REPLICATIVE HELICASE dnaB OF STAPHYLOCOCCUS AUREUS

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

Description: REPLICATIVE HELICASE dnaB OF STAPHYLOCOCCUS AUREUS FIELD OF THE INVENTION This invention relates to newly identifiisd polynucleotides and polypeptides. and their production .and uses, as well as their vanants, agonists and antagom.sts, and then: uses In paiHcular. the invention relates to polynucleotides and polypeptides of the Rephcative Heluase family, hereinafter referred to as "dnaB" BACKGROUND OF THE INVENTION It is particularly preferred to employ Staphvlococcal genes and gene products as targets for the development of antibiotics The Staphylococci make up a medically important genera of microbes They are known to produce two types of disease, i volve .and toxigenic Invasive infections are characterized generally by abscess formation effecting both skm surfaces and deep tissues S aureus is the second leading cause of bacteremia in cancer patients Osteomvelitis, septic arώntis, septtc thrombophlebitis -and acute bacteπal endocarditis are also relatively common There are at least three clinical conditions resulting from the toxigenic properties of Staph\ lococci The mamfe.station of these diseases result from the actions of exotoxins as opposed to tissue invasion and bacteremia These conditions include Staphvlococcal food poisoning, scalded skm s\τιdrome .and toxic shock syndrome The frequency of Staphylococcus aureus infections has πsen dramatically in the paΛ few decades This has been attnbuted to the emergence of multiply antibiotic resistant strains and an incrasing population of people with weakened immune systems It is no longer uncommon to isolate Staphylococcus aureus strains which are resistant to some or all of the standard antibiotics This phenomenon has created a demand for both new anti-microbial agents, vaccmes. and diagnostic te.sts for this organism Clearly, there exists a need for factors, such as the dnaB 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 characteirzation of such factors and then- antagonι.sts and agom.sts to find ways to prevent, ameliorate or correct such infection, dysfunction and dise^e Certain of the polypeptides of the invention possess ammo acid sequence homology to a known hekcsses from S pneumomae. E coll. B subtilis. H pylon. Synechoc} stis sp . M tuberculosis. S typhimunum. H influenzae protem (see Gen Bank Accession Nos KOI 174 and P37469) SUMMARY OF THE INVENTION It is an object of the mvention to provide polypeptides that have been identified as dnaB polypeptides by homology between the ammo acid sequence set out m Table 1 [SEQ ID NO 2] and a known ammo acid sequence or sequences of other proteins such as hehcases from S pneumomae. E co . B subtilis. H pylon. Synechocystis sp . M tuberculosis. S typhimunum. H influenzae protem It is a further object of the mvention to provide polynucleotides that encode dnaB polypeptides. particularly polynucleotides that encode the polypeptide herem designated dnaB In a particularly preferred embodiment of the mvention the polynucleotide compnses a region encoding dnaB polypeptides compnsmg a sequence set out m Table 1 [SEQ ID NO 1] which includes a full length gene, or a vanant thereof In another particularly preferred embodiment of the invention there is a dnaB protein from Staphylococcus aureus compnsmg the amino acid sequence of Table 1 [SEQ ID NO 2], or a variant thereof As a further aspect of the mvention there are provided isolated nucleic acid molecules encoding dnaB. particularly Staphylococcus aureus dnaB. including mRNAs. cDN.As. genomic DN-As Further embodiments of the mvention mclude biologically, diagnostically. proph\ lacticalh . clinically or therapeutically useful vanants thereof, and compositions compnsmg the same In accordance with another aspect of the invention, there is provided the use of a polynucleotide of the mvention for therapeutic or prophylactic purposes, in particular genetic immunization Among the particularly preferred embodiments of the mvention are natural!} occurring alle c vanants of dnaB and polypeptides encoded thereby In another aspect of the mvention there are provided polypeptides of Staphylococcus aureus referred to herem as dnaB as well as biologically, diagnostically. prophylacticalh . clinicalh or therapeutically useful vanants thereof, and compositions compnsmg the same Among the particularly preferred embodiments of the mvention are vanants of dnaB polypeptide encoded by naturally occurring alleles of the diraB gene - 2 - In a preferred embodiment of the mvention there are provided methods for producmg the aforementioned dnaB polypeptides In accordance with yet another aspect of the mvention. there are provided inhibitors to such polypeptides. useful as antibactenal agents, including, for example, antibodies In accordance with certain preferred embodiments of the mvention. there are provided products, compositions and methods for assessmg dnaB expression, treating disease, assaying genetic variation, and administering a dnaB polypeptide or polynucleotide to an organism to raise an lmmunological response against a bacten^ especially a Staphylococcus aureus bactena hi accordance with certain preferred embodiments of this and other aspects of the mvention there are provided polynucleotides that hybndize to dnaB polynucleotide sequences, particularly under stringent conditions In certain preferred embodiments of the mvention there are provided antibodies against dnaB polypeptides In other embodiments of the mvention there are provided methods for identifying compounds which bmd to or otherwise mteract with and inhibit or activate an activity of a polypeptide or polynucleotide of the mvention compnsmg contacting a polypeptide or polynucleotide of the mvention with a compound to be screened under conditions to permit bmdmg to or other mteraction between the compound and the polypeptide or polynucleotide to assess the bmdmg to or other mteraction with the compound, such bmdmg or mteraction bemg associated with a second component capable of providmg a detectable signal m response to the bmdmg or mteraction of the pohpeptide or polynucleotide with the compound, and determining whether the compound bmds to or otherwise interacts with and activates or inhibits an activity of the polypeptide or pohnucleotide b\ detectmg the presence or absence of a signal generated from the bmdmg or mteraction of the compound with the polypeptide or polynucleotide In accordance with yet another aspect of the mvention. there are provided dnaB agonists and antagonists, preferably bactenostatic or bactenocu l agonists and antagonists In a further aspect of the mvention there are provided compositions compnsmg a dnaB pohnucleotide or a dnaB polypeptide for administration to a cell or to a multicellular organism In another embodiment of the mvention there is provided a computer readable medium havmg stored thereon a member selected from the group consisting of a pohnucleotide comprising the sequence of SEQ ID NO 1. a polypeptide compnsmg the sequence of SEQ ID NO 2. a set of polynucleotide sequences wherem at least one of said sequences compπses the - 3 sequence of SEQ ID NO 1. a set of polypeptide sequences wherein at least one of said sequences compnses the sequence of SEQ ID NO 2. a data set representing a pohnucleotide sequence compnsmg the sequence of SEQ ID NO 1. a data set representmg a polynucleotide sequence encodmg a polypeptide sequence compnsmg the sequence of SEQ ID NO 2. a polynucleotide compnsmg the sequence of SEQ ID NO 1. a polypeptide compnsmg the sequence of SEQ ID NO 2, a set of polynucleotide sequences wherem at least 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 representmg a polynucleotide sequence compnsmg the sequence of SEQ ID NO 1. a data set representing a polynucleotide sequence encoding a polypeptide sequence comprising the sequence of SEQ ID NO 2 A further embodiment of the invention provides a computer based method for performing homology identification, said method compnsmg the steps of providmg a polynucleotide sequence compnsmg the sequence of SEQ ID NO 1 in a computer readable medium, and comparing said polynucleotide sequence to at least one polynucleotide or pohpeptide sequence to identify homology A further embodiment of the mvention provides a computer based method for performing homology identification, said method comprising the steps of providing a polypeptide sequence compnsmg the sequence of SEQ ID NO 2 in a computer readable medium, and companng said polypeptide sequence to at least one polynucleotide or pohpeptide sequence to identify homology A further embodiment of the invention provides a computer based method for pohnucleotide assembly, said method comprising the steps of providing a first pohnucleotide sequence compnsmg the sequence of SEQ ID NO 1 in a computer readable medium, and screening for at least one overlapping region between said first polynucleotide sequence and a second polynucleotide sequence A further embodiment of the invention provides a computer based method for performing homology identification, said method comprising the steps of providing a pohnucleotide sequence compnsmg the sequence of SEQ ID NO 1 in a computer readable medium, and companng said polynucleotide sequence to at least one pohnucleotide or pohpeptide sequence to identify homology A further embodiment of the invention provides a computer based method for performing homology identification, said method compnsmg the steps of providing a pohpeptide sequence compnsmg the sequence of SEQ ID NO 2 m a computer readable medium, and comparing said polypeptide sequence to at least one pohnucleotide or polypeptide sequence to identify homology A further embodiment of the mvention provides a computer based method for polynucleotide assembly, said method comprising the steps of providing a first polynucleotide sequence compnsmg the sequence of SEQ ID NO 1 in a computer readable medium, and screening for at least one overlappmg region between said first pohnucleotide sequence and a second polynucleotide sequence Vanous changes and modifications within the spint .and scope of the disclosed mvention will become readily apparent to those skilled m the art from readmg the following descnptions and from reading the other parts of the present disclosure DESCRIPTION OF THE INVENTION The mvention relates to dnaB polypeptides and polynucleotides as descnbed m greater detail below In particular, the mvention relates to polypeptides and pohnucleotides of a dnaB of Staphylococcus aureus, which is related by ammo acid sequence homology to hehcases from S pneumoniae. E coh. B subtilis. H pylon. Synechocystis sp . M tuberculosis. S typhimunum, H influenzae polypeptide The mvention relates especially to dnaB havmg the nucleotide and ammo acid sequences set out m Table 1 as SEQ ID NO 1 and SEQ ID NO 2 respective.} TABLE 1 dnaB Polynucleotide and Polypeptide Sequences (A) Sequences from Staphylococcus aureus dnaB polynucleotide sequence [SEQ ID NO 1] 5 ' - ACGAATGTACCTGTTAAATTAGATAAAGAAGTTGAAGGTACAATTCGCGTACACACAGTTG75.ACAATAA AGTTGGATTGA AATAAGAGGTGTAACCATTCATGGATAGAATGTATGAGCAAAATCAAATGCCACATAACAATGAAGCTG AACAGTCTGTC TTAGGTTCAATTATTATAGATCCAGAATTGATTAATACTACTCAGGAAGTGTTGCTTCCTGAGTCATTT TATAGGGGTGC CCATCAACATATTTTCCGTGCAATGATGCACTTAAATGAAGATAATAAAGAAATTGATGTTGTAACATT GATGGATCAAT TATCGACGGAAGGTACGTTGAATGAAGCGGGTGGCCCGCAATATCTTGCAGAGTTATCTACAAATGTAC CAACGACGCGA AATGTTCAGTATTATACTGATATCGTTTCTAAGCATGCATTAAAACGTAGATTGATTCAAACTGCAGAT AGTATTGCCAA TGATGGATATAATGATGAACTTGAACTAGATGCGATTTTAAGTGATGCAGAACGTCGAATTTTAGAGCT ATCATCTTCTC GTGAAAGCGATGGCTTTAAAGACATTCGAGATGTCTTAGGACAAGTATATGAAACAGCTGAAGAGCTTG ATCAAAATAGT GGTCAAACACCAGGTATTCCTACAGGATATCGAGATTTAGACCAAATGACAGCAGGGTTCAACCGAAAT GATTTAATTAT CCTTGCAGCGCGTCCATCTGTAGGTAAGACTGCGTTCGCACTTAATATTGCACAAAAAGTTGCAACGCA TGAAGATATGT ATACAGTTGGTATTTTCTCACTAGAGATGGGTGCTGATCAGTTAGCCACACGTATGATTTGTAGTTCTG GTAATGTTGAC TCAAACCGCTTAAGAACCGGTACTATGACTGAGGAAGATTGGAGTCGTTTTACTATAGCGGTAGGTAAA TTATCACGTAC GAAGATTTTTATTGATGATACACCGGGCATTCGAATTAATGATCTACGTTCTAAATGTCGTCGATTAAA GCAAGAACATG GCTTAGACATGATTGTAATTGACTACTTACAGTTGATTCAAGGTAGTGGTTCACGTGCGTCCGATAACA GACAACAGGAA GTTTCTGAAATCTCTCGTACATTAAAAGCATTAGCTCGTGAATTAGAATGTCCAGTTATCGCGTTGAGT CAGTTATCTCG TGGTGTTGAACAACGACAAGATAAACGTCCAATGATGAGTGATATTCGTGAATCTGGTTCGATTGAGCA AGATGCCGATA TCGTTGCATTCTTATACCGTGATGATTACTATAACCGTGGCGGCGATGAAGATGATGACGATGATAGTG GTTTTGAGCCA CAAACGAATGATGAAAACGGTGAAATTGAAATCATCATTGCTAAGCAACGTAATGGTCCAACAGGCACA GTTAAGTTACA CTTTATGAAACAATATAATAAATTTACAGATATCGATTATGCACATGCTGATATGATGTAAAAAAGTTT TTCCGTACAAT AATCATCTCGATGATAAAATTGTACGGTTTTTATTTCGTTCTGAACGGGTTGATATATGTTAAGTTTGT GTATTTGAAGT G-3 1 (B) Staphylococcus aureus dnaB polypeptide sequence deduced from the pohnucleotide sequence in this table [SEQ ID NO:2]. NH ; - MDRMYEQNQMPHNNEAEQSVLGSIIIDPELINTTQEVLLPESFYRGAHQHIFRAMMHLNEDNKEIDWT LMDQLSTEGTL -6- NEAGGPQYLAELSTNVPTTRNVQYYTDIVSKHALKRRLIQTADSIANDGYNDELELDAILSDAERRILE LSSSRESDGFK DIRDVLGQVYETAEELDQNSGQTPGIPTGYRDLDQMTAGFNR DLIILAARPSVGKTAFALNIAQKVAT HEDMYTVGIFS LEMGADQLATRMICSSGNVDSNRLRTGTMTEEDWSRFTIAVGKLSRTKIFIDDTPGIRINDLRSKCRRL KQEHGLDMIVI DYLQLIQGSGSRASDNRQQEVSEISRTLKALARELECPVIALSQLSRGVEQRQDKRPMMSDIRESGSIE QDADIVAFLYR DDYYNRGGDEDDDDDSGFEPQTNDENGEIEIIIAKQRNGPTGTVKLHFMKQYNKFTDIDYAHADMM.- COOH (C) Polynucleotide sequences comprising Staphylococcus aureus dnaB ORF sequence [SEQ ID NO 3] 5 ' -ATCCCTAGGATATACGAATGTNCCTGTTAAATTAGATAAAGAAGTTGAAGGTACAATTCGCGTACA CACAGTTGANCAATAAAGTTGGATTGAAATAAGAGGTGTAACCATTCATGGATAGAATGTATGAGC AAAATCAANTGCCACATAACAATGAAGCTGAACAGTCTGTCTTAGGTTCANTTATTATAGATCCAGA ATTGATTAATACTACTCAGGAAGTTTNGCTTCCTGAGTCGTTTTATAGGGGTGCCCATCAACATATT TTCCGTGCAATGATGCACTTAAATGAAGATAATAAAGAAATTGATGTTGTAACATTGATGGATCAAT TATCGACGGAAGGTACGTTGAATGAAGCGGGTGGCCCGCAATATCTTGCAGAGTTATCTACAAATGT NCCAACGACGCGAAATGTCCAGTATTATACTGATATCGNCTCTTANGCATGCATTAAANACGTAGGA TTGATTCAAACTGCAGATAGTATTGCCAATGATGGATATANTGATGAACTNGGACTAGATGCGATTT AAGNGATGCAGAACGTCGNATTTTAGAG-3 ' (D) Staphylococcus aureus dnaB polypeptide sequence deduced from the pohnucleotide ORF sequence m this table [SEQ ID NO 4] NH ; - PDIRMXLLNIKKLKVQFAYTQLXNKVGLKEVPFMDRMYEQNQXPHNNEAEQSVLGSXI IDPELINTTQE VXLPES FYRGAHQHI FRAMMHLNEDNKEIDλΛ/TLMDQLSTEGTLNEAGGPQYLAELSTNVPTTRNVQYY TDIXSXACI KXVGLIQTADS IANDGYXDELGLDAIXMQNVXF-COOH Deposited materials A deposit containing a Staphylococcus aureus WCUH 29 strain has been deposited with the National Collections of Industπal .and Marme Bactena Ltd (herem "NCIMB"), 23 St Machar Dnve. Aberdeen AB2 1RY. Scotland on 11 September 1995 and assigned NCIMB Deposit No 40771. and referred to as Staphylococcus aureus WCUH29 on deposit The Staphylococcus aureus strain deposit is referred to herem as "the deposited strain" or as "the DNA of the deposited strain " - 7 - The deposited strain contains the full length dnaB gene The sequence of the polynucleotides contained m the deposited stram. as well as the ammo acid sequence of the polypeptide encoded thereby, are controlling in the event of any conflict with any descnption 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 restnction 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 mav be required to make, use or sell the deposited strain, and compounds denved 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 Staphylococcus aureus WCUH 29 stram contained m the deposited stram Further provided by the mvention are dnaB nucleotide sequences of the DNA m the deposited stram and ammo acid sequences encoded thereby Also provided by the mvention are dnaB polypeptide sequences isolated from the deposited stram and ammo acid sequences denved therefrom Polypeptides The polypeptides of the mvention include a pohpeptide 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 dnaB, 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 soil 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 generalh containing at least 30 ammo acids and more preferably at least 50 ammo acids The mvention also mcludes polypeptides of the formula X-(R 1 ) m -(R 2 )-(R 3 ) n -Y wherem. at the .ammo termmus, X is hydrogen or a metal, and at the carboxvl termmus. Y is hydrogen or a metal. R\ and R3 are any ammo acid residue, m is an integer between 1 and 1000 or zero, n is an integer between 1 and 1000 or zero, and R 2 is an ammo acid sequence of the mvention, particularh an ammo acid sequence selected from Table 1 In the formula above R 2 is onented so that its ammo terminal residue is at the left, bound to R\ 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 vanant polypeptide havmg an ammo acid sequence that entireh is the same as part but not all of the ammo acid sequence of the aforementioned polypeptides As with dnaB polypeptides fragments may be "free-standing." or compnsed within a larger polypeptide of which they form a part or region, most preferably as a smgle continuous region, a smgle larger polypeptide Preferred fragments include, for example, truncation polypeptides havmg a portion of an ammo acid sequence of Table 1 [SEQ ID NO 2]. or of vanants thereof, such as a continuous senes of residues that mcludes the ammo termmus. or a contmuous senes of residues that mcludes the carboxvl termmus Degradation forms of the polypeptides of the mvention m a host cell, particularly a Staphylococcus aureus. are also prefened Further preferred are fragments characterized by structural or functional attributes such as fragments that compπse alpha-helix and alpha-helix forming regions, beta-sheet and beta-sheet-formmg regions, turn and turn-forming regions, coil and coil-formmg regions, hydrophilic regions, hydrophobic regions, alpha amphipathic regions, beta amphipathic regions, flexible regions, surface-forming regions, substrate bmdmg region, and high antigemc mdex regions Also preferred are biologically active fragments which are those fragments that mediate activities of dnaB. including those with a similar activity or an improved activity, or with a decreased undesirable activity Also mcluded are those fragments that are antigemc or mimunogemc m an animal, especially m a human Particularly prefened are fragments compnsmg receptors or domains of enzymes that confer a function essential for viability of Staphylococcus aureus or the ability to initiate, or maintain cause disease m an individual, particularly a human Vanants that are fragments of the polypeptides of the mvention may be employed for producmg the correspondmg full-length polypeptide by peptide synthesis, therefore, these vanants may be employed as intermediates for producmg the full-length polypeptides of the mvention In addition to the standard single and triple letter representations for amino acids, the term "X" or "Xaa" may also be used m descnbmg certain polypeptides of the invention "X" and "Xaa" mean that any of the twenty naturally occurring ammo acids may appear at such a designated position m the polypeptide sequence Polynucleotides - 9 - Another aspect of the mvention relates to isolated polynucleotides. including the full length gene, that encode the dnaB polypeptide havmg a deduced ammo acid sequence of Table 1 [SEQ ID NO 2] and polynucleotides closely related thereto and vanants thereof Usmg the information provided herein, such as a polynucleotide sequence set out m Table 1 [SEQ ED NO 1], a polynucleotide of the mvention encoding dnaB polypeptide may be obtained usmg stand^d cloning and screening methods, such as those for cloning and sequencmg chromosomal DNA fragments from bacteπa usmg Staphylococcus aureus WCUH 29 cells as starting matenal. followed by obtaining a full length clone For example, to obtam a polynucleotide sequence of the mvention. such as a sequence given in Table 1 [SEQ ID NO 1], typically a library of clones of chromosomal DNA of Staphylococcus aureus WCUH 29 in E coll or some other suitable host is probed with a radiolabeled ohgonucleotide. preferably a 17-mer or longer, denved from a partial sequence Clones carrying DNA identical to that of the probe can then be distinguished usmg stringent conditions By sequencing the individual clones thus identified with sequencmg primers designed from the onginal sequence it is then possible to extend the sequence m both directions to determine the full gene sequence Convemently. such sequencing is performed usmg denatured double stranded DNA prepared from a plasmid clone Suitable techniques are descnbed by Maniatis, T , Fntsch, E F and Sambrook et al , MOLECULAR CLONING. A LABORATORY MANUAL. 2nd Ed . Cold Spring Harbor Laboratory Press. Cold Spring Harbor. New York (1989) (see in particular Screening By Hybndization 1 90 and Sequencing Denatured Double-Stranded DNA Templates 13 70) Illustrative of the mvention. the pohnucleotide set out m Table 1 [SEQ ID NO 1 ] was discovered m a DNA hbrar} denved from Staphylococcus aureus WCUH 29 The DNA sequence set out m Table 1 [SEQ ID NO 1] contains an open readmg frame encoding 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 ID NO 1. between nucleotide number 101 and the stop codon which begins at nucleotide number 1499 of SEQ ID NO 1. encodes the polypeptide of SEQ ID NO 2 The dnaB protem of the mvention is structurally related to other proteins of the Replicative Hehcase family 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 - 10 - polypeptide or a fragment in readmg frame with other codmg sequence, such as those encoding 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 transcnbed. non-translated sequences, termination signals, nbosome bmdmg sites, sequences that stabilize mRNA. mtrons. polyadenylation signals, and additional codmg sequence which encode additional ammo acids For example, a marker sequence that facilitates purification of the fused polypeptide can be encoded In certain embodiments of the mvention, the marker sequence is a hexa-histidine peptide. as provided m the pQE vector (Qiagen. Inc ) and descnbed in Gentz et al , Proc Natl Acad Sci USA 86 821-824 (1989), or an HA tag (Wilson et al . Cell 37 161 (1984) Polynucleotides of the mvention also mclude. but are not limited to. polynucleotides compnsmg a structural gene and its naturally associated sequences that control gene expression A preferred embodiment of the mvention is a polynucleotide of compnsmg nucleotide 101 to the nucleotide immediately upstream of or including nucleotide 1499 set forth m SEQ ED NO 1 of Table 1. both of which encode the dnaB 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 R j and R3 is independently any nucleic acid residue, m is an integer between 1 and 3000 or zero , n is an integer between 1 and 3000 or zero, and R 2 is a nucleic acid sequence of the invention, particularly a nucleic acid sequence selected from Table 1 In the polynucleotide formula above R 2 is oriented so that its 5' end residue is at the left, bound to R\ and its 3' end residue is at the right, 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 wherein the formula shows a first strand to which the second strand is complementary In another prefened embodiment m and/or n is an integer between 1 and 1000. It is most prefened that the polynucleotides of the inventions are denved from Staphylococcus aureus, however, they may preferably be obtained from organisms of the same - 1 1 - taxonomic genus They mav also be obtamed. 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 encodmg a polypeptide of the mvention. particularly a bacteπal polypeptide and more particularly a polypeptide of the Staphylococcus aureus dnaB havmg an ammo acid sequence set out m Table 1 [SEQ ID NO 2] The term also encompasses polynucleotides that mclude a smgle continuous region or discontinuous regions encodmg the polypeptide (for example, interrupted by mtegrated phage or an insertion sequence or editing) together with additional regions, that also may contain codmg and/or non-coding sequences The mvention further relates to vanants of the polynucleotides descnbed herem that encode for vanants of the polypeptide havmg a deduced ammo acid sequence of Table 1 [SEQ ID NO 2] Vanants that are fragments of the polynucleotides of the mvention may be used to synthesize full- length polynucleotides of the mvention Further particularly prefened embodiments are polynucleotides encodmg dnaB vanants. that have the ammo acid sequence of dnaB 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, m any combination Especially preferred among these are silent substitutions, additions and deletions, that do not alter the properties and activities of dnaB Further prefened embodiments of the mvention are polynucleotides that are at least 70% identical over their entire length to a polynucleotide encodmg dnaB 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 prefened are polynucleotides that compnse a region that is at least 80% identical over its entire length to a polynucleotide encodmg dnaB pohpeptide and pohnucleotides complementary thereto In this regard, polynucleotides at least 90% identical over their entire length to the same are particularly prefened. and among these particularh prefened pohnucleotides. those with at least 95% are especially prefened Furthermore, those with at least 97% are highly prefened among those with at least 95%. and among these those with at least 98% and at least 99% are particularly highly prefened. with at le^ 99% bemg the more prefened Prefened 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 1] The mvention further relates to polynucleotides that hybπdize to the herem above-descnbed sequences In this regard, the mvention especially relates to polynucleotides that h}bndιze under - 12 - .stringent conditions to the herem above-descnbed polynucleotides As herem used, the terms "stringent conditions" and "stringent hybndization conditions" mean h\bndιzation will occur only if there is at least 95% and preferably at least 97% identity between the sequences An example of stringent hybndization conditions is overnight incubation at 42°C in a solution compnsmg 50% formamide. 5x SSC (150mM NaCl. 15mM tnsodium citrate). 50 mM sodium phosphate (pH7 6). 5x Denhardt's solution. 10% dextran sulfate. and 20 micrograms/ml denatured, sheared salmon sperm DNA, followed by washmg the hybridization support in 0 lx SSC at about 65 °C Hybndization and wash conditions are well known and exemplified in Sambrook. et αl . Molecular Cloning A Laboratory Manual. Second Edition. Cold Spring Harbor. N Y . (1 89), particularly Chapter 11 therem The mvention also provides a polynucleotide consistmg essentially of a polynucleotide sequence obtainable by screenmg an appropnate library containing the complete gene for a polynucleotide sequence set forth in SEQ ID NO 1 under stringent hybridization conditions with a probe having the sequence of said polynucleotide sequence set forth in SEQ ID NO 1 or a fragment thereof, and isolating said DNA sequence Fragments useful for obtaimng such a polynucleotide mclude. for example, probes and pnmers descnbed elsewhere herem As discussed additionally herem regarding polynucleotide assays of the mvention, for instance, polynucleotides of the mvention as discussed above, may be used as a hybndization probe for RNA. cDNA and genomic DNA to isolate full-length cDNAs and genomic clones encodmg dnaB and to isolate cDNA and genomic clones of other genes that have a high sequence identity to the dnaB gene Such probes generally will compnse at least 15 bases Preferably, such probes will have at least 30 bases and may have at least 50 bases Particularly prefened probes will have at least 30 bases and will have 50 bases or less For example, the codmg region of the dnaB gene may be isolated by screenmg usmg a DNA sequence provided m Table 1 [SEQ ID NO 1] to synthesize an ohgonucleotide probe A labeled ohgonucleotide havmg a sequence complementary to that of a gene of the mvention is then used to screen a library of cDNA, genomic DNA or RNA to determine which members of the library the probe hybndizes 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 relatmg to polynucleotide assa}s Polynucleotides of the invention that are ohgonucleotides denved from the sequences of Table 1 [SEQ ID NOS 1 or 2] may be used in the processes herein as described, but preferabK - 13 - for PCR. to determine whether or not the polynucleotides identified herein in whole or in part are transcribed m bactena m infected tissue It is recognized that such sequences will also have utility in diagnosis of the stage of mfection 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-termmal ammo acids, or ammo acids mtenor to the mature polypeptide (when the mature form has more than one polypeptide chain, for instance) Such sequences may play a role m processmg of a protem from precursor to a mature form, may allow protem transport, may lengthen or shorten protem half-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 mav be an inactive form of the polypeptide When prosequences are removed such inactive precursors generally are activated Some or all of the prosequences may be removed before activation Generally, such precursors are called proproteins In addition to the standard A, G. C. T U representations for nucleic acid bases, the term "N" may also be used m descπbmg certain polynucleotides of the invention "N" means that any of the four DNA or RNA bases may appear at such a designated position in the DNA or RNA sequence, except it is preferred that N is not a base that when taken in combmation with adjacent nucleotide positions, when read in the correct reading frame, would have the effect of generatmg a premature termination codon m such reading frame In sum. a polynucleotide of the mvention may encode a mature protem. a mature protem plus a leader sequence (which may be referred to as a preprotem), a precursor of a mature protem havmg one or more prosequences that are not the leader sequences of a preprotem. or a preproprotein, which is a precursor to a proprotem. havmg a leader sequence and one or more prosequences, which generally are removed dunng processmg steps that produce acti e and mature forms of the polypeptide The mvention further compnses an isolated polynucleotide compnsmg a pohnucleotide having at least a 70% identity to a polynucleotide encodmg a polypeptide compnsmg the ammo acid sequence of SEQ ID NO 4 The mvention further compnses an isolated polynucleotide compnsmg a pohnucleotide havmg at least a 70% identity to the polynucleotide sequence of SEQ ID NO 3 Vectors, host cells, expression The mvention also relates to vectors that compnse a polynucleotide or polynucleotides of the mvention. host cells that are genetically engmeered with vectors of the mvention and the production - 14 - of polypeptides of the mvention by recombinant techniques Cell-free translation systems can also be employed to produce such proteins usmg RNAs denved from the DNA constructs of the mvention For recombinant production, host cells can be genetically engineered to incorporate expression systems or portions thereof or polynucleotides of the mvention Introduction of a pohnucleotide mto the host cell can be effected by methods descnbed m many standard laborator} manuals, such as Davis et al. BASIC METHODS IN MOLECULAR BIOLOGY. (1986) and Sambrook et al . MOLECULAR CLONING A LABORATORY MANUAL, 2nd Ed . Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N Y (1989), such as, calcium phosphate transfection, DEAE-dextran mediated transfection, transvection, micromjection. cationic hpid- mediated transfection. electroporatio transduction. scrape loadmg. balhstic mtroduction and infection Representative examples of appropnate hosts mclude bactenal cells, such as .streptococci, staphylococci. enterococci E cob. streptomyces and Bacillus subtilis cells, fungal cells, such as } east 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-denved vectors. e g . vectors denved from bactenal plasmids. from bactenophage. from transposons. from yeast episomes. from insertion elements, from yeajst chromosomal elements, from viruses such as baculσv ruses. papova viruses, such as SV40. vaccinia viruses, adeno\τruses. fowl pox viruses, pseudorabies viruses and retroviruses. and vectors denved from combinations thereof, such as those denved from plasmid and bactenophage genetic elements, such as cosmids and phagemids The expression system constructs may contain control regions that regulate as well as engender expression Generally, any system or vector suitable to mamtain. propagate or express polynucleotides and/or to express a polypeptide m a host may be used for expression m this regard The appropnate DNA sequence may be inserted mto the expression system by any of a vanety of well-known and routme techniques, 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 penplasmic space or mto the extracellular environment, appropnate secretion signals may be incorporated mto the expressed polypeptide These signals may be endogenous to the pohpeptide or they may be heterologous signals - 15 - Polypeptides of the mvention can be recovered and purified from recombinant cell cultures by well-known methods including ammomum sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography. phosphocellulose chromatography. hydrophobic mteraction chromatography. affinity chromatography. hydroxylapatite chromatograph} and lectin chromatography Most preferably, high performance liquid chromatography is employed for purification Well known techniques for refolding protem may be employed to regenerate active conformation when the polypeptide is denatured dunng isolation and or purification Diagnostic, Prognostic, Serotyping and Mutation Assays This mvention is also related to the use of the dnaB polynucleotides of the m ention for use as diagnostic reagents Detection of dnaB m a eukarvote. particularly a mammal, and especially a human, w ll provide a diagnostic method for diagnosis of a disease Eukaryotes (herem also "ιndιvιdual(s)"), particularly mammals, and especially humans, particularly those infected or suspected to be infected with an organism compnsmg the dnaB gene may be detected at the nucleic acid level by a vanety of techniques Nucleic acids for diagnosis may be obtained from an infected individual's cells and tissues, such as bone, blood, muscle, cartilage, and skm Genomic DNA may be used directh for detection or may be amplified enzymatically by usmg PCR or other amplification technique pnor to analysis RNA. cDNA and genomic DNA may also be used m the same ways Usmg amplification, charactenzation of the species and stram of prokarvote present m an individual, may be made by an analysis of the genotype of the prokarvote gene Deletions and insertions can be detected by a change m size of the amplified product m companson to the genotype of a reference sequence Pomt mutations can be identified by hybndizmg amplified DNA to labeled dnaB polynucleotide sequences Perfectly matched sequences can be distinguished from mismatched duplexes by RNase digestion or by differences m meltmg temperatures DNA sequence differences may also be detected by alterations m the electrophoretic mobility of the DNA fragments m gels, with or without denaturmg agents, or by direct DNA 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 S 1 protection or a chemical cleavage method See. e g , Cotton et al . Proc Natl Acad Sci , USA, 85 4397-4401 (1985) Cells carrying mutations or polymorphisms (allehc vanations) m the gene of the mvention may also be detected at the DNA or RNA level by a vanety of techniques, to allow for serotyping. for example For example. RT-PCR can be used to detect mutations m the RNA It is particularh prefened to used RT-PCR m conjunction with automated detection systems, such as. for example. - 16 - GeneScan RNA. cDNA or genomic DNA may also be used for the same purpose. PCR or RT- PCR As an example. PCR pπmers complementary to a nucleic acid encodmg dnaB can be used to identif} and anah ze mutations Examples of representative primers are shown below m Table 2 Table 2 Primers for amplification of dnaB polynucleotides SEQ ID NO PRIMER SEQUENCE 5 5 ' -AAATTAGATAAAGAAGTTGAAGGT-3 ' 6 5 ' -CGAGATGATTATTGTACGGAAAAA-3 ' The mvention also mcludes primers of the formula X-(R 1 ) 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, Rj and R3 is any nucleic acid residue, m is an mteger between 1 and 20 or zero . n is an mteger between 1 and 20 or zero, and R is a primer sequence of the invention. particul.arly a primer sequence selected from Table 2 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 nght. 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 prefened embodiment m and/or n is an mteger betwi n 1 and 10. The mvention further provides these primers with 1. 2. 3 or 4 nucleotides removed from the 5' and/or the 3' end These primers may be used for. among other things, amplifying dnaB DNA isolated from a sample denved from an mdividual The primers may be used to amplify the gene isolated from an infected mdividual such that the gene may then be subject to vanous techniques for elucidation of the DNA sequence In this way. mutations m the DNA sequence mav be detected and used to diagnose infection and to serotype and/or classify the infectious agent The mvention further provides a process for diagnosing, disease, preferabh bacterial infections, more preferably infections by Staphylococcus aureus. compnsmg determining from a sample denved from an mdividual a increased level of expression of polynucleotide having a sequence of Table 1 [SEQ ID NO 1] Increased or decreased expression of dnaB polvnucleotide can be measured using any on of the methods well known in the art for the - 17 - quantitation of polynucleotides. such as. for example, amplification. PCR. RT-PCR. RNase protection. Northern blotting and other hybridization methods In addition, a dιagno.stιc assay m accordance with the mvention for detecting over- expression of dnaB protem compared to normal control tissue samples mav be used to detect the presence of an infection, for example Assay techniques that can be used to determine levels of a dnaB protein, m a sample denved from a host are well-known to those of skill m the art Such assa\ methods mclude radioimmunoassays. 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 hybndize with, a particular location on an mdividual microbial chromosome, particularly a Staphylococcus aureus chromosome The mapping of relevant sequences to a chromosome according to the present mvention is an important first step m conelatmg those sequences with gene associated with microbial pathogenicity and disease, or to chromosomal regions cntical 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 conelated with genetic map data Such data are found m. for example, microbial genomic sequences available on the World Wide Web The relationship between genes and microbial pathogenicity. disease, or to genome regions cntical to the growth, survival and/or ecological mche that have been mapped to the same chromosomal region are then identified usmg methods to define a genetic relationship between the gene and another gene or phenotype. such as b\ linkage analysis (coinhentance of physically adjacent genes) The differences in 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 certain 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 pathogemcit} . growth charactenstics. survival charactenstics and or ecological mche characteπstics Differential Expression The polynucleotides and polynucleotides of the mvention ma\ be used as reagents for differential screenmg methods There are many differential screenmg and differential dιspla\ methods known m the art m which the polynucleotides and polypeptides of the mvention may be used For example, the differential display technique is described by Chuang et al . J Bactenol 175 2026-2036 (1993) This method identifies those genes which are expressed m - 18 - an organism b} identifying mRNA present using randomly-primed RT-PCR B\ comparmg pre-infection and post infection profiles, genes up and down regulated dunng infection can be identified and the RT-PCR product sequenced and matched to ORF 'unknowns' In Vivo Expression Technology (IVET) is descnbed by Camilh et αl Proc Nαt'l Acαd Sci USA 91 2634-2638 (1994) IVET identifies genes up-regulated dunng 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 in a plasmid vector This construct is introduced into the target organism which carnes an antibiotic resistance gene flanked by resolvase sites Growth in the presence of the antibiotic removes from the population those fragments cloned into the plasmid vector capable of supporting transcnption of the recombmase gene and therefore have caused loss of antibiotic resistance The resistant pool is introduced into a host and at various times after infection bacteria may be recovered and assessed for the presence of antibiotic resistance The chromosomal fragment earned by each antibiotic sensitive bactenum should carry a promoter or portion of a gene normally upregulated dunng infection Sequencing upstream of the recombmase gene allows identification of the up regulated gene RT-PCR may also be used to analyze gene expression patterns For RT PCR using the polynucleotides of the invention, messenger RNA is isolated from bacterial infected tissue, e g . 48 hour munne lung infections, and the amount of each mRNA species assessed b\ reverse transcnption of the RNA sample primed with random hexanucleotides followed b} 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 bactenal genes which are transcnbed in the infected tissue Anahsis of gene transcnption can be earned out at different times of infection to gain a detailed knowledge of gene regulation in bactenal pathogenesis allowing for a clearer understanding of which gene products represent targets for screens for antibactenals Because of the gene specific nature of the PCR pnmers employed it should be understood that the bacterial mRNA preparation need not be free of mammalian RNA This allows the investigator to carry out a simple and quick RNA preparation from infected tissue to obtain bactenal mRNA species which are very short lived in the bactenum (in the order of 2 minute halflives) Optimally the bactenal mRNA is prepared from infected munne lung tissue bv mechanical disruption m the presence of TRIzole - 19 - (GIBCO-BRL) for very short penods of time, subsequent processing according 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 Staphylococcus aureus 16S nbosomal RNA as detected by probing Northerns with a suitably labelled sequence specific ohgonucleotide probe Typically a 5' dye labelled pnmer is used m each PCR pnmer pair in a PCR reaction which is terminated optimally between 8 and 25 cycles The PCR products are separated on 6% polyacrylamide gels with detection and quantification usmg GeneScanner (manufactured by .ABI) Each of these techniques may have advantages or disadvantage dependmg on the particular application The skilled artisan would choose the approach that is the most relevant w ith the particular end use in mind Antibodies The polypeptides of the mvention or vanants thereof, or cells expressmg them can be used as an immunogen to produce antibodies immunospecific for such polypeptides "Antibodies" as used herem mcludes monoclonal and polyclonal antibodies, chimenc. smgle chain, simianized antibodies and humanized antibodies, as well as Fab fragments, including the products of an Fab lmmunolglobulm expression library Antibodies generated against the polypeptides of the mvention can be obtained b} administering the polypeptides or epitope-beanng fragments, analogues or cells to an animal. preferably a nonhuman, usmg routme protocols For preparation of monoclonal antibodies, am technique known m the art that provides antibodies produced by contmuous cell lme cultures can be used Examples mclude vanous techniques, such as those m Kohler. G and Milstem. C . Nature 256 495-497 (1975), Kozbor et al , Immunology Today 4 72 (1983). Cole et al . pg 77-96 m MONOCLONAL ANTIBODIES AND CANCER THERAPY. Alan R Liss. Inc (1985) Techniques for the production of smgle chain antibodies (U S Patent No 4.946 778) can be adapted to produce smgle 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 antibod genes with bmdmg activities towards the polypeptide either from repertoires of PCR amplified v-genes of hmphocytes from humans screened for possessmg anti-dnaB or from naive hbranes (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 improved bv chain shuffling (Clackson. T et al . (1991) Nature 352. 624-628) - 20 - If two antigen bmdmg domams are present each domain may be directed agamst a different epitope - termed 'bispecific' antibodies The above-descnbed antibodies may be employed to isolate or to identify clones expressmg the polypeptides to punfy the polypeptides by affinity chromatography Thus, among others, antibodies against dnaB-polypeptide may be employed to treat infections, particularly bactenal infections Polypeptide variants include antigenicall}. epitopically or lmmunologically equivalent vanants that form a particular aspect of this mvention The term "antigenically equivalent deπvative" as used herein encompasses a polypeptide or its equivalent which will be specifically recogmzed by certain antibodies which, when raised to the protein or polypeptide accordmg to the invention, interfere with the immediate physical interaction between pathogen and mammalian host The term "lmmunologically equivalent denvative" as used herein encompasses a peptide or its equivalent which when used m a suitable formulation to raise antibodies in a vertebrate, the antibodies act to interfere with the immediate physical interaction between pathogen and mammalian host The polypeptide, such as an antigenically or lmmunologically equivalent denvative or a fusion protein thereof is used as an antigen to immunize a mouse or other animal such as a rat or chicken The fusion protein may provide stability to the polypeptide The antigen may be associated, for example by conjugation, with an lmmunogenic earner protein for example bovme serum albumin (BSA) or keyhole limpet haemocyanm (KLH) Altemativeh a multiple antigemc peptide comprising multiple copies of the protem or pohpeptide. or an antigenically or lmmunologically equivalent polypeptide thereof may be sufficiently antigemc to improve lmmunogenicity so as to obviate the use of a earner Preferably, the antibody or variant thereof is modified to make it less lmmunogenic in the individual For example, if the individual is human the antibody may most preferably be "humanized", where the comphmentaπty determining regιon(s) of the hybndoma-deπved antibody has been transplanted into a human monoclonal antibody . for example as descnbed 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 in genetic immunization will preferably employ a suitable delivery method such as direct injection of plasmid DNA into muscles (Wolff et al . Hum Mol Genet 1992. 1 363. Manthorpe et al . Hum Gene Ther 1963 4. 419). deliver} of DNA complexed with specific protein carriers (Wu et al . J Biol Chem 1989 264.16985). - 21 - coprecipitation of DNA with calcium phosphate (Benvemsty & Reshef. PNAS USA. 1986 83.9551). encapsulation of DNA in various forms of hposomes (Kaneda et al . Science 1989 243.375). particle bombardment (Tang et al . Nature 1992. 356 152. Eisenbraun et al DNA Cell Biol 1993. 12 791) and in vivo infection using cloned retroviral vectors (Seeger et al . PNAS USA 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 ligands m. for example, cells, cell-free preparations, chemical hbranes. and natural product mixtures These substrates and ligands may be natural substrates and ligands or may be structural or functional mimetics See. e g . Coligan et al , Current Protocols in Immunology 1(2) Chapter s (1991) The mvention also provides a method of screenmg compounds to identify those which enhance (agonist) or block (antagonist) the action of dnaB polypeptides or pohnucleotides. particularly those compounds that are bactenostatic and/or bactenocidal The method of screenmg ma}- mvolve high-throughput techniques For example, to screen for agonists or antagonι.sts. a s}nthetιc reaction mix. a cellular compartment, such as a membrane, cell envelope or cell wall, or a preparation of any thereof, compnsmg diraB polypeptide and a labeled substrate or ligand of such pohpeptide is mcubated m the absence or the presence of a candidate molecule that may be a dnaB agonist or antagonist The ability of the candidate molecule to agonize or antagonize the dnaB pohpeptide is reflected in decreased bmdmg of the labeled hgand or decreased production of product from such substrate Molecules that bmd gratuitously. i e . without mducmg the effects of dnaB pohpeptide are most likely to be good antagonists 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 s} stems that may be useful m this regard mclude but are not limited to colonmetnc labeled substrate converted mto product, a reporter gene that is responsive to changes dnaB polynucleotide or pohpeptide activit} . and bmdmg assays known m the art Another example of an assay for dnaB antagonists is a competitive assay that combmes dnaB and a potential antagonist with dnaB-bmdmg molecules, recombinant dnaB bmdmg molecules. natural substrates or ligands. or substrate or ligand mimetics, under appropnate conditions for a competitive inhibition assay The dnaB molecule can be labeled, such as by radioactivity or a colonmetnc compound, such that the number of dnaB molecules bound to a bmdmg molecule or 22 - converted to product can be determined accurately to assess the effectiveness of the potential antagonist Potential antagonists mclude small organic molecules, peptides. polypeptides and antibodies that bmd to a polynucleotide or polypeptide of the mvention and thereby inhibit or extinguish its activity Potential antagonists also may be small organic molecules, a peptide. a polypeptide such as a closely related protem or antibody that bmds the same sites on a bmdmg molecule, such as a bmdmg molecule, without mducmg dnaB-induced activities, thereby preventmg the action of dnaB by excluding dnaB from bmdmg Potential antagonists mclude a small molecule that b ds to and occupies the bmdmg site of the polypeptide thereby preventmg bmdmg to cellular bmdmg molecules, such that normal biological activity is prevented Examples of small molecules mclude but are not limited to small organic molecules, peptides or peptide- ke molecules Other potential antagonists mclude antisense molecules (see Okano. J Neurochem 56 560 (1991), OLIGODEOXYNUCLEOTIDES AS ANTISENSE INHIBITORS OF GENE EXPRESSION, CRC Press. Boca Raton. FL (1988), for a descnption of these molecules) Prefened potential antagonists mclude compounds related to and vanants of dnaB Each of the DNA sequences provided herem may be used in the discovery and development of antibactenal compounds The encoded protem. upon expression, can be used as a target for the screening of antibactenal drugs Additionally, the DNA sequences encoding the ammo terminal regions of the encoded protein or Shme-Delgarno or other translation facilitating sequences of the respective mRNA can be used to construct antisense sequences to control the expression of the codmg sequence of interest The invention also provides the use of the pohpeptide. pohnucleotide or inhibitor of the invention to interfere with the initial physical interaction between a pathogen and mammalian host responsible for sequelae of infection In particular the molecules of the invention may be used in the prevention of adhesion of bacteria, in particular gram positive bacteria, to mammalian extracellular matnx proteins on in-dwelling devices or to extracellular matrix proteins in wounds, to block dnaB protein-mediated mammalian cell invasion by. for example, initiating phosphorylation of mammalian tyrosine kmases (Rosenshine et αl . Infect Immun 60 2211 (1992). to block bactenal adhesion between mammalian extracellular matnx proteins and bacterial dnaB proteins that mediate tissue damage and. to block the normal progression of pathogenesis in infections initiated other than by the implantation of in-dwelling devices or by other surgical techniques - 23 - The antagonists and agonists of the mvention may be employed, for instance, to inhibit and treat diseases Helwobacter pylori (herein H pylori) bacteria infect the stomachs of over one-third of the world's population causmg stomach cancer, ulcers, and gastntis (International Agency for Research on Cancer (1994) Schistosomes. Liver Flukes and Ηehcobacter Pylori (International Agency for Research on Cancer. Lyon. France, http //www uicc ch/ecp/ecp2904 htm) Moreover, the international Agency for Research on Cancer recently recognized a cause-and- effect relationship between H pylori and gastnc adenocarcinoma. classifying the bactenum as a Group I (definite) carcinogen Prefened antimicrobial compounds of the invention (agomsts and antagonists of dnaB) found using screens provided by the invention, particularly broad- spectrum antibiotics, should be useful m the treatment of H pylori infection Such treatment should decrease the advent of H y /on -induced cancers, such as gastrointestinal carcinoma Such treatment should also cure gastnc ulcers and gastntis Vaccines Another aspect of the invention relates to a method for inducing an immunological response in an individual, particularly a mammal which compnses inoculating the mdividual with dnaB. 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 particularh Staphylococcus aureus infection Also provided are methods whereby such immunological response slows bacterial replication Yet another aspect of the invention relates to a method of inducing immunological response in an individual which comprises delivering to such individual a nucleic acid vector to direct expression of dnaB. or a fragment or a variant thereof, for expressing αnaB. or a fragment or a vanant thereof in vivo m order to induce an immunological response, such as. to produce antibody and/ or T cell immune response. including, for example, cytokme-producing T cells or cytotoxic T cells, to protect said individual from disease, whether that disease is already established within the individual or not One w ay of administering the gene is by accelerating it into the desired cells as a coating 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 invention relates to an immunological composition which, when introduced into an individual capable or having induced withm it an immunological response, induces an immunological response m such individual to a dnaB or protem coded therefrom, w herein the composition comprises a recombinant dnaB or protem coded therefrom comprising - 24 - DNA which codes for and expresses an antigen of said dnaB 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 ansmg from CTL or CD4+ T cells A dnaB polypeptide or a fragment thereof may be fused with co-protein which may not by itself produce antibodies, but is capable of stabilizing the first protem and producing a fused protem which will have lmmunogenic and protective properties Thus fused recombinant protem. preferably further comprises an antigemc co-protem. such as hpoprotein D from Hemophilus influenzae. Glutathione-S-transferase (GST) or beta-galactosidase. relatively large co-protems which solubihze the protein and facilitate production and punfication thereof Moreover, the co-protem may act as an adjuvant in the sense of providing a generalized stimulation of the immune system The co-protein may be attached to either the ammo or carboxy termmus of the first protein Provided by this invention are compositions, particularly vaccine compositions, and methods compnsmg the polypeptides or polynucleotides of the mvention and lmmunostimulatory DNA sequences, such as those described in Sato. Y et al Science 273 352 (1996) Also, provided by this invention are methods usmg the described polynucleotide or particular fragments thereof which have been shown to encode non-vanable regions of bacterial cell surface proteins in DNA constructs used in such genetic immunization experiments in animal models of infection with Staphylococcus aureus will be particularh 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 successfulh resistmg or clearing infection for the development of prophylactic agents or therapeutic treatments of bactenal infection, particularly Staphylococcus aureus infection, in mammals, particularh humans The pohpeptide may be used as an antigen for vaccination of a host to produce specific antibodies which protect against invasion of bacteria, for example b} blocking adherence of bacteria to damaged tissue Examples of tissue damage include wounds in skin or connective tissue caused, e g , by mechanical, chemical or thermal damage or by implantation of indwelling devices, or wounds in the mucous membranes, such as the mouth, mammarv glands, urethra or vagina 25 - The mvention also mcludes a vacc e formulation which comprises an lmmunogenic recombinant protem of the mvention together with a suitable carrier Since the protem may be broken down in the stomach, it is preferably administered parenterally. including, for example, admmistration that is subcutaneous, intramuscular, intravenous, or mtradermal Formulations suitable for parenteral admmistration include aqueous and non-aqueous sterile injection solutions which may contain anti-oxidants. buffers, bactenostats and solutes which render the formulation insotomc with the bodily fluid, preferably the blood, of the mdividual. and aqueous and non-aqueous stenle suspensions which may include suspendmg agents or thickening agents The formulations may be presented in unit-dose or multi-dose containers, for example. sealed ampules and vials and may be stored in a freeze-dned condition requiring only the addition of the sterile liquid earner immediately prior to use The vaccine formulation may also include adjuvant systems for enhancing the immunogenicity of the formulation, such as oil-in water systems and other systems known in the art The dosage will depend on the specific activity of the vaccine and can be readily determined by routme experimentation While the invention has been described with reference to certain dnaB protem. it is to be understood that this covers fragments of the naturally occurring protein and similar proteins with additions, deletions or substitutions which do not substantial!} affect the lmmunogenic properties of the recombinant protein Compositions, lots and administration The mvention also relates to compositions compnsmg the polynucleotide or the polypeptides discussed above or their agonists or antagonists The polypeptides of the mvention may be employed m combination with a non-sterile or stenle earner or earners for use with cells, tissues or organisms, such as a pharmaceutical earner suitable for admmistration to a subject Such compositions compnse. for instance, a media additive or a therapeutically effective amount of a pohpeptide of the mvention and a pharmaceutically acceptable earner or excipient Such earners may mclude. but are not limited to. sa ne, buffered saline, dextrose, water, glycerol. ethanol and combinations thereof The formulation should suit the mode of admmistration 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 26 - The pharmaceutical compositions may be administered m any effective, convenient manner including, for instance, administration by topical, oral. anal, vaginal, mtravenous. mtrapentoneal. intramuscular, subcutaneous, intranasal or mtradermal routes among others In therapy or as a prophylactic, the active agent may be administered to an mdividual as an mjectable composition, for example as a stenle aqueous dispersion, preferabh lsotomc Alternatively the composition may be formulated for topical application for example m the form of ointments, creams, lotions, eye ointments, eye drops, ear drops, mouthwash. impregnated dressmgs and sutures and aerosols, and may contam appropnate conventional additives, including, for example, preservatives, solvents to assist drug penetration, and emollients in ointments and creams Such topical formulations may also contain compatible conventional carriers, for example cream or ointment bases, and ethanol or oleyl alcohol for lotions Such carriers may constitute from about 1% to about 98% by weight of the formulation, more usually they will constitute up to about 80% by weight of the formulation 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 nig/Teg, typicalh around 1 mg/kg The physician m any event will determine the actual dosage which will be most suitable for an individual and will vary with the age. weight and response of the particular individual The above dosages are exemplary of the average case There can. of course, be mdividual instances where higher or lower dosage ranges are mented, and such are within the scope of this invention In-dwelling devices include surgical implants, prosthetic devices and catheters, I e . devices that are introduced to the body of an individual and remain in position for an extended time Such devices include, for example, artificial joints, heart valves, pacemakers, vascular grafts, vascular catheters, cerebrospmal fluid shunts, urinary catheters, continuous ambulatory pentoneal dialysis (CAPD) catheters The composition of the invention may be administered b} injection to achieve a systemic effect against relevant bacteria shortly before insertion of an in-dvvellmg device Treatment may be continued after surgery during the ln-body time of the device In addition. the composition could also be used to broaden penoperative cover for any surgical technique to prevent bacterial wound infections, especially Staphylococcus aureus wound infections Many orthopaedic surgeons consider that humans with prosthetic jomts should be considered for antibiotic prophylaxis before dental treatment that could produce a bacteremia - 27 - Late deep infection is a senous complication sometimes leading to loss of the prosthetic joint 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 in 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 bactena to matnx protems exposed m wound tissue and for prophylactic use m dental treatment as an alternative to. or in conjunction with, antibiotic prophylaxis Alternatively, the composition of the invention may be used to bathe an indwelling device immediately before insertion The active agent will preferably be present at a concentration of 1 μg/ml to lOmg/ml for bathing of wounds or indwelling devices A vaccine composition is conveniently m injectable form Conventional adjuvants may be employed to enhance the immune response A suitable unit dose for vaccination is 0 5-5 microgram kg of antigen, and such dose is preferably administered 1-3 times and with an interval of 1 -3 weeks With the indicated dose range, no adverse toxicological effects will be observed with the compounds of the invention which would preclude their admimstration to suitable individuals Sequence Databases and Algorithms The polynucleotide and polypeptide sequences of the invention are particularly useful as components in databases useful for search analyses as well as m sequence analysis algonthms As used in this section entitled Databases and Algonthms and in claims related thereto, the terms "polynucleotide of the invention" and "polynucleotide sequence of the invention" mean any detectable chemical or physical characteristic 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 Algonthms and m claims related thereto, the terms "polypeptide of the invention" and "polypeptide sequence of the invention" mean any detectable chemical or physical characteristic of a polypeptide of the invention that is or may be reduced to or stored in a 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 having stored thereon sequences of the mvention For example, a computer readable medium is provided having stored thereon a member selected from the group consisting of a polynucleotide compnsmg the sequence of a - 28 - pohnucleotide of the invention, a polypeptide compnsmg the sequence of a polypeptide sequence of the invention, a set of polynucleotide sequences wherem at least one of said sequences comprises the sequence of a polynucleotide sequence of the invention, a set of polypeptide sequences wherem at least one of said sequences compnses the sequence of a pohpeptide sequence of the invention, a data set representing a polynucleotide sequence compnsmg the sequence of polynucleotide sequence of the mvention. a data set representmg a polynucleotide sequence encodmg a polypeptide sequence compnsmg the sequence of a polypeptide sequence of the invention, a polynucleotide compnsmg the sequence of a polynucleotide sequence of the mvention. a polypeptide compnsmg the sequence of a polypeptide sequence of the mvention. a set of polynucleotide sequences wherein at least one of said sequences comprises the sequence of a polynucleotide sequence of the invention, a set of pohpeptide sequences wherein at least one of said sequences compnses the sequence of a polypeptide sequence of the invention, a data set representmg a polynucleotide sequence compnsmg the sequence of a polynucleotide sequence of the invention, a data set representmg a polynucleotide sequence encodmg a polypeptide sequence compnsmg the sequence of a polypeptide sequence of the invention The computer readable medium can be any composition of matter used to store information or data, mcludmg, for example, commercially available floppy disks, tapes, hard drives, compact disks, and video disks Also provided by the mvention are methods for the analysis of character sequences. particularly genetic sequences Prefened methods of sequence analysis include, for example, methods of sequence homology analysis, such as identity and similarity anahsis. RNA structure analysis, sequence assembly, cladistic analysis, sequence motif analysis, open reading frame determination, nucleic acid base calling, and sequencmg chromatogram pe-ak analysis A computer based method is provided for performing homology identification This method compnses the steps of providing a polynucleotide sequence compnsmg the sequence a pohnucleotide of the mvention m a computer readable medium, and companng said pohnucleotide 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 comprising the steps of providing a polypeptide sequence compnsmg the sequence of a polypeptide of the invention in a computer readable medium, and companng said pohpeptide sequence to at least one polynucleotide or polypeptide sequence to identify homology - 29 - A computer based method is still further provided for polynucleotide assembly, said method compnsmg the steps of providmg a first polynucleotide sequence compnsmg the sequence of a polynucleotide of the invention in a computer readable medium, and screenmg for at least one overlapping region between said first polynucleotide sequence and a second polynucleotide sequence A further embodiment of the invention provides a computer based method for performing homology identification, said method comprising the steps of providmg a polynucleotide sequence compnsmg the sequence of a polynucleotide of the invention m a computer readable medium, and comparing said polynucleotide sequence to at least one pohnucleotide or polypeptide sequence to identify homology A further embodiment of the invention provides a computer based method for performing homology identification, said method comprising the steps of providmg a pohpeptide sequence compnsmg the sequence of a polypeptide of the invention in a computer readable medium, and companng said polypeptide sequence to at least one polynucleotide or polypeptide sequence to identify homology A further embodiment of the invention provides a computer based method for polynucleotide assembly, said method comprising the steps of providing a first polynucleotide sequence compnsmg the sequence of a polynucleotide of the invention m a computer readable medium, and screening for at least one overlapping region between said first pohnucleotide sequence and a second polynucleotide sequence Each reference disclosed herein is incorporated by reference herein m its entirety An} patent application to which this application claims prionty is also incorporated b} reference herein in its entirety GLOSSARY The following definitions are provided to facilitate understanding of certain terms used frequently herem "Dιsease(s)" means and disease caused by or related to infection by a bactena. including disease, such as. infections of the upper respiratory tract (e g . otitis media, bactenal tracheitis. acute epiglottitis. thyroiditis), lower respiratory (e g . empyema. lung abscess), cardiac (e g . infective endocarditis), gastromtestmal (e g . secretory dianhoea. splemc abscess, retropentoneal abscess). CNS (e g . cerebral abscess), eye (e g . blephantis. conjunctivitis, keratitis. endophthalmitis preseptal and orbital celluhtis. darcryocystitis). kidnev and urinary tract (e g . epididvmitis. intrarenal and peπnephnc abscess, toxic shock syndrome), skm (e g , impetigo, fol culitis. cutaneous - 30 - abscesses, celluhtis. wound infection, bactenal myositis) bone and jomt (e g . septic arthntis. osteomyelitis) "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 m the art, is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as the case may be. as determined by companng 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. includmg but not limited to those described 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 oj Sequence Data, Part I, Gnffin, A M . and Griffin, H G . eds . Humana Press. New Jersey, 1994. Sequence Analysis in Molecular Biology, von Heinje, G , Academic Press. 1987. and Sequence Analysis Primer. Gnbskov. M and Devereux, J . eds , M Stockton Press. New York. 1991, and Carillo. H . and Lipman. D . SIAM J Applied Math 48 1073 (1988) Methods to determine identity are designed to give the largest match between the sequences tested Moreover, methods to determine identity are codified m publicly available computer programs Computer program methods to determine identity between two sequences include, but are not limited to. the GCG program package (Devereux. J , et al . Nucleic Acids Research 12(1) 387 (1984)). BLASTP. BLASTN. and FASTA (Atschul. S F et al . J Molec B ol 215 403-410 (1990) The BLAST X program is publicly available from NCBI and other sources (BLAST Manual. Altschul. S . et al . NCBI NLM NIH Bethesda. MD 20894. Altschul. S . et al . J Mol Biol 215 403-410 (1990) The well known Smith Waterman algonthm may also be used to determine identity Parameters for polypeptide sequence companson include the following 1) Algorithm Needleman and Wunsch. J Mol Biol 48 443-453 (1970) Comparison matrix BLOSSUM62 from Hentikoff and Hentikoff. Proc Natl Acad Sci USA 89 10915-10919 (1992) Gap Penalty 12 Gap Length Penalty 4 31 A program useful with these parameters is publicly available as the "gap" program from Genetics Computer Group. Madison WI The aforementioned parameters are the default parameters for peptide compansons (along with no penalty for end gaps) Parameters for polynucleotide companson mclude the following 1) Algorithm Needleman and Wunsch. J Mol Biol 48 443-453 (1970) Comparison matnx matches = +10. mismatch = 0 Gap Penalty 50 Gap Length Penalty 3 Available as The "gap" program from Genetics Computer Group, Madison WI These are the default parameters for nucleic acid compansons A prefened meaning for "identity" for polynucleotides and polypeptides. as the case may be. are provided m (1) and (2) below (1) Polynucleotide embodiments further mclude an isolated polynucleotide compnsmg a pohnucleotide sequence having at least a 50. 60, 70, 80, 85, 90. 95. 97 or 100% identify to the reference sequence of SEQ ID NO 1. wherein said polynucleotide sequence may be identical to the reference sequence of SEQ ID NO 1 or may include up to a certain integer number of nucleotide alterations as compared to the reference sequence, wherem said alterations are selected from the group consisting of at least one nucleotide deletion, substitution, including transition and transversion. or insertion, and wherem said alterations may occur at the 5' or 3' terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among the nucleotides in the reference sequence or in one or more contiguous groups within the reference sequence, and wherein said number of nucleotide alterations is determined by multiplying the total number of nucleotides in SEQ ID NO 1 by the integer defining the percent identity divided b} 100 and then subtracting that product from said total number of nucleotides in SEQ ID NO 1. or n n ≤ n " ( x n * y)- wherein n n is the number of nucleotide alterations. x n is the total number of nucleotides in SEQ ID NO 1. y is 0 50 for 50%. 0 60 for 60%. 0 70 for 70%, 0 80 for 80%. 0 85 for 85%. 0 90 for 90%, 0 95 for 95%. 0 97 for 97% or 1 00 for 100%, and • is the symbol for the multiplication operator, and wherein any non-integer product of x n and y is rounded down to the nearest integer pnor to subtracting it from x n Alterations of a polynucleotide sequence - 32 - encoding the polypeptide of SEQ ID NO 2 may create nonsense, missense or frameshift mutations in this codmg sequence and thereby alter the polypeptide encoded by the polynucleotide following such alterations By way of example, a polynucleotide sequence of the present invention 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 certain 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, includmg transition and transversion. or insertion, and wherem said alterations may occur at the 5' or 3' terminal positions of the reference polynucleotide sequence or anywhere between those terminal positions, mterspersed either individually among the nucleic acids m the reference sequence or in one or more contiguous groups within the reference sequence The number of nucleic acid alterations for a given percent identity is determined by multiplying the total number of ammo acids m SEQ ID NO 2 by the integer defining the percent identity divided by 100 and then subtracting that product from said total number of amino acids in SEQ ID NO 2. or n n < x n - (x n • y), wherein n n is the number of amino acid alterations, x n is the total number of ammo acids in SEQ ID NO 2. y is, for instance 0 70 for 70%. 0 80 for 80%. 0 85 for 85% etc . • is the s}τnbol for the multiplication operator, and wherein any non-mteger product of x n and y is rounded down to the nearest mteger prior to subtracting it from x n (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 include up to a certain integer number of ammo acid alterations as compared to the reference sequence, wherein said alterations are selected from the group consisting of at least one ammo acid deletion, substitution, includmg conservative and non-conservative substitution, or insertion, and wherem said alterations may occur at the ammo- or carboxv-termmal positions of the reference polypeptide sequence or anywhere between those terminal positions, interspersed either individually among the am o acids m the reference sequence or in one or more contiguous groups within the reference sequence, and wherein said number of ammo acid alterations is determined by multiplying the - 33 - total number of ammo acids in SEQ ID NO 2 by the mteger defining the percent identify divided by 100 and then subtracting that product from said total number of amino acids m SEQ ID NO 2. or n a < x a - (x a • y). wherein n a is the number of ammo acid alterations. x a is the total number of amino 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 integer prior to subtracting it from x a By way of example, a polypeptide sequence of the present invention may be identical to the reference sequence of SEQ ID NO 2. that is it may be 100% identical, or it may include up to a certain 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, including 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, interspersed either individually among the ammo acids in the reference sequence or m one or more contiguous groups within 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 defining the percent identity divided b} 100 and then subtracting that product from said total number of ammo acids in SEQ ID NO 2. or n a ≤ x a ( χ a • y)> wherein n a is the number of ammo acid alterations. x a is the total number of ammo acids in SEQ ID NO 2, y is, for instance 0 70 for 70%, 0 80 for 80%. 0 85 for 85% etc . and • is the symbol for the multiplication operator, and wherein any non-mteger product of x a and y is rounded down to the nearest integer prior to subtracting it from x a "Isolated" means altered "by the hand of man" from its natural state, l e . if it occurs in nature, it has been changed or removed from its onginal environment, or both For example, a - 34 - polynucleotide or a polypeptide naturally present m a living organism is not "isolated. " but the same polynucleotide or polypeptide separated from the coexi^mg matenals of its natural state is "isolated", as the term is employed herem Moreover, a polynucleotide or polypeptide that is introduced mto an organism by transformation, genetic manipulation or by any other recombinant method is "isolated" even if it is still present m said organism, which organism may be living or nonliving "Polynucleotide(s)" generally refers to any polynbonucleotide or polydeoxnbonucleotide. 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 smgle- and double- stranded regions or smgle-. double- and tnple-stranded regions, smgle- and double-stranded RNA. and RNA that is mixture of smgle- and double-stranded regions, hybnd molecules compnsmg DNA and RNA that may be single-stranded or. more typically, double-stranded, or tnple-Λranded regions, or a mixture of smgle- and double-stranded regions In addition, "polynucleotide" as used herem refers to tnple-stranded regions compnsmg RNA or DNA or both RNA and DNA The strands m such regions may be from the same molecule or from different molecules The regions may mclude all of one or more of the molecules, but more typically mvolve only a region of some of the molecules One of the molecules of a tnple-hehcal region often is an ohgonucleotide As used herein, the term "polynucleotιde(s)" also mcludes DNAs or RNAs as descnbed above that contain one or more modified bases Thus, DNAs or RNAs with backbones modified for stability or for other reasons are "polynucleotide(s)" as that term is mtended herem Moreover. DNAs or RNAs compnsmg unusual bases, such as mosme. or modified b.ases. such as tnfylated 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 charactenstic of viruses and cells, including, for example, simple and complex cells "Polynucleotιde(s)" also embraces short polynucleotides often refened to as ohgonucleotide(s) "Polypeptιde(s)" refers to any peptide or protem compnsmg two or more ammo acids jomed to each other by peptide bonds or modified peptide bonds "Polypeptide(s)" refers to both short chains, commonly refened to as peptides. ohgopeptides and o gomers and to longer chains generalh refened to as proteins Polypeptides may contain ammo acids other than the 20 gene encoded ammo acids "Polypeptide(s)" mclude those modified either by natural processes, such as processmg and - 35 - other post-translational modifications, but also by chemical modification techniques Such modifications are well descnbed m 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 contain many types of modifications Modifications can occur anywhere m a polypeptide, including the peptide backbone, the ammo acid side-chains, and the ammo or carboxvl 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 phosphotidylmositol. cross-linking, cvckzation. disulfide bond formation, demethylation. formation of covalent cross-links, formation of cy^eme. formation of pyroglutamate. formylation, gamma-carboxylation. glycosylation. GPI anchor formation, hydroxylation. lodmation. methylation. mynstoylation, oxidation, proteolytic processmg, phosphorylation. prenylation. racemization. glycosylation. hpid attachment, sulfation. gamma- carboxvlation 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 Creightoa W H Freeman and Company. New York (1993) and Wold, F , Posttranslational Protem Modifications Perspectives and Prospects, pgs 1-12 m POSTTRANSLATIONAL COVALENT MODIFICATION OF PROTEINS. B C Johnson. Ed , Academic Press. New York (1983), Seifter et al . Meth Enzymol 182 626-646 (1990) and Rattan et al . Protein Synthesis Posttranslational Modifications and Aging, Asm. N Y Acad Sci 663 48- 62 (1992) Polypeptides may be branched or cyclic, with or without branching Cvclic. branched and branched circular polypeptides may result from post-translational natural processes and may be made by entirely synthetic methods, as well 'Naπant(s)" as the term is used herein, is a polynucleotide or polypeptide that differs from a reference polynucleotide or polypeptide respectively, but retains essential properties A typical variant of a polynucleotide differs in nucleotide sequence from another, reference polynucleotide Ch.anges m the nucleotide sequence of the vanant may or may not alter the ammo acid sequence of a polypeptide encoded by the reference pohnucleotide Nucleotide changes may result in amino acid substitutions, additions, deletions, fusions and truncations in the polypeptide encoded by the reference sequence, as discussed below A typical variant of a polypeptide differs in ammo acid sequence from another, reference polypeptide Generally, - 36 - differences are limited so that the sequences of the reference polypeptide and the v anant are closely similar overall and. in many regions, identical A variant and reference polypeptide ma} differ in ammo acid sequence by one or more substitutions, additions, deletions in any combmation A substituted or inserted amino acid residue may or may not be one encoded by the genetic code A variant of a polynucleotide or polypeptide may be a naturalh occurring such as an alle c vanant. or it may be a variant that is not known to occur naturally Non- naturally occurring variants of polynucleotides and polypeptides may be made b} mutagenesis techniques, by direct synthesis, and by other recombinant methods known to skilled artisans EXAMPLES The examples below are earned out usmg standard techniques, which are well known and routine to those of skill m the art. except where otherwise descnbed m detail The examples are illustrative, but do not limit the mvention Ex.ample 1 Strain selection, Library Production and Sequencing The polynucleotide having a DNA sequence given m Table 1 [SEQ ID NO 1] was obtained from a library of clones of chromosomal DNA of Staphylococcus aureus m E coli The sequencing data from two or more clones containing overlapping Staphylococcus aureus DNAs was used to construct the contiguous DNA sequence in SEQ ID NO 1 Libranes may be prepared by routine methods, for example Methods 1 and 2 below Total cellular DNA is isolated from Staphylococcus aureus WCUH 29 according to standard procedures and size-fractionated bv either of two methods Method 1 Total cellular DNA is mechanically sheared by passage through a needle in order to size-fractionate accordmg to standard procedures DNA fragments of up to 1 lkbp m size are rendered blunt by treatment with exonuclease and DNA polymerase. and EcoRI linkers added Fragments are hgated into the vector Lambda ZapII that has been cut with EcoRI. the library packaged by standard procedures and E cob infected with the packaged hbrarv The library is amplified by standard procedures Method 2 Total cellular DNA is partially hydrolyzed with a one or a combmation of restnction enzymes appropnate to generate a series of fragments for clomng into library vectors (e . 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 into the - 37 - vector Lambda ZapII that have been cut with EcoRI. the library packaged by standard procedures, and E coh infected with the packaged library The library is amplified by standard procedures Example 2 dnaB Characterization S aureus DnaB expression Usmg PCR amplification from S aureus WCUH29 genomic DNA (5' pnmer AGCATCATCCCATGGATAGAATGTATGAGCAA. [SEQ ID NO 7] 3' pnmer ATCTATTCCTCGAGCATCATATCAGCATGTGCAT [SEQ ID NO 8]), the DnaB gene was isolated and subcloned (Ncol Xhol) mto a suitable protem expression vector. pBluepET28a. made in house from pBIuescnpt (Stratagene)and pET28a (Invitrogen), linked to a C-terminal polyhistidine affinity tag Protem expression was earned out in the E coh stram LW29(DE3) contaming pRI952 which encodes rare E coh tRNAs for He and Arg Induction with 0 3 mM IPTG at 37C for 3hrs yielded a 53kD MW product on a 4-12% NuPAGE gel (Novex). consistent with the expected size of the protein fusion The protein was insoluble hen induced at 37C. solubility improved when mduction temperature was lowered to 24C - 38 -

Claims: What is claimed is: 1 An isolated polynucleotide compnsmg a polynucleotide havmg at least a 70% identity to a pohnucleotide encodmg a polypeptide compnsmg the ammo acid sequence of SEQ ED NO 2 2 An isolated polynucleotide compnsmg a polynucleotide havmg at least a 70% identity to a pohnucleotide encodmg the same mature polypeptide expressed by the dnaB gene contained m the Staphylococcus aureus 3 An isolated polynucleotide compnsmg a polynucleotide encodmg a polypeptide compnsmg an ammo acid sequence which is at least 70% identical to the ammo acid sequence of SEQ ED 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 ED NO 1 7 The polynucleotide of Claim 1 compnsmg nucleotide 101 to the stop codon which begins at nucleotide number 1499 set forth m SEQ ID NO 1 8 The polynucleotide of Claim 1 which encodes a polypeptide compnsmg the ammo acid sequence of SEQ ID NO 2 9 A vector compnsmg the polynucleotide of Claim 1 10 A host cell compnsmg the vector of Claim 9 11 A process for producmg a polypeptide compnsmg expressmg from the host cell of Claim 10 a pohpeptide encoded by said DNA 12 A process for producing a dnaB polypeptide or fragment compnsmg cultunng a host of claim 10 under conditions sufficient for the production of said pohpeptide 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 compnsmg an ammo acid sequence as set forth m 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 - 39 17 A method for the treatment of an mdividual m need of dnaB polypeptide compnsmg administering to the mdividual a therapeutically effective amount of the polypeptide of claim 14 18 A method for the treatment of an mdividual havmg need to inhibit dnaB pohpeptide compnsmg administering to the mdividual a therapeutically effective amount of the antagonist of Claim 14 19 A process for dragnosing a disease related to expression or activity of the polypeptide of claim 14 m an mdividual compnsmg (a) determining a nucleic acid sequence encodmg said polypeptide. and/or (b) analv2αng for the presence or amount of said polypeptide m a sample denved from the mdividual 20 A method for identifying compounds which mteract with and inhibit or activate .an activity of the polypeptide of claim 14 compnsmg contacting a composition compnsmg the polypeptide with the compound to be screened under conditions to permit mteraction between the compound and the polypeptide to assess the mteraction of a compound, such mteraction bemg associated with a second component capable of providmg a detectable signal m response to the mteraction of the polypeptide with the compound, 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 mteraction of the compound with the polypeptide 21 A method for inducing an immunological response m a mammal which compnses inoculating the mammal with dnaB 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 mducing immunological response m a mammal which compnses dehvenng a nucleic acid vector to direct expression of dnaB polypeptide of claim 14. or fragment or a vanant thereof, for expressing said dnaB polypeptide. or a fragment or a vanant thereof in vivo m 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 consistmg of a polynucleotide comprising the sequence of SEQ ID NO 1. a polypeptide compnsmg the sequence of SEQ ID NO 2, a set of polynucleotide sequences wherem at least one of said sequences compnses the sequence of SEQ ID NO 1. a set of - 40 - polypeptide sequences wherem at least one of said sequences compnses the sequence of SEQ ID NO 2. a data set representmg a polynucleotide sequence compnsmg the sequence of SEQ ID NO 1 , a data set representmg a polynucleotide sequence encodmg a polypeptide sequence compnsmg the sequence of SEQ ID NO 2, a polynucleotide compnsmg the sequence of SEQ ID NO 1 , a polypeptide compnsmg the sequence of SEQ ID NO 2, a set of polynucleotide sequences wherem at least one of said sequences compnses the sequence of SEQ ID NO 1, a set of polypeptide sequences wherein at least one of said sequences compnses the sequence of SEQ ID NO 2, a data set representmg a polynucleotide sequence compnsmg the sequence of SEQ ID NO 1. a data set representmg a polynucleotide sequence encoding 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 compnsmg the sequence of SEQ ID NO 1 in a computer readable medium, and companng said polynucleotide sequence to at least one polynucleotide or polypeptide sequence to identify homology 25 A further embodiment of the invention provides a computer based method for polynucleotide assembly, said method compnsmg the steps of providing a first polynucleotide sequence compnsmg the sequence of SEQ ID NO 1 m a computer readable medium, and screening for at least one overlapping region between said first polynucleotide sequence and a second polynucleotide sequence 26 An isolated polynucleotide compnsmg a polynucleotide having at least a 70% identify to a polynucleotide encodmg a pohpeptide compnsmg the ammo acid sequence of SEQ ID NO.4 27 An isolated polynucleotide compnsmg a polynucleotide havmg at least a 70% identity to the polynucleotide sequence of SEQ ID NO 3 - 41

Inventors: EARNSHAW DAVID L, MAY EARL W, MCDEVITT DAMIEN, EARNSHAW, DAVID, L., MAY, EARL, W., MCDEVITT, DAMIEN
Applicants: SMITHKLINE BEECHAM CORP, SMITHKLINE BEECHAM PLC, SMITHKLINE BEECHAM CORPORATION, SMITHKLINE BEECHAM, PLC
Application year: 1999
Main classification: C07H21
IPC codes: A61K31, A61K38, A61K39, A61K45, A61K48, A61P31, A61P43, C07K14, C07K16, C12N1, C12N9, C12N15, C12Q1, G06F17