pyrH GENE AND PROTEIN OF STREPTOCOCCUS PNEUMONIAE

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

Description: pyrH GENE AND PROTEIN OF STREPTOCOCCUS PNEUMONIAE 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 UMP (undine monophosphate) l nase famih. hereinafter referred to as "pyrH" 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 particularlv 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 mateπal was predicated on the work of Griffith and of Avery, Macleod and McCarty using this microbe Despite the vast amount of research with S 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 antibioUcs This phenomenon has created a demand for both new anti-microbial agents, vaccines, and diagnostic tests for this organism UMP kinase is involved in the biosynthesis of pynmidine tnphosphate nucleosides from glucose metabolism intermediates via the de novo pathway or from exogenous uracil and undine The pynmidine tnphosphate nucleotides are precursors in the biosynthesis of macromolecules such as RNA DNA phosphohpids and peptidoglycan The essential nature of the gene product of pyrH in Eschenchia colt has been demonstrated by the construction of temperature sensitive mutants (Yamanaka. K , Ogura. T , Niki, H . and Hiraga, S 1992 J Bacteπol 174, 7517-7526) Cold sensitive mutants have also been isolated in Eschenchia coh (Yamanaka, K . Ogura, T , Niki, H , and Hiraga, S 1992 J Bactenol 174, 7517-7526 Bucurenci. N , Senna. L , Zahana. C . Landais, S , Danchin, A , and Barzu 0 1998 J Bactenol - 1 - 180. 473-477) and Salmonella typhimunum (Ingraham, J L , and Neuhard, J 1972 J Biol Chem 247. 6259-6265) Furthermore, consistent with the important physiological role of UMP lαnase, the pyrH mutants show pleiotrophic effects including inhibition of macromolecule synthesis, defects m the membrane and change in the cell morphology (Yamanaka. K , Ogura, T , Niki, H , and Hiraga, S 1992 J Bactenol 174, 7517-7526) Clearly, there exists a need for factors, such as the pyrH embodiments of the invention, that have a present benefit of being useful to screen compounds for antibiotic 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 charactemation of such factors and then * antagonists and agonists to find ways to prevent, ameliorate or correct such infection, dysfunction and disease Certain of the polypeptides of the invention possess ammo acid sequence homology to a known Bacillus subtilis smbA, Synechocystis sp pyrH. Mycobactenum leprae pyrH, Mycobactenum tuberculosis pyrH, Eschenchia coli smbA, Haemophilus influenzae pyrH, Hehcobacter pylon pyrH, Mycoplasma pneumomae pyrH, Chlamydia trachomatis pyrH, Mycoplasma gemtahum smbA, Thermus aquaticus pyrH. Archaeoglobus fulgidus pyrH, Methanococcus jannaschu pyrH, Pyrococcus honkoshii pyrH and Borrelia burgdorfen smbA protein See GeneBank Z99112, GeneBank D90915, GeneBank Z97369. GeneBank Z74024, GeneBank D26562 and X78809, GeneBank U32786, GeneBank AE000589. GeneBank AE000021, GeneBank U60196, GeneBank U39730, GeneBank X83598, GeneBank AE000962, GeneBank U67566, GeneBank AB005215, GeneBank AE001158 SUMMARY OF THE INVENTION It is an object of the invention to provide polypeptides that have been identified as pyrH polypeptides by homology between the ammo acid sequence set out in Table 1 [SEQ ID NO 2] and a known ammo acid sequence or sequences of other proteins such as Bacillus subtilis smbA, Synechocystis sp pyrH, Mycobactenum leprae pyrH, Mycobactenum tuberculosis pyrH, Eschenchia coli smbA. Haemophilus influenzae pyrH, Hehcobacter pylon pyrH. Mycoplasma pneumomae pyrH, Chlamydia trachomatis pyrH, Mycoplasma gemtahum smbA Thermus aquaticus pyrH. Archaeoglobus fulgidus pyrH, Methanococcus jannaschu pyrH. Pyrococcus honkoshii pyrH and Borrelia burgdorfen smbA protein It is a further object of the invention to provide polynucleotides that encode pyrH polypeptides. particularly polynucleotides that encode the polypeptide herein designated pyrH - 2 In a particularly preferred embodiment of the invention the polynucleotide comprises a region encoding pyrH polypeptides compπsing a sequence set out m Table 1 [SEQ ID NO 1] which includes a full length gene, or a variant thereof In another particularly preferred embodiment of the mvention there is a pyrH protein from Streptococcus pneumomae compπsmg the ammo acid sequence of Table 1 [SEQ ID NO 2], or a vaπant thereof As a further aspect of the invention there are provided isolated nucleic acid molecules encoding pyrH, particularly Streptococcus pneumomae pyrH, including mRNAs, cDNAs, genomic DNAs Further embodiments of the invention include biologically, diagnosUcally, prophylactically, clinically or therapeuucally useful vaπaπts thereof, and compositions compπsmg the same In accordance with another aspect of the mvention, there is provided the use of a polynucleotide of the mvention for therapeutic or prophylactic purposes, m particular genetic immunization Among the particularly preferred embodiments of the invention are naturally occurring allehc vaπants of pyrH and polypeptides encoded thereby In another aspect of the invention there are provided polypeptides of Streptococcus pneumomae referred to herein as pyrH as well as biologically, diagnostically, prophylactically, clinically or therapeuucally useful vaπants thereof, and compositions compπsmg the same Among the particularly preferred embodiments of the mvention are vaπants of pyrH polypeptide encoded by naturally occurring alleles of the pyrH gene In a prefeπed embodiment of the mvention there are provided methods for producing the aforementioned pyrH polypeptides In accordance with yet another aspect of the mvention. there are provided inhibitors to such polvpeptides, useful as antibacteπal agents, including, for example, antibodies In accordance with certain prefeπed embodiments of the mvention. there are provided products, compositions and methods for assessing pyrH expression, treatmg disease, assavmg genetic vanaϋon. and administering a pyrH polypeptide or polynucleotide to an organism to raise an immunological response against a bactena. especially a Streptococcus pneumomae bacteπa In accordance with certain prefeπed embodiments of this and other aspects of the mvention there are provided polynucleotides that hybπdize to pyrH polynucleotide sequences, particularly under stringent conditions In certain prefeπed embodiments of the mvention there are provided antibodies against pyrH polypeptides In other embodiments of the mvention there are provided methods for identifying compounds which bind to or otherwise interact with and inhibit or activate an activity of a polypeptide or polynucleotide of the mvention compπsmg contacting a polypeptide or polynucleotide of the invention with a compound to be screened under conditions to permit bmdmg to or other interaction between the compound and the polypeptide or polynucleotide to assess the binding to or other interaction with the compound, such binding or mteraction being associated with a second component capable of providing a detectable signal m response to the bmdmg or mteraction of the polypeptide or polynucleotide with the compound, and determining whether the compound binds to or otherwise interacts with and activates or inhibits an activity of the polypeptide or polynucleotide by detecting the presence or absence of a signal generated from the binding or interaction of the compound with the polypeptide or polynucleotide In accordance with yet another aspect of the mvention, there are provided pyrH agonists and antagonists, preferably bacteπostatic or bacteπocidal agonists and antagonists In a further aspect of the mvention there are provided compositions compπsing a pyrH polynucleotide or a pyrH polypeptide for administration to a cell or to a multicellular organism In another embodiment of the mvention there is provided a computer readable medium having stored thereon a member selected from the group consistmg of a polynucleotide compπsmg the sequence of SEQ ID NO 1 , a polypeptide compπsmg the sequence of SEQ ID NO 2, a set of polynucleotide sequences wherem at least one of said sequences compπses the sequence of SEQ ID NO 1 , a set of polypeptide sequences wherem at least one of said sequences comprises the sequence of SEQ ID NO 2, a data set representmg a polynucleotide sequence compπsing the sequence of SEQ ID NO 1 , a data set representmg a polynucleotide sequence encodmg a polypeptide sequence compπsmg the sequence of SEQ ID NO 2. a polynucleotide comprising the sequence of SEQ ID NO 1 , a polypeptide compπsmg the sequence of SEQ ID NO 2, a set of polynucleotide sequences wherem at least one of said sequences compπses the sequence of SEQ ID NO 1, a set of polypeptide sequences wherem at least one of said sequences compπses the sequence of SEQ ID NO 2, a data set representmg a polynucleotide sequence compπsmg the sequence of SEQ ID NO 1, a data set representmg a polynucleotide sequence encoding a polypeptide sequence compπsmg the sequence of SEQ ID NO 2 A further embodiment of the invention provides a computer based method for performing homology identification, said method compπsmg the steps of providing a polynucleotide sequence compπsmg the sequence of SEQ ID NO 1 m a computer readable medium, and comparing said polynucleotide sequence to at least one polynucleotide or polypeptide sequence to identify homology A further embodiment of the mvention provides a computer based method for performing homology identification, said method compπsmg the steps of providing a polypeptide sequence compπsmg the sequence of SEQ ID NO 2 m 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 mvention provides a computer based method for polynucleotide assembly, said method compπsmg the steps of providing a first polynucleotide sequence compπsmg the sequence of SEQ ID NO 1 m a computer readable medium, and screening for at least one overlappmg region between said first polynucleotide sequence and a second polynucleotide sequence A further embodiment of the mvention provides a computer based method for performing homology identification, said method compπsmg the steps of providing a polynucleotide sequence compπsmg the sequence of SEQ ID NO 1 m a computer readable medium, and comparing said polynucleotide sequence to at least one polynucleotide or polypeptide sequence to identify homology A further embodiment of the mvention provides a computer based method for performing homology identification, said method compπsmg the steps of providmg a polypeptide sequence compπsmg the sequence of SEQ ID NO 2 m 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 mvention provides a computer based method for polynucleotide assembly, said method compπsmg the steps of providmg a first polynucleotide sequence compπsmg the sequence of SEQ ID NO 1 m a computer readable medium, and screening for at least one overlappmg region between said first polynucleotide sequence and a second polynucleotide sequence Vaπous changes and modifications within the spiπt and scope of the disclosed mvention will become readily apparent to those skilled m the art from reading the following descπptions and from reading the other parts of the present disclosure DESCRIPTION OF THE INVENTION The mvention relates to pyrH polypeptides and polynucleotides as descπbed m greater detail below In particular, the mvention relates to polypeptides and polynucleotides of a pyrH of Streptococcus pneumomae. which is related by ammo acid sequence homology to Bacillus subtilis smbA Synechocysύs sp pyrH, Mycobactenum leprae pyrH, Mycobactenum tuberculosis pyrH, - 5 - Eschenchia coli smbA, Haemophilus influenzae pyrH, Hehcobacter pylon pyrH, Mycoplasma pneumomae pyrH. Chlamydia trachomatis pyrH, Mycoplasma gemtahum smbA Thermus aquaticus pyrH, Archaeoglobus fulgidus pyrH, Methanococcus jannaschu pyrH, Pyrococcus honkoshii pyrH and Borrelia burgdorfen smbA polypeptide The mvention relates especially to pyrH havmg the nucleotide and ammo acid sequences set out m Table 1 as SEQ ID NO 1 and SEQ ID NO 2 respectively TABLE 1 PyrH Polynucleotide and Polypeptide Sequences (A) Sequences from Streptococcus pneumomae pyrH polynucleotide sequence [SEQ ID NO 1] 5 ' -ATGGCGAATCCCAAGTATAAACGTATTTTAATCAAGTTATCAGGTGAAGCCCTTGCCGGT GAACGTGGCGTAGGGATTGATATCCAAACAGTTCAAACAATCGCAAAAGAGATTCAAGAA GTTCATAGCTTAGGTATCGAAATTGCCCTTGTTATTGGTGGAGGAAATCTCTGGCGTGGA GAACCTGCAGCAGAAGCAGGTATGGACCGTGTTCAGGCAGATTACACTGGAATGCTTGGG ACTGTTATGAATGCTCTTGTGATGGCAGATTCATTGCAACAAGTTGGGGTTGATACGCGT GTACAAACAGCTATTGCTATGCAACAAGTGGCAGAGCCTTATGTCCGTGGACGTGCCCTT CGTCACCTTGAAAAAGGCCGTATCGTTATCTTTGGTGCTGGAATTGGTTCACCATATTTC TCGACAGATACAACAGCGGCCCTTCGTGCAGCTGAAATCGAAGCAGATGCCATCCTCATG GCTAAAAATGGCGTCGATGGTGTGTACAATGCCGATCCTAAGAAGGACAAGACAGCCGTT AAGTTTGAAGAATTGACCCACCGTGATGTTATCAACAAAGGTCTTCGTATCATGGACTCA ACAGCCTCAACCCTCTCAATGGACAACGACATTGACTTGGTTGTCTTCAACATGAACCAA T CAGGCAACAT CAAAC GT GTC GT ATT GGT GAAAATAT CGGAACAACAGTTT CAAATAAT ATCGAAGAAAAGGAATAA-3 ' (B) Streptococcus pneumomae pyrH polypeptide sequence deduced from the polvnucleotide sequence in this table [SEQ ID NO 2] NH 2 -MANPKYKRILIKLSGEALAGERGVGIDIQTVQTIAKEIQEVHS GIEIALVIGGGNLWRG EPAAEAGMDRVQADYTGMLGTVMNALλ ADSLQQVGVDTRVQTAIAMQQVAEPYVRGRAL RHLEKGRI VI FGAGI GS PYFSTDTTAALRAAEI EADAI MAKNGVDGVYNADPKKDKTAV KFEELTHRDVINKGLRIMDSTASTLSMDNDIDLWFNMNQSGNIKRWFGENI GTTVSNN IEEKE-COOH Deposited materials A deposit containing a Streptococcus pneumomae 0100993 strain has been deposited with the National Collections of Industπal and Maπne Bacteπa Ltd (herem "NCIMB"), 23 St Machar - 6 - Dπve. Aberdeen AB2 1RY. Scotland on 11 April 1996 and assigned deposit number 40794 The deposit was descπbed as Streptococcus pneumomae 0100993 on deposit On 17 Apπl 1996, a Streptococcus pneumomae 0100993 DNA library m E coli was similarly deposited with the NCIMB and assigned deposit number 40800 The Streptococcus pneumomae stram deposit is refeπed to herem as "the deposited stram" or as "the DNA of the deposited stra " The deposited stram contains the full length pyrH gene The sequence of the polynucleotides contained m the deposited strain, as well as the ammo acid sequence of the polypeptide encoded thereby, are controlling m the event of any conflict with any descπption of sequences herem The deposit of the deposited stram 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 stram will be irrevocably and without restriction or condition released to the public upon the issuance of a patent The deposited stram is provided merely as convenience to those of skill m 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 deπved therefrom, and no such license is hereby granted One aspect of the mvention there is provided an isolated nucleic acid molecule encoding a mature polypeptide expressible by the Streptococcus pneumomae 0100993 stram contained m the deposited stram Further provided by the mvention are pyrH nucleotide sequences of the DNA m the deposited stram and ammo acid sequences encoded thereby Also provided by the mvention are pyrH polypeptide sequences isolated from the deposited stram and ammo acid sequences deπved therefrom Polypeptides The polypeptides of the mvention mclude a polypeptide of Table 1 [SEQ ID NO 2] (m particular the mature polypeptide) as well as polypeptides and fragments, particularly those which have the biological activity of pyrH, and also those which have at least 70% identity to a polypeptide of Table 1 [SEQ ID NO l]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 mclude 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 polypeptides of the formula X-(R 1 ) m -(R 2 )-(R 3 ) n -Y wherein, at the ammo terminus, X is hydrogen or a metal, and at the carboxyl terminus, Y is hydrogen or a metal, Ri and R3 are any ammo acid residue, m is an integer between 1 and 1000 or zero, n is an - 7 - integer 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 In the formula above R 2 is oπented so that its ammo terminal residue is at the left, bound to Ri and its carboxy terminal residue is at the πght, bound to R3 Any stretch of ammo acid residues denoted by either R group, where m and/or n is greater than 1, may be either a heteropolymer or a homopolymer, preferably a heteropolymer A fragment is a vaπant polypeptide having an ammo acid sequence that entirely is the same as part but not all of the ammo acid sequence of the aforementioned polypeptides As with pyrH polypeptides fragments may be "free-standing," or compπsed within a larger polypeptide of which they form a part or region, most preferably as a single contmuous region, a single larger polypeptide Prefeπed fragments mclude, for example, truncation polypeptides having a portion of an ammo acid sequence of Table 1 [SEQ ID NO 2], or of vaπants thereof, such as a contmuous seπes of residues that mcludes the ammo terminus, or a contmuous seπes of residues that mcludes the carboxyl terminus Degradation forms of the polypeptides of the mvention in a host cell, particularly a Streptococcus pneumomae, are also prefeπed Further prefeπed are fragments characterized by structural or functional attπbutes such as fragments that comprise alpha-he x and alpha-hehx forming regions, beta-sheet and beta-sheet-forming regions, turn and turn-forming regions, coil and coil- forming regions, hydrophihc regions, hydrophobic regions, alpha amphipathic regions, beta amphipathic regions, flexible regions, surface-forming regions, substrate binding region, and high anugenic mdex regions Also prefeπed are biologically active fragments which are those fragments that mediate activities of pyrH, including those with a similar activity or an improved activity, or with a decreased undesirable activity Also mcluded are those fragments that are aπύgemc or immunogenic m an animal, especially m a human Particularly prefeπed are fragments compπsmg receptors or domains of enzymes that confer a function essential for viability of Streptococcus pneumomae or the ability to initiate, or maintain cause disease m an individual, particularly a human Vaπants that are fragments of the polypeptides of the mvention may be employed for producing the coπesponding full-length polypeptide by peptide synthesis, therefore, these vaπants may be employed as intermediates for producing the full-length polypeptides of the mvention In addition to the standard smgle and tπple letter representations for ammo acids, the term "X" or "Xaa" may also be used m descπbmg certam polypeptides of the mvention "X" and "Xaa" mean that any of the twenty naturally occurring ammo acids may appear at such a designated position m the polypeptide sequence 8 - Polynucleotides Another aspect of the mvention relates to isolated polynucleotides, including the full length gene, that encode the pyrH polypeptide havmg a deduced ammo acid sequence of Table 1 [SEQ ID NO.2] and polynucleotides closely related thereto and vaπants thereof Using the information provided herein, such as a polynucleotide sequence set out m Table 1 [SEQ ID NO 1], a polynucleotide of the mvention encoding pyrH polypeptide may be obtained using standard cloning and screenmg methods, such as those for cloning and sequencing chromosomal DNA fragments from bacteπa usmg Streptococcus pneumomae 0100993 cells as starting material, followed by obtaining a full length clone For example, to obtain a polynucleotide sequence of the mvention, such as a sequence given m Table 1 [SEQ ID NO 1], typically a library of clones of chromosomal DNA of Streptococcus pneumomae 0100993 m E coli or some other suitable host is probed with a radiolabeled ohgonucleotide. preferably a 17-mer or longer, deπved from a partial sequence Clones carrying DNA identical to that of the probe can then be distinguished usmg stringent conditions By sequencmg the individual clones thus identified with sequencmg primers designed from the oπgmal sequence it is then possible to extend the sequence m both directions to determine the full gene sequence Convemently, such sequencmg is performed usmg denatured double stranded DNA prepared from a plasmid clone Suitable techniques are descπbed by Maniatis, T , Fπtsch, 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 in particular Screenmg By Hybπdization 1 90 and Sequencmg Denatured Double-Stranded DNA Templates 13 70) Illustrative of the mvention, the polynucleotide set out m Table 1 [SEQ ID NO 1] was discovered m a DNA library deπved from Streptococcus pneumomae 0100993 The DNA sequence set out m Table 1 [SEQ ID NO 1] contains an open reading frame encodmg a protem havmg about the number of ammo acid residues set forth m Table 1 [SEQ ID NO 2] with a deduced molecular weight that can be calculated usmg ammo acid residue molecular weight values well known m the art The polynucleotide of SEQ ED NO 1. between nucleotide number 1 and the stop codon which begins at nucleotide number 736 of SEQ ID NO.l, encodes the polypeptide of SEQ ID NO 2 PyrH of the mvention is structurally related to other proteins of the UMP (undine monophosphate) kinase family See GeneBank Z99112, GeneBank D90915, GeneBank Z97369, GeneBank Z74024, GeneBank D26562 and X78809, GeneBank U32786. GeneBank AE000589, GeneBank AE000021, GeneBank U60196, GeneBank U39730, GeneBank X83598, GeneBank AE000962, GeneBank U67566, GeneBank AB005215, GeneBank AE001158 - 9 - The mvention provides a polynucleotide sequence identical over its entire length to a coding sequence m Table 1 [SEQ ID NO 1] Also provided by the mvention is the coding sequence for the mature polypeptide or a fragment thereof, by itself as well as the coding sequence for the mature polypeptide or a fragment m reading frame with other coding sequence, such as those encodmg a leader or secretory sequence, a pre-, or pro- or prepro- protem sequence The polynucleotide may also contain non-coding sequences, including for example, but not limited to non-coding 5' and 3' sequences, such as the transcπbed, non-translated sequences, termination signals, πbosome binding sites, sequences that stabilize mRNA, introns, polyadenylation signals, and additional coding sequence which encode additional ammo acids For example, a marker sequence that facilitates purification of the fused polypeptide can be encoded In certam embodiments of the mvention, the marker sequence is a hexa-histidine peptide, as provided m the pQE vector (Qiagen, Inc ) and descπbed m Gentz et al , Proc Natl Acad Sci USA 86 821-824 (1989), or an HA tag (Wilson et al , Cell 37 767 (1984) Polynucleotides of the mvention also mclude, but are not limited to, polynucleotides compπsmg a structural gene and its naturally associated sequences that control gene expression A prefeπed embodiment of the mvention is a polynucleotide of compπsing nucleotide 1 to the nucleotide immediately upstream of or including nucleotide 736 set forth m SEQ ID NO 1 of Table 1, both of which encode the pyrH polypeptide The mvention also mcludes polynucleotides of the formula X-(R 1 ) m -(R 2 )-(R 3 ) n -Y wherem, at the 5' end of the molecule, X is hydrogen or a metal or together with Y defines a covalent bond, and at the 3' end of the molecule, Y is hydrogen or a metal or together with X defines the covalent bond, each occurrence of Ri and R3 is mdependently any nucleic acid residue, m is an mteger between 1 and 3000 or zero , n is an mteger between 1 and 3000 or zero, and R is a nucleic acid sequence of the mvention, particularly a nucleic acid sequence selected from Table 1 In the polynucleotide formula above R is oπented so that its 5' end residue is at the left, bound to Ri and its 3' end residue is at the πght, bound to R3 Any stretch of nucleic acid residues denoted by either R group, where m and/or n is greater than 1, may be either a heteropolymer or a homopolymer, preferably a heteropolymer Where, m 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 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. - 10 It is most prefeπed that the polynucleotides of the inventions are deπved from Streptococcus pneumomae, however, they may preferably be obtained from organisms of the same taxonomic genus They may also be obtained, for example, from organisms of the same taxonomic family or order The term "polynucleotide encodmg a polypeptide" as used herem encompasses polynucleotides that mclude a sequence encoding a polypeptide of the mvention, particularly a bacteπal polypeptide and more particularly a polypeptide of the Streptococcus pneumomae pyrH havmg an ammo acid sequence set out m Table 1 [SEQ ID NO 2] The term also encompasses polynucleotides that mclude a single contmuous region or discontinuous regions encoding the polypeptide (for example, interrupted by integrated phage or an insertion sequence or editing) together with additional regions, that also may contain coding and/or non-coding sequences The mvention further relates to vaπants of the polynucleotides descπbed herem that encode for vaπants of the polypeptide having a deduced ammo acid sequence of Table 1 [SEQ ID NO 2] Vaπants that are fragments of the polynucleotides of the mvention may be used to synthesize full- length polynucleotides of the mvention Further particularly prefeπed embodiments are polynucleotides encoding pyrH vaπants, that have the ammo acid sequence of pyrH 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, deleted or added, in any combination Especially prefeπed among these are silent substitutions, additions and deletions, that do not alter the properties and activities of pyrH Further prefeπed embodiments of the mvention are polynucleotides that are at least 70% identical over their entire length to a polynucleotide encodmg pyrH polypeptide havmg an ammo acid sequence set out m Table 1 [SEQ ID NO 2], and polynucleotides that are complementary to such polynucleotides Alternatively, most highly prefeπed are polynucleotides that compπse a region that is at least 80% identical over its entire length to a polynucleotide encodmg pyrH polypeptide and polynucleotides complementary thereto In this regard, polynucleotides at least 90% identical over their entire length to the same are particularly prefeπed. and among these particularly prefeπed polynucleotides, those with at least 95% are especially prefeπed Furthermore, those with at least 97% are highly prefeπed among those with at least 95%, and among these those with at least 98% and at least 99% are particularly highly prefeπed, with at least 99% bemg the more prefeπed Prefeπed embodiments are polynucleotides that encode 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] The mvention further relates to polynucleotides that hybπdize to the herem above-descπbed sequences In this regard, the mvention especially relates to polynucleotides that hybπdize under - 1 1 - stringent conditions to the herem above-descπbed polynucleotides As herem used, the terms "stringent conditions" and "stringent hybπdization conditions" mean hybπdization will occur only if there is at least 95% and preferably at least 97% identity between the sequences An example of stringent hybπdization conditions is overnight mcubation at 42°C m a solution compπsmg 50% formamide, 5x SSC (150 mM NaCl, 15 mM tπsodium citrate), 50 mM sodium phosphate (pH7 6), 5x Denhardt's solution, 10% dextran sulfate, and 20 micrograms/ml denatured, sheared salmon sperm DNA. followed by washing the hybπdization support m 0 lx SSC at about 65°C Hybπdization and wash conditions are well known and exemplified m Sambrook, et al , Molecular Cloning A Laboratory Manual, Second Edition, Cold Spring Harbor, N Y , (1989), particularly Chapter 11 therein The mvention also provides a polynucleotide consistmg essentially of a polvnucleotide sequence obtainable by screemng an appropπate library containing the complete gene for a polynucleotide sequence set forth m SEQ ID NO 1 under stringent hybndization 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 DNA sequence Fragments useful for obtaining such a polynucleotide mclude. for example, probes and primers descπbed elsewhere herem As discussed additionally herem regarding polynucleotide assays of the invention, for instance, polynucleotides of the mvention as discussed above, may be used as a hybπdization probe for RNA cDNA and genomic DNA to isolate full-length cDNAs and genomic clones encodmg pyrH and to isolate cDNA and genomic clones of other genes that have a high sequence identity to the pyrH gene Such probes generally will compπse at least 15 bases Preferably, such probes will have at least 30 bases and may have at least 50 bases Particularly prefeπed probes will have at least 30 bases and will have 50 bases or less For example, the coding region of the pyrH gene may be isolated by screenmg usmg a DNA sequence provided in Table 1 [SEQ ID NO 1] to synthesize an ohgonucleotide probe A labeled ohgonucleotide having a sequence complementary to that of a gene of the mvention is then used to screen a library of cDNA genomic DNA or mRNA to determine which members of the library the probe hvbπdizes to The polynucleotides and polypeptides of the mvention may be employed, for example, as research reagents and mateπals for discovery of treatments of and diagnostics for disease, particularly human disease, as further discussed herem relating to polynucleotide assays Polynucleotides of the mvention that are ohgonucleotides deπved from the sequences of Table 1 [SEQ ID NOS 1 or 2] may be used m the processes herem as descπbed. but preferably for PCR. to determine whether or not the polynucleotides identified herem m whole or m part are - 12 - transcπbed in bacteπa m infected tissue It is recognized that such sequences will also have utihtv m diagnosis of the stage of infection and type of infection the pathogen has attained The mvention also provides polynucleotides that may encode a polypeptide that is the mature protem plus additional ammo or carboxyl-terminal ammo acids, or ammo acids lnteπor to the mature polypeptide (when the mature form has more than one polypeptide chain, for instance) Such sequences may play a role m processing of a protem from precursor to a mature form, may allow protem transport, may lengthen or shorten protem half-life or may facilitate manipulation 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 A precursor protein, havmg the 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 mav be removed before activation Generally, such precursors are called proproteins In addition to the standard A, G, C, TAJ representations for nucleic acid bases, the term "N" may also be used m descπbing certam polynucleotides of the mvention "N" means that any of the four DNA or RNA bases may appear at such a designated position m the DNA or RNA sequence, except it is prefeπed that N is not a base that when taken m combination with adjacent nucleotide positions, when read in the coπect readmg frame, would have the effect of generating a premature termination codon m such readmg frame In sum, a polynucleotide of the mvention may encode a mature protein, a mature protem plus a leader sequence (which may be refeπed to as a preprotein), a precursor of a mature protem havmg one or more prosequences that are not the leader sequences of a preprotein, 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 The mvention also relates to vectors that compπse 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 deπved from the DNA constructs of the mvention For recombinant production, 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 descπbed m many standard laboratory manuals, such as Davis et aL, BASIC METHODS IN MOLECULAR BIOLOGY, (1986) and - 13 - Sambrook et al , MOLECULAR CLONING A LABORATORY MANUAL, 2nd Ed . Cold Spπng Harbor Laboratory Press Cold Spπng Harbor. N Y (1989), such as. calcium phosphate transfection, DEAE-dextran mediated transfection, transvection, micromjection. cationic hpid-mediated transfection. electroporation, transduction, scrape loading, ballistic introduction and infection Representative examples of appropπate hosts mclude bacteπal cells, such as streptococci, staphylococci, enterococci E coli, streptomyces and Bacillus subtilis cells, fungal cells, such as yeast cells and Aspergillus cells, insect cells such as Drosophύa S2 and Spodoptera Sf9 cells, animal cells such as CHO COS, HeLa, C127, 3T3. BHK, 293 and Bowes melanoma cells, and plant cells A great vaπety of expression systems can be used to produce the polypeptides of the mvention Such vectors mclude among others, chromosomal, episomal and virus-deπved vectors, e g , vectors deπved from bacteπal 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 and retroviruses, and vectors deπved from combinations thereof, such as those deπved 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 this regard The appropπate DNA sequence may be inserted mto the expression system by any of a vaπety of well-known and routine techmques, such as, for example, those set forth m Sambrook et al , MOLECULAR CLONING, A LABORATORY MANUAL, (supra) For secretion of the translated protem mto the lumen of the endoplasmic reticulum, mto the peπplasmic 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 purified from recombinant cell cultures by well-known methods including ammonium sulfate or ethanol precipitation, acid extraction, amon or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatographv, affinity chromatography, hydroxylapatite chromatography, and lectin chromatography Most preferably, high performance hqmd chromatography is employed for purification Well known techmques for refolding protem may be employed to regenerate active conformation when the polypeptide is denatured during isolation and or purification Diagnostic, Prognostic, Serotyping and Mutation Assays 14 - This mvention is also related to the use of the pyrH polynucleotides of the mvention for use as diagnostic reagents Detection of pyrH m a eukaryote, particularly a mammal, and especially a human, will provide a diagnostic method for diagnosis of a disease Eukaryotes (herem also "ιndrvιdual(s)"), particularly mammals, and especially humans, particularly those infected or suspected to be infected with an organism compπsmg the pyrH gene may be detected at the nucleic acid level by a vaπety of techmques Nucleic acids for diagnosis may be obtained from an infected individual's cells and tissues, such as bone, blood, muscle, cartilage, and skin Genomic DNA may be used directly for detection or may be amplified enzymatically by usmg PCR or other amplification technique pπor to analysis RNA cDNA and genomic DNA may also be used m the same ways Using amplification, characterization of the species and stram of prokaryote present m an individual, may be made by an analysis of the genotype of the prokaryote gene Deletions and insertions can be detected by a change m size of the amplified product m comparison to the genotype of a reference sequence Pomt mutations can be identified by hybπdizing amplified DNA to labeled pyrH polynucleotide sequences Perfectly matched sequences can be distinguished from mismatched duplexes by RNase digestion or by differences m melting temperatures DNA sequence differences may also be detected by alterations m the electrophoretic mobility of the DNA fragments m gels, with or without denaturing agents, or by direcrDNA sequencmg See, e g , Myers et al , Science, 230 1242 (1985) Sequence changes at specific locations also may be revealed by nuclease protection assays, such as RNase and SI protection or a chemical cleavage method See, e g , Cotton et al , Proc Natl Acad Sci , USA, 85 4397-44OI (1985) Cells carrying mutations or polymorphisms (allehc vaπations) m the gene of the mvention may also be detected at the DNA or RNA level by a vaπety of techmques, to allow for serotypmg, for example For example, RT-PCR can be used to detect mutations m the RNA It is particularly prefeπed to used RT-PCR m conjunction with automated detection systems, such as, for example, GeneScan RNA cDNA or genomic DNA may also be used for the same purpose, PCR or RT-PCR As an example, PCR primers complementary to a nucleic acid encodmg pyrH can be used to identify and analyze mutations Examples of representative pπmers are shown below m Table 2 Table 2 Primers for amplification of pyrH polynucleotides SEQ ID NO PRIMER SEQUENCE 3 5 I -GGTAGGATGAAAGAAGGAGAG-3 I - 15 - 5'-GCCATATTCTTTCTTATTCC-3' The mvention also mcludes primers of the formula X-(Rι ) m -(R 2 )-(R 3 ) n -Y wherein, at the 5' end of the molecule, X is hydrogen or a metal, and at the 3' end of the molecule, Y is hydrogen or a metal, Ri and R3 is any nucleic acid residue, m is an integer between 1 and 20 or zero , n is an mteger between 1 and 20 or zero, and R 2 is a pπmer sequence of the mvention. particularly a pπmer sequence selected from Table 2 In the polynucleotide formula above R 2 is onented so that its 5' end residue is at the left, bound to R and its 3' end residue is at the πght, bound to R3 Any stretch of nucleic acid residues denoted by either R group, where 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 prefeπed embodiment m and/or n is an mteger between 1 and 10. The mvention further provides these pπmers with 1, 2, 3 or 4 nucleotides removed from the 5' and/or the 3' end These pπmers may be used for, among other things, amplifying pyrH DNA isolated from a sample deπved from an individual The pπmers may be used to amplify the gene isolated from an infected individual such that the gene may then be subject to vaπous techmques for elucidation of the DNA sequence In this way, mutations m the DNA sequence may be detected andmsed to diagnose infection and to serotype and/or classify the infectious agent The mvention further provides a process for diagnosing, disease, preferably bacteπal infections, more preferably infections by Streptococcus pneumomae, compπsmg determining from a sample deπved from an individual a mcreased level of expression of polynucleotide havmg a sequence of Table 1 [SEQ ID NO 1] Increased or decreased expression of pyrH polynucleotide can be measured usmg any on of the methods well known m the art for the quantitation of polynucleotides, such as. for example, amplification, PCR, RT-PCR. RNase protection, Northern blotting and other hybridization methods In addition, a diagnostic assay m accordance with the mvention for detecting over-expression of pyrH protem 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 pyrH protein, m a sample deπved from a host are well-known to those of skill m the art Such assay methods mclude radiounmunoassays, competitive-binding assays, Western Blot analysis and ELISA assays The polynucleotide sequences of the present mvention are also valuable for chromosome identification The sequence is specifically targeted to, and can hybπdize with, a particular location on an individual microbial chromosome, particularly a Streptococcus pneumomae chromosome The mapping of relevant sequences to a chromosome according to the present mvention is an important - 16 - first step m coπelating those sequences with gene associated with microbial pathogemcity and disease, or to chromosomal regions cπtical to the growth, survival and/or ecological mche Once a sequence has been mapped to a precise chromosomal location, the physical position of the sequence on the chromosome can be coπelated with genetic map data Such data are found in. for example, microbial genomic sequences available on the World Wide Web The relationship between genes and microbial pathogemcity, disease, or to genome regions cπtical to the growth, survival and/or ecological mche that have been mapped to the same chromosomal region are then identified using methods to define a genetic relationship between the gene and another gene or phenotype, such as by linkage analysis (coinheπtance of physically adjacent genes) The differences m the RNA or genomic sequence between microbes of differing phenotypes can also be determined If a mutation or sequence is observed m some or all of the microbes of a certam phenotype, but not in any microbes lacking that phenotype, then the mutation or sequence is likely to be the causative agent of the phenotype In this way, chromosomal regions may be identified that confer microbial pathogemcity, growth characteristics, survival characteπstics and/or ecological mche characteπstics Differential Expression The polynucleotides and polynucleotides of the mvention may be used as reagents for differential screenmg methods There are many differential screenmg and differential display methods known m the art m which the polynucleotides and polypeptides of the mvention may be used For example, the differential display technique is descπbed 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 usmg 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 descπbed by Camilh et al , Proc Nat'l Acad Sci USA 91 2634-2638 (1994) IVET identifies genes up-regulated during infection when compared to laboratory cultivation, implying an important role m infection ORF 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 m a plasmid vector This construct is mtroduced mto the target organism which carries an antibiotic resistance gene flanked bv resolvase sites Growth m the presence of the antibiotic removes from the population those fragments cloned mto the plasmid vector capable of supporting transcπption of the recombmase gene and therefore have caused loss of antibiotic resistance The resistant pool is mtroduced mto a host and at - 17 - vaπous times after infection bacteπa may be recovered and assessed for the presence of antibiotic resistance The chromosomal fragment earned by each antibiotic sensitive bactenum should cany a promoter or portion of a gene normally upregulated during infection Sequencmg 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 usmg the polynucleotides of the mvention, messenger RNA is isolated from bactenal infected tissue, e g , 48 hour munne lung infections, and the amount of each mRNA species assessed by reverse transcnption of the RNA sample pruned 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 bacteπal genes which are transcnbed m the infected tissue Analysis of gene transcnption can be earned out at different times of infection to gam a detailed knowledge of gene regulation m bacteπal pathogenesis allowing for a clearer understanding of which gene products represent targets for screens for antibacteπals Because of the gene specific nature of the PCR pπmers employed it should be understood that the bacteπal mRNA preparation need not be free of mammalian RNA This allows the mvestigator to carry out a simple and quick RNA preparation from infected tissue to obtain bacteπal mRNA species which are very short lived m the bactenum (m the order of 2 minute halflives) Optimally the bactenal mRNA is prepared from infected munne lung tissue bv mechanical disruption in the presence of TRIzole (GIBCO-BRL) for very short penods of time, subsequent processmg accordmg to the manufacturers of TRIzole reagent and DNAase treatment to remove contaminating DNA Preferably the process is optimised by finding those conditions which give a maximum amount of Streptococcus pneumomae 16S nbosomal RNA as detected by probing Northerns with a suitably labelled sequence specific ohgonucleotide probe Typically a 5' dye labelled pπmer is used in each PCR pnmer pair in a PCR reaction which is termmated optimally between 8 and 25 cycles The PCR products are separated on 6% pohacrylamide gels with detection and quantification usmg GeneScanner (manufactured by ABI) Each of these techmques may have advantages or disadvantage depending on the particular application The skilled artisan would choose the approach that is the most relevant with the particular end use m mind Antibodies The polypeptides of the mvention or vaπants thereof, or cells expressmg them can be used as an immunogen to produce antibodies lmmunospecific for such polypeptides "Antibodies" as used herem mcludes monoclonal and polyclonal antibodies, chimeπc, single chain, simiamzed antibodies and humanized antibodies, as well as Fab fragments, including the products of an Fab lmmunolglobuhn expression library Antibodies generated against the polypeptides of the mvention can be obtained by administering the polypeptides or epitope-beanng fragments, analogues or cells to an ammal, preferably a nonhuman, usmg routine protocols For preparation of monoclonal antibodies, any technique known m the art that provides antibodies produced by continuous cell line cultures can be used Examples mclude vanous techmques, such as those m Kohler, G and Milstein, 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 single chain antibodies to polypeptides of this mvention Also, transgenic mice, or other organisms such as other mammals, may be used to express humanized antibodies Alternatively phage display technology may be utilized to select antibody genes with bmdmg activities towards the polypeptide either from repertoires of PCR amplified v-genes of lymphocytes from humans screened for possessmg anti-pyrH or from naive libranes (McCafferty, J et al , (1990), Nature 348, 552-554, Marks, J et al , (1992) Biotechnology 10, 779-783) The affinity of these antibodies can also be unproved by chain shuffling (Clackson, T et*, (1991) Nature 352, 624-628) If two antigen bmdmg domams are present each domam may be directed against a different epitope - termed 'bispecific' antibodies The above-descπbed antibodies may be employed to isolate or to identify clones expressing the polypeptides to purify the polypeptides by affinity chromatography Thus, among others, antibodies against pyrH-polypeptide may be employed to treat infections, particularly bacteπal infections Polypeptide vanants mclude antigenically, epitopically or immunologically equivalent vaπants that form a particular aspect of this mvention The term "antigenically equivalent denvative" as used herem encompasses a polypeptide or its equivalent which will be specifically recognized by certam antibodies which, when raised to the protem or polypeptide accordmg to the mvention, interfere with the immediate physical mteraction between pathogen and mammalian host The term "immunologically equivalent denvative" as used herem encompasses a peptide or its equivalent which when used m a suitable formulation to raise antibodies m a vertebrate, the antibodies act to interfere with the immediate physical mteraction between pathogen and mammalian host 19 The polypeptide, such as an antigenically or immunologically equivalent denvative or a fusion protem thereof is used as an antigen to immunize a mouse or other animal such as a rat or chicken The fusion protem may provide stability to the polypeptide The antigen may be associated, for example by conjugation, with an lmmunogemc earner protem for example bovine serum albumm (BSA) or keyhole limpet haemocyanm (KLH) Alternatively a multiple antigemc peptide compnsmg multiple copies of the protem or polypeptide, or an antigenically or immunologically equivalent polypeptide thereof may be sufficiently antigemc to improve immunogenicity so as to obviate the use of a earner Preferably, the antibody or vaπant thereof is modified to make it less immunogenic m the mdividual For example, if the mdividual is human the antibody may most preferably be "humanized", where the complimentanty determining regιon(s) of the hybndoma-denved antibody has been transplanted mto a human monoclonal antibody , for example as descπbed m Jones. P et al (1986), Nature 321, 522-525 or Tempest et al , (1991) Biotechnology 9, 266- 273 The use of a polynucleotide of the mvention m genetic immunization will preferably employ a suitable delivery method such as direct injection of plasmid DNA mto muscles (Wolff et al . Hum Mol Genet 1992. 1 363, Manthorpe et al , Hum Gene Ther 1963 4, 419)rdehvery of DNA complexed with specific protem earners (Wu et al , J Biol Chem 1989 264,16985), coprecipitation of DNA with calcium phosphate (Benvenisty & Reshef, PNAS USA 1986 83,9551), encapsulation of DNA m vanous 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 usmg cloned retroviral vectors (Seeger et al , PNAS USA 1984 81,5849) Antagonists and agonists - assays and molecules Polypeptides of the mvention may also be used to assess the bmdmg of small molecule substrates and hgands in, for example, cells, cell-free preparations, chemical libranes. 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) The mvention also provides a method of screening compounds to identify those which enhance (agonist) or block (antagonist) the action of pyrH polypeptides or polynucleotides, particularly those compounds that are bactenostatic and/or bactenocidal The method of screening may mvolve high-throughput techmques For example, to screen for agonists or antagonists, a synthetic reaction mix, a cellular compartment, such as a membrane, cell envelope or cell wall, or a - 20 - preparation of any thereof, compπsing pyrH polypeptide and a labeled substrate or gand of such polypeptide is incubated m the absence or the presence of a candidate molecule that may be a pyrH agonist or antagonist The ability of the candidate molecule to agonize or antagonize the pyrH polypeptide is reflected m decreased binding of the labeled hgand or decreased production of product from such substrate Molecules that bmd gratuitously, i e , without mducmg the effects of pyrH polypeptide are most likely to be good antagomsts Molecules that bmd well and mcrease the rate of product production from substrate are agonists Detection of the rate or level of production of product from substrate may be enhanced by usmg a reporter system Reporter systems that may be useful m this regard mclude but are not limited to coloπmetnc labeled substrate converted mto product, a reporter gene that is responsive to changes m pyrH polynucleotide or polypeptide activity, and bmdmg assays known m the art Another example of an assay for pyrH antagomsts is a competitive assay that combines pyrH and a potential antagonist with pyrH-binding molecules, recombinant pyrH bmdmg molecules, natural substrates or hgands, or substrate or hgand mimetics, under appropπate conditions for a competitive inhibition assay PyrH can be labeled, such as by radioactivity or a colonmetnc compoimd, such that the number of pyrH 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 small orgamc molecules, peptides, polypeptides and antibodies that bmd to a polynucleotide or polypeptide of the mvention and thereby inhibit or extinguish its activity Potential 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 binding molecule, without mducmg pyrH-mduced activities, thereby preventing the action of pyrH by excluding pyrH from bmdmg Potential antagomsts mclude a small molecule that bmds to and occupies the bmdmg site of the polypeptide thereby preventing bmdmg to cellular bmdmg molecules, such that normal biological activity is prevented Examples of small molecules mclude but are not limited to small orgamc molecules, peptides or peptide-like molecules Other potential antagomsts mclude antisense molecules (see Okano, J Neurochem 56 560 (1991), OUGODEOXYNUCLEOTIDES AS ANTISENSE INHIBITORS OF GENE EXPRESSION, CRC Press, Boca Raton, FL (1988), for a descπption of these molecules) Prefeπed potential antagonists mclude compounds related to and vaπants of pyrH Each of the DNA sequences provided herem may be used m the discovery and development of antibacteπal compounds The encoded protem, upon expression, can be used as a target for the screemng of antibactenal drugs Additionally, the DNA sequences encodmg the ammo terminal regions of the encoded protein or Shine-Delgarno or other translation facilitating - 21 - sequences of the respective mRNA can be used to construct antisense sequences to control the expression of the codmg sequence of mterest The invention also provides the use of the polypeptide, polynucleotide or inhibitor of the invention to interfere with the initial physical mteraction between a pathogen and mammalian host responsible for sequelae of infection In particular the molecules of the mvention may be used m the prevention of adhesion of bactena. m particular gram positive bacteπa, to mammalian extracellular matnx proteins on in-dwelling devices or to extracellular matnx protems m wounds, to block pyrH protem-mediated mammalian cell mvasion by. for example, initiating phosphorylation of mammalian tyrosine kinases (Rosenshine et al , Infect Immun 60 2211 (1992), to block bacterial adhesion between mammalian extracellular matnx protems and bacterial pyrH proteins that mediate tissue damage and, to block the normal progression of pathogenesis m infections initiated other than by the implantation of in-dwelling devices or by other surgical techmques The antagonists and agonists of the mvention may be employed, for instance, to inhibit and treat diseases Hehcobacter pylori (herein H pylon) bactena 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).Schιstosomes. Liver Flukes and Hehcobacter Pylon (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 Preferred antimicrobial compounds of the mvention (agonists and antagomsts of pyrH) found using screens provided by the mvention, particularly broad-spectrum antibiotics, should be useful in the treatment of H pylori infection Such treatment should decrease the advent of H pylori -induced cancers, such as gastrointestinal carcmoma Such treatment should also cure gastnc ulcers and gastntis Vaccines Another aspect of the invention relates to a method for mducmg an immunological response in an mdividual, particularly a mammal which comprises inoculating the mdividual with pyrH, or a fragment or vanant thereof, adequate to produce antibody and/ or T cell immune response to protect said individual from infection, particularly bactenal infection and most particularly Streptococcus pneumomae infection Also provided are methods whereby such immunological response slows bacteπal replication Yet another aspect of the mvention relates to a method of mducmg immunological response m an individual which compπses delivering to - 22 - such mdividual a nucleic acid vector to direct expression of pyrH, or a fragment or a vanant thereof, for expressmg pyrH, or a fragment or a vanant thereof in vivo m order to mduce an immunological response, such as, to produce antibody and/ or T cell immune response, including, for example, cytokine-producing T cells or cytotoxic T cells, to protect said mdividual from disease, whether that disease is already established within the individual or not One way of administering the gene is by accelerating it mto the desired cells as a coatmg on particles or otherwise Such nucleic acid vector may compnse DNA, RNA, a modified nucleic acid, or a DNA RNA hybnd A further aspect of the mvention relates to an immunological composition which, when mtroduced into an mdividual capable or havmg mduced within it an immunological response, mduces an immunological response m such individual to a pyrH or protem coded therefrom, wherem the composition compnses a recombinant pyrH or protem coded therefrom compnsmg DNA which codes for and expresses an antigen of said pyrH or protem coded therefrom The immunological response may be used therapeutically or prophylactically and may take the form of antibody immunity or cellular immunity such as that ansing from CTL or CD4+ T cells A pyrH polypeptide or a fragment thereof may be fused with co-protem which may not by itself produce antibodies, but is capable of stabilizing the first protem and producmg a fused protem which will have lmmunogenic and protective properties Thus fused recombinant protem, preferably further compnses an antigemc co-protein, such as poprotem D from Hemophilus influenzae, Glutathione-S-transferase (GST) or beta-galactosidase, relatively large co-proteins which solubihze the protem and facilitate production and punfication thereof Moreover, the co-protem may act as an adjuvant m the sense of providmg a generalized stimulation of the immune system The co-protem may be attached to either the ammo or carboxy terminus of the first protem Provided by this mvention are compositions, particularly vaccme compositions, and methods compπsmg the polypeptides or polynucleotides of the mvention and lmmunostimulatory DNA sequences, such as those descπbed in Sato, Y et al Science 273 352 (1996) Also, provided by this mvention are methods usmg the descnbed polynucleotide or particular fragments thereof which have been shown to encode non-vanable regions of bacteπal cell surface protems m DNA constructs used m such genetic unmumzation experiments m animal models of mfection with Streptococcus pneumomae will be particularly useful for identifying protem 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 from the requisite organ of the animal successfully resisting or clearing mfection - 23 - for the development of prophylactic agents or therapeutic treatments of bactenal infection, particularly Streptococcus pneumomae infection, m mammals, particularly humans The polypeptide may be used as an antigen for vaccination of a host to produce specific antibodies which protect against invasion of bactena, for example by blocking adherence of bactena to damaged tissue Examples of tissue damage mclude wounds in skin or connective tissue caused, e g , by mechanical, chemical or thermal damage or by implantation of indwelling devices, or wounds m the mucous membranes, such as the mouth, mammary glands, urethra or vagma The mvention also mcludes a vaccme formulation which compnses an lmmunogenic recombmant protem of the mvention together with a suitable earner Smce the protem may be broken down in the stomach, it is preferably administered parenterally, mcludmg, for example, administration that is subcutaneous, intramuscular, intravenous, or lntradermal Formulations suitable for parenteral administration mclude aqueous and non-aqueous steπle injection solutions which may contain anti-oxidants, buffers, bactenostats and solutes which render the formulation msotomc with the bodily fluid, preferably the blood, of the mdividual, and aqueous and non- aqueous stenle suspensions which may mclude suspendmg agents or thickening agents The formulations may be presented m umt-dose or multi-dose containers, for example^ sealed ampules and vials and may be stored m a freeze-dπed condition requiring only the addition of the stenle liquid earner immediately prior to use The vaccme formulation may also mclude adjuvant systems for enhancmg the immunogemcity 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 vaccme and can be readily determined by routine experimentation While the mvention has been descnbed with reference to certam pyrH protein, it is to be understood that this covers fragments of the naturally occurring protem and similar protems with additions, deletions or substitutions which do not substantially affect the unmunogemc properties of the recombinant protein Compositions, kits and administration The mvention also relates to compositions compπsing the polynucleotide or the polypeptides discussed above or their agonists or antagomsts The polypeptides of the mvention may be employed m combination with a non-steπle or steπle earner or earners for use with cells, tissues or organisms, such as a pharmaceutical earner suitable for administration to a subject Such compositions compnse, for instance, a media additive or a therapeutically effective amount of a polypeptide of the mvention and a pharmaceutically acceptable earner or excipient Such earners may mclude, but are not limited to, saline, buffered saline, dextrose, water, glycerol, ethanol and combinations thereof The - 24 - formulation should smt 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 and other compounds of the mvention may be employed alone or m conjunction with other compounds, such as therapeutic compounds The pharmaceutical compositions may be administered m any effective, convenient manner including, for instance, administration by topical, oral, anal, vaginal, intravenous, lntrapeπtoneal, intramuscular, subcutaneous, mtranasal or intradermal routes among others In therapy or as a prophylactic, the active agent may be administered to an mdividual as an injectable composition, for example as a stenle aqueous dispersion, preferably isotomc Alternatively the composition may be formulated for topical application for example m the form of omtments. creams, lotions, eye omtments, eye drops, ear drops, mouthwash, impregnated dressmgs and sutures and aerosols, and may contam appropnate conventional additives, mcludmg, for example, preservatives, solvents to assist drug penetration, and emollients m omtments and creams Such topical formulations may also contam compatible conventional earners, for example cream or ointment bases, and ethanol or oleyl alcohol for lotions Such earners 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 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 m any event will determine the actual dosage which will be most suitable for an mdividual 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 mdividual instances where higher or lower dosage ranges are mented, and such are withm the scope of this mvention In-dwelling devices include surgical implants, prosthetic devices and catheters, i.e., devices that are mtroduced to the body of an individual and remain in position for an extended tune Such devices mclude, for example, artificial joints, heart valves, pacemakers, vascular grafts, vascular catheters, cerebrospinal fluid shunts, unnary catheters, continuous ambulatory peπtoneal dialysis (CAPD) catheters The composition of the mvention may be administered by injection to achieve a systemic effect agamst relevant bacteπa shortly before insertion of an in-dwelling 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 peπoperative cover for any surgical technique to prevent bacteπal wound infections, especially Streptococcus pneumomae wound infections - 25 - Many orthopaedic surgeons consider that humans with prosthetic jomts should be considered for antibiotic prophylaxis before dental treatment that could produce a bacteremia Late deep mfection is a senous complication sometimes leadmg to loss of the prosthetic jomt and is accompanied by significant morbidity and mortality It may therefore be possible to extend the use of the active agent as a replacement for prophylactic antibiotics m this situation In addition to the therapy descnbed above, the compositions of this invention may be used generally as a wound treatment agent to prevent adhesion of bacteπa to matnx protems exposed in wound tissue and for prophylactic use m dental treatment as an alternative to, or m conjunction with, antibiotic prophylaxis Alternatively, the composition of the mvention may be used to bathe an indwelling device immediately before insertion The active agent will preferably be present at a concentration of lμg/ml to lOmg/ml for bathing of wounds or indwelling devices A vaccme composition is convemently m injectable form Conventional adjuvants may be employed to enhance the immune response A suitable umt dose for vaccination is 0 5-5 microgram kg of antigen, and such dose is preferably admmistered 1 -3 tunes and with an mterval of 1-3 weeks With the mdicated 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 and Algorithms The polynucleotide and polypeptide sequences of the mvention are particularly useful as components in databases useful for search analyses as well as m sequence analysis algoπthms As used in this section entitled Databases and Algonthms and in claims related thereto, the terms "polvnucleotide of the invention" and "polynucleotide sequence of the mvention" mean any detectable chemical or physical charactenstic of a polynucleotide of the mvention that is or may be reduced to or stored in 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 m this section entitled Databases and Algoπthms and m claims related thereto, the terms "polypeptide of the invention" and "polypeptide sequence of the mvention" mean any detectable chemical or physical characteristic of a polypeptide of the mvention that is or may be reduced to or stored m a computer readable form For example, chromatographic scan data or peak data, photographic data or scan data therefrom, and mass spectrographic data The mvention provides computer readable medium havmg stored thereon sequences of the invention For example, a computer readable medium is provided havmg stored thereon a member selected from the group consisting of a polynucleotide compnsmg the sequence of a - 26 - polynucleotide of the invention, a polypeptide compnsmg the sequence of a polypeptide sequence of the mvention, a set of polynucleotide sequences wherem at least one of said sequences compnses the sequence of a polynucleotide sequence of the mvention, a set of polypeptide sequences wherem at least one of said sequences compnses the sequence of a polypeptide sequence of the mvention, a data set representmg a polynucleotide sequence compπsmg the sequence of polynucleotide sequence of the mvention, a data set representmg a polynucleotide sequence encodmg a polypeptide sequence compπsmg the sequence of a polypeptide sequence of the invention, a polynucleotide compπsmg the sequence of a polynucleotide sequence of the mvention, a polypeptide compπsmg the sequence of a polypeptide sequence of the mvention; a set of polynucleotide sequences wherem at least one of said sequences compπses the sequence of a polynucleotide sequence of the mvention, a set of polypeptide sequences wherein at least one of said sequences compnses the sequence of a polypeptide sequence of the mvention. a data set representmg a polynucleotide sequence compnsmg the sequence of a polynucleotide sequence of the mvention, a data set representmg a polynucleotide sequence encodmg a polypeptide sequence compπsmg the sequence of a polypeptide sequence of the mvention The computer readable medium can be any composition of matter used to store information or data, including, for example, commercially available floppy disks, tapes, hard dπves, compact disks, and video disks- Also provided by the mvention are methods for the analysis of character sequences, particularly genetic sequences Prefeπed methods of sequence analysis mclude, for example, methods of sequence homology analysis, such as identity and smulanty analysis, RNA structure analysis, sequence assembly, cladistic analysis, sequence motif analysis, open readmg frame determination, nucleic acid base calling, and sequencing chromatogram peak analysis A computer based method is provided for performing homology identification This method comprises the steps of providing a polynucleotide sequence compnsmg the sequence a polynucleotide of the invention in a computer readable medium, and comparing said polynucleotide sequence to at least one polynucleotide or polypeptide sequence to identify homology A computer based method is also provided for performing homology identification, said method compnsmg the steps of: providmg a polypeptide sequence compnsmg the sequence of a polypeptide of the mvention in a computer readable medium, and comparing said polypeptide sequence to at least one polynucleotide or polypeptide sequence to identify homology A computer based method is still further provided for polynucleotide assembly, said method compπsmg the steps of providmg a first polynucleotide sequence compπsmg the - 27 - sequence of a polynucleotide of the mvention in a computer readable medium, and screenmg for at least one overlappmg region between said first polynucleotide sequence and a second polynucleotide sequence A further embodiment of the mvention provides a computer based method for performing homology identification, said method compnsmg the steps of providmg a polynucleotide sequence compnsmg the sequence of a polynucleotide of the mvention m a computer readable medium, and comparing said polynucleotide sequence to at least one polynucleotide or polypeptide sequence to identify homology A further embodiment of the mvention provides a computer based method for performing homology identification, said method compπsmg the steps of providmg a polypeptide sequence compπsmg the sequence of a polypeptide of the mvention m 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 mvention provides a computer based method for polynucleotide assembly, said method compnsmg the steps of providmg a first polynucleotide sequence compπsmg the sequence of a polynucleotide of the mvention m a computer readable medium, and screenmg for at least one overlappmg region between said first polyπαcleotide sequence and a second polynucleotide sequence Each reference disclosed herein is incorporated by reference herem m its entirety Any patent application to which this application claims pnonty is also mcorporated by reference herem m its entirety GLOSSARY The following definitions are provided to facilitate understanding of certam terms used frequently herem "Dιsease(s)" means and disease caused by or related to mfection by a bactena, including otitis media, conjunctivitis, pneumonia, bacteremia, meningitis, sinusitis, pleural empyema and endocarditis, and most particularly meningitis, such as for example infection of cerebrospinal fluid "Host cell" is a cell which has been transformed or transfected, or is capable of transformation or transfection by an exogenous polynucleotide sequence "Identity," as known in the art, is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as the case may be, as determined by comparing the sequences In the art, "identity" also means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as the case may be, as determined by the match between strings of such sequences "Identity" can be readily calculated by known methods, mcludmg but not limited - 28 - to those descnbed m {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, Gnffin, A M , and Gnffin, H G , eds , Humana Press, New Jersey, 1994, Sequence Analysis m Molecular Biology, von Hemje, 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 , SLAM 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 m publicly available computer programs Computer program methods to determine identitv 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 (Atschul, 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 NM Bethesda, MD 20894, Altschul, S , et al , J Mol Biol 215 403-410 (1990) The well known Smith Waterman algoπthm may also be used to determine identity Parameters for polypeptide sequence companson mclude the following (1) Algonthm Needleman and Wunsch, J Mol Biol 48 443-453 (1970), (2) Companson matnx BLOSSUM62 from Hentikoff and Hentikoff, Proc Natl Acad Sci USA 89 10915-10919 (1992), (3) Gap Penalty 12, and (4) 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 include the following (1) Algonthm Needleman and Wunsch. J Mol Biol 48 443-453 (1970), (2) Companson matnx matches = +10. mismatch = 0, (3) Gap Penalty 50, and (4) Gap Length Penalty 3 Available as The "gap" program from Genetics Computer Group, Madison WI These are the default parameters for nucleic acid compansons 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 50, 60, 70, 80, 85, 90, 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 certam mteger number of nucleotide alterations as compared to the reference sequence, wherem said alterations - 29 - are selected from the group consistmg of at least one nucleotide deletion, substitution, including transition and trans version, 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, mterspersed either mdividually among the nucleotides m the reference sequence or m one or more contiguous groups within the reference sequence, and wherem said number of nucleotide alterations is determined by multiplying the total number of nucleotides m SEQ ID NO 1 by the integer defining the percent identity divided by 100 and then subtracting that product from said total number of nucleotides m SEQ ID NO 1, or n n ≤ x n - ( x n * y)> wherem n n is the number of nucleotide alterations, x n is the total number of nucleotides m 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 wherem any non-integer product of x n and y is rounded down to the nearest mteger pnor to subtractmg it from x n Alterations of a polynucleotide sequence encodmg the polypeptide of SEQ ID NO 2 may create nonsense, nussense or frameshift mutations m 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 2, that is it may be 100% identical, or it may mclude up to a certam mteger number of ammo 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 consistmg 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, mterspersed either mdividually among the nucleic acids in the reference sequence or m 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 ammo acids m SEQ ID NO 2 by the integer defining the percent identity divided by 100 and then subtractmg that product from said total number of ammo acids in SEQ ID NO 2, or n n ≤ x n - ( x n • y)» wherem n n is the number of ammo acid alterations, x n is the total number of ammo acids m SEQ ID NO 2, 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 wherem any non-mteger product of x n and y is rounded down to the nearest integer pnor to subtractmg it from x n - 30 - (2) Polypeptide embodiments further mclude an isolated polypeptide compnsmg a polypeptide havmg at least a 50,60, 70, 80, 85, 90, 95, 97 or 100% identity to a polypeptide reference sequence of SEQ ID NO 2, wherem said polypeptide sequence may be identical to the reference sequence of SEQ ID NO 2 or may mclude up to a certam integer number of ammo acid alterations as compared to the reference sequence, wherem said alterations are selected from the group consistmg of at least one ammo 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, mterspersed either mdividually among the ammo acids m the reference sequence or m one or more contiguous groups within the reference sequence, and wherem said number of ammo acid alterations is determined by multiplying the total number of ammo acids m SEQ ID NO 2 by the mteger definmg the percent identity divided by 100 and then subtracting that product from said total number of ammo acids m SEQ ID NO 2, or n a ≤ x a - ( x a *» y), wherem n a is the number of ammo acid alterations, x a is the total number of ammo acids m 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 wherem any non-mteger product of x a and y is rounded down to the nearest mteger pnor to subtractmg 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 mclude up to a certam mteger number of ammo 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 consistmg of at least one ammo acid deletion, substitution, mcludmg conservative and non- conservative substitution, or insertion, and wherem said alterations may occur at the ammo- or carboxy-terminal positions of the reference polypeptide sequence or anywhere between those terminal positions, mterspersed either mdividually among the a mo acids m the reference sequence or in one or more contiguous groups withm the reference sequence The number of ammo acid alterations for a given % identity is determined by multiplying the total number of ammo acids m SEQ ID NO 2 by the mteger definmg the percent identity divided by 100 and then subtractmg that product from said total number of ammo acids m SEQ ID NO 2, or n a ≤ x a - ( χ a • y)» wherem n a is the number of ammo acid alterations, x a is the total number of ammo acids m 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 - 31 - for the multiplication operator, and wherem any non-mteger product of x a and y is rounded down to the nearest mteger pnor to subtractmg it from x a "Isolated" means altered "by the hand of man" from its natural state, ; e , if it occurs m nature, it has been changed or removed from its onginal 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 mateπals 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 m sard organism, which organism may be living or non-living "Polynucleσtιde(s)" generally refers to any polynbonucleotide or polydeoxπbonucleσtide, which may be unmodified RNA or DNA or modified RNA or DNA "Polynucleotide(s)" mclude, without limitation, smgle- and double-stranded DNA DNA that is a mixture of single- and double- stranded regions or single-, double- and tnple-stranded regions, single- 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 smgle- and double-stranded regions In addition, "polynucleotide" as used herem refers to tπple-stranded regions compπsmg RNA or DNA or both RNA and DNA The strands m sucrrregions 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-hehcal region often is an ohgonucleotide As used herein, the term "polynucleotide(s)" also mcludes DNAs or RNAs as descnbed above that contam one or more modified bases Thus, DNAs or RNAs with backbones modified for stability or for other reasons are "polynucleotide(s)" as that term is intended herem Moreover, DNAs or RNAs compπsmg unusual bases, such as mosme, or modified bases, such as tπtylated 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 metabolically modified forms of polynucleotides, as well as the chemical forms of DNA and RNA characteπstic of viruses and cells, including, for example, simple and complex cells "Polynucleotide(s)" also embraces short polynucleotides often refeπed to as ohgonucleotide(s) "Polypeptide(s)" refers to any peptide or protem compπsing two or more ammo acids jomed to each other by peptide bonds or modified peptide bonds "Polypeptide(s)" refers to both short chains, commonly refeπed to as peptides. okgopeptides and ohgomers and to longer chains generally refeπed to as proteins Polypeptides may contam ammo acids other than the 20 gene encoded ammo acids - 32 - "Polypeptide(s)" mclude those modified either by natural processes, such as processing and other post- translational modifications, but also by chemical modification techmques Such modifications are well descnbed in basic texts and m more detailed monographs, as well as m 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 contam many types of modifications Modifications can occur anywhere m a polypeptide, including the peptide backbone, the ammo acid side-chains, and the ammo or carboxyl termini Modifications mclude, for example, acetylation, acylation, ADP-nbosylation, amidation, covalent attachment of flavin, 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 phosphotidyhnositol, cross-linking, cychzation, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylatiσn, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, lodination, methylation, myπstoylation, 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 - 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 mPOSTTRANSLATIONAL COVALENT MODIFICATION OF PROTEINS, B C Johnson, Ed , Academic Press, New York (1983), Seifter et al , Meth Enzymol 182626-646 (1990) and Rattan et al , Protein Synthesis Posttranslational Modifications and Aging, Ann NY Acad Sci 663 48-62 (1992) Polypeptides may be branched or cyclic, with or without branching Cyclic, branched and branched circular polypeptides may result from post-translational natural processes and may be made by entirely synthetic methods, as well 'Nanant(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 vanant of a polynucleotide differs m nucleotide sequence from another reference polynucleotide Changes in the nucleotide sequence of the vanant 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, fusions 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 - 33 - closely similar overall and, m many regions, identical A vanant and reference polypeptide may differ m ammo acid sequence by one or more substitutions, additions, deletions m any combmation A substituted or inserted ammo acid residue may or may not be one encoded by the genetic code A vanant of a polynucleotide or polypeptide may be a naturally occurring such as an allelic vanant, or it may be a vanant that is not known to occur naturally Non-naturally occurring vanants of polynucleotides and polypeptides may be made by mutagenesis techmques, by direct synthesis, and by other recombmant methods known to skilled artisans EXAMPLES The examples below are earned out using standard techmques, which 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 m Table 1 [SEQ ID NO 1] was obtamed from a library of clones of chromosomal DNA of Streptococcus pneumomae m E coli The sequencmg data from two or more clones containing overlappmg Streptococcus pneumomae DNAs was used to construct the contiguous DNA sequence m SEQ ID NO 1 Libranes may be prepared by routme methods, for example Methods 1 and 2 below Total cellular DNA is isolated from Streptococcus pneumomae 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 accordmg to standard procedures DNA fragments of up to l lkbp m size are rendered blunt by treatment with exonuclease and DNA polvmerase, and EcoRI linkers added Fragments are hgated mto 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 by standard procedures Method 2 Total cellular DNA is partially hydrolyzed with a one or a combmation of restriction enzymes appropπate 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 hgated to the DNA and the fragments then hgated mto the vector 34 Lambda ZapII that have been cut with EcoRJ, the library packaged by standard procedures, and E.co infected with the packaged library. The library is amplified by standard procedures. - 35

Claims: What is claimed is: 1 An isolated polynucleotide compπsmg a polynucleotide havmg at least a 70% identity to a polynucleotide encodmg a polypeptide compπsing the ammo acid sequence of SEQ ID NO 2 2 An isolated polynucleotide compπsmg a polynucleotide having at least a 70% identity to a polynucleotide encoding the same mature polypeptide expressed by the pyrH gene contained m the Streptococcus pneumomae 3 An isolated polynucleotide compπsing a polynucleotide encoding a polypeptide comprising an ammo acid sequence which is at least 70% identical to the ammo acid sequence of SEQ ID NO 2 4 An isolated polynucleotide that is complementary to the polynucleotide of claim 1 5 The polynucleotide of Claim 1 wherem the polynucleotide is DNA or RNA 6 The polynucleotide of Claim 1 compnsmg the nucleic acid sequence set forth m SEQ ID NO l 7 The polynucleotide of Claim 1 compnsmg nucleotide 1 to the stop codon which begins at nucleotide number 736 set forth m SEQ ID NO 1 8 The polynucleotide of Claim 1 which encodes a polypeptide compπsing the ammo acid sequence of SEQ ID NO 2 9 A vector compnsmg the polynucleotide of Claim 1 10 A host cell compπsmg the vector of Claim 9 11 A process for producing a polypeptide compπsmg expressing from the host cell of Claim 10 a polypeptide encoded by said DNA 12 A process for producmg a pyrH polypeptide or fragment compπsmg cultuπng a host of claim 10 under conditions sufficient for the production of said polypeptide or fragment 13 A polypeptide compnsmg an ammo acid sequence which is at least 70% identical to the ammo acid sequence of SEQ ID NO 2 14 A polypeptide compπsmg an ammo acid sequence as set forth in SEQ ID NO 2 15 An antibody against the polypeptide of claim 14 16 An antagonist which inhibits the activity or expression of the polypeptide of claim 14 17 A method for the treatment of an mdividual m need of pyrH polypeptide compπsmg administering to the mdividual a therapeutically effective amount of the polypeptide of claim 14 36 18. A method for the treatment of an individual having need to inhibit pyrH polypeptide comprising: administering to the individual a therapeutically effective amount of the antagonist of Claim 16. 19. A process for diagnosing a disease related to expression or activity of the polypeptide of claim 14 in an individual comprising: (a) determining a nucleic acid sequence encoding said polypeptide, and/or (b) analyzing for the presence or amount of said polypeptide in a sample derived from the individual. 20. A method for identifying compounds which interact with and inhibit or activate an activity of the polypeptide of claim 14 comprising: contacting a composition comprising the polypeptide with the compound to be screened under conditions to permit interaction between the compound and the polypeptide to assess the interaction of a compound, such interaction being associated with a second component capable of providing a detectable signal in response to the interaction of the polypeptide with the compoimd; and determining whether the compound interacts with and activates or inhibits an activity of the polypeptide by detecting the presence or absence of a signal generated from the interaction of the compound with the polypeptide. 21. A method for inducing an immunological response in a mammal which comprises inoculating the mammal with pyrH polypeptide of claim 14, or a fragment or variant thereof, adequate to produce antibody and/or T cell immune response to protect said animal from disease. 22. A method of inducing immunological response in a mammal which comprises delivering a nucleic acid vector to direct expression of pyrH polypeptide of claim 14, or fragment or a variant thereof, for expressing said pyrH polypeptide, or a fragment or a variant thereof in vivo in order to induce an immunological response to produce antibody and/ or T cell immune response to protect said animal from disease. 23. 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 - 37 - one of said sequences compnses the sequence of SEQ ID NO 1, a set of polypeptide sequences wherem at least one of said sequences compnses the sequence of SEQ ID NO 2, a data set representing a polynucleotide sequence compnsmg the sequence of SEQ ID NO 1 , a data set representing a polynucleotide sequence encodmg a polypeptide sequence compnsmg the sequence of SEQ ID NO 2 24 A computer based method for performing homology identification, said method compnsmg the steps of providmg a polynucleotide sequence compπsmg the sequence of SEQ ID NO 1 m a computer readable medium, and comparing said polynucleotide sequence to at least one polynucleotide or polypeptide sequence to identify homology 25 A further embodiment of the mvention provides a computer based method for polynucleotide assembly, said method compnsmg the steps of providmg a first polynucleotide sequence compnsmg the sequence of SEQ ID NO 1 m a computer readable medium, and screenmg for at least one overlappmg region between said first polynucleotide sequence and a second polynucleotide sequence 38 -

Inventors: PETIT CHANTAL M, PETIT, CHANTAL, M.
Applicants: SMITHKLINE BEECHAM CORP, SMITHKLINE BEECHAM CORPORATION
Application year: 1999
Main classification: C07H21
IPC codes: A61K31, A61K38, A61K39, A61K45, A61K48, A61P31, A61P37, C07K14, C07K16, C12N1, C12N9, C12N15, C12P21, G06F17