WO2001007463A1 - Trer - Google Patents

Abstract

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

Description

TreR RELATED APPLICATIONS

This application claims benefit to US Provisional Patent Application Number 60/144.990. filed July 22, 1999

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 treR (repressor proteins) family, as well as their vanants, herein referred to as "treR." "treR polynucleotιde(s)," and "treR polypeptιde(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 cerebrospinal 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 S pneumoniae, 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 pneumoniae 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 w th weakened immune systems It is no longer uncommon to isolate Streptococcu pneumoniae strains that are resistant to some or all of the standard antibiotics This phenomenon has created an unmet medical need and demand for new anti-microbial agents, vaccines, drug screening methods, and diagnostic tests for this organism

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 vanous tools of biornformatics 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 characterize 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 treR embodiments of the mvention, that have a present benefit of, among other thmgs. bemg useful to screen compounds for antimicrobial activity Such factors are also useful to determme their role m 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 treR. m particular treR polypeptides and treR polynucleotides. recombinant matenals and methods for their production In another aspect, the mvention relates to methods for usmg such polypeptides and polynucleotides. mcludmg treatment of microbial diseases, amongst others In a further aspect, the mvention relates to methods for identifying agonists and antagonists using the matenals provided by the invention, and for treating microbial infections and conditions associated with such infections with the identified agomst or antagonist compounds In a still further aspect, the mvention relates to diagnostic assays for detecting diseases associated with microbial infections and conditions associated with such infections, such as assays for detectmg treR expression or activity

Various changes and modifications within the spint and scope of the disclosed mvention will become readily apparent to those skilled m the art from readmg the following descnptions and from readmg the other parts of the present disclosure

DESCRIPTION OF THE INVENTION

The mvention relates to treR polypeptides and polynucleotides as descnbed m greater detail below In particular, the mvention relates to polypeptides and polynucleotides of a treR of Streptococcus pneumoniae, that is related by ammo acid sequence homology to B subtihs treR polypeptide The mvention relates especially to treR having a nucleotide and ammo acid sequences set out m Table 1 as SEQ ID NO 1 and SEQ ID NO 2 respectively Note that sequences recited in the Sequence Listmg 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 treR Polynucleotide and Polypeptide Sequences

(A) Streptococcus pneumoniae treR polynucleotide sequence [SEQ ID NO 1] 5 ' -

ATGAAGAAATACCAAC7ATTATTTAAGCAAATCCAAGAAACCATTCA7Λ7λACGAGACTTACGCTGTCGGAGATTTC CTTCCTAGCGAGCACGACCTTATGGAGCAATATCAAGTGAGTCGTGATACCGTCCGAAAGGCCCTGTCTCTCCTC CAAGAGGAAGGATTGATCAAAAAGATAAGAGGGCAAGGTTCTCAAGTCGTCAAAGAAGAAACCGTCAATTTCCCT GTATCCAACCTAACC

AGCTACCAAGAACTAGTTAAAGAACTTGGACTGCGCTCTAAAACCAACGTGGTCAGTCTGGACAAGATTATTATT GATAAAAAATCCTCACTGATAACCGGTTTCCCAGAGTTTCGGATGGTTTGGAAGGTGGTCCGCCAGCGTGTGGTG GATGATCTGGTATCCGTTCTGGATACAGACTATCTGGATATGGAACTAATTCCAAATCTCACTCGCCAAATTGCT GAGCAGTCTATCTAT

TCTTATATAGAAAATGGCCTCAAACTCCTTATTGATTATGCTCAGAAGGAAATCACCATTGACCACTCAAGCGAC CGAGACAAGATTCTCATGGACATTGGCAAAGACCCTTATGTCGTTTCGATTAAATCAAAAGTCTATCTCCAAGAC GGACGCCAATTTCAGTTTACCGAAAGTCGCCATAAGTTAGAAAAATTTAGATTTGTAGATTTTGCAAAACGCAAG AAATAA-3'

(B) Streptococcus pneumoniae treR polypeptide sequence deduced from a polynucleotide sequence in this table [SEQ ID NO:2].

NH₂- MKKYQQLFKQIQETIQNETYAVGDFLPSEHDLMEQYQVSRDTVRKALSLLQEEGLI KKI RGQGSQWKEETVNFP VSNLTSYQELVKELGLRS KTNWS LDKI I I DKKS SLITGFPEFRMVTΛ/KWRQRWDDLVSVLDTDYLDMELI PNL TRQIAEQS IYSYIENGLKLLIDYAQKEITIDHS SDRDKILMDIGKDPYλ/VS I KSKVYLQDGRQFQFTESRHKLEK FRFVDFAKRKK-COOH

Deposited materials

A deposit comprising a Streptococcus pneumoniae 0100993 strain has been deposited with the National Collections of Industrial and Marine Bacteria Ltd. (herein "NCIMB"), 23 St. Machar Drive, Aberdeen AB2 IRY, Scotland on 11 April 1996 and assigned deposit number 40794. The deposit was described as Streptococcus pneumoniae 0100993 on deposit.

On 17 April 1996 a Streptococcus pneumomae 0100993 DNA library in E. coli was similarly deposited with the NCIMB and assigned deposit number 40800. The Streptococcus pneumoniae strain deposit is referred to herein as "the deposited strain" or as "the DNA of the deposited strain."

The deposited strain comprises a full length treR gene. The sequence of the polynucleotides comprised 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 any description 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 restriction or condition released to the public upon the issuance of a patent. The deposited strain is provided merely as convenience 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 stram, and compounds denved therefrom, and no such license is hereby granted

In one aspect of the mvention there is provided an isolated nucleic acid molecule encodmg a mature polypeptide expressible by the Streptococcus pneumoniae 0100993 strain, which polypeptide is compnsed m the deposited stram Further provided by the mvention are treR polynucleotide sequences m the deposited strain, such as DNA and RNA, and ammo acid sequences encoded thereby Also provided by the mvention are treR polypeptide and polynucleotide sequences isolated from the deposited stram

Polypeptides

TreR polypeptide of the mvention is substantially phylogenetically related to other proteins of the treR (repressor protems) family

In one aspect of the mvention there are provided polypeptides of Streptococcus pneumoniae referred to herem as "treR" and "treR polypeptides" as well as biologically, diagnostically. prophylactically. clinically or therapeutically useful vanants thereof, and compositions compnsmg the same

Among the particularly preferred embodiments of the mvention are vanants of treR polypeptide encoded by naturally occurring alleles of a treR gene

The present mvention further provides for an isolated polypeptide that (a) comprises or consists of an ammo acid sequence that has 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 compπsmg or consisting of a polynucleotide sequence that has 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 compnsmg or consisting of a polynucleotide sequence encodmg a polypeptide that has at least 95% identity, even more preferably at least 97-99% or exact identity, to the ammo acid sequence of SEQ ID NO 2, over the entire length of SEQ ID NO 2 The polypeptides of the mvention mclude a polypeptide of Table 1 [SEQ ID NO 2] (m particular a mature polypeptide) as well as polypeptides and fragments, particularly those that has a biological activity of treR, and also those that have at least 95% identity to a polypeptide of Table 1 [SEQ ID NO 2] and also mclude portions of such polypeptides with such portion of the polypeptide generally compnsmg at least 30 ammo acids and more preferably at least 50 ammo acids The mvention also mcludes a polypeptide consistmg of or compnsmg a polypeptide of the formula

X-(R₁)_rn-(R₂)-(R₃)_n-Y wherem. at the ammo terminus. X is hydrogen, a metal or any other moiety descnbed herem for modified polypeptides, and at the carboxyl terminus, Y is hydrogen, a metal or any other moiety descnbed herem for modified polypeptides, Ri and R3 are any ammo acid residue or modified ammo acid residue, m is an mteger between 1 and 1000 or zero, n is an mteger between 1 and 1000 or zero, and R₂ 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, R₂ is onented so that its ammo terminal ammo acid residue is at the left, covalently bound to Ri and its carboxy terminal ammo acid residue is at the ngh covalently bound to R3 Any stretch of ammo acid residues denoted by either Rj 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 pneumoniae. however, it may preferably be obtamed from other orgamsms of the same taxonomic genus A polypeptide of the mvention may also be obtamed, for example, from orgamsms of the same taxonomic family or order

A fragment is a vanant polypeptide havmg 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 treR polypeptides. fragments may be "free-standing," or compπsed within a larger polypeptide of which they form a part or regioa most preferably as a smgle contmuous region m a smgle larger polypeptide Preferred fragments mclude. for example, truncation polypeptides havmg a portion of an ammo acid sequence of Table 1 [SEQ ID NO 2], or of vanants thereof, such as a contmuous seπes 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 pneumoniae, are also preferred Further preferred are fragments charactenzed by structural or functional attributes such as fragments that compnse alpha-hehx and alpha-he x formmg regions, beta-sheet and beta-sheet-formmg regions, turn and turn-formmg regions, coil and coil-forming regions, hydrophilic regions, hydrophobic regions, alpha amphipathic regions, beta amphipathic regions, flexible regions, surface-forming regions, substrate bmdmg regioa and high antigenic index regions

Further preferred fragments mclude an isolated polypeptide comprising an amino acid sequence having at least 15, 20, 30, 40, 50 or 100 contiguous amino acids from the ammo 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 amino acids truncated or deleted from the amino acid sequence of

SEQ ID NO:2

Fragments of the polypeptides of the mvention may be employed for producmg the corresponding full-length polypeptide by peptide synthesis, therefore, these vanants may be employed as mtermediates for producmg the full-length polypeptides of the mvention Polynucleotides It is an object of the mvention to provide polynucleotides that encode treR polypeptides. particularly polynucleotides that encode a polypeptide herem designated treR In a particularly preferred embodiment of the mvention the polynucleotide compπses a region encodmg treR polypeptides compπsmg a sequence set out m Table 1 [SEQ ID NO 1] that mcludes a full length gene, or a vanant thereof This mvention provides that this full length gene is essential to the growth and/or survival of an orgamsm that possesses it, such as Streptococcus pneumoniae As a further aspect of the mvention there are provided isolated nucleic acid molecules encodmg and/or expressmg treR polypeptides and polynucleotides, particularly Streptococcus pneumoniae treR polypeptides and polynucleotides, mcludmg, for example, unprocessed RNAs, nbozyme RNAs, mRNAs, cDNAs, genomic DNAs, 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 compπsmg the same

Another aspect of the mvention relates to isolated polynucleotides, mcludmg at least one full length gene, that encodes a treR polypeptide havmg a deduced ammo acid sequence of Table 1 [SEQ ID NO 2] and polynucleotides closely related thereto and vanants thereof

In another particularly prefened embodiment of the mvention there is a treR polypeptide from Streptococcus pneumoniae compnsmg or consistmg of an amino acid sequence of Table 1 [SEQ ID NO 2], or a variant thereof

Usmg the information provided herein, such as a polynucleotide sequence set out m Table 1 [SEQ ID NO 1], a polynucleotide of the mvention encodmg treR polypeptide may be obtained usmg standard cloning and screenmg methods, such as those for cloning and sequencmg chromosomal DNA fragments from bacteπa using Streptococcus pneumoniae 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 m Table 1 [SEQ ID NO 1], typically a library of clones of chromosomal DNA of Streptococcus pneumoniae 0100993 m E coh or some other suitable host is probed with a radiolabeled ohgonucleotide, preferably a 17-mer or longer, denved from a partial sequence Clones carrying DNA identical to that of the probe can then be distmgmshed using strmgent hybndization conditions By sequencing the individual clones thus identified by hybndization with sequencmg primers designed from the ongmal polypeptide or polynucleotide sequence it is then possible to extend the polynucleotide sequence in both directions to determine a full length gene sequence Conveniently, such sequencing is performed, for example, usmg denatured double stranded DNA prepared from a plasmid clone Suitable techniques are descnbed by Maniatis, T , Fntsch, E F and Sambrook et al , MOLECULAR CLONING, A LABORATORY MANUAL, 2nd E , Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York (1989) (see in particular Screemng By Hybndization 1 90 and Sequencmg Denatured Double-Stranded DNA Templates 13 70) Direct genomic DNA sequencing may also be performed to obtain a full length gene sequence. Illustrative of the invention, each polynucleotide set out in Table 1 [SEQ ID NO:l] was discovered in a DNA hbrary derived from Streptococcus pneumoniae 0100993.

Moreover, each DNA sequence set out in Table 1 [SEQ ID NOT] contains an open reading frame encoding a protein having about the number of amino acid residues set forth in Table 1 [SEQ ID NO:2] with a deduced molecular weight that can be calculated using amino acid residue molecular weight values well known to those skilled in the art. The polynucleotide of SEQ ID NO: 1, between nucleotide number 1 and the stop codon that begins at nucleotide number 709 of SEQ ID NOT, encodes the polypeptide of SEQ ID NO:2. In a further aspect, the present invention provides for an isolated polynucleotide comprising or consisting of: (a) a polynucleotide sequence that has 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 NOT, or the entire length of that portion of SEQ ID NO: 1 which encodes SEQ ID NO:2; (b) a polynucleotide sequence encoding a polypeptide that has at least 95% identity, even more preferably at least 97-99% or 100% exact, to the amino acid sequence of SEQ ID NO:2, over the entire length of SEQ ID NO:2.

A polynucleotide encoding a polypeptide of the present invention, including homologs and orthologs from species other than Streptococcus pneumoniae, may be obtained by a process that comprises the steps of screening an appropriate hbrary under stringent hybridization conditions with a labeled or detectable probe consisting of or comprising the sequence of SEQ ID NOT or a fragment thereof; and isolating a full-length gene and/or genomic clones comprising said polynucleotide sequence.

The invention provides a polynucleotide sequence identical over its entire length to a coding sequence (open reading frame) in Table 1 [SEQ ID NOT]. Also provided by the invention is a coding sequence for a mature polypeptide or a fragment thereof, by itself as well as a coding sequence for a mature polypeptide or a fragment in reading frame with another coding sequence, such as a sequence encoding a leader or secretory sequence, a pre-, or pro- or prepro-protein sequence. The polynucleotide of the invention may also comprise at least one non-coding sequence, including for example, but not limited to at least one non-coding 5' and 3' sequence, such as the transcribed but non-translated sequences, termination signals (such as rho-dependent and rho-independent termination signals), ribosome binding sites, Kozak sequences, sequences that stabilize mRNA, introns, and polyadenylation signals. The polynucleotide sequence may also comprise additional coding sequence encoding additional amino acids. For example, a marker sequence that facilitates purification of a fused polypeptide can be encoded. In certain embodiments of the invention, the marker sequence is a hexa-histidine peptide, as provided in the pQE vector (Qiagen, Inc.) and described in Gentz et al, Proc. Natl. Acad. Set, USA 86: 821-824 (1989), or an HA peptide tag (Wilson et al, Cell 37: 767 (1984), both of that may be useful in purifying polypeptide sequence fused to them. Polynucleotides of the invention also include, but are not limited to, polynucleotides comprising a structural gene and its naturally associated sequences that control gene expression. A prefened embodiment of the mvention is a polynucleotide of consisting of or compπsmg nucleotide 1 to the nucleotide immediately upstream of or mcludmg nucleotide 709 set forth m SEQ ID NO 1 of Table 1, both of that encode a treR polypeptide

The mvention also mcludes a polynucleotide consisting of or compπsmg a polynucleotide of the formula

X-(Rl)m-(R2)-(R₃)n-Y wherem, 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 occunence of Ri and R3 is mdependently 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 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, R₂ is onented so that its 5¹ end nucleic acid residue is at the left, bound to Ri and its 3' end nucleic acid residue is at the right, bound to R3 Any stretch of nucleic acid residues denoted by either Ri and/or R , where m and/or n is greater than 1, may be either a heteropolymer or a homopolymer, preferably a heteropolymer Where, m a prefened embodiment, X and Y together define a covalent bond, the polynucleotide of the above formula is a closed, circular polynucleotide, that can be a double-stranded polynucleotide wherem the formula shows a first strand to which the second strand is complementary In another preferred embodiment m and/or n is an mteger between 1 and 1000. Other prefened 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 prefened that a polynucleotide of the mvention is denved from Streptococcus pneumoniae. 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 encodmg a polypeptide" as used herem encompasses polynucleotides that mclude a sequence encodmg a polypeptide of the mvention, particularly a bactenal polypeptide and more particularly a polypeptide of the Streptococcus pneumoniae treR havmg an ammo acid sequence set out m Table 1 [SEQ ID NO 2] The term also encompasses polynucleotides that mclude a smgle contmuous region or discontmuous regions encoding the polypeptide (for example, polynucleotides mterrupted by mtegrated phage, an mtegrated insertion sequence, an mtegrated vector sequence, an mtegrated transposon sequence, or due to RNA editing or genomic DNA reorganization) together with additional regions, that also may compnse codmg and/or non-coding sequences The mvention further relates to vanants of the polynucleotides descnbed herem that encode vanants of a polypeptide havmg a deduced ammo acid sequence of Table 1 [SEQ ID NO 2] Fragments of polynucleotides of the mvention may be used, for example, to synthesize full-length polynucleotides of the mvention Further particularly prefened embodiments are polynucleotides encodmg treR vanants, that have the ammo acid sequence of treR 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 treR polypeptide Prefened isolated polynucleotide embodiments also mclude polynucleotide fragments, such as a polynucleotide comprising a nuchc acid sequence having at least 15, 20, 30, 40, 50 or 100 contiguous nucleic acids from the polynucleotide sequence of SEQ ID NO: l, or an polynucleotide comprising a nucleic acid sequence having at least 15, 20, 30, 40, 50 or 100 contiguous nucleic acids truncated or deleted from the 5' and/or 3' end of the polynucleotide sequence of SEQ ID NO: l.

Further prefened embodiments of the mvention are polynucleotides that are at least 95 % or 97% identical over their entire length to a polynucleotide encodmg treR polypeptide havmg an ammo acid sequence set out m Table 1 [SEQ ID NO 2], and polynucleotides that are complementary to such polynucleotides Most highly prefened are polynucleotides that compnse a region that is at least 95 % are especially prefened Furthermore, those with at least 97% are highly prefened among those with at least 95%, and among these those with at least 98% and at least 99% are particularly highly prefened, with at least 99% bemg the more prefened

Prefened embodiments are polynucleotides encodmg polypeptides that retain substantially the same biological function or activity as a mature polypeptide encoded by a DNA of Table 1 [SEQ ED NO 1] In accordance with certain prefened embodiments of this mvention there are provided polynucleotides that hybndize, particularly under stnngent conditions, to treR polynucleotide sequences, such as those polynucleotides in Table 1

The mvention further relates to polynucleotides that hybndize to the polynucleotide sequences provided herem In this regard, the mvention especially relates to polynucleotides that hybndize under stnngent conditions to the polynucleotides descnbed herem A specific example of stnngent 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 hybndization support in 0 lx SSC at about 65°C Hybridization and wash conditions are well known and exemplified in Sambrook, et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor, N.Y., (1989), particularly Chapter 11 therein. Solution hybridization may also be used with the polynucleotide sequences provided by the invention.

The invention also provides a polynucleotide consisting of or comprising a polynucleotide sequence obtained by screening an appropriate library comprising a complete gene for a polynucleotide sequence set forth in SEQ ID NOT under stringent hybridization conditions with a probe having the sequence of said polynucleotide sequence set forth in 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 herein. As discussed elsewhere herein regarding polynucleotide assays of the invention, for instance, the polynucleotides of the invention, may be used as a hybridization probe for RNA, cDNA and genomic DNA to isolate full-length cDNAs and genomic clones encoding treR and to isolate cDNA and genomic clones of other genes that have a high identity, particularly high sequence identity, to a treR gene. Such probes generally will comprise 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 coding region of a treR gene may be isolated by screening using a DNA sequence provided in Table 1 [SEQ ED NOT] to synthesize an oligonucleotide probe. A labeled ohgonucleotide having a sequence complementary to that of a gene of the invention is then used to screen a library of cDNA, genomic DNA or mRNA to determine which members of the Hbrary the probe hybridizes to.

There are several methods available and well known to those skilled in the art to obtain full- length DNAs, or extend short DNAs, for example those based on the method of Rapid Amplification of cDNA ends (RACE) (see, for example, Frohman, et al, PNAS 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 primer 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 usmg 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 denved 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 determme whether or not the polynucleotides identified herein in whole or m part are transcnbed m bactena in infected tissue It is recognized that such sequences will also have utility m diagnosis of the stage of mfection and type of infection the pathogen has attained

The mvention also provides polynucleotides that encode a polypeptide that is a mature protem plus additional ammo or carboxyl-terminal ammo acids, or ammo acids mtenor to a mature polypeptide (when a mature form has more than one polypeptide cham, for instance) Such sequences may play a role m processmg of a protem from precursor to a mature form, may allow protem transport, may lengthen or shorten protem half- fe or may facilitate mampulation of a protem for assay or production, among other thmgs As generally is the case in vivo, the additional ammo acids may be processed away from a mature protem by cellular enzymes

For each and every polynucleotide of the mvention 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 protein, havmg a mature form of the polypeptide fused to one or more prosequences may be an inactive form of the polypeptide When prosequences are removed such inactive precursors generally are activated Some or all of the prosequences may be removed before activation Generally, such precursors are called proproteins As will be recognized, the entire polypeptide encoded by an open readmg frame is often not required for activity Accordingly, it has become routme m molecular biology to map the boundaπes of the primary structure required for activity with N-terminal and C-terminal deletion experiments These experiments utilize exonuclease digestion or convenient restnction sites to cleave codmg nucleic acid sequence For example, Promega (Madison, WI) sell an Erase-a-base™ system that uses Exonuclease Q designed to facilitate analysis of the deletion products (protocol available at wwwpromega com) The digested endpomts can be repaired (e g , by ligation to synthetic linkers) to the extent necessary to preserve an open reading frame In this way. the nucleic acid of SEQ ID NO 1 readily provides contiguous fragments of SEQ ED NO 2 sufficient to provide an activity, such as an enzymatic, bmdmg or antibody-inducing activity Nucleic acid sequences encodmg such fragments of SEQ ED NO 2 and vanants thereof as descnbed herem are within the mvention. as are polypeptides so encoded

As is known mthe art, portions of the N-termmal and/or C-terminal sequence of a protem can generally be removed without seπous consequence to the function of the protem The amount of sequence that can be removed is often quite substantial The nucleic acid cutting and deletion methods used for creatmg such deletion vanants are now quite routine Accordingly, any contiguous fragment of SEQ ID NO 2 which retains at least 20%, preferably at least 50%, of an activity of the polypeptide encoded by the gene for SEQ ID NO 2 is within the invention, as are corresponding fragment which are 70%, 80%, 90%, 95%,97%, 98% or 99% identical to such contiguous fragments In one embodiment, the contiguous fragment compnses at least 70% of the ammo acid residues of SEQ ID NO 2, preferably at least 80%. 90% or 95% of the residues

In sum, a polynucleotide of the mvention may encode a mature protem, a mature protem plus a leader sequence (that may be refened to as a preprotern). a precursor of a mature protem havmg one or more prosequences that are not the leader sequences of a preprotern, or a preproprotein, that is a precursor to a proprotein, havmg a leader sequence and one or more prosequences, that generally are removed dunng processmg steps that produce active and mature forms of the polypeptide

Vectors, Host Ceils, Expression Systems

The mvention also relates to vectors that compnse a polynucleotide or polynucleotides of the mvention, host cells that are genetically engineered with vectors of the mvention and the production of polypeptides of the mvention by recombinant techmques 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 m those skilled m the art from genetically engineered host cells compnsmg expression systems Accordmgly, m a further aspect, the present mvention relates to expression systems that compnse a polynucleotide or polynucleotides of the present mvention, to host cells that are genetically engineered with such expression systems, and to the production of polypeptides of the mvention by recombinant techmques

For recombinant production of the polypeptides of the mvention, host cells can be genetically engineered 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, microinjection, catiomc lipid-mediated transfection. electroporation, transduction. scrape loading, ballistic introduction and infection Representative examples of appropπate hosts mclude bactenal ceUs. such as cells of streptococci, staphylococci, enterococci E coh, streptomyces, cyanobactena, Bacillus subtihs, and Streptococcus pneumoniae. fungal cells, such as cells of a yeast. Kluveromyces, Saccharomyces, a basidiomycete. Candida albicans and Aspergillus, insect cells such as cells of Drosophila 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-deπved vectors, for example, vectors denved from bactenal plasmids, from bacteπophage, 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 bacteπophage genetic elements, such as cosmids and phagemids The expression system constructs may compnse control regions that regulate as well as engender expression Generally, any system or vector suitable to mamtam, propagate or express polynucleotides and/or to express a polypeptide m a host may be used for expression m this regard The appropnate DNA sequence may be inserted mto the expression system by any of a vanety of well-known and routme techmques, such as. for example, those set forth m Sambrook et al . MOLECULAR CLONING, A LABORATORY MANUAL, (supra)

In recombinant expression systems in eukaryotes. for secretion of a translated protem mto the lumen of the endoplasmic reticulum, mto the penplasmic space or mto the extracellular environment, appropπate 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 puπfied from recombinant cell cultures by well- known methods mcludmg ammonium sulfate or ethanol precipitation, acid extraction, amon or cation exchange chromatography, phosphocellulose chromatography. hydrophobic mteraction chromatography, affinity chromatography, hydroxylapatite chromatography, and lectm chromatography Most preferably, high performance liquid chromatography is employed for puπfication Well known techmques for refolding protem may be employed to regenerate active conformation when the polypeptide is denatured dunng isolation and or punfication Diagnostic, Prognostic, Serotyping and Mutation Assays

This mvention is also related to the use of treR polynucleotides and polypeptides of the mvention for use as diagnostic reagents Detection of treR polynucleotides and/or polypeptides m a eukaryote, particularh. a mammal, and especially a human, will provide a diagnostic method for diagnosis of disease, staging of disease or response of an infectious orgamsm to drugs Eukaryotes, particularly mammals, and especially humans, particularly those infected or suspected to be infected with an orgamsm compπsmg the treR gene or protein, 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 infected 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, characterization of the species and stram of infectious or resident orgamsm present in an mdividual, may be made by an analysis of the genotype of a selected polynucleotide of the orgamsm 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 orgamsm, 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 treR polynucleotide sequences Perfectly or significantly matched sequences can be distmgmshed from imperfectly or more significantly mismatched duplexes by DNase or RNase digestion, for DNA or RNA respectively, or by detecting differences m melting temperatures or renaturation kinetics Polynucleotide sequence differences may also be detected by alterations in 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 sequencmg 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 SI protection assay or a chemical cleavage method See, for example. Cotton et al . Proc Natl Acad Sci , USA, 85 4397-4401 (1985)

In another embodiment, an array of ohgonucleotides probes compπsmg treR nucleotide sequence or fragments thereof can be constructed to conduct efficient screenmg of. for example, genetic mutations, serotype, taxonomic classification or identification Anay 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 vaπabihty (see, for example, Chee et al , Science, 274 610 (1996))

Thus m another aspect, the present mvention relates to a diagnostic kit that 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 mvention. preferably the polypeptide of SEQ ID NO 2 or a fragment thereof, or (d) an antibody to a polypeptide 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 compnse a substantial component Such a kit will be of use m diagnosing a disease or susceptibility to a Disease, among others This invention also relates to the use of polynucleotides of the present invention as diagnostic reagents. Detection of a mutated form of a polynucleotide of the invention, preferable, SEQ ED NO: 1, that 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, that results from under-expression, over-expression or altered expression of the polynucleotide. Organisms, particularly infectious organisms, carrying mutations in such polynucleotide may be detected at the polynucleotide level by a variety of techniques, such as those described elsewhere herein.

The differences in a polynucleotide 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 (allelic variations) in a polynucleotide and/or polypeptide of the invention may also be detected at the polynucleotide or polypeptide level by a variety of techniques, to allow for serotyping, for example. For example, RT-PCR can be used to detect mutations in the RNA. It is particularly 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 treR polypeptide can be used to identify and analyze mutations. The invention further provides these primers with 1, 2, 3 or 4 nucleotides removed from the 5' and/or the 3' end. These primers may be used for, among other things, amphfying treR DNA and/or RNA isolated from a sample derived from an individual, such as a bodily material. The primers may be used to amplify a polynucleotide isolated from an infected individual, such that the polynucleotide may then be subject to various techniques for elucidation of the polynucleotide sequence. In this way, mutations in the polynucleotide sequence may be detected and used to diagnose and/or prognose the infection or its stage or course, or to serotype and/or classify the infectious agent.

The invention further provides a process for diagnosing, disease, preferably bacterial infections, more preferably infections caused by Streptococcus pneumoniae, 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 NOT]. Increased or decreased expression of a treR polynucleotide can be measured using any on of the methods well known in the art for the quantitation of polynucleotides, such as, for example, amplification, PCR, RT-PCR, RNase protection, Northern blotting, spectrometry and other hybridization methods.

In addition, a diagnostic assay in accordance with the invention for detecting over-expression of treR 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 determme levels of a treR 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

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 hgands m, for example, cells, cell-free preparations, chemical hbranes, and natural product mixtures These substrates and hgands may be natural substrates and hgands or may be structural or functional mimetics See, e g , Cohgan 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, m particular the Diseases herem mentioned It is therefore desirable to devise screenmg methods to identify compounds that agomze (e g , stimulate) or that antagonize (e g ,ιnhιbιt) the function of the polypeptide or polynucleotide Accordmgly, m a further aspect, the present mvention provides for a method of screenmg compounds to identify those that agomze or that antagomze the function of a polypeptide or polynucleotide of the mvention, as well as related polypeptides and polynucleotides In general, agomsts or antagomsts (e g , inhibitors) may be employed for therapeutic and prophylactic purposes for such Diseases as herem mentioned Compounds may be identified from a vanety of sources, for example, cells, cell-free preparations, chemical hbranes, and natural product mixtures Such agomsts and antagomsts so-identified may be natural or modified substrates, hgands. receptors, enzymes, etc , as the case may be. of treR 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 bmdmg of a candidate compound to the polypeptide or polynucleotide, or to cells or membranes beanng the polypeptide or polynucleotide, or a fusion protem of the polypeptide by means of a label directly or mdirectly associated with the candidate compound Alternatively, the screening method may involve competition with a labeled competitor Further, these screemng methods may test whether the candidate compound results in a signal generated by activation or inhibition of the polypeptide or polynucleotide. using detection systems appropriate to the cells compnsmg 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 m screening methods for inverse agonists, m the absence of an agomst or antagonist, by testing whether the candidate compound results m inhibition of activation of the polypeptide or polynucleotide. as the case may be Further, the screening methods may simply compnse the steps of mixing a candidate compound with a solution compnsmg a polypeptide or polynucleotide of the present mvention, to form a mixture, measunng treR polypeptide and/or polynucleotide activity in the mixture, and companng the treR polypeptide and or polynucleotide activity of the mixture to a standard Fusion proteins, such as those made from Fc portion and treR polypeptide, as herein described, can also be used for high-throughput screenmg assays to identify antagomsts of the polypeptide of the present mvention, as well as of phylogenetically and and/or functionally related polypeptides (see D Bennett et al , ] Mol Recognition, 8 52-58 (1995), and K Johanson et al , J Biol Chem, 270(16) 9459-9471 (1995))

The polynucleotides, polypeptides and antibodies that bind to and/or interact with a polypeptide of the present mvention may also be used to configure screemng 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 that may inhibit or enhance the production of polypeptide (also called antagonist or agomst, respectively) from suitably manipulated cells or tissues

The mvention also provides a method of screening compounds to identify those that enhance (agomst) or block (antagonist) the action of treR polypeptides or polynucleotides, particularly those compounds that are bactenstatic and/or bactencidal The method of screenmg 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 treR polypeptide and a labeled substrate or hgand of such polypeptide is mcubated m the absence or the presence of a candidate molecule that may be a treR agomst or antagonist The ability of the candidate molecule to agomze or antagonize the treR polypeptide is reflected m decreased bmdmg of the labeled hgand or decreased production of product from such substrate Molecules that bmd gratuitously. / e . without mducmg the effects of treR 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 coloπmetπc, labeled substrate converted mto product, a reporter gene that is responsive to changes m treR polynucleotide or polypeptide activity, and bmdmg assays known m the art

Polypeptides of the mvention may be used to identify membrane bound or soluble receptors, if any, for such polypeptide. through standard receptor bindmg techmques known m the art These techniques include, but are not limited to, hgand bmdmg and crosslinking assays in which the polypeptide is labeled with a radioactive isotope (for instance. 1^1). chemically modified (for instance, biotinylated). or fused to a peptide sequence suitable for detection or punfication, and incubated with a source of the putative receptor (e g , cells, cell membranes, cell supernatants, tissue extracts, bodily matenals) Other methods mclude biophysical techniques such as surface plasmon resonance and spectroscopy These screenmg methods may also be used to identify agomsts and antagomsts of the polypeptide that compete with the bmdmg of the polypeptide to its receptor(s), if any Standard methods for conductmg 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 Protem complexes, such as formed by treR polypeptide associatmg with another treR polypeptide or other polypeptide, labeled to comprise a fluorescently- labeled molecule will have higher polarization values than a fluorescently labeled monomenc protem It is preferred that this method be used to charactenze small molecules that disrupt polypeptide complexes

Fluorescence energy transfer may also be used charactenze small molecules that interfere with the formation of treR polypeptide dimers. tnmers. tetramers or higher order structures, or structures formed by treR polypeptide bound to another polypeptide TreR 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 dimenzation will inhibit fluorescence energy transfer

Surface plasmon resonance can be used to momtor the effect of small molecules on treR polypeptide self-association as well as an association of treR polypeptide and another polypeptide or small molecule TreR polypeptide can be coupled to a sensor chip at low site density such that covalently bound molecules will be monomenc Solution protem can then passed over the treR polypeptide -coated surface and specific bmding can be detected m real-time by momtormg the change in resonance angle caused by a change in local refractive mdex This technique can be used to charactenze the effect of small molecules on kmetic rates and eqmhbnum binding constants for treR polypeptide self-association as well as an association of treR polypeptide and another polypeptide or small molecule A scintillation proximity assay may be used to characterize the interaction between an association of treR polypeptide with another treR polypeptide or a different polypeptide TreR polypeptide can be coupled to a scmtillation-filled bead Addition of radio-labeled treR polypeptide results m binding where the radioactive source molecule is m close proximity to the scintillation fluid Thus, signal is emitted upon treR polypeptide bmdmg and compounds that prevent treR polypeptide self-association or an association of treR polypeptide and another polypeptide or small molecule will diminish signal.

In other embodiments of the invention there are provided methods for identifying compounds that bind to or otherwise interact with and inhibit or activate an activity or expression of a polypeptide and/or polynucleotide of the invention comprising: contacting a polypeptide and/or polynucleotide of the invention with a compound to be screened under conditions to permit binding to or other interaction between the compound and the polypeptide and/or polynucleotide to assess the binding to or other interaction with the compound, such binding or interaction preferably being associated with a second component capable of providing a detectable signal in response to the binding or interaction of the polypeptide and/or polynucleotide with the compound; and determining whether the compound binds to or otherwise interacts with and activates or inhibits an activity or expression of the polypeptide and/or polynucleotide by detecting the presence or absence of a signal generated from the binding or interaction of the compound with the polypeptide and/or polynucleotide. Another example of an assay for treR agonists is a competitive assay that combines treR and a potential agonist with treR-binding molecules, recombinant treR binding molecules, natural substrates or hgands, or substrate or ligand mimetics, under appropriate conditions for a competitive inhibition assay. TreR can be labeled, such as by radioactivity or a colorimetric compound, such that the number of treR molecules bound to a binding molecule or converted to product can be determined accurately to assess the effectiveness of the potential antagonist.

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 agonist or antagonist of the polypeptide and/or polynucleotide, by: (a) deteπnining 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 site(s), binding site(s) or motif(s) of an agonist or antagonist; (c) synthesizing candidate compounds that are predicted to bind to or react with the deduced binding site(s), reactive site(s), and/or motif(s); and (d) testing whether the candidate compounds are indeed agonists or antagonists. 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 invention provides methods of treating abnormal 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 treR 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 compπses administering to an mdividual m need thereof an inhibitor compound (antagonist) as herem descnbed, optionally m combination with a pharmaceutically acceptable earner, m 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 hgands, 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 bmdmg the hgand, substrate, enzymes, receptors, etc in competition with endogenous polypeptide and/or polynucleotide may be admimstered Typical examples of such competitors include fragments of the treR polypeptide and/or polypeptide

In still another approach, expression of the gene encoding endogenous treR polypeptide can be inhibited usmg expression blockmg 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 admimstered (see, for example, O'Connor, J Neurochem (1991) 56 560 ιn Ohgodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton. FL (1988)) Alternatively, ohgonucleotides that 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 jeer se or the relevant ohgomers can be expressed in vivo

Each of the polynucleotide sequences provided herein may be used m the discovery and development of antibacterial compounds The encoded protem. upon expression, can be used as a target for the screening of antibacterial drugs Additionally, the polynucleotide sequences encodmg the ammo terminal regions of the encoded protein or Shrne-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 mvention also provides the use of the polypeptide. polynucleotide, agomst or antagonist of the mvention 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 m the prevention of adhesion of bactena. m particular gram positive and/or gram negative bactena, to eukaryotic. preferably mammalian, extracellular matrix protems on m-dwellmg devices or to extracellular matnx protems in wounds, to block bacterial adhesion between eukaryotic, preferably mammalian, extracellular matnx protems and bacterial treR protems that mediate tissue damage and or, to block the normal progression of pathogenesis m infections initiated other than by the implantation of in-dwelling devices or by other surgical techmques

In accordance with yet another aspect of the mvention, there are provided treR 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

Antagomsts of the mvention 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 Antagomsts also may be small orgamc 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 treR-induced activities, thereby preventmg the action or expression of treR polypeptides and/or polynucleotides by excluding treR polypeptides and or polynucleotides from bmdmg

Antagomsts of the mvention also 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 hmited to small orgamc molecules, peptides or peptide-like molecules Other 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 antagomsts mclude compounds related to and vanants of treR Other examples of polypeptide antagomsts mclude antibodies or, m some cases, ohgonucleotides or proteins that are closely related to the hgands, substrates, receptors, enzymes, etc , as the case may be, of the polypeptide, e g . a fragment of the hgands, substrates, receptors, enzymes, etc . or small molecules that bmd to the polypeptide of the present mvention but do not elicit a response, so that the activity of the polypeptide is prevented Small molecules of the invention preferably have a molecular weight below 2,000 daltons, more preferably between 300 and 1,000 daltons, and most preferably between 400 and 700 daltons It is prefened that these small molecules are orgamc molecules

Hehcobacter pylori (herem "H pylori") bacteria infect the stomachs of over one-third of the world's population causing stomach cancer, ulcers, and gastntis (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 gastnc adenocarcmoma, classifying the bactenum as a Group I (definite) carcinogen Prefened antimicrobial compounds of the invention (agonists and antagonists of treR polypeptides and/or polynucleotides) found using screens provided by the mvention, or known in the art, particularly narrow-spectrum antibiotics, should be useful m the treatment of H pylori mfection Such treatment should decrease the advent of H /?y /on -induced cancers, such as gastrointestinal carcmoma Such treatment should also prevent, inhibit and or cure gastric ulcers and gastntis

All publications and references, mcludmg but not limited to patents and patent applications, cited m this specification are herein incorporated by reference in their entirety as if each individual publication or reference were specifically and individually indicated to be incorporated by reference herein as being fully set forth Any patent application to which this application claims pnonty is also incorporated by reference herein in its entirety in the manner descnbed above for publications and references

GLOSSARY

The following definitions are provided to facilitate understanding of certain terms used frequently herem

"Bodily mateπal(s) means any matenal denved from an mdividual or from an organism infecting, infesting or inhabiting an mdividual, mcludmg but not limited to, cells, tissues and waste, such as. bone, blood, serum, cerebrospinal 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, pneumonia, bacteremra, meningitis, sinusitis, pleural empyema and endocarditis, and most particularly meningitis, such as for example infection of cerebrospmal fluid

"Host cell(s)" is a cell that has been mtroduced (e g , transformed or transfected) or is capable of mtroduction (e g , 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 determmed by comparmg 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, mcludmg but not limited to those described m (Computational Molecular Biology, Lesk, A M , ed , Oxford University Press, New York. 1988, Bwcomputing Informatics and Genome Projects, Smith, D W , ed , Academic Press, New York, 1993, Computer Analysis of Sequence Data, Part I. Griffin. A M . and Griffin. H G . eds , Humana Press, New Jersey. 1994, Sequence Analysis in Molecular Biology, von Heinje, G , Academic Press, 1987, and Sequence Analysis Primer. Gπbskov. M and Devereux, J , eds , M Stockton Press, New York, 1991, and Canllo, H , and Lipman, D , SEAM J Applied Math , 48 1073 (1988) Methods to determme identity are designed to give the largest match between the sequences tested Moreover, methods to determme identity are codified in publicly available computer programs Computer program methods to determme identity between two sequences mclude, 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 NEH Bethesda, MD 20894, Altschul, S , et al , J Mol Biol 215 403-410 (1990) The well known Smith Waterman algorithm may also be used to determme identity' Parameters for polypeptide sequence companson mclude the following Algonthm Needleman and Wunsch. J Mol Biol 48 443-453 (1970)

Companson 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 compansons (along with no penalty for end gaps)

Parameters for polynucleotide companson mclude the following Algonthm Needleman and Wunsch, J Mol Biol 48 443-453 (1970)

Companson matnx 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 prefened 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 compnsmg a polynucleotide sequence havmg at least a 95, 97 or 100% identity to the reference sequence of SEQ ID NO 1, wherem said polynucleotide sequence may be identical to the reference sequence of SEQ ID NO 1 or may include up to a certain mteger number of nucleotide alterations as compared to the reference sequence, wherein said alterations are selected from the group consistmg of at least one nucleotide deletion, substitution, mcludmg transition and transversion. or insertion, and wherem 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 nucleotides in the reference sequence or in one or more contiguous groups within the reference sequence, and wherein said number of nucleotide alterations is determined by multiplying the total number of nucleotides in SEQ ID NOT by the integer defining the percent identity divided by 100 and then subtracting that product from said total number of nucleotides in SEQ ID NOT, or:

ⁿn ≤ ^xn - (^xn ^# )>

wherein n_n is the number of nucleotide alterations, x_n is the total number of nucleotides in SEQ ID NOT, y is 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 prior 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. (2) Polypeptide embodiments further include an isolated polypeptide comprising a polypeptide having at least a 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 wherein said alterations may occur at the amino- or carboxy-terminal positions of the reference polypeptide sequence or anywhere between those terminal positions, interspersed either individually among the amino acids in the reference sequence or in one or more contiguous groups within the reference sequence, and wherein said number of amino acid alterations is determined by multiplying the total number of amino acids in SEQ ID NO:2 by the integer defimng the percent identity divided by 100 and then subtracting that product from said total number of amino acids in SEQ ID NO:2, or:

ⁿa ≤ ^xa " (^xa ^# j),

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 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_a and y is rounded down to the nearest integer prior to subtracting it from x_a. "Indιvιdual(s)" means a multicellular eukaryote, mcludmg. but not hmited 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, 1 e , if it occurs in nature, it has been changed or removed from its onginal environment, or both For example, a polynucleotide or a polypeptide naturally present in a living orgamsm 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 orgamsm by transformation, genetic mampulation or by any other recombinant method is "isolated" even if it is still present m said orgamsm, which orgamsm may be living 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, Enterobacter, Yersinia, Fancisella, Pasturella, Moraxella, Acinetobacter, Erysipelothnx, Branhamella, Actinobacillus, Streptobacillus, Listena, Calymmatobactenum, Brucella, Bacillus, Clostndium, Treponema, Eschenchia, Salmonella, Kleibsiella, Vibno, Proteus, Erwinia, Borrelia, Leptospira, Spinllum, Campylobacter, Shigella, Legionella, Pseudomonas, Aeromonas, Rickettsia, Chlamydia, Borrelia and Mycoplasma, 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 pneumoniae, Streptococcus pyogenes, Streptococcus agalactiae, Streptococcus faecahs, Streptococcus faecium, Streptococcus durans, Neissena gonorrheae, Neissena meningitidis, Staphylococcus aureus, Staphylococcus epidermidis, Corynebactenum dipthenae, Gardnerella vaginahs, Mycobactenum tuberculosis, Mycobactenum bovis, Mycobactenum ulcerans, Mycobactenum leprae, Actinomyctes israeln, Listena monocytogenes, Bordetella pertusis, Bordatella parapertusis, Bordetella bronchiseptica, Eschenchia coh, Shigella dysentenae, Haemophilus influenzae, Haemophilus aegypt us, Haemophilus parainfluenzae, Haemophilus ducreyi, Bordetella, Salmonella typhi, Citrobacter freundu, Proteus mirabilis, Proteus vulgans, Yersinia pestis, Kleibsiella pneumoniae, Serratia marcessens, Serratia hquefaciens, Vibno cholera, Shigella dysentem, Shigella flexnen, Pseudomonas aeruginosa, Franscisella tularensis, Brucella abortis, Bacillus anthracis, Bacillus cereus, Clostndium perfringens, Clostndium tetani, Clostndium botulinum, Treponema pallidum, Rickettsia nckettsii and Chlamydia trachomitis, (n) an archaeon, mcludmg but not limited to Archaebacter, and (m) a umceUular 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

"Polynucleotide(s)" generally refers to any polynbonucleotide or polydeoxynbonucleotide, that may be unmodified RNA or DNA or modified RNA or DNA "Polynucleotide(s)" mclude. without limitation, single- and double-stranded DNA, DNA that is a mixture of smgle- and double-stranded regions or smgle-, double- and tπple-stranded regions, smgle- and double-stranded RNA. and RNA that is mixture of smgle- and double-stranded regions, hybπd molecules compπsmg DNA and RNA that may be single-stranded or, more typically, double-stranded, or tπple-stranded regions, or a mixture of single- 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 m 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 ohgonucleotide As used herem, the term "polynucleotide(s)" also mcludes DNAs or RNAs as descnbed above that compnse one or more modified bases Thus, DNAs or RNAs with backbones modified for stability or for other reasons are "polynucleotιde(s)" as that term is mtended herem Moreover, DNAs or RNAs compnsmg unusual bases, such as mosme. or modified bases, such as tiitylated 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 term "polynucleotide(s)" as it is employed herem embraces such chemically, enzymatically or metabohcally 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 ohgonucleotide(s)

"Polypeptide(s)" refers to any peptide or protem compπsmg two or more ammo acids jomed to each other by peptide bonds or modified peptide bonds "Polypeptide(s)" refers to both short chains, commonly refened to as peptides, ohgopeptides and ohgomers and to longer chains generally refened to as proteins Polypeptides may compnse ammo acids other than the 20 gene encoded ammo acids "Polypeptide(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 m more detailed monographs, as well as in a voluminous 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 compnse 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, acetvlation. acylation, ADP-πbosylation, amidation, covalent attachment of flavm, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide denvative, covalent attachment of a hpid or hpid denvative, covalent attachment of phosphotidylmositol. cross-linking, cychzation, disulfide bond formation, demethylation, formation of covalent cross-hnks, formation of cysteine, formation of pyroglutamate, formylation, gamma-carboxylation. GPI anchor formation, hydroxylation, lodination, methylation. mynstoylabon, oxidation, proteolytic processmg, phosphorylabon, 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 - STRUCTURE 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 cychc, with or without branching Cyclic, branched and branched circular polypeptides may result from posttranslational 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 "Vanant(s)" as the term is used herem, 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 m nucleotide sequence from another, reference polynucleotide Changes m the nucleotide sequence of the variant may or may not alter the ammo acid sequence of a polypeptide encoded by the reference polynucleotide Nucleotide changes may result m ammo acid substitutions, additions, deletions, fusion protems and truncations m the polypeptide encoded by the reference sequence, as discussed below A typical vanant of a polypeptide differs m ammo 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 vanant and reference polypeptide may differ in ammo acid sequence by one or more substitutions, additions. deletions in any combmation A substituted or mserted ammo 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 m which several. 5-10, 1-5. 1-3, 1-2 or 1 ammo acids are substituted, deleted, or added m any combmation A vanant of a polynucleotide or polypeptide may be a naturally occurring such as an allehc vanant, or it may be a variant that is not known to occur naturally Non-naturally occuπrng vanants of polynucleotides and polypeptides may be made by mutagenesis techmques, by direct synthesis, and by other recombinant methods known to skilled artisans

EXAMPLES

The examples below are earned out usmg standard techmques, that are well known and routine 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 havmg a DNA sequence given in Table 1 [SEQ ID NO 1] was obtained from a library of clones of chromosomal DNA of Streptococcus pneumoniae m E coh The sequencmg data from two or more clones compnsmg overlapping Streptococcus pneumoniae DNAs was used to construct the contiguous DNA sequence m 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 pneumoniae 0100993 accordmg 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 m size are rendered blunt by treatment with exonuclease and DNA polymerase, and EcoRI linkers added Fragments are ligated mto the vector Lambda ZapII that has been cut with EcoRI, the library packaged by standard procedures and E coh mfected with the packaged library The library is amplified by standard procedures

Method 2

Total cellular DNA is partially hydrolyzed with a one or a combmation of restnction enzymes appropnate to generate a senes of fragments for clonmg mto library vectors (e g , Rsal, Pall, Alul, Bshl235I), and such fragments are size-fractionated accordmg to standard procedures EcoRI linkers are ligated to the DNA and the fragments then ligated mto the vector Lambda ZapII that have been cut with EcoRI, the library packaged by standard procedures, and E coh 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:

(i) an isolated polypeptide comprising an amino acid having at least 95% identity to the amino acid sequence of SEQ ID NO:2 over the entire length of SEQ ID NO:2; (ii) an isolated polypeptide comprising the amino acid sequence of SEQ ID NO:2, (iii) an isolated polypeptide that is the amino acid sequence of SEQ ID NO:2, and (iv) a polypeptide that is encoded by a recombinant polynucleotide comprising the polyncleotide sequence of SEQ ID NOT.

2. An isolated polynucleotide selected from the group consisting of:

(i) an isolated polynucleotide comprising a polynucleotide sequence encoding a polypeptide that has at least 95% identity to the amino acid sequence of SEQ ED NO:2, over the entire length of SEQ ED NO:2;

(ii) an isolated polynucleotide comprising a polynucleotide sequence that has at least 95% identity over its entire length to a polynucleotide sequence encoding the polypeptide of SEQ ED

NO:2;

(iii) an isolated polynucleotide comprising a nucleotide sequence that has at least 95% identity to that of SEQ ID NOT over the entire length of SEQ ID NOT;

(iv) an isolated polynucleotide comprising a nucleotide sequence encoding the polypeptide of SEQ ED

NO:2;

(v) an isolated polynucleotide that is the polynucleotide of SEQ ID NO: 1 ;

(vi) an isolated polynucleotide of at least 30 nucleotides in length obtainable by screening an appropriate library under stringent hybridization conditions with a probe having the sequence of SEQ

ID NO: 1 or a fragment thereof of of at least 30 nucleotides in length;

(vii) an isolated polynucleotide encoding a mature polypeptide expressed by the treR gene comprised in the Streptococcus pneumoniae; and

(viii) a polynucleotide sequence complementary to said isolated polynucleotide of (i), (h), (hi), (iv), (v), (vi) or (vii).

3. A method for the treatment of an individual:

(i) in need of enhanced activity or expression of or immunological response to the polypeptide of claim 1 comprising the step of: administering to the individual a therapeutically effective amount of an antagonist to said polypeptide; or (n) havmg need to inhibit activity or expression of the polypeptide of claim 1 compnsmg

(a) admimstenng to the mdividual a therapeutically effective amount of an antagonist to said polypeptide, or

(b) admimstenng to the mdividual a nucleic acid molecule that inhibits the expression of a polynucleotide sequence encoding said polypeptide,

(c) admimstenng to the mdividual a therapeutically effective amount of a polypeptide that competes with said polypeptide for its hgand, substrate, or receptor, or

(d) admimstenng to the individual an amount of a polypeptide that mduces an rmmunological lesponse to said polypeptide in said individual

4 A process for diagnosing or prognosmg a disease or a susceptibility to a disease m an mdividual related to expression or activity of the polypeptide of claim 1 m an mdividual compnsmg the step of

(a) determining the presence or absence of a mutation m the nucleotide sequence encoding said polypeptide in an organism in said mdividual, or

(b) analyzing for the presence or amount of said polypeptide expression m a sample denved from said mdividual

5 A process for producing a polypeptide selected from the group consistmg of

(l) an isolated polypeptide compnsmg an ammo acid sequence selected from the group havmg at least 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 compnsmg the ammo acid sequence of SEQ ID NO 2, (m) an isolated polypeptide that is the ammo acid sequence of SEQ ID NO 2, and (iv) a polypeptide that is encoded by a recombmant polynucleotide compnsmg the polynucleotide sequence of SEQ ID NO 1, compnsmg the step of cultunng a host cell under conditions sufficient for the production of the polypeptide

6 A process for producing a host cell comprising an expression system or a membrane thereof expressmg a polypeptide selected from the group consisting of (1) an isolated polypeptide compnsmg an ammo acid sequence selected from the group havmg at least 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 compnsmg the ammo acid sequence of SEQ ID NO 2, (in) an isolated polypeptide that is the ammo acid sequence of SEQ ID NO 2, and (iv) a polypeptide that is encoded by a recombmant polynucleotide compnsmg the polynucleotide sequence of SEQ ID NO 1, said process compnsmg the step of transforming or transfectrng a cell with an expression system compnsmg a polynucleotide capable of producing said polypeptide of (l), (n), (in) or (iv) when said expression system is present m a compatible host cell such the host cell, under appropnate culture conditions, produces said polypeptide of (I), (u). (m) or (iv)

7 A host cell or a membrane expressmg a polypeptide selected from the group consistmg of (I) an isolated polypeptide compnsmg an a mo acid sequence selected from the group havmg at least 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 compnsmg the ammo acid sequence of SEQ ID NO 2, (m) an isolated polypeptide that is the ammo acid sequence of SEQ ID NO 2, and (iv) a polypeptide that is encoded by a recombmant polynucleotide compnsmg the polynucleotide sequence of SEQ ID NO 1

8 An antibody lmmunospecifϊc for the polypeptide of claim 1

9 A method foi screenmg to identify compounds that agonize or that inhibit the function of the polypeptide of claim 1 that compnses a method selected from the group consisting of

(a) measunng the bmdmg of a candidate compound to the polypeptide (or to the cells or membranes bearmg the polypeptide) or a fusion protem thereof by means of a label directly or mdirectly associated with the candidate compound,

(b) measunng the bmdmg of a candidate compound to the polypeptide (or to the cells or membranes beanng the polypeptide) or a fusion protem 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 appropnate to the cells or cell membranes beanng the polypeptide, (d) mixing a candidate compound with a solution compnsmg a polypeptide of claim 1. to form a mixture, measuring activity of the polypeptide m the mixture, and comparmg the activity of the mixture to a standard, or

(e) detectmg the effect of a candidate compound on the production of mRNA encodmg said polypeptide and said polypeptide m cells, usmg for instance, an ELISA assay

10 An agomst or antagonist to the polypeptide of claim 1