labeled monomeπc protein It is preferred that this method be used to characterize small molecules that disrupt polypeptide complexes Fluorescence energy transfer may also be used characterize small molecules that interfere with the formation of ratC polypeptide dimers. tπmers. tetramers or higher order structures, or structures formed by ratC polypeptide bound to another polypeptide ratC polypeptide can be labeled with both a donor and acceptor fluorophore Upon mixing of the two labeled species and excitation of the donor fluorophore, fluorescence energy transfer can be detected by observing fluorescence of the acceptor Compounds that block dimeπzation will inhibit fluorescence energy transfer Surface plasmon resonance can be used to monitor the effect of small molecules on ratC polypeptide self-association as well as an association of ratC polypeptide and another polypeptide or small molecule ratC polypeptide can be coupled to a sensor chip at low site density such that covalently bound molecules will be monomeπc Solution protein can then passed over the ratC polypeptide -coated surface and specific bmdmg can be detected m real- time by monitoring the change in resonance angle caused by a change m local refractive index This technique can be used to characterize the effect of small molecules on kinetic rates and equilibrium binding constants for ratC polypeptide self-association as well as an association of ratC polypeptide and another polypeptide or small molecule A scintillation proximity assay may be used to characterize the interaction between an association of ratC polypeptide with another ratC polypeptide or a different polypeptide ratC polypeptide can be coupled to a scintillation-filled bead Addition of radio-labeled ratC polypeptide results in binding where the radioactive source molecule is in close proximity to the scintillation fluid Thus, signal is emitted upon ratC polypeptide binding and compounds that prevent ratC polypeptide self-association or an association of ratC polypeptide and another polypeptide or small molecule will diminish signal ICS biosensors have been described by AMBRI (Australian Membrane Biotechnology Research Institute) They couple the self-association of macromolecules to the closing of gramacidin-facilitated ion channels m suspended membrane bilay'ers and hence to a measurable change in the admittance (similar to impedence) of the biosensor This approach is linear over six decades of admittance change and is ideally suited for large scale, high through-put screening of small molecule combinatorial libraries In other embodiments of the mvention there are provided methods for identifying compounds which bmd to or otherwise mteract with and inhibit or activate an activity or expression of a polypeptide and/or polynucleotide of the mvention compnsmg contacting a polypeptide and/or polynucleotide of the mvention with a compound to be screened under conditions to permit bmdmg to or other mteraction between the compound and the polypeptide and/or polynucleotide to assess the bmdmg to or other mteraction with the compound, such bmdmg or mteraction preferably bemg associated with a second component capable of providing a detectable signal in response to the bmdmg or mteraction of the polypeptide and/or polynucleotide with the compound, and determimng whether the compound bmds to or otherwise mteracts w th and activates or inhibits an activity or expression of the polypeptide and/or polynucleotide by detectmg the presence or absence of a signal generated from the binding or mteraction of the compound with the polypeptide and/or polynucleotide Another example of an assay for ratC agomsts is a competitive assay that combines ratC and a potential agomst with ratC-binding molecules, recombinant ratC bmdmg molecules, natural substrates or ligands. or substrate or ligand mimetics. under appropnate conditions for a competitive inhibition assay ratC can be labeled, such as by radioactivity or a colonmetnc compound, such that the number of ratC molecules bound to a bmdmg molecule or converted to product can be determined accurately to assess the effectiveness of the potential antagonist Potential antagomsts mclude. among others, small organic molecules, peptides. polypeptides and antibodies that bmd to a polynucleotide and/or polypeptide of the mvention and thereby inhibit or extinguish its activity or expression Potential antagomsts also may be small organic molecules, a peptide. a polypeptide such as a closely related protem or antibody that bmds the same sites on a bmdmg molecule, such as a bmdmg molecule, without mducmg ratC-mduced activities, thereby preventmg the action or expression of ratC polypeptides and/or polynucleotides by excluding ratC polypeptides and/or polynucleotides from bmdmg Potential antagomsts mclude a small molecule that bmds to and occupies the bmdmg site of the polypeptide thereby preventmg bmdmg to cellular bmdmg molecules, such that normal biological activity is prevented Examples of small molecules mclude but are not limited to small organic molecules, peptides or peptide-like molecules Other potential antagomsts mclude antisense molecules (see Okano, J Neurochem 56 560 (1991), OLIGODEOXYNUCLEOTIDES AS ANTISENSE INHIBITORS OF GENE EXPRESSION CRC Press. Boca Raton. FL (1988). for a descnption of these molecules) Prefened potential antagomsts mclude compounds related to and vanants of ratC Other examples of potential polypeptide antagomsts mclude antibodies or. m some cases, oligonucleotides or protems which are closely related to the ligands. substrates, receptors, enzymes, etc . as the case may be. of the polypeptide. e g . a fragment of the ligands. substrates, receptors, enzymes, etc , or small molecules winch bmd to the polypeptide of the present mvention but do not elicit a response, so that the activity of the polypeptide is prevented Certain of the polypeptides of the mvention are biomimetics. functional mimetics of the natural ratC polypeptide These functional mimetics may be used for. among other things, antagonizing the activity of ratC polypeptide or as a antigen or lmmunogen m a manner descnbed elsewhere herem Functional mimetics of the polypeptides of the mvention mclude but are not limited to truncated polypeptides For example, prefened functional mimetics include, a polypeptide compnsmg the polypeptide sequence set forth m SEQ ID NO 2 lacking 20. 30. 40. 50. 60. 70 or 80 ammo- or carboxy- terminal ammo acid residues, mcludmg fusion protems compnsmg one or more of these truncated sequences Polynucleotides encoding each of these functional mimetics may' be used as expression cassettes to express each mimetic polypeptide It is prefened that these cassettes compnse 5' and 3' restnction sites to allow for a convenient means to ligate the cassettes together when desired It is further prefened that these cassettes compnse gene expression signals known m the art or descnbed elsewhere herem Thus, in another aspect, the present invention relates to a screening kit for identifying agonists, antagonists, ligands. receptors, substrates, enzymes, etc for a polypeptide and/or polynucleotide of the present invention, or compounds which decrease or enhance the production of such polypeptides and or polynucleotides , which comprises (a) a polypeptide and/or a polynucleotide of the present invention, (b) a recombinant cell expressmg a polypeptide and/or polynucleotide of the present invention, (c) a cell membrane expressing a poly peptide and/or polynucleotide of the present invention, or (d) antibody to a polypeptide and/or polynucleotide of the present invention, which polypeptide is preferably that of SEQ ID NO 2. and which polynucleotide is preferably that of SEQ ID NO 1 It will be appreciated that in any such kit, (a), (b), (c) or (d) may comprise a substantial component It will be readily appreciated by the skilled artisan that a polypeptide and/or polynucleotide of the present invention may also be used in a method for the structure-based design of an agomst, antagonist or inhibitor of the polypeptide and/or polynucleotide. by (a) determining in the first instance the three-dimensional structure of the polypeptide and/or polynucleotide. or complexes thereof, (b) deducing the three-dimensional structure for the likely reactive sιte(s). binding sιte(s) or motifts) of an agonist, antagonist or inhibitor, (c) synthesizing candidate compounds that are predicted to bind to or react with the deduced binding sιte(s). reactive sιte(s). and/or motιf(s). and (d) testing whether the candidate compounds are indeed agonists, antagonists or inhibitors It will be further appreciated that this will normally be an iterative process, and this iterative process may be performed using automated and computer-controlled steps In a further aspect, the present my ention provides methods of treating abnonnal conditions such as. for instance, a Disease, related to either an excess of, an under-expression of. an elevated activity of, or a decreased activity of ratC polypeptide and/or polynucleotide If the expression and/or activity of the polypeptide and/or polynucleotide is m excess, several approaches are available One approach compnses administering to an individual m need thereof an inhibitor compound (antagonist) as herem descnbed, optionally m combmation with a pharmaceutically acceptable earner, in an amount effective to inhibit the function and/or expression of the polypeptide and/or polynucleotide. such as, for example, by blockmg the bmdmg of ligands. substrates receptors, enzymes, etc . or by inhibiting a second signal, and thereby alleviating the abnormal condition In another approach, soluble forms of the polypeptides still capable of binding the ligand. substrate, enzymes, receptors, etc in competition with endogenous polypeptide and/or polynucleotide may be administered Typical examples of such competitors include fragments of the ratC polypeptide and/or polypeptide In a further aspect, the present mvention relates to genetically engineered soluble fusion proteins compnsing a polypeptide of the present invention, or a fragment thereof, and various portions of the constant regions of heavy' or light chains of immunoglobulms of various subclasses (IgG. IgM. IgA. IgE) Preferred as an mimunoglobuhn is the constant part of the heavy chain of human IgG, particularly IgG 1 , where fusion takes place at the hmge 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 protem technology can be found in International Patent Application Nos W094/29458 and W094/22914 In still another approach, expression of the gene encoding endogenous ratC polypeptide can be inhibited using expression blocking techniques This blocking may be targeted against any step in gene expression, but is preferably targeted against transcription and/or translation An examples of a known technique of this sort involve the use of antisense sequences, either internally generated or separately administered (see, for example. O'Connor. J Neurochem (1991) 56 560 in Ohgodeoxynucleotides as Antisense Inhibitors of Gene Expression. CRC Press, Boca Raton, FL (1988)) Alternatively, ohgonucleotides which form tnple helices with the gene can be supplied (see, for example. Lee et al , Nucleic Acids Res (1979) 6 3073, Cooney et al , Science (1988) 241 456, Dervan et al , Science (1991) 251 1360) These ohgomers can be administered per se or the relevant ohgomers can be expressed in vivo 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 protem 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 protems on m-dwelhng devices or to extracellular matrix proteins m wounds, to block bacterial adhesion between eukaryotic. preferably mammalian, extracellular matrix proteins and bacterial ratC proteins that mediate tissue damage and/or. to block the normal progression of 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 mvention, there are provided ratC agomsts and antagomsts, preferably bactenstatic or bactencidal agomsts and antagomsts The antagomsts and agomsts of the mvention may be employed, for instance, to prevent, inhibit and/or treat diseases Hehcobacter pylori (herem "H pylori") bacteria infect the stomachs of over one-third of the world's population causing stomach cancer, ulcers, and gastritis (International Agency for Research on Cancer (1994) Schistosomes Liver Flukes and Hehcobacter Pylori (International Agency for Research on Cancer. Lyon. France, http //www uicc ch/ecp/ecp2904 htm) Moreover, the International Agency for Research on Cancer recently recognized a cause-and-effect relationship between H pylori and gastric adenocarcmoma. classifying the bacterium as a Group I (definite) carcinogen Preferred antimicrobial compounds of the invention (agonists and antagonists of ratC polypeptides and/or polynucleotides) found usmg screens provided by the invention, or known m the art, particularly narrow-spectrum antibiotics, should be useful in the treatment of // pylori infection Such treatment should decrease the advent of H p\ Ion -induced cancers, such as gastrointestinal carcinoma Such treatment should also prevent, inhibit and/or cure gastric ulcers and gastritis Vaccines There are provided by the invention, products, compositions and methods for assessmg ratC expression, treatmg disease, assaying genetic vanation. and administering a ratC polypeptide and or polynucleotide to an organism to raise an immunological response agamst a bactena especially a Streptococcus pneumomae bactena Another aspect of the invention relates to a method for inducing an immunological response in an individual, particularly a mammal which comprises inoculating the individual with ratC 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 Streptococcus pneumomae 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 m an individual which comprises delivering to such individual a nucleic acid vector, sequence or πbozyme to direct expression of ratC polynucleotide and/or polypeptide. or a fragment or a variant thereof, for expressing ratC polynucleotide and or polypeptide. or a fragment or a variant thereof in vivo m order to induce an immunological response, such as, to produce antibody and/ or T cell immune response, including, for example, cytokine-producmg 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 πbozyme. a modified nucleic acid, a DNA/RNA hybrid, a DNA-protein complex or an RNA- protem complex A further aspect of the invention relates to an immunological composition that when introduced into an individual, preferably a human, capable of having mduced withm it an immunological response, induces an immunological response m such individual to a ratC polynucleotide and/or polypeptide encoded therefrom, wherein the composition comprises a recombinant ratC polynucleotide and or polypeptide encoded therefrom and or comprises DNA and/or RNA which encodes and expresses an antigen of said ratC 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 CTL or CD4+ T cells A ratC polypeptide or a fragment thereof may be fused with co-protem 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 antigemc and/or immunogenic properties, and preferably protective properties Thus fused recombinant protem, preferably further comprises an antigemc co-protem. such as hpoprotein D from Hemophilus influenzae. Glutathione-S-transferase (GST) or beta-galactosidase. or any other relatively large co-protem which solubihzes 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-protem may be attached to either the ammo- or carboxy-terminus of the first protem Provided by this invention are compositions, particularly vaccine compositions, and methods comprising the polypeptides and/or polynucleotides of the invention and lmmunostimulatory DNA sequences, such as those described in Sato. Y et al Science 273 352 (1996) 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 protems. in polynucleotide constructs used m such genetic immunization experiments in animal models of infection with Streptococcus pneumomae 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 Streptococcus pneumomae infection, in mammals, particularly humans A polypeptide of the invention may be used as an antigen for vaccination of a host to produce specific antibodies which protect against invasion of bacteria, for example by blocking adherence of bacteria to damaged tissue Examples of tissue damage include wounds m skin or connective tissue caused, for example b y mechanical, chemical, thermal or radiation damage or by implantation of indwelling devices, or wounds in the mucous membranes, such as the mouth, throat, mammary glands, urethra or vagma The invention also includes a vaccme formulation which comprises an immunogenic recombmant 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, bactenstatic compounds and solutes which render the formulation lsotomc 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 multi-dose containers, for example, sealed ampoules and vials and may be stored in a freeze-dπed condition requiring only the addition of the sterile liquid carrier inmiediately prior to use The vaccine formulation may also mclude adjuvant systems for enhancing the lmmunogemcity of the formulation, such as oil-in water systems and other systems known in the art The dosage will depend on the specific activity of the vaccine and can be readily determined by routine experimentation While the invention has been described with reference to certain ratC 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 hi a further aspect of the mvention there are provided compositions compnsmg a ratC polynucleotide and/or a ratC polypeptide for administration to a cell or to a multicellular organism The mvention also relates to compositions compnsmg a polynucleotide and/or a polypeptides discussed herem or their agomsts or antagomsts The polypeptides and polynucleotides of the mvention may be employed m combmation with a non-stenle or stenle earner or earners for use with cells, tissues or organisms, such as a pharmaceutical earner suitable for admimstration to an individual Such compositions compnse, for instance, a media additive or a therapeutically effective amount of a polypeptide and/or polynucleotide of the mvention and a pharmaceutically acceptable earner or excipient Such earners may mclude, but are not limited to, salme. buffered sahne. dextrose, water, glycerol, ethanol and combinations thereof The formulation should suit the mode of administration The mvention further relates to diagnostic and pharmaceutical packs and kits compnsmg one or more containers filled with one or more of the ingredients of the aforementioned compositions of the mvention Polypeptides, polynucleotides and other compounds of the mvention may be employed alone or in conjunction with other compounds, such as therapeutic compounds The pharmaceutical compositions may be administered m any effective, convenient manner mcludmg. for instance, administration by topical, oral, anal, vaginal, mtravenous, mtrapentoneal. intramuscular, subcutaneous, mtranasal 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 lsotomc Alternatively the composition may be formulated for topical application for example in the fonn of ointments, creams, lotions, eye ointments, eye drops ear drops, mouthwash. impregnated dressings and sutures and aerosols, and mav contain appropriate conventional additives, including, for example, preservatives, solvents to assist drug penetration, and emollients in ointments and creams Such topical fonnulations may also contain compatible conventional carriers, for example cream or ointment bases, and ethanol or oleyl alcohol for lotions Such carriers may constitute from about 1% to about 98% by weight of the formulation, more usually they will constitute up to about 80% by weight of the formulation In a further aspect, the present mvention provides for pharmaceutical compositions compnsmg a therapeutically effective amount of a polypeptide and/or polynucleotide. such as the soluble form of a polypeptide and/or polynucleotide of the present mvention. agonist or antagonist peptide or small molecule compound, m combmation with a pharmaceutically acceptable earner or excipient Such earners mclude. but are not limited to. salme. buffered salme. dextrose, water, glycerol. ethanol. and combinations thereof The mvention further relates to pharmaceutical packs and kits compnsmg one or more containers filled with one or more of the ingredients of the aforementioned compositions of the mvention Polypeptides, polynucleotides and other compounds of the present mvention mav be employed alone or m conjunction with other compounds, such as therapeutic compounds The composition will be adapted to the route of admimstration. for instance by a systemic or an oral route Preferred forms of systemic admimstration mclude injection, typically by intravenous injection Other injection routes, such as subcutaneous, intramuscular, or mtrapentoneal. can be used Alternative means for systemic admimstration mclude transmucosal and transdeπnal admimstration usmg penetrants such as bile salts or fusidic acids or other detergents In addition, if a polypeptide or other compounds of the present mvention can be formulated m an entenc or an encapsulated formulation, oral admimstration may also be possible Admimstration of these compounds may also be topical and/or localized, m the form of salves, pastes, gels, and the like 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 mg/kg 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 ithm the scope of this invention In-dwelling devices include surgical implants, prosthetic devices and catheters, I e . devices that are introduced to the body of an individual and remain in position for an extended time Such devices include, for example, artificial joints, heart valves, pacemakers, vascular grafts, vascular catheters, cerebrospmal fluid shunts, urinary' catheters continuous ambulatory peritoneal dialysis (CAPD) catheters The composition of the mvention may be administered by injection to achieve a systemic effect against relevant bacteria shortly before insertion of an in-dwellmg device Treatment may be continued after surgery during the m-body time of the device In addition, the composition could also be used to broaden penoperative cover for any surgical technique to prevent bacterial wound infections, especially Streptococcus pneumomae yyound infections Many orthopedic surgeons consider that humans with prosthetic joints should be considered for antibiotic prophylaxis before dental treatment that could produce a bacteremia Late deep infection is a serious complication sometimes leading to loss of the prosthetic joint and is accompanied by significant morbidity and mortality It mav therefore be possible to extend the use of the active agent as a replacement for prophylactic antibiotics in this situation In addition to the therapy described above, the compositions of this invention may be used generally as a wound treatment agent to prevent adhesion of bacteria to matrix proteins exposed in wound tissue and for prophylactic use in dental treatment as an alternative to. or in conjunction with, antibiotic prophylaxis Alternatively, the composition of the invention may be used to bathe an indwelling device immediately before insertion The active agent will preferably be present at a concentration of 1 μg/ml to 1 Omg/ml for bathing of wounds or indwelling devices A vaccine composition is conveniently in mjectable 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 1-3 times and with an interval of 1-3 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 Sequence 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-dιmensιonal structures as well as to identify' further sequences of similar homology These approaches are most easily facilitated by storing the sequence m a computer readable medium and then usmg the stored data m a known macromolecular structure program or to search a sequence database usmg well known searching tools, such as GCC The polynucleotide and polypeptide sequences of the invention are particularly useful as components in databases useful for search analyses as well as in sequence analysis algorithms As used in this section entitled "Sequence Databases. Sequences m a Tangible Medium, and Algorithms." and in claims related to this section, the terms "polynucleotide of the invention" and "polynucleotide sequence of the invention" mean any detectable chemical or physical characteristic of a pol nucleotide of the invention that is or may be reduced to or stored in a tangible medium. preferably a computer readable form For example, chromatographic scan data or peak data, photographic data or scan data therefrom, called bases, and mass spectrographic data As used in this section entitled Databases and Algorithms and in claims related thereto, the terms "polypeptide of the invention" and "polypeptide sequence of the invention" mean any detectable chemical or physical characteristic of a polypeptide of the invention that is or may be reduced to or stored in a tangible medium, preferably a computer readable fonn For example, chromatographic scan data or peak data, photographic data or scan data therefrom, and mass spectrographic data The mvention provides a computer readable medium havmg stored thereon polypeptide sequences of the invention and/or polynucleotide sequences of the invention For example, a computer readable medium is provided comprising and having stored thereon a member selected from the group consisting of a polynucleotide comprising the sequence of a polynucleotide of the invention, a polypeptide comprising the sequence of a polypeptide sequence of the invention, a set of polynucleotide sequences wherein at least one of the sequences comprises the sequence of a polynucleotide sequence of the invention, a set of polypeptide sequences wherein at least one of the sequences comprises the sequence of a polypeptide sequence of the mvention, a data set representing a polynucleotide sequence comprising the sequence of polynucleotide sequence of the invention, a data set representing a polynucleotide sequence encoding a polypeptide sequence comprising the sequence of a polypeptide sequence of the invention, a polynucleotide comprising the sequence of a polynucleotide sequence of the invention, a polypeptide compnsing the sequence of a polypeptide sequence of the invention, a set of polynucleotide sequences wherein at least one of the sequences comprises the sequence of a polynucleotide sequence of the invention, a set of polypeptide sequences wherein at least one of said sequences comprises the sequence of a polypeptide sequence of the invention, a data set representing a polynucleotide sequence comprising the sequence of a polynucleotide sequence of the invention, a data set representing a polynucleotide sequence encoding a polypeptide sequence comprising the sequence of a polypeptide sequence of the invention The computer readable medium can be any composition of matter used to store infonnation or data, including, for example, commercially available floppy disks, tapes, chips, hard drives, compact disks, and video disks Also provided by the invention are methods for the analysis of character sequences or strings, particularly genetic sequences or encoded genetic sequences Preferred methods of sequence analysis include, for example, methods of sequence homology analysis, such as identity and similarity analysis. RNA structure analysis, sequence assembly, cladistic analysis, sequence motif analysis, open reading frame determination, nucleic acid base calling, 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 compnsmg the sequence a polynucleotide of the invention m 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 compnsing the sequence of a polypeptide of the mvention m a computer readable medium, and comparing said first polypeptide sequence to at least one second polynucleotide or polypeptide sequence to identify homology A computer based method is still further provided for polynucleotide assembly, said method comprising the steps of providing a first polynucleotide sequence comprising the sequence of a polynucleotide of the invention in a computer readable medium, and screening for at least one overlapping region between said first polynucleotide sequence and at least one second polynucleotide or polypeptide sequence A computer based method is still further provided for polynucleotide assembly, said method comprising the steps of providing a first polypeptide sequence comprising a polypeptide of the invention in a computer readable medium, and screening for at least one overlapping region between said first polypeptide sequence and at least one second polynucleotide or polypeptide sequence In another prefened embodiment of the mvention there is provided a computer readable medium having stored thereon a member selected from the group consisting of a polynucleotide comprising the sequence of SEQ ID NO 1, a polypeptide comprising the sequence of SEQ ID NO 2, a set of polynucleotide sequences wherein at least one of said sequences comprises the sequence of SEQ ID NO 1 , a set of polypeptide sequences wherein at least one of said sequences comprises the sequence of SEQ ID NO 2. a data set representing a polynucleotide sequence comprising the sequence of SEQ ID NO 1. a data set representing a polynucleotide sequence encoding a polypeptide sequence comprising the sequence of SEQ ID NO 2. a polynucleotide comprising the sequence of SEQ ID NO 1. a polypeptide comprising the sequence of SEQ ID NO 2. a set of polynucleotide sequences wherein at least one of said sequences comprises the sequence of SEQ ID NO 1. a set of polypeptide sequences wherein at least one of said sequences comprises the sequence of SEQ ID NO 2, a data set representing a polynucleotide sequence comprising the sequence of SEQ ID NO 1. a data set representing a polynucleotide sequence encoding a polypeptide sequence comprising the sequence of SEQ ID NO 2 A further preferred embodiment of the invention provides a computer based method for performing homology identification, said method comprising the steps of providing a polynucleotide sequence comprising the sequence of SEQ ID NO 1 in a computer readable medium, and comparing said polynucleotide sequence to at least one polynucleotide or polypeptide sequence to identify homology A still further preferred embodiment of the invention provides a computer based method for performing homology identification, said method comprising the steps of providing a polypeptide sequence comprising the sequence of SEQ ID NO 2 in a computer readable medium and comparing said polypeptide sequence to at least one polynucleotide or polypeptide sequence to identify homology A further embodiment of the invention provides a computer based method for polynucleotide assembly, said method comprising the steps of providing a first polynucleotide sequence comprising the sequence of SEQ ID NO 1 in a computer readable medium, and screenmg for at least one overlapping region between said first polynucleotide sequence and a second polynucleotide sequence A further embodiment of the invention provides a computer based method for performing homology identification, said method comprising the steps of providing a polynucleotide sequence comprising the sequence of SEQ ID NO 1 in a computer readable medium, and comparing said polynucleotide sequence to at least one polynucleotide or polypeptide sequence to identify homology All publications and references including but not limited to patents and patent applications, cited in this specification are herein mcorporated by reference in their entirety as if each individual publication or reference were specifically and individually indicated to be incorporated by reference herem 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 GLOSSARY The following definitions are provided to facilitate understanding of certain tenns used frequently herem 'Αntιbody(ιes)" as used herein includes polyclonal and monoclonal antibodies chimeπc. single chain, and humamzed antibodies, as well as Fab fragments, including the products of an Fab or other lmmunoglobuhn expression library "Antigemcally equivalent denvatιve(s)" as used herein encompasses a polypeptide. polynucleotide. or the equivalent of either which will be specifically recognized by certain antibodies which, when raised to the protem. polypeptide or polynucleotide according to the invention, interferes with the immediate physical interaction between pathogen and mammalian host "Bispecific antιbody(ιes)" means an antibody comprising at least two antigen binding domains, each domain directed against a different epitope "Bodily matenal(s) means any' matenal denved from an individual or from an organism infecting, infesting or inhabiting an individual, mcludmg but not limited to, cells, tissues and waste, such as, bone, blood, serum, cerebrospmal fluid, semen, saliva, muscle, cartilage, organ tissue, skin, urine, stool or autopsy matenals "Dιsease(s)" means any disease caused by or related to infection by a bactena, mcludmg . for example, otitis media, conjunctivitis, pneumoma, bacteremia. meningitis, sinusitis, pleural empyema and endocarditis, and most particularly meningitis, such as for example infection of cerebrospmal fluid "Fusion proteιn(s)" refers to a protem encoded by two, often unrelated, fused genes or fragments thereof In one example. EP-A-0464 discloses fusion protems comprising various portions of constant region of immunoglobulm molecules together with another human protein or part thereof In many cases, employing an immunoglobulm Fc region as a part of a fusion protein is advantageous for use in therapy and diagnosis resulting m. for example, improved pharmacokinetic properties [see, e g . EP-A 0232262] On the other hand, for some uses it would be desirable to be able to delete the Fc part after the fusion protein has been expressed, detected and purified "Host cell(s)" is a cell which has been transformed or transfected. or is capable of transformation or transfection by an exogenous polynucleotide sequence "Identity." as known m 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 determined by the match between strings of such sequences "Identity" can be readily calculated by known methods, including but not limited to those described in (Computational Molecular Biology. Lesk. A M . ed . Oxford University Press. New York. 1988. 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 m Molecular Biology, von Heinje, G . Academic Press. 1987. and Sequence Analysis Primer. Gnbskoy. M and Devereux. J , eds . M Stockton Press. New York. 1991. and Canllo. 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 determine identity between two sequences include, but are not limited to. the GCG program package (Devereux, J , et al . Nucleic Acids Research 12(1) 387 (1984)). BLASTP. BLASTN. and FASTA (Altschul, S F et al . J Molec Biol 215 403-410 (1990) The BLAST X program is publicly available from NCBI and other sources (BLAST Manual Altschul. S . et al , NCBI NLM NIH Bethesda. MD 20894. Altschul. S . et l . 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 (1970) Comparison matrix BLOSSUM62 from Hentikoff and Hentikoff. Proc Natl Acad Sci USA 89 10915-10919 (1992) Gap Penalty 12 Gap Length Penalty 4 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 Algonthm Needleman and Wunsch. J Mol Biol 48 443-453 (1970) Comparison matrix matches = +10. mismatch = 0 Gap Penalty 50 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 be. are provided in (1) and (2) below (1) Polynucleotide embodiments further mclude an isolated polynucleotide comprising a polynucleotide sequence having at least a 50. 60. 70. 80. 85. 90. 95. 97 or 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 mclude 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 nucleotide deletion, substitution, including transition and transversion, or insertion, and wherein said alterations may occur at the 5' or 3' terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among the nucieotides in the reference sequence or in one or more contiguous groups within the reference sequence, and wherein said number of nucleotide alterations is detenmned by multiplying the total number of nucieotides 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 nucieotides m SEQ ID NO 1, or n n ≤ x n - ( x n • y)> wherein n n is the number of nucleotide alterations. x n is the total number of nucieotides in SEQ ID NO 1, 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 operator, and wherein any non-integer product of x n and y is rounded down to the nearest integer pnor to subtracting it from x n Alterations of a polynucleotide sequence encoding the polypeptide of SEQ ID NO 2 may create nonsense, missense or frameshift mutations in this coding sequence and thereby alter the polypeptide encoded by the polynucleotide following such alterations By way of example, a polynucleotide sequence of the present mvention 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 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 m 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 ≤ x n " ( x n * y)> wherein n n is the number of nucleic acid alterations. x n 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 . • is the symbol for the multiplication operator, and wherein any non-integer product of x n and y is rounded down to the nearest integer prior to subtracting it from x n (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 NO 2, wherein said polypeptide sequence may be identical to the reference sequence of SEQ ID NO 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 wherem 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 ammo acids in the reference sequence or in one or more contiguous groups withm the reference sequence, and wherein said number of amino acid alterations is determined by multiplying the total number of ammo acids in SEQ ID NO 2 by the integer defining the percent identity divided by 100 and then subtractmg that product from said total number of amino acids m SEQ ID NO 2, or n a < x a - (x a • y), wherein n a is the number of amino acid alterations, x a is the total number of ammo acids in SEQ ID NO 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 operator, and wherein any non-mteger product of x a and y is rounded down to the nearest integer prior to subtracting it from x a By way of example, a polypeptide sequence of the present mvention may be identical to the reference sequence of SEQ ID NO 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 wherem 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 ammo acids in SEQ ID NO 2 by the integer defining the percent identity divided by 100 and then subtracting that product from said total number of amino acids m SEQ ID NO 2. or n a ≤ x a " ( a • Y)> wherein n a is the number of amino acid alterations. x a is the total number of amino acids in SEQ ID NO 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 x a and y is rounded down to the nearest integer prior to subtracting it from x a "Immunologically equivalent deπvatιve(s)" as used herein encompasses a polypeptide, polynucleotide. or the equivalent of either which when used in a suitable formulation to raise antibodies in a vertebrate, the antibodies act to interfere with the immediate physical interaction between pathogen and mammalian host "Immunospecific' " means that charactenstic of an antibody whereby it possesses substantially greater affinity for the polypeptides of the mvention or the polynucleotides of the mvention than its affinity for other related polypeptides or polynucleotides respectively, particularly those polypeptides and polynucleotides m the pnor art "Indιvιdual(s)" means a multicellular eukaryote. mcludmg, 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 m nature, it has been changed or removed from its ongmal environment, or both For example, a polynucleotide or a polypeptide naturally present m a living organism is not "isolated." but the same polynucleotide or polypeptide separated from the coexisting matenals of its natural state is "isolated", as the term is employed herem Moreover, a polynucleotide or polypeptide that is mtroduced mto an organism by transformation, genetic manipulation or by any other recombinant method is "isolated" even if it is still present in said organism, yvhich organism may be Irving or non-living "Organιsm(s)" means a (I) prokaryote. mcludmg but not limited to. a member of the genus Streptococcus, Staphylococcus, Bordetella. Corynebactenum. Mycobactenum, Neissena, Haemophilus, Actinomycetes, Streptomycetes Nocardia, Enter obacter, Yersinia. Fanasella, Pasturella. Moraxella, Acinetobacter, Erysipelothnx, Branhamella, Actinobacillus Streptobacillus, Liste a, Calymmatobacte um, Brucella, Bacillus. Clostndium. Treponema, Escherichia, Salmonella, Kleibsiella, Vibrio Proteus, Erwinia. Borrelia. Leptospira, Spinllum. Campylobacter Shigella, Legwnella, Pseudomonas, Aeromonas. Rickettsia, Chlamydia. Borrelia and Mycopla.sma. and further mcludmg. but not limited to. a member of the species or group, Group A Streptococcus. Group B Streptococcus: Group C Streptococcus Group D Streptococcus. Group G Streptococcus, Streptococcus pneumomae, Streptococcus pyogenes, Streptococcus agalactiae Streptococcus faecahs Streptococcus jaecium, Streptococcus durans, Neissena gonorrheae, Neisse a meningitidis. Staphylococcus aureus, Staphylococcus epidermidis, Corynebactenum dipthenae, Gardnerella vaginahs, Mycobactenum tuberculosis, Mycobactenum bovis, Mycobacterium ulcerans, Mycobacterium leprae, Actinomyctes israeln, Listena monocytogenes, Bordetella pertusis, Bordatella parapertusis, Bordetella bronchiseptica, Eschenchia coli, Shigella dysentenae, Haemophύus influenzae, Haemophilus aegyptius, Haemophύus parainfluenzae, Haemophύus ducreyi, Bordetella, Salmonella typhi, Citrobacter freundn, Proteus mirabihs, Proteus vulgans, Yersima pestis. Kleibsiella pneumomae, Serratia marcessens, Serratia hquefaciens, Vibrio cholera, Shigella dysenteni, Shigella flexnen, Pseudomonas aerugmosa, Franscisella tularensis, Brucella abortis. Bacillus anthracis, Bacillus cereus, Clostndium perfrmgens, Clostndium tetani, Clostndium botulmum, Treponema palhdum, Rickettsia nckettsii and Chlamydia trachomitis, (u) an archaeon, mcludmg but not limited to Archaebacter. and (in) a unicellular or filamentous eukaryote. mcludmg but not limited to, a protozoan, a fungus, a member of the genus Saccharomyces, Kluveromyces, or Candida, and a member of the species Saccharomyces cenviseae, Kluveromyces lactis, or Candida albicans "Polynucleotιde(s)" generally refers to any polynbonucleotide or polydeoxynbonucleotide. which may be unmodified RNA or DNA or modified RNA or DNA "Polynucleotιde(s)" mclude, without limitation, smgle- and double-stranded DNA, DNA that is a mixture of smgle- and double- stranded regions or smgle-, double- and tnple-stranded regions, smgle- and double-stranded RNA. and RNA that is mixture of smgle- and double-stranded regions, hybnd molecules compnsmg DNA and RNA that may be single-stranded or, more typically, double-stranded, or tnple-stranded regions, or a mixture of smgle- and double-stranded regions In addition, "polynucleotide" as used herem refers to tnple-stranded regions compnsmg RNA or DNA or both RNA and DNA The strands in such regions may be from the same molecule or from different molecules The regions may mclude all of one or more of the molecules, but more typically mvolve only a region of some of the molecules One of the molecules of a tnple-he cal region often is an oligonucleotide As used herem, the term "polynucleotide(s)" also mcludes DNAs or RNAs as descnbed above that contain one or more modified bases Thus, DNAs or RNAs with backbones modified for stability or for other reasons are "pofynucleotide(s)" as that term is mtended herem Moreover. DNAs or RNAs compnsmg unusual bases, such as mosme. or modified bases, such as tntylated bases, to name just two examples, are polynucleotides as the term is used herem It will be appreciated that a great vanety of modifications have been made to DNA and RNA that serve many useful purposes known to those of skill m the art The tenn "polynucleotιde(s)" as it is employed herem embraces such chemically, enzymatically or metabo cally modified forms of polynucleotides. as well as the chemical forms of DNA and RNA charactenstic of viruses and cells, mcludmg, for example, simple and complex cells "Polynucleotide(s)" also embraces short polynucleotides often refened to as ohgonucleotιde(s) "Polypeptιde(s)" refers to any peptide or protem compnsmg two or more ammo acids joined to each other by peptide bonds or modified peptide bonds "Polypeptide(s)" refers to both short chams, commonly refened to as peptides, o gopeptides and ohgomers and to longer chains generally refened to as protems Polypeptides may contain ammo acids other than the 20 gene encoded ammo acids "Polypeptιde(s)" mclude those modified either by natural processes, such as processmg and other post- translational modifications, but also by chemical modification techmques Such modifications are well descnbed m basic texts and in more detailed monographs, as well as m a volummous research literature, and they are well known to those of skill m the art It will be appreciated that the same type of modification may be present m the same or varying degree at several sites m a given polypeptide Also, a given polypeptide may contain many types of modifications Modifications can occur anywhere m a polypeptide, mcludmg the peptide backbone, the ammo acid side-chains, and the ammo or carboxyl termini Modifications mclude, for example, acetylation. acylation, ADP-nbosylation. anudation. covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide denvative. covalent attachment of a pid or pid denvative. covalent attachment of phosphotidylmositol. cross-linking, cyclization. disulfide bond formation, demethylation fonnation of covalent cross-links, formation of cysteme. formation of pyroglutamate. formylation. gamma- carboxylation GPI anchor formation, hydroxylation, lodination. methylation, mynstoylation, oxidation, proteolytic processmg. phosphorylation. prenylation. racemization. glycosylation, hpid attachment, sulfation. gamma-carboxylation of glutamic acid residues, hydroxylation and ADP-nbosylation. selenoylation, sulfation, transfer-RNA mediated addition of ammo acids to proteins, such as arginylation. and ubiquitination See. for instance. PROTEINS - STR UCTURE AND MOLECULAR PROPERTIES, 2nd Ed , T E Creighton, W H Freeman and Company. New York (1993) and Wold, F , Posttranslational Protem Modifications Perspectives and Prospects, pgs 1-12 m POSTTRANSLATIONAL COVALENT MODIFICATION OF PROTEINS B C Johnson, Ed , Academic Press, New York (1983), Seifter et al . Meth Enzymol 182 626-646 (1990) and Rattan et al , Protein Synthesis Posttranslational Modifications and Aging. Ann N Y Acad Sci 663 48-62 (1992) Polypeptides may be branched or cyclic, with or without branclnng Cyclic, branched and branched circular polypeptides may result from post-translational natural processes and may be made by entirely synthetic methods, as well "Recombinant expression system(s)" refers to expression systems or portions thereof or polynucleotides of the mvention mtroduced or transformed mto a host cell or host cell lysate for the production of the polynucleotides and polypeptides of the mvention "Subtraction set" is one or more, but preferably less than 100, polynucleotides comprising at least one polynucleotide of the invention 'Naπant(s)" as the term is used herein, is a polynucleotide or polypeptide that differs from a reference polynucleotide or polypeptide respectively, 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 ammo acid substitutions, additions, deletions, fusion proteins and truncations in 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 vanant 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 The present mvention also mcludes mclude vanants of each of the polypeptides of the mvention. that is polypeptides that vary from the referents by conservative ammo acid substitutions, whereby a residue is substituted by another with like charactenstics Typical such substitutions are among Ala. Val. Leu and He. among Ser and Thr. among the acidic residues Asp and Glu, among Asn and Gin. and among the basic residues Lys and Arg, or aromatic residues Phe and Tyr Particularly prefened are vanants in which several. 5-10. 1-5. 1-3. 1-2 or 1 ammo acids are substituted, deleted or added m any combmation 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 variants of polynucleotides and polypeptides may be made by mutagenesis techniques, by direct synthesis, and by other recombinant methods known to skilled artisans EXAMPLES The examples below are earned out usmg standard techniques, which are well known and routme to those of skill m the art, except where otherwise descnbed m detail The examples are illustrative, but do not limit the mvention Example 1 Strain selection, Library Production and Sequencing The polynucleotide having a DNA sequence given in Table 1 [SEQ ID NO 1] was obtained from a library of clones of chromosomal DNA of Streptococcus pneumomae in E coli The sequencing data from two or more clones containing overlapping Streptococcus pneumomae DNAs was used to construct the contiguous DNA sequence in SEQ ID NO 1 Libraries may be prepared by routine methods, for example Methods 1 and 2 below Total cellular DNA is isolated from Streptococcus pneumomae 0100993 according to standard procedures and size-fractionated by either of two methods Method 1 Total cellular DNA is mechanically sheared by passage through a needle m order to size- fractionate according to standard procedures DNA fragments of up to 1 lkbp in size are rendered blunt by treatment with exonuclease and DNA polymerase. and EcoRI linkers added Fragments are ligated into the vector Lambda ZapII that has been cut with EcoRI. the library packaged by standard procedures and E coli infected with the packaged library The library is amplified b> standard procedures Method 2 Total cellular DNA is partially hydrolyzed with a one or a combination of restriction enzymes appropriate to generate a series of fragments for cloning mto library vectors (e g . Rsal. Pall. Alul, Bshl235I), and such fragments are size-fractionated according to standard procedures EcoRI linkers are ligated to the DNA and the fragments then ligated into the vector Lambda ZapII that have been cut with EcoRI, the library packaged by standard procedures, and E coli infected with the packaged library The library is amplified by standard procedures

Claims: What is claimed is: 1 An isolated polypeptide selected from the group consisting of (1) an isolated polypeptide comprising an amino acid having at least (a) 70% identity, (b) 80% identity. (c) 90% identity, or (d) 95% identity to the amino acid sequence of SEQ ID NO 2 over the entire length of SEQ ID NO 2, (n) an isolated polypeptide comprising the ammo acid sequence of SEQ ID NO 2 (in) an isolated polypeptide which is the amino acid sequence of SEQ ID NO 2, and (iv) a polypeptide which is encoded by a recombinant polynucleotide comprising the polynucleotide sequence of SEQ ID NO 1 2 An isolated polynucleotide selected from the group consisting of (i) an isolated polynucleotide compnsmg a polynucleotide sequence encodmg a polypeptide that has at least (a) 70% identity. (b) 80% identity, (c) 90% identity, or (d) 95% identity. to the ammo acid sequence of SEQ ID NO 2. over the entire length of SEQ ID NO 2 (u) an isolated polynucleotide compnsmg a polynucleotide sequence that has at least (a) 70% identity (b) 80% identity. (c) 90% identity, or (d) 95% identity. over its entire length to a polynucleotide sequence encodmg the polypeptide of SEQ ID NO 2. (in) an isolated polvnucleotide compnsmg a nucleotide sequence which has at least (a) 70% identity (b) 80% identity. (c) 90% identity, or (d) 95% identity, to that of SEQ ID NO 1 over the entire length of SEQ ID NO 1 , (iv) an isolated polynucleotide compnsmg a nucleotide sequence encodmg the polypeptide of SEQ ID NO 2, (v) an isolated polynucleotide which is the polynucleotide of SEQ ID NO 1 , (vi) an isolated polynucleotide obtainable by screenmg an appropnate library under stnngent hybndization conditions with a probe havmg the sequence of SEQ ID NO 1 or a fragment thereof. (vn) an isolated polynucleotide encoding a mature polypeptide expressed by the ratC gene contained in the Streptococcus pneumomae. and (vui) a polynucleotide sequence complementary to said isolated polynucleotide of (I). (n), (in), (iv). (v). (vi) or (vn) 3 An antibody antigemc to or immunospecific for the polypeptide of claim 1 4 A method for the treatment of an mdividual (l) in need of enhanced activity or expression of the polypeptide of claim 1 comprising the step of (a) administering to the individual a therapeutically effective amount of an agonist to said polypeptide, or (b) providing to the individual an isolated polynucleotide compnsmg a polynucleotide sequence encodmg said polypeptide m a form so as to effect production of said polypeptide activity in vivo, or (n) having need to inhibit activity or expression of the polypeptide of claim 1 comprising (a) administering to the individual a therapeutically effective amount of an antagonist to said polypeptide. or (b) administering to the individual a nucleic acid molecule that inhibits the expression of a polynucleotide sequence encoding said polypeptide, or (c) administering to the individual a therapeutically effective amount of a polypeptide that competes with said polypeptide for its ligand. substrate , or receptor 5 A process for diagnosing or prognosmg a disease or a susceptibility to a disease in an individual related to expression or activity of the polypeptide of claim 1 m an mdividual compnsing the step of (a) determining the presence or absence of a mutation in the nucleotide sequence encoding said polypeptide in the genome of said individual, or (b) analyzing for the presence or amount of said polypeptide expression m a sample derived from said individual 6 A method for screening to identify compounds that activate or that inhibit the function of the polypeptide of claim 1 which compnses a method selected from the group consisting of (a) measuring the bmdmg of a candidate compound to the polypeptide or to the cells or membranes beanng the polypeptide or a fusion protein thereof by means of a label directly or indirectly associated with the candidate compound (b) measuring the bmdmg of a candidate compound to the polypeptide or to the cells or membranes bearing the polypeptide or a fusion protein thereof in the presence of a labeled competitor, (c) testing whether the candidate compound results in a signal generated by activation or inhibition of the polypeptide. using detection systems appropriate to the cells or cell membranes bearing the polypeptide. (d) mixing a candidate compound with a solution containing a polypeptide of claim 1. to form a mixture, measuring activity of the polypeptide m the mixture, and comparing the activity of the mixture to a standard, (e) detecting the effect of a candidate compound on the production of mRNA encoding said polypeptide and said polypeptide in cells, usmg for instance, an ELISA assay, or (f) (1) contacting a composition compnsmg the polypeptide with the compound to be screened under conditions to permit mteraction between the compound and the polypeptide to assess the mteraction of a compound, such mteraction bemg associated with a second component capable of providing a detectable signal m response to the mteraction of the polypeptide with the compound, and (2) determining whether the compound interacts with and activates or inhibits an activity of the polypeptide by detectmg the presence or absence of a signal generated from the mteraction of the compound with the polypeptide 7 An agonist or an antagonist of the activity or expression polypeptide of claim 1 8 An expression system compnsmg a polynucleotide capable of producing a polypeptide of claim 1 when said expression system is present in a compatible host cell 9 A host cell comprising the expression system of claim 8 or a membrane thereof expressing a polypeptide selected from the group consisting of (I) an isolated polypeptide comprising an ammo acid sequence selected from the group having at least (a) 70% identity, (b) 80% identity, (c) 90% identity, or (d) 95% identity to the amino acid sequence of SEQ ID NO 2 over the entire length of SEQ ID NO 2, (n) an isolated polypeptide comprising the amino acid sequence of SEQ ID NO 2. (in) an isolated polypeptide which is the ammo acid sequence of SEQ ID NO 2. and (iv) a polypeptide which is encoded by a recombmant polynucleotide comprising the polynucleotide sequence of SEQ ID NO 1 10 A process for producing a polypeptide selected from the group consisting of (I) an isolated polypeptide comprising an ammo acid sequence selected from the group having at least (a) 70% identity. (b) 80% identity, (c) 90% identity, or (d) 95% identity to the ammo acid sequence of SEQ ID NO 2 over the entire length of SEQ ID NO 2, (n) an isolated polypeptide comprising the ammo acid sequence of SEQ ID NO 2 (in) an isolated polypeptide which is the ammo acid sequence of SEQ ID NO 2, and (iv) a polypeptide which is encoded by a recombmant polynucleotide compnsing the polynucleotide sequence of SEQ ID NO 1, comprising the step of culturing a host cell of claim 9 under conditions sufficient for the production of said polypeptide 11 A process for producing a host cell compnsing the expression system of claim 8 or a membrane thereof expressing a polypeptide selected from the group consisting of (l) an isolated polypeptide comprising an amino acid sequence selected from the group having at least (a) 70% identity, (b) 80% identity, (c) 90% identity, or (d) 95% identity to the amino acid sequence of SEQ ID NO 2 over the entire length of SEQ ID NO 2, (n) an isolated polypeptide comprising the ammo acid sequence of SEQ ID NO 2. (in) an isolated polypeptide which is the ammo acid sequence of SEQ ID NO 2, and (iv) a polypeptide which is encoded by a recombinant polynucleotide comprising the polynucleotide sequence of SEQ ID NO 1. said process comprising the step of transforming or transfecting a cell with an expression system compnsmg a polynucleotide capable of producing said polypeptide of (I). (u), (in) or (iv) when said expression system is present in a compatible host cell such the host cell under appropriate culture conditions, produces said polypeptide of (I), (n), (in) or (iv) 12 A host cell produced by the process of claim 11 or a membrane thereof expressing a polypeptide selected from the group consisting of (l) an isolated polypeptide comprising an ammo acid sequence selected from the group having at least (a) 70% identity, (b) 80% identity, (c) 90% identity, or (d) 95% identity to the amino acid sequence of SEQ ID NO 2 over the entire length of SEQ ID NO 2, (n) an isolated polypeptide comprising the amino acid sequence of SEQ ID NO 2, (in) an isolated polypeptide which is the ammo acid sequence of SEQ ID NO 2, and (iv) a polypeptide which is encoded by a recombmant polynucleotide compnsing the polynucleotide sequence of SEQ ID NO 1 13 A computer readable medium having stored thereon a member selected from the group consisting of a polynucleotide compnsmg the sequence of SEQ ID NO 1 , a polypeptide compnsing the sequence of SEQ ID NO 2, a set of polynucleotide sequences wherein at least one of said sequences comprises the sequence of SEQ ID NO 1, a set of polypeptide sequences wherein at least one of said sequences comprises the sequence ofSEQ ID NO 2, a data set representing a polynucleotide sequence compnsing the sequence of SEQ ID NO 1. a data set representing a polynucleotide sequence encoding a polypeptide sequence comprising the sequence of SEQ ID NO 2. a polynucleotide comprising the sequence of SEQ ID NO 1, a polypeptide comprising the sequence of SEQ ID NO 2, a set of polynucleotide sequences wherein at least one of said sequences comprises the sequence of SEQ ID NO 1. a set of polypeptide sequences wherein at least one of said sequences comprises the sequence of SEQ ID NO 2, a data set representing a polynucleotide sequence comprising the sequence of SEQ ID NO 1. a data set representing a polynucleotide sequence encoding a polypeptide sequence comprising the sequence of SEQ ID NO 2 14 A computer based method for performing homology identification, said method comprising the steps of providing a polynucleotide sequence compnsing the sequence of SEQ ID NO 1 in a computer readable medium, and comparing said polynucleotide sequence to at least one polynucleotide or polypeptide sequence to identify homology 15 A further embodiment of the invention provides a computer based method for polynucleotide assembly, said method comprising the steps of providmg a first polynucleotide sequence comprising the sequence of SEQ ID NO 1 m a computer readable medium, and screening for at least one overlapping region between said first polynucleotide sequence and a second polynucleotide sequence

Inventors: KALLENDER HOWARD, KALLENDER, HOWARD
Applicants: SMITHKLINE BEECHAM CORP, SMITHKLINE BEECHAM CORPORATION
Application year: 1999
Main classification: C07H21
IPC codes: A61K31, A61K38, A61K39, A61K45, A61P31, A61P35, C07K14, C07K16, C12N1, C12N5, C12N15, C12P21, C12Q1, G01N33, G01N37