The invention provides ileS polypeptides and DNA (RNA) encoding ileS polypeptides and methods for producing such polypeptides by recombinant techniques. Also provided are methods for utilizing ileS polypeptides to screen for antibacterial compounds.

FIELD OF THE INVENTION
 This invention relates to newly identified polynucleotides and
 polypeptides, and their production and uses, as well as their variants,
 agonists and antagonists, and their uses. In particular, in these and in
 other regards, the invention relates to novel polynucleotides and
 polypeptides of the isoleucyl tRNA synthetase family, hereinafter referred
 to as "ileS".
 BACKGROUND OF THE INVENTION
 The Streptococci make up a medically important genera of microbes known to
 cause several types of disease in humans, including, for example, otitis
 media, conjunctivitis, pneumonia, bacteremia, meningitis, sinusitis,
 pleural empyema and endocarditis, and most particularly meningitis, such
 as for example infection of cerebrospinal fluid. Since its isolation more
 than 100 years ago, Streptococcus pneumoniae has been one of the more
 intensively studied microbes. For example, much of our early understanding
 that DNA is, in fact, the genetic material was predicated on the work of
 Griffith and of Avery, Macleod and McCarty using this microbe. Despite the
 vast amount of research with S. pneumoniae, many questions concerning the
 virulence of this microbe remain. It is particularly preferred to employ
 Streptococcal genes and gene products as targets for the development of
 antibiotics.
 The frequency of Streptococcus pneumoniae infections has risen dramatically
 in the past 20 years. This has been attributed to the emergence of
 multiply antibiotic resistant strains and an increasing population of
 people with weakened immune systems. It is no longer uncommon to isolate
 Streptococcus pneumoniae strains which are resistant to some or all of the
 standard antibiotics. This has created a demand for both new
 anti-microbial agents and diagnostic tests for this organism.
 t-RNA synthetases have a primary role in protein synthesis according to the
 following scheme:
 Enzyme+ATP+AA.revreaction.Enzyme.AA-AMP+PPi
 Enzyme.AA-AMP+t-RNA.revreaction.Enzyme+AMP+AA-t-RNA
 in which AA is an amino acid.
 Inhibition of this process leads to a reduction in the levels of charged
 t-RNA and this triggers a cascade of responses known as the stringent
 response, the result of which is the induction of a state of dormancy in
 the organism. As such selective inhibitors of bacterial t-RNA synthetase
 have potential as antibacterial agents. One example of such is mupirocin
 which is a selective inhibitor of isoleucyl t-RNA synthetase. Other t-RNA
 synthetases are now being examined as possible anti-bacterial targets,
 this process being greatly assisted by the isolation of the synthetase.
 Clearly, there is a need for factors, such as the novel compounds 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 characterization of such factors and their
 antagonists and agonists which can play a role in preventing, ameliorating
 or correcting infections, dysfunctions or diseases.
 The polypeptides of the invention have amino acid sequence homology to a
 known Staphylococcus aureus isoleucyl tRNA synthetase protein.
 SUMMARY OF THE INVENTION
 It is an object of the invention to provide polypeptides that have been
 identified as novel ileS polypeptides by homology between the amino acid
 sequence set out in Table 1 [SEQ ID NO: 2, 6 and 9] and a known amino acid
 sequence or sequences of other proteins such as Staphylococcus aureus
 isoleucyl tRNA synthetase protein.
 It is a further object of the invention to provide polynucleotides that
 encode ileS polypeptides, particularly polynucleotides that encode the
 polypeptide herein designated ileS.
 In a particularly preferred embodiment of the invention the polynucleotide
 comprises a region encoding ileS polypeptides comprising the sequence set
 out in Table 1 [SEQ ID NO: 1, 5, 8 and 10] which includes, for example, a
 full length gene, or a variant thereof.
 In another particularly preferred embodiment of the invention there is a
 novel ileS protein from Streptococcus pneumoniae comprising the amino acid
 sequence of Table 1 [SEQ ID NO: 2, 6 and 9], or a variant thereof.
 In accordance with another aspect of the invention there is provided an
 isolated nucleic acid molecule encoding a mature polypeptide expressible
 by the Streptococcus pneumoniae 0100993 strain contained in the deposited
 strain.
 A further aspect of the invention there are provided isolated nucleic acid
 molecules encoding ileS, particularly Streptococcus pneumoniae ileS,
 including mRNAs, cDNAs, genomic DNAs. Further embodiments of the invention
 include biologically, diagnostically, prophylactically, clinically or
 therapeutically useful variants thereof, and compositions comprising the
 same.
 In accordance with another aspect of the invention, there is provided the
 use of a polynucleotide of the invention for therapeutic or prophylactic
 purposes, in particular genetic immunization. Among the particularly
 preferred embodiments of the invention are naturally occurring allelic
 variants of ileS and polypeptides encoded thereby.
 Another aspect of the invention there are provided novel polypeptides of
 Streptococcus pneumoniae referred to herein as ileS as well as
 biologically, diagnostically, prophylactically, clinically or
 therapeutically useful variants thereof, and compositions comprising the
 same.
 Among the particularly preferred embodiments of the invention are variants
 of ileS polypeptide encoded by naturally occurring alleles of the ileS
 gene.
 In a preferred embodiment of the invention there are provided methods for
 producing the aforementioned ileS polypeptides.
 In accordance with yet another aspect of the invention, there are provided
 inhibitors to such polypeptides, useful as antibacterial agents,
 including, for example, antibodies.
 In accordance with certain preferred embodiments of the invention, there
 are provided products, compositions and methods for assessing ileS
 expression, treating disease, for example, otitis media, conjunctivitis,
 pneumonia, bacteremia, meningitis, sinusitis, pleural empyema and
 endocarditis, and most particularly meningitis, such as for example
 infection of cerebrospinal fluid, assaying genetic variation, and
 administering a ileS polypeptide or polynucleotide to an organism to raise
 an immunological response against a bacteria, especially a Streptococcus
 pneumoniae bacteria.
 In accordance with certain preferred embodiments of this and other aspects
 of the invention there are provided polynucleotides that hybridize to ileS
 polynucleotide sequences, particularly under stringent conditions.
 In certain preferred embodiments of the invention there are provided
 antibodies against ileS polypeptides.
 In other embodiments of the invention there are provided methods for
 identifying compounds which bind to or otherwise interact with and inhibit
 or activate an activity of a polypeptide or polynucleotide of the
 invention comprising: contacting a polypeptide or polynucleotide of the
 invention with a compound to be screened under conditions to permit
 binding to or other interaction between the compound and the polypeptide
 or polynucleotide to assess the binding to or other interaction with the
 compound, such binding or interaction being associated with a second
 component capable of providing a detectable signal in response to the
 binding or interaction of the polypeptide or polynucleotide with the
 compound; and determining whether the compound binds to or otherwise
 interacts with and activates or inhibits an activity of the polypeptide or
 polynucleotide by detecting the presence or absence of a signal generated
 from the binding or interaction of the compound with the polypeptide or
 polynucleotide.
 In accordance with yet another aspect of the invention, there are provided
 ileS agonists and antagonists, preferably bacteriostatic or bactericidal
 agonists and antagonists.
 In a further aspect of the invention there are provided compositions
 comprising a ileS polynucleotide or a ileS polypeptide for administration
 to a cell or to a multicellular organism.
 Various changes and modifications within the spirit and scope of the
 disclosed invention will become readily apparent to those skilled in the
 art from reading the following descriptions and from reading the other
 parts of the present disclosure.
 GLOSSARY
 The following definitions are provided to facilitate understanding of
 certain terms used frequently herein.
 "Host cell" is a cell which has been transformed or transfected, or is
 capable of transformation or transfection by an exogenous polynucleotide
 sequence.
 "Identity," as known in the art, is a relationship between two or more
 polypeptide sequences or two or more polynucleotide sequences, as
 determined by comparing the sequences. In the art, "identity" also means
 the degree of sequence relatedness between polypeptide or polynucleotide
 sequences, as the case may be, as determined by the match between strings
 of such sequences. "Identity" and "similarity" can be readily calculated
 by known methods, including but not limited to those described in
 (Computational Molecular Biology, Lesk, A. M., ed., Oxford University
 Press, New York, 1988; Biocomputing: Informatics and Genome Projects,
 Smith, D. W., ed., Academic Press, New York, 1993; Computer Analysis of
 Sequence Data, Part I, Griffin, A. M., and Griffin, H. G., eds., Humana
 Press, New Jersey, 1994; Sequence Analysis in Molecular Biology, von
 Heinje, G., Academic Press, 1987; and Sequence Analysis Primer, Gribskov,
 M. and Devereux, J., eds., M Stockton Press, New York, 1991; and Carillo,
 H., and Lipman, D., SIAM J. Applied Math., 48: 1073 (1988). Preferred
 methods to determine identity are designed to give the largest match
 between the sequences tested. Methods to determine identity and similarity
 are codified in publicly available computer programs. Preferred computer
 program methods to determine identity and similarity 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. Biol. 215: 403-410 (1990). The BLAST X
 program is publicly available from NCBI and other sources (BLAST Manual,
 Altschul, S., et al., NCBI NLM NIH Bethesda, Md. 20894; Altschul, S., et
 al., J. Mol. Biol. 215: 403-410 (1990). As an illustration, by a
 polynucleotide having a nucleotide sequence having at least, for example,
 95% "identity" to a reference nucleotide sequence of SEQ ID NO: 1 it is
 intended that the nucleotide sequence of the polynucleotide is identical
 to the reference sequence except that the polynucleotide sequence may
 include up to five point mutations per each 100 nucleotides of the
 reference nucleotide sequence of SEQ ID NO: 1. In other words, to obtain a
 polynucleotide having a nucleotide sequence at least 95% identical to a
 reference nucleotide sequence, up to 5% of the nucleotides in the
 reference sequence may be deleted or substituted with another nucleotide,
 or a number of nucleotides up to 5% of the total nucleotides in the
 reference sequence may be inserted into the reference sequence. These
 mutations of the reference sequence may occur at the 5' or 3' terminal
 positions of the reference nucleotide sequence or anywhere between those
 terminal positions, interspersed either individually among nucleotides in
 the reference sequence or in one or more contiguous groups within the
 reference sequence. Analogously , by a polypeptide having an amino acid
 sequence having at least, for example, 95% identity to a reference amino
 acid sequence of SEQ ID NO: 2 is intended that the amino acid sequence of
 the polypeptide is identical to the reference sequence except that the
 polypeptide sequence may include up to five amino acid alterations per
 each 100 amino acids of the reference amino acid of SEQ ID NO: 2. In other
 words, to obtain a polypeptide having an amino acid sequence at least 95%
 identical to a reference amino acid sequence, up to 5% of the amino acid
 residues in the reference sequence may be deleted or substituted with
 another amino acid, or a number of amino acids up to 5% of the total amino
 acid residues in the reference sequence may be inserted into the reference
 sequence. These alterations of the reference sequence may occur at the
 amino or carboxy terminal positions of the reference amino acid sequence
 or anywhere between those terminal positions, interspersed either
 individually among residues in the reference sequence or in one or more
 contiguous groups within the reference sequence.
 "Isolated" means altered "by the hand of man" from its natural state, ie.,
 if it occurs in nature, it has been changed or removed from its original
 environment, or both. For example, a polynucleotide or a polypeptide
 naturally present in a living organism is not "isolated," but the same
 polynucleotide or polypeptide separated from the coexisting materials of
 its natural state is "isolated", as the term is employed herein.
 "Polynucleotide(s)" generally refers to any polyribonucleotide or
 polydeoxribonucleotide, which may be unmodified RNA or DNA or modified RNA
 or DNA. "Polynucleotide(s)" include, without limitation, single- and
 double-stranded DNA, DNA that is a mixture of single- and double-stranded
 regions or single-, double- and triple-stranded regions, single- and
 double-stranded RNA, and RNA that is mixture of single- and
 double-stranded regions, hybrid molecules comprising DNA and RNA that may
 be single-stranded or, more typically, double-stranded, or triple-stranded
 regions, or a mixture of single- and double-stranded regions. In addition,
 "polynucleotide" as used herein refers to triple-stranded regions
 comprising RNA or DNA or both RNA and DNA. The strands in such regions may
 be from the same molecule or from different molecules. The regions may
 include all of one or more of the molecules, but more typically involve
 only a region of some of the molecules. One of the molecules of a
 triple-helical region often is an oligonucleotide. As used herein, the
 term "polynucleotide(s)" also includes DNAs or RNAs as described 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 intended herein. Moreover, DNAs or RNAs comprising unusual
 bases, such as inosine, or modified bases, such as tritylated bases, to
 name just two examples, are polynucleotides as the term is used herein. It
 will be appreciated that a great variety of modifications have been made
 to DNA and RNA that serve many useful purposes known to those of skill in
 the art. The term "polynucleotide(s)" as it is employed herein embraces
 such chemically, enzymatically or metabolically modified forms of
 polynucleotides, as well as the chemical forms of DNA and RNA
 characteristic of viruses and cells, including, for example, simple and
 complex cells. "Polynucleotide(s)" also embraces short polynucleotides
 often referred to as oligonucleotide(s).
 "Polypeptide(s)" refers to any peptide or protein comprising two or more
 amino acids joined to each other by peptide bonds or modified peptide
 bonds. "Polypeptide(s)" refers to both short chains, commonly referred to
 as peptides, oligopeptides and oligomers and to longer chains generally
 referred to as proteins. Polypeptides may contain amino acids other than
 the 20 gene encoded amino acids. "Polypeptide(s)" include those modified
 either by natural processes, such as processing and other
 post-translational modifications, but also by chemical modification
 techniques. Such modifications are well described in basic texts and in
 more detailed monographs, as well as in a voluminous research literature,
 and they are well known to those of skill in the art. It will be
 appreciated that the same type of modification may be present in the same
 or varying degree at several sites in a given polypeptide. Also, a given
 polypeptide may contain many types of modifications. Modifications can
 occur anywhere in a polypeptide, including the peptide backbone, the amino
 acid side-chains, and the amino or carboxyl termini. Modifications
 include, for example, acetylation, acylation, ADP-ribosylation, amidation,
 covalent attachment of flavin, covalent attachment of a heme moiety,
 covalent attachment of a nucleotide or nucleotide derivative, covalent
 attachment of a lipid or lipid derivative, covalent attachment of
 phosphotidylinositol, cross-linking, cyclization, disulfide bond
 formation, demethylation, formation of covalent cross-links, formation of
 cysteine, formation of pyroglutamate, formylation, gamma-carboxylation,
 glycosylation, GPI anchor formation, hydroxylation, iodination,
 methylation, myristoylation, oxidation, proteolytic processing,
 phosphorylation, prenylation, racemization, glycosylation, lipid
 attachment, sulfation, gamma-carboxylation of glutamic acid residues,
 hydroxylation and ADP-ribosylation, selenoylation, sulfation, transfer-RNA
 mediated addition of amino acids to proteins, such as arginylation, and
 ubiquitination. See, for instance, PROTEINS--STRUCTURE AND MOLECULAR
 PROPERTIES, 2nd Ed., T. E. Creighton, W. H. Freeman and Company, New York
 (1993) and Wold, F., Posttranslational Protein Modifications: Perspectives
 and Prospects, pgs. 1-12 in POSTTRANSLATIONAL COVALENT MODIFICATION OF
 PROTEINS, B. C. Johnson, Ed., Academic Press, New York (1983); Seifter et
 al., Meth. Enzymol. 182:626-646 (1990) and Rattan et al., Protein
 Synthesis: Posttranslational Modifications and Aging, Ann. N.Y. Acad. Sci.
 663: 48-62 (1992). Polypeptides may be branched or cyclic, with or without
 branching. Cyclic, branched and branched circular polypeptides may result
 from post-translational natural processes and may be made by entirely
 synthetic methods, as well.
 "Variant(s)" as the term is used herein, is a polynucleotide or polypeptide
 that differs from a reference polynucleotide or polypeptide respectively,
 but retains essential properties. A typical variant of a polynucleotide
 differs in nucleotide sequence from another, reference polynucleotide.
 Changes in the nucleotide sequence of the variant may or may not alter the
 amino acid sequence of a polypeptide encoded by the reference
 polynucleotide. Nucleotide changes may result in 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 amino acid sequence from another, reference
 polypeptide. Generally, differences are limited so that the sequences of
 the reference polypeptide and the variant are closely similar overall and,
 in many regions, identical. A variant and reference polypeptide may differ
 in amino acid sequence by one or more substitutions, additions, deletions
 in any combination. A substituted or inserted amino acid residue may or
 may not be one encoded by the genetic code. A variant of a polynucleotide
 or polypeptide may be a naturally occurring such as an allelic variant, or
 it may be a variant that is not known to occur naturally. Non-naturally
 occurring variants of polynucleotides and polypeptides may be made by
 mutagenesis techniques, by direct synthesis, and by other recombinant
 methods known to skilled artisans.
 DESCRIPTION OF THE INVENTION
 The invention relates to novel ileS polypeptides and polynucleotides as
 described in greater detail below. In particular, the invention relates to
 polypeptides and polynucleotides of a novel ileS of Streptococcus
 pneumoniae, which is related by amino acid sequence homology to
 Staphylococcus aureus isoleucyl tRNA synthetase polypeptide. The invention
 relates especially to ileS having the nucleotide and amino acid sequences
 set out in Table 1 [SEQ ID NO: 1] and Table 1 [SEQ ID NO: 2] respectively,
 and to the ileS nucleotide sequences of the DNA in the deposited strain
 and amino acid sequences encoded thereby.
 TABLE 1
 ileS Polynucleotide and Polypeptide Sequences
 (A) Sequences from Streptococcus pneumoniae ileS polynucleotide
 sequence [SEQ ID NO:1].
 5'-1 ATGAAACTCA AAGACACCCT TAATCTTGGG AAAACTGAAT TCCCAATGCG
 51 TGCAGGCCTT CCTACCAAAG AGCCAGTTTG GCAAAAGGAA TGGGAAGATG
 101 CAAAACTTTA TCAACGTCGT CAAGAATTGA ACCAAGGAAA ACCTCATTTC
 151 ACCTTGCATG ATGGCCCTCC ATACGCTAAC GGAAATATCC ACGTTGGACA
 201 TGCTATGAAC AAGATTTCAA AAGATATCAT TGTTCGTTCT AAGTCTATGT
 251 CAGGATTTTA CGCGCCATTT ATTCCTGGTT GGGATACTCA TGGTCTGCCA
 301 ATCGAGCAAG TCTTGTCAAA ACAAGGTGTC AAACGTAAAG AAATGGACTT
 351 GGTTGAGTAC TTGAAACTTT GCCGTGAGTA CGCTCTTTCT CAAGTAGATA
 401 AACAACGTGA AGATTTTAAA CGTTTGGGTG TTTCTGGTGA CTGGGAAAAT
 451 CCATATGTGA CCTTGACTCC TGACTATGAA GCAGCTCAAA TTCGTGTATT
 501 TGGTGAGATG GCTAATAAGG GTTATATCTA CCGTGGTGCC AAGCCAGTTT
 551 ACTGGTCATG GTCATCTGAG TCAGCCCTTG CTGAAGCAGA GATTGAATAC
 601 CATGACTTGG TTTCAACTTC CCTTTACTAT GCCAACAAGG TAAAAGATGG
 651 CAAAGGAGTT CTAGATACAG ATACTTATAT CGTTGTCTGG ACAACGACTC
 701 CATTTACCAT CACAGCTTCT CGTGGTTTGA CGGTTGGTGC AGATATTGAT
 751 TACGTTTTGG TTCAACCTGC TGGTGAAGCT CGTAAGTTTG TCGTTGCTGC
 801 TGAATTATTG ACTAGCTTGT CTGAGAAATT TGGCTGGGCT GATGTTCAAG
 851 TTTTGGAAAC TTACCGTGGC CAAGAACTTA ACCACATCGT AACAGAACAC
 901 CCATGGGATA CAGCTGTAGA AGAGTTGGTA ATTCTTGGTG ACCACGTTAC
 951 GACTGACTCT GGTACAGGTA TTGTCCATAC AGCCCCTGGT TTTGGTGAGG
 1001 ACGACTACAA TGTTGGTATT GCTAATAATC TTGAAGTCGC AGTGACTGTT
 1051 GATGAACGTG GTATCATGAT GAAGAATGCT GGTCCTGAGT TTGAAGGTCA
 1101 ATTCTATGAA AAGGTAGTTC CAACTGTTAT TGAAAAACTT GGTAACCTCC
 1151 TTCTTGCCCA AGAAGAAATC TCTCACTCAT ATCCATTTGA CTGGCGTACT
 1201 AAGAAACCAA TCATCTGGCG TGCAGTTCCA CAATGGTTTG CCTCAGTTTC
 1251 TAAATTCCGT CAAGAAATCT TGGACGAAAT TGAAAAAGTG AAATTCCACT
 1301 CAGAATGGGG TAAAGTCCGT CTTTACAATA TGATCCGTGA CCGTGGTGAC
 1351 TGGGTTATCT CTCGTCAACG TGCTTGGGGT GTTCCACTTC CAATCTTCTA
 1401 TGCAGAAGAC GGTACAGCTA TCATGGTAGC TGAAACGATT GAACACGTAG
 1451 CTCAACTTTT TGAAGAACAT GGTTCAAGCA TTTGGTGGGA ACGTGATGCC
 1501 AAAGATCTCT TGCCAGAAGG ATTTACTCAT CCAGGTTCAC CAAACGGCGA
 1551 GTTCAAAAAA GAAACTGATA TCATGGACGT TTGGTTTGAC TCAGGTTCAT
 1601 CATGGAATGG AGTGGTGGTA AACCGTCCTG AATTGACTTA CCCAGCCGAC
 1651 CTTTACCTAG AAGGTTCTGA CCAATACCGT GGTTGGTTTA ACTCATCACT
 1701 TATCACATCT GTTGCCAACC ATGGCGTAGC ACCTTACAAA CAAATCTTGT
 1751 CACAAGGTTT TGCCCTTGAT GGTAAAGGTG AGAAGATGTC TAAATCTCTT
 1801 GGAAATACCA TTGCTCCAAG CGATGTTGAA AAACAATTCG GTGCTGAAAT
 1851 CTTGCGTCTC TGGGTAACAA GTGTTGACTC AAGCAATGAC GTGCGTATCT
 1901 CTATGGATAT TTTGAGCCAA GTTTCTGAAA CTTACCGTAA GATTCGTAAC
 1951 ACTCTTCGTT TCTTGATTGC CAATACATCT GACTTTAACC CAGCTCAAGA
 2001 TACAGTCGCT TACGATGAGC TTCGTTCAGT TGATAAGTAC ATGACGATTC
 2051 GCTTTAACCA GCTTGTCAAG ACCATTCGTG ATGCCTATGC AGACTTTGAA
 2101 TTCTTGACGA TCTACAAGGC CTTGGTGAAC TTTATCAACG TTGACTTGTC
 2151 AGCCTTCTAC CTTGATTTTG CCAAAGATGT TGTTTACATT GAAGGTGCCA
 2201 AATCACTGGA ACGCCGTCAA ATGCAGACTG TCTTCTATGA CATTCTTGTC
 2251 AAAATCACCA AACTCTTGAC ACCAATCCTT CCTCACACTG CGGAAGAAAT
 2301 TTGGTCATAT CTTGAGTTTG AAACAGAAGA CTTCGTCCAA TTGTCAGAAT
 2351 TACCAGAGGC TCAAACTTTT GCTAATCAAG AAGAAATCTT GGATACATGG
 2401 GCAGCCTTCA TGGACTTCCG TGGACAAGCT CAAAAAGCCT TGGAAGAAGC
 2451 TCGTAATGCA AAAGTAATCG GTAAATCACT TGAAGCACAC TTGACAGTTT
 2501 ATCCAAACGA AGTTGTGAAA ACTCTACTCG AAGCAGTAAA CAGCAATGTG
 2551 GCTCAACTTT TGATCGTGTC AGACTTGACC ATCGCAGAAG GACCAGCTCC
 2601 AGAAGCTGCC CTTAGCTTCG AAGATGTAGC CTTCACAGTT GAACGCGCTG
 2651 CAGGTGAAGT ATGTGACCGT TGCCGTCGTA TTGACCCAAC AACAGCAGAA
 2701 CGTAGCTACC AGGCAGTTAT CTGTGACCAC TGTGCAAGCA TCGTAGAAGA
 2751 AAACTTTGCG GAAGCAGTCG CAGAAGGATT TGAAGAGAAA TAA-3'
 (B) ileS polypeptide sequence deduced from tbe polynucleotide
 sequence in this table [SEQ ID NO:2].
 NH.sub.2 -1 MKLKDTLNLG KTEFPMRAGL PTKEPVWQKE WEDAKLYQRR QELNQGKPHF
 51 TLHDGPPYAN GNIHVGHAMN KISKDIIVRS KSMSGFYAPF IPGWDTHGLP
 101 IEQVLSKQGV KRKEMDLVEY LKLCREYALS QVDKQREDFK RLGVSGDWEN
 151 PYVTLTPDYE AAQIRVFGEM ANKGYIYRGA KPVYWSWSSE SALAEAEIEY
 201 HDLVSTSLYY ANKVKDGKGV LDTDTYIVVW TTTPFTITAS RGLTVGADID
 251 YVLVQPAGEA RKFVVAAELL TSLSEKFGWA DVQVLETYRG QELNHIVTEH
 301 PWDTAVEELV ILGDHVTTDS GTGIVHTAPG FGEDDYNVGI ANNLEVAVTV
 351 DERGIMMKNA GPEFEGQFYE KVVPTVIEKL GNLLLAQEEI SHSYPFDWRT
 401 KKPIIWRAVP QWFASVSKFR QEILDEIEKV KFHSEWGKVR LYNMIRDRGD
 451 WVISRQRAWG VPLPIFYAED GTAIMVAETI EHVAQLFEEH GSSIWWERDA
 501 KDLLPEGFTH PGSPNGEFKK ETDIMDVWFD SGSSWNGVVV NRPELTYPAD
 551 LYLEGSDQYR GWFNSSLITS VANHGVAPYK QILSQGFALD GKGEKMSKSL
 601 GNTIAPSDVE KQFGAEILRL WVTSVDSSND VRISMDILSQ VSETYRKIRN
 651 TLRFLIANTS DFNPAQDTVA YDELRSVDKY MTIRFNQLVK TIRDAYADFE
 701 FLTIYKALVN FINVDLSAFY LDFAKDVVYI EGAKSLERRQ MQTVFYDILV
 751 KITKLLTPIL PHTAEEIWSY LEFETEDFVQ LSELPEAQTF ANQEEILDTW
 801 AAFMDFRGQA QKALEEARNA KVIGKSLEAH LTVYPNEVVK TLLEAVNSNV
 851 AQLLIVSDLT IAEGPAPEAA LSFEDVAFTV ERAAGEVCDR CRRIDPTTAE
 901 RSYQAVICDH CASIVEENFA EAVAEGFEEK-COOH
 (C) Polynucleotide sequence embodiments [SEQ ID NO: 1].
 X-(R.sub.1).sub.N -1 ATGAAACTCA AAGACACCCT TAATCTTGGG AAAACTGAAT TCCCAATGCG
 51 TGCAGGCCTT CCTACCAAAG AGCCAGTTTG GCAAAAGGAA TGGGAAGATG
 101 CAAAACTTTA TCAACGTCGT CAAGAATTGA ACCAAGGAAA ACCTCATTTC
 151 ACCTTGCATG ATGGCCCTCC ATACGCTAAC GGAAATATCC ACGTTGGACA
 201 TGCTATGAAC AAGATTTCAA AAGATATCAT TGTTCGTTCT AAGTCTATGT
 251 CAGGATTTTA CGCGCCATTT ATTCCTGGTT GGGATACTCA TGGTCTGCCA
 301 ATCGAGCAAG TCTTGTCAAA ACAAGGTGTC AAACGTAAAG AAATGGACTT
 351 GGTTGAGTAC TTGAAACTTT GCCGTGAGTA CGCTCTTTCT CAAGTAGATA
 401 AACAACGTGA AGATTTTAAA CGTTTGGGTG TTTCTGGTGA CTGGGAAAAT
 451 CCATATGTGA CCTTGACTCC TGACTATGAA GCAGCTCAAA TTCGTGTATT
 501 TGGTGAGATG GCTAATAAGG GTTATATCTA CCGTGGTGCC AAGCCAGTTT
 551 ACTGGTCATG GTCATCTGAG TCAGCCCTTG CTGAAGCAGA GATTGAATAC
 601 CATGACTTGG TTTCAACTTC CCTTTACTAT GCCAACAAGG TAAAAGATGG
 651 CAAAGGAGTT CTAGATACAG ATACTTATAT CGTTGTCTGG ACAACGACTC
 701 CATTTACCAT CACAGCTTCT CGTGGTTTGA CGGTTGGTGC AGATATTGAT
 751 TACGTTTTGG TTCAACCTGC TGGTGAAGCT CGTAAGTTTG TCGTTGCTGC
 801 TGAATTATTG ACTAGCTTGT CTGAGAAATT TGGCTGGGCT GATGTTCAAG
 851 TTTTGGAAAC TTACCGTGGC CAAGAACTTA ACCACATCGT AACAGAACAC
 901 CCATGGGATA CAGCTGTAGA AGAGTTGGTA ATTCTTGGTG ACCACGTTAC
 951 GACTGACTCT GGTACAGGTA TTGTCCATAC AGCCCCTGGT TTTGGTGAGG
 1001 ACGACTACAA TGTTGGTATT GCTAATAATC TTGAAGTCGC AGTGACTGTT
 1051 GATGAACGTG GTATCATGAT GAAGAATGCT GGTCCTGAGT TTGAAGGTCA
 1101 ATTCTATGAA AAGGTAGTTC CAACTGTTAT TGAAAAACTT GGTAACCTCC
 1151 TTCTTGCCCA AGAAGAAATC TCTCACTCAT ATCCATTTGA CTGGCGTACT
 1201 AAGAAACCAA TCATCTGGCG TGCAGTTCCA CAATGGTTTG CCTCAGTTTC
 1251 TAAATTCCGT CAAGAAATCT TGGACGAAAT TGAAAAAGTG AAATTCCACT
 1301 CAGAATGGGG TAAAGTCCGT CTTTACAATA TGATCCGTGA CCGTGGTGAC
 1351 TGGGTTATCT CTCGTCAACG TGCTTGGGGT GTTCCACTTC CAATCTTCTA
 1401 TGCAGAAGAC GGTACAGCTA TCATGGTAGC TGAAACGATT GAACACGTAG
 1451 CTCAACTTTT TGAAGAACAT GGTTCAAGCA TTTGGTGGGA ACGTGATGCC
 1501 AAAGATCTCT TGCCAGAAGG ATTTACTCAT CCAGGTTCAC CAAACGGCGA
 1551 GTTCAAAAAA GAAACTGATA TCATGGACGT TTGGTTTGAC TCAGGTTCAT
 1601 CATGGAATGG AGTGGTGGTA AACCGTCCTG AATTGACTTA CCCAGCCGAC
 1651 CTTTACCTAG AAGGTTCTGA CCAATACCGT GGTTGGTTTA ACTCATCACT
 1701 TATCACATCT GTTGCCAACC ATGGCGTAGC ACCTTACAAA CAAATCTTGT
 1751 CACAAGGTTT TGCCCTTGAT GGTAAAGGTG AGAAGATGTC TAAATCTCTT
 1801 GGAAATACCA TTGCTCCAAG CGATGTTGAA AAACAATTCG GTGCTGAAAT
 1851 CTTGCGTCTC TGGGTAACAA GTGTTGACTC AAGCAATGAC GTGCGTATCT
 1901 CTATGGATAT TTTGAGCCAA GTTTCTGAAA CTTACCGTAA GATTCGTAAC
 1951 ACTCTTCGTT TCTTGATTGC CAATACATCT GACTTTAACC CAGCTCAAGA
 2001 TACAGTCGCT TACGATGAGC TTCGTTCAGT TGATAAGTAC ATGACGATTC
 2051 GCTTTAACCA GCTTGTCAAG ACCATTCGTG ATGCCTATGC AGACTTTGAA
 2101 TTCTTGACGA TCTACAAGGC CTTGGTGAAC TTTATCAACG TTGACTTGTC
 2151 AGCCTTCTAC CTTGATTTTG CCAAAGATGT TGTTTACATT GAAGGTGCCA
 2201 AATCACTGGA ACGCCGTCAA ATGCAGACTG TCTTCTATGA CATTCTTGTC
 2251 AAAATCACCA AACTCTTGAC ACCAATCCTT CCTCACACTG CGGAAGAAAT
 2301 TTGGTCATAT CTTGAGTTTG AAACAGAAGA CTTCGTCCAA TTGTCAGAAT
 2351 TACCAGAGGC TCAAACTTTT GCTAATCAAG AAGAAATCTT GGATACATGG
 2401 GCAGCCTTCA TGGACTTCCG TGGACAAGCT CAAAAAGCCT TGGAAGAAGC
 2451 TCGTAATGCA AAAGTAATCG GTAAATCACT TGAAGCACAC TTGACAGTTT
 2501 ATCCAAACGA AGTTGTGAAA ACTCTACTCG AAGCAGTAAA CAGCAATGTG
 2551 GCTCAACTTT TGATCGTGTC AGACTTGACC ATCGCAGAAG GACCAGCTCC
 2601 AGAAGCTGCC CTTAGCTTCG AAGATGTAGC CTTCACAGTT GAACGCGCTG
 2651 CAGGTGAAGT ATGTGACCGT TGCCGTCGTA TTGACCCAAC AACAGCAGAA
 2701 CGTAGCTACC AGGCAGTTAT CTGTGACCAC TGTGCAAGCA TCGTAGAAGA
 2751 AAACTTTGCG GAAGCAGTCG CAGAAGGATT TGAAGAGAAA TAA-(R.sub.2).sub.N
 -Y
 (D) Polypeptide sequence embodiments [SEQ ID NO:2].
 X-(R.sub.1).sub.n -1 MKLKDTLNLG KTEFPMRAGL PTKEPVWQKE WEDAKLYQRR QELNQGKPHF
 51 TLHDGPPYAN GNIHVGHAMN KISKDIIVRS KSMSGFYAPF IPGWDTHGLP
 101 IEQVLSKQGV KRKEMDLVEY LKLCREYALS QVDKQREDFK RLGVSGDWEN
 151 PYVTLTPDYE AAQIRVFGEM ANKGYIYRGA KPVYWSWSSE SALAEAEIEY
 201 HDLVSTSLYY ANKVKDGKGV LDTDTYIVVW TTTPFTITAS RGLTVGADID
 251 YVLVQPAGEA RKFVVAAELL TSLSEKFGWA DVQVLETYRG QELNHIVTEH
 301 PWDTAVEELV ILGDHVTTDS GTGIVHTAPG FGEDDYNVGI ANNLEVAVTV
 351 DERGIMMKNA GPEFEGQFYE KVVPTVIEKL GNLLLAQEEI SHSYPFDWRT
 401 KKPIIWRAVP QWFASVSKFR QEILDEIEKV KFHSEWGKVR LYNMIRDRGD
 451 WVISRQRAWG VPLPIFYAED GTAIMVAETI EHVAQLFEEH GSSIWWERDA
 501 KDLLPEGFTH PGSPNGEFKK ETDIMDVWFD SGSSWNGVVV NRPELTYPAD
 551 LYLEGSDQYR GWFNSSLITS VANHGVAPYK QILSQGFALD GKGEKMSKSL
 601 GNTIAPSDVE KQFGAEILRL WVTSVDSSND VRISMDILSQ VSETYRKIRN
 651 TLRFLIANTS DFNPAQDTVA YDELRSVDKY MTIRFNQLVK TIRDAYADFE
 701 FLTIYKALVN FINVDLSAFY LDFAKDVVYI EGAKSLERRQ MQTVFYDILV
 751 KITKLLTPIL PHTAEEIWSY LEFETEDFVQ LSELPEAQTF ANQEEILDTW
 801 AAFMDFRGQA QKALEEARNA KVIGKSLEAH LTVYPNEVVK TLLEAVNSNV
 851 AQLLIVSDLT IAEGPAPEAA LSFEDVAFTV ERAAGEVCDR CRRIDPTTAE
 901 RSYQAVICDH CASIVEENFA EAVAEGFEEK-(R.sub.2).sub.n -Y
 (E) Sequences from Streptococcus pneumoniae ileS polynucleotide
 sequence.
 Fragment 1 [SEQ ID NO:5]
 5'- ATGAAACTCA AAGACACCCT TAATCTTGGG AAAACTGAAT TCCCAATGCG
 TGCAGGCCTT CCTACCAAAG AGCCAGTTTG GCAAAAGGAA TGGGAAGATG
 CAAAACTTTA TCAACGTCGT CAAGAATTGA ACCAAGGAAA ACCTCATTTC
 ACCTTGCATG ATGGCCCTCC ATACGCTAAC GGAAATATCC ACGTTGGACA
 TGCTATGAAC AAGATTTCAA AAGATATCAT TGTTCGTTCT AAGTCTATGT
 CAGGATTTTA CGCGCCATTT ATTCCTGGTT GGGATACTCA TGGTCTGCCA
 ATCGAGCAAG TCTTGTCAAA ACAAGGTGTC AAACGTAAAG AAATGGACTT
 GGTTGAGTAC TTGAAACTTT GCCGTGAGTA CGCTCTTTCT CAAGTAGATA
 AACAACGTGA AGATTTTAAA CGTTTGGGTG TTTCTGGTGA CTGGGAAAAT
 CCATATGTGA CCTTGACTCC TGACTATGAA GCAGCTCAAA TTCGTGTATT
 TGGTGAGATG GCTAATAAGG GTTATATCTA CCGTGGTGCC AAGCCAGTTT
 ACTGGTCATG GTCATCTGAG TCAGCCCTTG CTGAAGCAGA GATTGAATAC
 CATGACTTGG TTTCAACTTC CCTTTACTAT GCCAACAAGG TAAAAGATGG
 CAAAGGAGTT CTAGATACAG ATACTTATAT CGTTGTCTGG ACAACGACTC
 CATTTACCAT CACAGCTTCT CGTGGTTTGA CGGTTGGTGC AGATATTGAT
 TACGTTTTGG TTCAACCTGC TGGTGAAGCT CGTAAGTTTG TCGTTGCTGC
 TGAATTATTG ACTAG-3'
 Fragment 2 [SEQ ID NO:8]
 5'- TTGTCTGAGA AATTTGGCTG GGCTGATGTT CAAGTTTTGG AAACTTACCG
 TGGCCAAGAA CTTAACCACA TCGTAACAGA ACACCCATGG GATACAGCTG
 TAGAAGAGTT GGTAATTCTT GGTGACCACG TTACGACTGA CTCTGGTACA
 GGTATTGTCC ATACAGCCCC TGGTTTTGGT GAGGACGACT ACAATGTTGG
 TATTGCTAAT AATCTTGAAG TCGCAGTGAC TGTTGATGAA CGTGGTATCA
 TGATGAAGAA TGCTGGTCCT GAGTTTGAAG GTCAATTCTA TGAAAAGGTA
 GTTCCAACTG TTATTGAAAA ACTTGGTAAC CTCCTTCTTG CCCAAGAAGA
 AATCTCTCAC TCATATCCAT TTGACTGGCG TACTAAGAAA CCAATCATCT
 GGCGTGCAGT TCCACAATGG TTTGCCTCAG TTTCTAAATT CCGTCAAGAA
 ATCTTGGACG AAATTGAAAA AGTGAAATTC CACTCAGAAT GGGGTAAAGT
 CCGTCTTTAC AATATGATCC GTGACCGTGG TGACTGGGTT ATCTCTCGTC
 AACGTGCTTG GGGTGTTCCA CTTCCAATCT TCTATGCAGA AGACGGTACA
 GCTATCATGG TAGCTGAAAC GATTGAACAC GTAGCTCAAC TTTTTGAAGA
 ACATGGTTCA AGCATTTGGT GGGAACGTGA TGCCAAAGAT CTCTTGCCAG
 AAGGATTTAC TCATCCAGGT TCACCAAACG GCGAGTTCAA AAAAGAAACT
 GATATCATGG ACGTTTGGTT TGACTCAGGT TCATCATGGA ATGGAGTGGT
 GGTAAACCGT CCTGAATTGA CTTACCCAGC CGACCTTTAC CTAGAAGGTT
 CTGACCAATA CCGTGGTTGG TTTAACTCAT CACTTATCAC ATCTGTTGCC
 AACCATGGCG TAGCACCTTA CAAACAAATC TTGTCACAAG GTTTTGCCCT
 TGATGGTAAA GGTGAGAAGA TGTCTAAATC TCTTGGAAAT ACCATTGCTC
 CAAGCGATGT TGAAAAACAA TTCGGTGCTG AAATCTTGCG TCTCTGGGTA
 ACAAGTGTTG ACTCAAGCAA TGACGTGCGT ATCTCTATGG ATATTTTGAG
 CCAAGTTTCT GAAACTTACC GTAAGATTCG TAACACTCTT CGTTTCTTGA
 TTGCCAATAC ATCTGACTTT AACCCAGCTC AAGATACAGT CGCTTACGAT
 GAGCTTCGTT CAGTTGATAA GTACATGACG ATTCGCTTTA ACCAGCTTGT
 CAAGACCATT CGTGATGCCT ATGCAGACTT TGAATTCTTG ACGATCTACA
 AGGCCTTGGT GAACTTTATC AACGTTGACT TGTCAGCCTT CTACCTTGAT
 TTTGCCAAAG ATGTTGTTTA CATTGAAGGT GCCAAATCAC TGGAACGCCG
 TCAAATGCAG ACTGTCTTCT ATGACATTCT TGTCAAAATC ACCAAACTCT
 TGACACCAAT CCTTCCTCAC ACTGCGGAAG AAATTTGGTC ATATCTTGAG
 TTTGAAACAG AAGACTTCGT CCAATTGTCA GAATTACCAG AGGCTCAAAC
 TTTTGCTAAT CAAGAAGAAA TCTTGGATAC ATGGGCAGCC TTCATGGACT
 TCCGTGGACA AGCTCAAAAA GCCTTGGAAG AAGCTCGTAA TGCAAAAGTA
 ATCGGTAAAT CACTTGAAGC ACACTTGACA GTTTATCCAA ACGAAGTTGT
 GAAAACTCTA CTCGAAGCAG TAAACAGCAA TGTGGCTCAA CTTTTGATCG
 TGTCAGACTT GACCATCGCA GAAGGACCAG CTCCAGAAGC TGCCCTTAGC
 TTCGAAGATG TAGCCTTCAC AGTTGAACGC GCTGCAGGTG AAGTATGTGA
 CCGTTGCCGT CGTATTGACC CAACAACAGC AGAACGTAGC TACCAGGCAG
 TTATCTGTGA CCACTGTGCA AGCATCGTAG AAGAAAACTT TGCGGAAGCA
 GTCGCAGAAG GATTTGAAGA GAAATAA- 3'
 (F) ileS polypeptide sequence deduced from the polynucleotide
 sequence of SEQ ID NO:5 [SEQ ID NO:6].
 NH.sub.2- MKLKDTLNLG KTEFPMRAGL PTKEPVWQKE WEDAKLYQRR QELNQGKPHF
 TLHDGPPYAN GNIHVGHAMN KISKDIIVRS KSMSGFYAPF IPGWDTHGLP
 IEQVLSKQGV KRKEMDLVEY LKLCREYALS QVDKQREDFK RLGVSGDWEN
 PYVTLTPDYE AAQIRVFGEM ANKGYIYRGA KPVYWSWSSE SALAEAEIEY
 HDLVSTSLYY ANKVKDGKGV LDTDTYIVVW TTTPFTITAS RGLTVGADID
 YVLVQPAGEA RKFVVAAELL T-COOH
 ileS polypeptide sequence deduced from the polynucleotide
 sequence of SEQ ID NO:8 [SEQ ID NO:9].
 NH.sub.2- LSEKFGWADY QVLETYRGQE LNHIVTEHPW DTAVEELVIL GDHVTTDSGT
 GIVHTAPGFG EDDYNVGIAN NLEVAVTVDE RGIMMKNAGP EFEGQFYEKV
 VPTVIEKLGN LLLAQEEISH SYPFDWRTKK PIIWRAVPQW FASVSKFRQE
 ILDEIEKVKF HSEWGKVRLY NMIRDRGDWV ISRQRAWGVP LPIFYAEDGT
 AIMVAETIEH VAQLFEEHGS SIWWERDAKD LLPEGFTHPG SPNGEFKKET
 DIMDVWFDSG SSWNGVVVNR PELTYPADLY LEGSDQYRGW FNSSLITSVA
 NHGVAPYKQI LSQGFALDGK GEKMSKSLGN TIAPSDVEKQ FGAEILRLWV
 TSVDSSNDVR ISMDILSQVS ETYRKIRNTL RFLIANTSDF NPAQDTVAYD
 ELRSVDKYMT IRFNQLVKTI RDAYADFEFL TIYKALVNFI NVDLSAFYLD
 FAKDVVYIEG AKSLERRQMQ TVFYDILVKI TKLLTPILPH TAEEIWSYLE
 FETEDFVQLS ELPEAQTFAN QEEILDTWAA FMDFRGQAQK ALEEARNAKV
 IGKSLEAHLT VYPNEVVKTL LEAVNSNVAQ LLIVSDLTIA EGPAPEAALS
 FEDVAFTVER AAGEVCDRCR RIDPTTAERS YQAVICDHCA SIVEENFAEA
 VAEGFEEK-COOH
 (G) Polynucleotide sequence embodiments.
 Fragent 1 [SEQ ID NO:5]
 X-(R.sub.1).sub.n - ATGAAACTCA AAGACACCCT TAATCTTGGG AAAACTGAAT TCCCAATGCG
 TGCAGGCCTT CCTACCAAAG AGCCAGTTTG GCAAAAGGAA TGGGAAGATG
 CAAAACTTTA TCAACGTCGT CAAGAATTGA ACCAAGGAAA ACCTCATTTC
 ACCTTGCATG ATGGCCCTCC ATACGCTAAC GGAAATATCC ACGTTGGACA
 TGCTATGAAC AAGATTTCAA AAGATATCAT TGTTCGTTCT AAGTCTATGT
 CAGGATTTTA CGCGCCATTT ATTCCTGGTT GGGATACTCA TGGTCTGCCA
 ATCGAGCAAG TCTTGTCAAA ACAAGGTGTC AAACGTAAAG AAATGGACTT
 GGTTGAGTAC TTGAAACTTT GCCGTGAGTA CGCTCTTTCT CAAGTAGATA
 AACAACGTGA AGATTTTAAA CGTTTGGGTG TTTCTGGTGA CTGGGAAAAT
 CCATATGTGA CCTTGACTCC TGACTATGAA GCAGCTCAAA TTCGTGTATT
 TGGTGAGATG GCTAATAAGG GTTATATCTA CCGTGGTGCC AAGCCAGTTT
 ACTGGTCATG GTCATCTGAG TCAGCCCTTG CTGAAGCAGA GATTGAATAC
 CATGACTTGG TTTCAACTTC CCTTTACTAT GCCAACAAGG TAAAAGATGG
 CAAAGGAGTT CTAGATACAG ATACTTATAT CGTTGTCTGG ACAACGACTC
 CATTTACCAT CACAGCTTCT CGTGGTTTGA CGGTTGGTGC AGATATTGAT
 TACGTTTTGG TTCAACCTGC TGGTGAAGCT CGTAAGTTTG TCGTTGCTGC
 TGAATTATTG ACTAG- (R.sub.2).sub.n -Y
 Fragent 2 [SEQ ID NO:8]
 X-(R.sub.1).sub.n- TTGTCTGAGA AATTTGGCTG GGCTGATGTT CAAGTTTTGG AAACTTACCG
 TGGCCAAGAA CTTAACCACA TCGTAACAGA ACACCCATGG GATACAGCTG
 TAGAAGAGTT GGTAATTCTT GGTGACCACG TTACGACTGA CTCTGGTACA
 GGTATTGTCC ATACAGCCCC TGGTTTTGGT GAGGACGACT ACAATGTTGG
 TATTGCTAAT AATCTTGAAG TCGCAGTGAC TGTTGATGAA CGTGGTATCA
 TGATGAAGAA TGCTGGTCCT GAGTTTGAAG GTCAATTCTA TGAAAAGGTA
 GTTCCAACTG TTATTGAAAA ACTTGGTAAC CTCCTTCTTG CCCAAGAAGA
 AATCTCTCAC TCATATCCAT TTGACTGGCG TACTAAGAAA CCAATCATCT
 GGCGTGCAGT TCCACAATGG TTTGCCTCAG TTTCTAAATT CCGTCAAGAA
 ATCTTGGACG AAATTGAAAA AGTGAAATTC CACTCAGAAT GGGGTAAAGT
 CCGTCTTTAC AATATGATCC GTGACCGTGG TGACTGGGTT ATCTCTCGTC
 AACGTGCTTG GGGTGTTCCA CTTCCAATCT TCTATGCAGA AGACGGTACA
 GCTATCATGG TAGCTGAAAC GATTGAACAC GTAGCTCAAC TTTTTGAAGA
 ACATGGTTCA AGCATTTGGT GGGAACGTGA TGCCAAAGAT CTCTTGCCAG
 AAGGATTTAC TCATCCAGGT TCACCAAACG GCGAGTTCAA AAAAGAAACT
 GATATCATGG ACGTTTGGTT TGACTCAGGT TCATCATGGA ATGGAGTGGT
 GGTAAACCGT CCTGAATTGA CTTACCCAGC CGACCTTTAC CTAGAAGGTT
 CTGACCAATA CCGTGGTTGG TTTAACTCAT CACTTATCAC ATCTGTTGCC
 AACCATGGCG TAGCACCTTA CAAACAAATC TTGTCACAAG GTTTTGCCCT
 TGATGGTAAA GGTGAGAAGA TGTCTAAATC TCTTGGAAAT ACCATTGCTC
 CAAGCGATGT TGAAAAACAA TTCGGTGCTG AAATCTTGCG TCTCTGGGTA
 ACAAGTGTTG ACTCAAGCAA TGACGTGCGT ATCTCTATGG ATATTTTGAG
 CCAAGTTTCT GAAACTTACC GTAAGATTCG TAACACTCTT CGTTTCTTGA
 TTGCCAATAC ATCTGACTTT AACCCAGCTC AAGATACAGT CGCTTACGAT
 GAGCTTCGTT CAGTTGATAA GTACATGACG ATTCGCTTTA ACCAGCTTGT
 CAAGACCATT CGTGATGCCT ATGCAGACTT TGAATTCTTG ACGATCTACA
 AGGCCTTGGT GAACTTTATC AACGTTGACT TGTCAGCCTT CTACCTTGAT
 TTTGCCAAAG ATGTTGTTTA CATTGAAGGT GCCAAATCAC TGGAACGCCG
 TCAAATGCAG ACTGTCTTCT ATGACATTCT TGTCAAAATC ACCAAACTCT
 TGACACCAAT CCTTCCTCAC ACTGCGGAAG AAATTTGGTC ATATCTTGAG
 TTTGAAACAG AAGACTTCGT CCAATTGTCA GAATTACCAG AGGCTCAAAC
 TTTTGCTAAT CAAGAAGAAA TCTTGGATAC ATGGGCAGCC TTCATGGACT
 TCCGTGGACA AGCTCAAAAA GCCTTGGAAG AAGCTCGTAA TGCAAAAGTA
 ATCGGTAAAT CACTTGAAGC ACACTTGACA GTTTATCCAA ACGAAGTTGT
 GAAAACTCTA CTCGAAGCAG TAAACAGCAA TGTGGCTCAA CTTTTGATCG
 TGTCAGACTT GACCATCGCA GAAGGACCAG CTCCAGAAGC TGCCCTTAGC
 TTCGAAGATG TAGCCTTCAC AGTTGAACGC GCTGCAGGTG AAGTATGTGA
 CCGTTGCCGT CGTATTGACC CAACAACAGC AGAACGTAGC TACCAGGCAG
 TTATCTGTGA CCACTGTGCA AGCATCGTAG AAGAAAACTT TGCGGAAGCA
 GTCGCAGAAG GATTTGAAGA GAAATAA-(R.sub.2).sub.n -Y
 (H) Polypeptide sequence embodiments [SEQ ID NO:6].
 X-(R.sub.1).sub.n - MKLKDTLNLG KTEFPMRAGL PTKEPVWQKE WEDAKLYQRR QELNQGKPHF
 TLHDGPPYAN GNIHVGHAMN KISKDIIVRS KSMSGFYAPF IPGWDTHGLP
 IEQVLSKQGV KRKEMDLVEY LKLCREYALS QVDKQREDFK RLGVSGDWEN
 PYVTLTPDYE AAQIRVFGEM ANKGYIYRGA KPVYWSWSSE SALAEAEIEY
 HDLVSTSLYY ANKVKDGKGV LDTDTYIVVW TTTPFTITAS RGLTVGADID
 YVLVQPAGEA RKFVVAAELL T-(R.sub.2).sub.n-Y
 [SEQ ID NO:9]
 X-(R.sub.1).sub.n- LSEKFGWADV QVLETYRGQE LNHIVTEHPW DTAVEELVIL GDHVTTDSGT
 GIVHTAPGFG EDDYNVGIAN NLEVAVTVDE RGIMMKNAGP EFEGQFYEKV
 VPTVIEKLGN LLLAQEEISH SYPFDWRTKK PIIWRAVPQW FASVSKFRQE
 ILDEIEKVKF HSEWGKVRLY NMIRDRGDWV ISRQRAWGVP LPIFYAEDGT
 AIMVAETIEH VAQLFEEHGS SIWWERDAKD LLPEGFTHPG SPNGEFKKET
 DIMDVWFDSG SSWNGVVVNR PELTYPADLY LEGSDQYRGW FNSSLITSVA
 NHGVAPYKQI LSQGFALDGK GEKMSKSLGN TIAPSDVEKQ FGAEILRLWV
 TSVDSSNDVR ISMDILSQVS ETYRKIRNTL RFLIANTSDF NPAQDTVAYD
 ELRSVDKYMT IRFNQLVKTI RDAYADFEFL TIYKALVNFI NVDLSAFYLD
 FAKDVVYIEG AKSLERRQMQ TVFYDILVKI TKLLTPILPH TAEETWSYLE
 FETEDFVQLS ELPEAQTFAN QEEILDTWAA FMDFRGQAQK ALEEARNAKV
 IGKSLEAHLT VYPNEVVKTL LEAVNSNVAQ LLIVSDLTIA EGPAPEAALS
 FEDVAFTVER AAGEVCDRCR RIDPTTAERS YQAVICDHCA SIVEENFAEA
 VAEGFEEK- (R.sub.2).sub.n -Y
 (I) Polynucleotide sequence embodiment [SEQ ID NO:10] .
 5'- CAACTTTTTG AAGAACATGG TTCAAGCATT TGGTGGGAAC GTGATGCCAA
 AGATCTCTTG CCAGAAGGAT TTACTCATCC AGGTTCACCA AACGGCGAGT
 TCAAAAAAGA AACTGATATC ATGGACGTTT GGTTTGACTC AGGTTCATCA
 TGGAATGGAG TGGTGGTAAA CCGTCCTGAA TTGACTTACC CAGCCGACCT
 TTACCTAGAA GGTTCTGACC AATACCGTGG TTGGTTTAAC TCATCACTTA
 TCACATCTGT TGCCAACCAT GGCGTAGCAC CTTACAAACA AATCTTGTCA
 CAAGGTTTTG CCCTTGATGG TAAAGGTGAG AAGATGTCTA AATCTCTTGG
 AAATACCATT GCTCCAAGCG ATGTTGAAAA ACAATTCGGG-3'
 Deposited materials
 A deposit containing a Streptococcus pneumoniae 0100993 strain has been
 deposited with the National Collections of Industrial and Marine Bacteria
 Ltd. (herein "NCIMB"), 23 St. Machar Drive, Aberdeen AB2 1RY, Scotland on
 Apr. 11, 1996 and assigned deposit number 40794. The deposit was described
 as Streptococcus peumnoniae 0100993 on deposit. On Apr. 17, 1996 a
 Streptococcus peumnoniae 0100993 DNA library in E. coli was similarly
 deposited with the NCIMB and assigned deposit number 40800. The
 Streptococcus pneumoniae strain deposit is referred to herein as "the
 deposited strain" or as "the DNA of the deposited strain."
 The deposited strain contains the full length ileS gene. The sequence of
 the polynucleotides contained in the deposited strain, as well as the
 amino acid sequence of the polypeptide encoded thereby, are controlling in
 the event of any conflict with any description of sequences herein.
 The deposit of the deposited strain has been made under the terms of the
 Budapest Treaty on the International Recognition of the Deposit of
 Micro-organisms for Purposes of Patent Procedure. The strain will be
 irrevocably and without restriction or condition released to the public
 upon the issuance of a patent. The deposited strain is provided merely as
 convenience to those of skill in the art and is not an admission that a
 deposit is required for enablement, such as that required under 35 U.S.C.
 .sctn.112.
 A license may be required to make, use or sell the deposited strain, and
 compounds derived therefrom, and no such license is hereby granted.
 Polypeptides
 The polypeptides of the invention include the polypeptide of Table 1 [SEQ
 ID NO: 2, 6 and 9] (in particular the mature polypeptide) as well as
 polypeptides and fragments, particularly those which have the biological
 activity of ileS, and also those which have at least 70% identity to the
 polypeptide of Table 1 [SEQ ID NO: 2, 6 and 9] or the relevant portion,
 preferably at least 80% identity to the polypeptide of Table 1 [SEQ ID NO:
 2, 6 and 9], and more preferably at least 90% similarity (more preferably
 at least 90% identity) to the polypeptide of Table 1 [SEQ ID NO: 2, 6 and
 9] and still more preferably at least 95% similarity (still more
 preferably at least 95% identity) to the polypeptide of Table 1 [SEQ ID
 NO: 2, 6 and 9] and also include portions of such polypeptides with such
 portion of the polypeptide generally containing at least 30 amino acids
 and more preferably at least 50 amino acids.
 The invention also includes polypeptides of the formula set forth in Table
 1 (D) wherein, at the amino terminus, X is hydrogen, and at the carboxyl
 terminus, Y is hydrogen or a metal, R.sub.1 and R.sub.2 is any amino acid
 residue, and n is an integer between 1 and 1000 or 2000. Any stretch of
 amino acid residues denoted by either R group, where n is an integer
 grater than 1, may be either a heteropolymer or a homopolymer, preferably
 a heteropolymer.
 The invention also includes polypeptides of the formula set forth in Table
 1 (H) wherein, at the amino terminus, X is hydrogen, and at the carboxyl
 terminus, Y is hydrogen or a metal, R.sub.1 and R.sub.2 is any amino acid
 residue, and n is an integer between 1 and 1000. Any stretch of amino acid
 residues denoted by either R group, where R is greater than 1, may be
 either a heteropolymer or a homopolymer, preferably a heteropolymer.
 A fragment is a variant polypeptide having an amino acid sequence that
 entirely is the same as part but not all of the amino acid sequence of the
 aforementioned polypeptides. As with ileS polypeptides fragments may be
 "free-standing," or comprised within a larger polypeptide of which they
 form a part or region, most preferably as a single continuous region, a
 single larger polypeptide.
 Preferred fragments include, for example, truncation polypeptides having a
 portion of the amino acid sequence of Table 1 [SEQ ID NO: 2, 6 and 9], or
 of variants thereof, such as a continuous series of residues that includes
 the amino terminus, or a continuous series of residues that includes the
 carboxyl terminus. Degradation forms of the polypeptides of the invention
 in a host cell, particularly a Streptococcus pneumoniae, are also
 preferred. Further preferred are fragments characterized by structural or
 functional attributes such as fragments that comprise alpha-helix and
 alpha-helix forming regions, beta-sheet and beta-sheet-forming regions,
 turn and turn-forming regions, coil and coil-forming regions, hydrophilic
 regions, hydrophobic regions, alpha amphipathic regions, beta amphipathic
 regions, flexible regions, surface-forming regions, substrate binding
 region, and high antigenic index regions.
 Also preferred are biologically active fragments which are those fragments
 that mediate activities of ileS, including those with a similar activity
 or an improved activity, or with a decreased undesirable activity. Also
 included are those fragments that are antigenic or immunogenic in an
 animal, especially in a human. Particularly preferred are fragments
 comprising receptors or domains of enzymes that confer a function
 essential for viability of Streptococcus pneumoniae or the ability to
 initiate, or maintain cause disease in an individual, particularly a
 human.
 Variants that are fragments of the polypeptides of the invention may be
 employed for producing the corresponding full-length polypeptide by
 peptide synthesis; therefore, these variants may be employed as
 intermediates for producing the full-length polypeptides of the invention.
 Polynucleotides
 Another aspect of the invention relates to isolated polynucleotides,
 including the full length gene, that encode the ileS polypeptide having
 the deduced amino acid sequence of Table 1 [SEQ ID NO: 2, 6 and 9] and
 polynucleotides closely related thereto and variants thereof.
 Using the information provided herein, such as the polynucleotide sequence
 set out in Table 1 [SEQ ID NO: 1, 5, 8 and 10], a polynucleotide of the
 invention encoding ileS polypeptide may be obtained using standard cloning
 and screening methods, such as those for cloning and sequencing
 chromosomal DNA fragments from bacteria using Streptococcus pneumoniae
 0100993 cells as starting material, followed by obtaining a full length
 clone. For example, to obtain a polynucleotide sequence of the invention,
 such as the sequence given in Table 1 [SEQ ID NO: 1, 5, 8 and 10],
 typically a library of clones of chromosomal DNA of Streptococcus
 pneumoniae 0100993 in E.coli or some other suitable host is probed with a
 radiolabeled oligonucleotide, preferably a 17-mer or longer, derived from
 a partial sequence. Clones carrying DNA identical to that of the probe can
 then be distinguished using stringent conditions. By sequencing the
 individual clones thus identified with sequencing primers designed from
 the original sequence it is then possible to extend the sequence in both
 directions to determine the full gene sequence. Conveniently, such
 sequencing is performed using denatured double stranded DNA prepared from
 a plasmid clone. Suitable techniques are described by Maniatis, T.,
 Fritsch, E. F. and Sambrook et al., MOLECULAR CLONING, A LABORATORY
 MANUAL, 2nd Ed.; Cold Spring Harbor Laboratory Press, Cold Spring Harbor,
 N.Y. (1989). (see in particular Screening By Hybridization 1.90 and
 Sequencing Denatured Double-Stranded DNA Templates 13.70). Illustrative of
 the invention, the polynucleotide set out in Table 1 [SEQ ID NO: 1, 5, 8
 and 10] was discovered in a DNA library derived from Streptococcus
 pneumoniae 0100993.
 The DNA sequence set out in Table 1 [ SEQ ID NO: 1, 5, 8 and 10] contains
 an open reading frame encoding a protein having about the number of amino
 acid residues set forth in Table 1 [SEQ ID NO: 2, 6 and 9] with a deduced
 molecular weight that can be calculated using amino acid residue molecular
 weight values well known in the art. The polynucleotide of SEQ ID NO: 1,
 between nucleotide number 1 through number 2790 encodes the polypeptide of
 SEQ ID NO: 2. The stop codon begins at nucleotide number 2791 of SEQ ID
 NO: 1.
 The other DNA sequences set out in Table 1 as SEQ ID NOS: 5 and 8 contain
 open reading frames encoding a protein having about the number of amino
 acid residues set forth in Table 1 as SEQ ID NO: 6 and 9, respectively,
 with a deduced molecular weight that can be calculated using amino acid
 residue molecular weight values well known in the art. The start codon of
 the DNA in Table 1 is nucleotide number 1 and last codon that encodes an
 amino acid is number 815 for "Fragment 1" herein, and analogously 1 to
 1974 for "Fragment 2" herein, the stop codon being the next codon
 following this last codon encoding an amino acid.
 ileS of the invention is structurally related to other proteins of the
 isoleucyl tRNA synthetase family, as shown by the results of sequencing
 the DNA encoding ileS of the deposited strain. The protein exhibits
 greatest homology to Staphylococcus aureus isoleucyl tRNA synthetase
 protein among known proteins. ileS of Table 1 [SEQ ID NO: 2, 6 and 9] has
 about 55% identity over its entire length and about 71% similarity over
 its entire length with the amino acid sequence of Staphylococcus aureus
 isoleucyl tRNA synthetase polypeptide.
 The invention provides a polynucleotide sequence identical over its entire
 length to the coding sequence in Table 1 [SEQ ID NO: 1, 5, 8 and 10]. Also
 provided by the invention is the coding sequence for the mature
 polypeptide or a fragment thereof, by itself as well as the coding
 sequence for the mature polypeptide or a fragment in reading frame with
 other coding sequence, such as those encoding a leader or secretory
 sequence, a pre-, or pro or prepro-protein 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 transcribed,
 non-translated sequences, termination signals, ribosome binding sites,
 sequences that stabilize mRNA, introns, polyadenylation signals, and
 additional coding sequence which encode additional amino acids. For
 example, a marker sequence that facilitates purification of the fused
 polypeptide can be encoded. In certain embodiments of the invention, the
 marker sequence is a hexa-histidine peptide, as provided in the pQE vector
 (Qiagen, Inc.) and described in Gentz et al., Proc. Natl. Acad. Sci., USA
 86: 821-824 (1989), or an HA tag (Wilson et al., Cell 37: 767 (1984).
 Polynucleotides of the invention also include, but are not limited to,
 polynucleotides comprising a structural gene and its naturally associated
 sequences that control gene expression.
 A preferred embodiment of the invention is the polynucleotide of comprising
 nucleotide 1 to 2790 set forth in SEQ ID NO: 1 of Table 1 which encodes
 the ileS polypeptide.
 Another preferred embodiment of the invention includes, for example, a
 polynucleotide comprising nucleotide 1 to 815 or 1 to 1974 set forth in
 SEQ ID NO: 5 and SEQ ID NO: 8 respectively of Table 1 each of which
 encodes ileS polypeptide.
 The invention also includes polynucleotides of the formula set forth in
 Table 1 (C) wherein, at the 5' end of the molecule, X is hydrogen, and at
 the 3' end of the molecule, Y is hydrogen or a metal, R.sub.1 and R.sub.2
 is any nucleic acid residue, and n is an integer between 1 and 1000, 2000
 or 3000. Any stretch of nucleic acid residues denoted by either R group,
 where R is greater than 1, may be either a heteropolymer or a homopolymer,
 preferably a heteropolymer.
 The invention also includes polynucleotides of the formula set forth in
 Table 1 (G) wherein, at the 5' end of the molecule, X is hydrogen, and at
 the 3' end of the molecule, Y is hydrogen or a metal, R.sub.1 and R.sub.2
 is any nucleic acid residue, and n is an integer between 1 and 1000. Any
 stretch of nucleic acid residues denoted by either R group, where R is
 greater than 1, may be either a heteropolymer or a homopolymer, preferably
 a heteropolymer.
 The term "polynucleotide encoding a polypeptide" as used herein encompasses
 polynucleotides that include a sequence encoding a polypeptide of the
 invention, particularly a bacterial polypeptide and more particularly a
 polypeptide of the Streptococcus pneumoniae ileS having the amino acid
 sequence set out in Table 1 [SEQ ID NO: 2, 6 and 9]. The term also
 encompasses polynucleotides that include a single continuous region or
 discontinuous regions encoding the polypeptide (for example, interrupted
 by integrated phage or an insertion sequence or editing) together with
 additional regions, that also may contain coding and/or non-coding
 sequences.
 The invention further relates to variants of the polynucleotides described
 herein that encode for variants of the polypeptide having the deduced
 amino acid sequence of Table 1 [SEQ ID NO: 2, 6 and 9]. Variants that are
 fragments of the polynucleotides of the invention may be used to
 synthesize full-length polynucleotides of the invention.
 Further particularly preferred embodiments are polynucleotides encoding
 ileS variants, that have the amino acid sequence of ileS polypeptide of
 Table 1 [SEQ ID NO: 2, 6 and 9] in which several, a few, 5 to 10, 1 to 5,
 1 to 3, 2, 1 or no amino acid residues are substituted, deleted or added,
 in any combination. Especially preferred among these are silent
 substitutions, additions and deletions, that do not alter the properties
 and activities of ileS.
 Further preferred embodiments of the invention are polynucleotides that are
 at least 70% identical over their entire length to a polynucleotide
 encoding ileS polypeptide having the amino acid sequence set out in Table
 1 [SEQ ID NO: 2, 6 and 9], and polynucleotides that are complementary to
 such polynucleotides. Alternatively, most highly preferred are
 polynucleotides that comprise a region that is at least 80% identical over
 its entire length to a polynucleotide encoding ileS polypeptide of the
 deposited strain and polynucleotides complementary thereto. In this
 regard, polynucleotides at least 90% identical over their entire length to
 the same are particularly preferred, and among these particularly
 preferred polynucleotides, those with at least 95% are especially
 preferred. Furthermore, those with at least 97% are highly preferred among
 those with at least 95%, and among these those with at least 98% and at
 least 99% are particularly highly preferred, with at least 99% being the
 more preferred.
 Preferred embodiments are polynucleotides that encode polypeptides that
 retain substantially the same biological function or activity as the
 mature polypeptide encoded by the DNA of Table 1 [SEQ ID NO: 1, 5, 8 and
 10].
 The invention further relates to polynucleotides that hybridize to the
 herein above-described sequences. In this regard, the invention especially
 relates to polynucleotides that hybridize under stringent conditions to
 the herein above-described polynucleotides. As herein used, the terms
 "stringent conditions" and "stringent hybridization conditions" mean
 hybridization will occur only if there is at least 95% and preferably at
 least 97% identity between the sequences. An example of stringent
 hybridization conditions is overnight incubation at 42.degree. C. in a
 solution comprising: 50% formamide, 5.times.SSC (150 mM NaCl, 15 mM
 trisodium citrate), 50 mM sodium phosphate (pH7.6), 5.times.Denhardt's
 solution, 10% dextran sulfate, and 20 micrograms/ml denatured, sheared
 salmon sperm DNA, followed by washing the hybridization support in
 0.1.times.SSC at about 65.degree. C. Hybridization and wash conditions are
 well known and exemplified in Sambrook, et al., Molecular Cloning: A
 Laboratory Manual, Second Edition, Cold Spring Harbor, N.Y., (1989),
 particularly Chapter 11 therein.
 The invention also provides a polynucleotide consisting essentially of a
 polynucleotide sequence obtainable by screening an appropriate library
 containing the complete gene for a polynucleotide sequence set forth in
 SEQ ID NO: 1, 5, 8 and 10 under stringent hybridization conditions with a
 probe having the sequence of said polynucleotide sequence set forth in SEQ
 ID NO: 1, 5, 8 and 10 or a fragment thereof; and isolating said DNA
 sequence. Fragments useful for obtaining such a polynucleotide include,
 for example, probes and primers described elsewhere herein.
 As discussed additionally herein regarding polynucleotide assays of the
 invention, for instance, polynucleotides of the invention as discussed
 above, may be used as a hybridization probe for RNA, cDNA and genomic DNA
 to isolate full-length cDNAs and genomic clones encoding ileS and to
 isolate cDNA and genomic clones of other genes that have a high sequence
 similarity to the ileS gene. Such probes generally will comprise at least
 15 bases. Preferably, such probes will have at least 30 bases and may have
 at least 50 bases. Particularly preferred probes will have at least 30
 bases and will have 50 bases or less.
 For example, the coding region of the ileS gene may be isolated by
 screening using the DNA sequence provided in SEQ ID NO: 1 to synthesize an
 oligonucleotide probe. A labeled oligonucleotide having a sequence
 complementary to that of a gene of the invention is then used to screen a
 library of cDNA, genomic DNA or mRNA to determine which members of the
 library the probe hybridizes to.
 The polynucleotides and polypeptides of the invention may be employed, for
 example, as research reagents and materials for discovery of treatments of
 and diagnostics for disease, particularly human disease, as further
 discussed herein relating to polynucleotide assays.
 Polynucleotides of the invention that are oligonucleotides derived from the
 sequences of SEQ ID NOS: 1 and/or 2 and/or 5 and/or 6 and/or 8 and/or 9
 and/or 10 may be used in the processes herein as described, but preferably
 for PCR, to determine whether or not the polynucleotides identified herein
 in whole or in part are transcribed in bacteria in infected tissue. It is
 recognized that such sequences will also have utility in diagnosis of the
 stage of infection and type of infection the pathogen has attained.
 The invention also provides polynucleotides that may encode a polypeptide
 that is the mature protein plus additional amino or carboxyl-terminal
 amino acids, or amino acids interior to the mature polypeptide (when the
 mature form has more than one polypeptide chain, for instance). Such
 sequences may play a role in processing of a protein from precursor to a
 mature form, may allow protein transport, may lengthen or shorten protein
 half-life or may facilitate manipulation of a protein for assay or
 production, among other things. As generally is the case in vivo, the
 additional amino acids may be processed away from the mature protein by
 cellular enzymes.
 A precursor protein, having the mature form of the polypeptide fused to one
 or more prosequences may be an inactive form of the polypeptide. When
 prosequences are removed such inactive precursors generally are activated.
 Some or all of the prosequences may be removed before activation.
 Generally, such precursors are called proproteins.
 In sum, a polynucleotide of the invention may encode a mature protein, a
 mature protein plus a leader sequence (which may be referred to as a
 preprotein), a precursor of a mature protein having one or more
 prosequences that are not the leader sequences of a preprotein, or a
 preproprotein, which is a precursor to a proprotein, having a leader
 sequence and one or more prosequences, which generally are removed during
 processing steps that produce active and mature forms of the polypeptide.
 Vectors, host cells, expression
 The invention also relates to vectors that comprise a polynucleotide or
 polynucleotides of the invention, host cells that are genetically
 engineered with vectors of the invention and the production of
 polypeptides of the invention by recombinant techniques. Cell-free
 translation systems can also be employed to produce such proteins using
 RNAs derived from the DNA constructs of the invention.
 For recombinant production, host cells can be genetically engineered to
 incorporate expression systems or portions thereof or polynucleotides of
 the invention. Introduction of a polynucleotide into the host cell can be
 effected by methods described in many standard laboratory manuals, such as
 Davis et al., BASIC METHODS IN MOLECULAR BIOLOGY, (1986) and Sambrook et
 al., MOLECULAR CLONING: A LABORATORY MANUAL, 2nd Ed., Cold Spring Harbor
 Laboratory Press, Cold Spring Harbor, N.Y. (1989), such as, calcium
 phosphate transfection, DEAE-dextran mediated transfection, transvection,
 microinjection, cationic lipid-mediated transfection, electroporation,
 transduction, scrape loading, ballistic introduction and infection.
 Representative examples of appropriate hosts include bacterial cells, such
 as streptococci, staphylococci, enterococci E. coli, streptomyces and
 Bacillus subtilis cells; fungal cells, such as yeast cells and Aspergillus
 cells; insect cells such as Drosophila 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 variety of expression systems can be used to produce the
 polypeptides of the invention. Such vectors include, among others,
 chromosomal, episomal and virus-derived vectors, e.g., vectors derived
 from bacterial plasmids, from bacteriophage, from transposons, from yeast
 episomes, from insertion elements, from yeast chromosomal elements, from
 viruses such as baculoviruses, papova viruses, such as SV40, vaccinia
 viruses, adenoviruses, fowl pox viruses, pseudorabies viruses and
 retroviruses, and vectors derived from combinations thereof, such as those
 derived from plasmid and bacteriophage genetic elements, such as cosmids
 and phagemids. The expression system constructs may contain control
 regions that regulate as well as engender expression. Generally, any
 system or vector suitable to maintain, propagate or express
 polynucleotides and/or to express a polypeptide in a host may be used for
 expression in this regard. The appropriate DNA sequence may be inserted
 into the expression system by any of a variety of well-known and routine
 techniques, such as, for example, those set forth in Sambrook et al.,
 MOLECULAR CLONING, A LABORATORY MANUAL, (supra).
 For secretion of the translated protein into the lumen of the endoplasmic
 reticulum, into the periplasmic space or into the extracellular
 environment, appropriate secretion signals may be incorporated into the
 expressed polypeptide. These signals may be endogenous to the polypeptide
 or they may be heterologous signals.
 Polypeptides of the invention can be recovered and purified from
 recombinant cell cultures by well-known methods including ammonium sulfate
 or ethanol precipitation, acid extraction, anion or cation exchange
 chromatography, phosphocellulose chromatography, hydrophobic interaction
 chromatography, affinity chromatography, hydroxylapatite chromatography,
 and lectin chromatography. Most preferably, high performance liquid
 chromatography is employed for purification. Well known techniques for
 refolding protein may be employed to regenerate active conformation when
 the polypeptide is denatured during isolation and or purification.
 Diagnostic Assays
 This invention is also related to the use of the ileS polynucleotides of
 the invention for use as diagnostic reagents. Detection of ileS in a
 eukaryote, particularly a mammal, and especially a human, will provide a
 diagnostic method for diagnosis of a disease. Eukaryotes (herein also
 "individual(s)"), particularly mammals, and especially humans,
 particularly those infected or suspected to be infected with an organism
 comprising the ileS gene may be detected at the nucleic acid level by a
 variety of techniques.
 Nucleic acids for diagnosis may be obtained from an infected individual's
 cells and tissues, such as bone, blood, muscle, cartilage, and skin.
 Genomic DNA may be used directly for detection or may be amplified
 enzymatically by using PCR or other amplification technique prior to
 analysis. RNA or cDNA may also be used in the same ways. Using
 amplification, characterization of the species and strain of prokaryote
 present in an individual, may be made by an analysis of the genotype of
 the prokaryote gene. Deletions and insertions can be detected by a change
 in size of the amplified product in comparison to the genotype of a
 reference sequence. Point mutations can be identified by hybridizing
 amplified DNA to labeled ileS polynucleotide sequences. Perfectly matched
 sequences can be distinguished from mismatched duplexes by RNase digestion
 or by differences in melting temperatures. DNA sequence differences may
 also be detected by alterations in the electrophoretic mobility of the DNA
 fragments in gels, with or without denaturing agents, or by direct DNA
 sequencing. 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 S1 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 in the gene of the invention may
 also be detected at the DNA level by a variety of techniques, to allow for
 serotyping, for example. For example, RT-PCR can be used to detect
 mutations. It is particularly preferred to used RT-PCR in conjunction with
 automated detection systems, such as, for example, GeneScan. RNA or cDNA
 may also be used for the same purpose, PCR or RT-PCR. As an example, PCR
 primers complementary to a nucleic acid encoding ileS can be used to
 identify and analyze mutations. Examples of representative primers are
 shown below in Table 2.
 TABLE 2
 Primers for amplification of ileS polynucleotides
 SEQ ID NO PRIMER SEQUENCE
 3 5'-ATGAAACTTCAAAGACACCCTTAAT-3'
 4 5'-TTATTTCTCTCAAATCCTTCTGC-3'
 The invention further provides these primers with 1, 2, 3 or 4 nucleotides
 removed from the 5' and/or the 3' end. These primers may be used for,
 among other things, amplifying ileS DNA isolated from a sample derived
 from an individual. The primers may be used to amplify the gene isolated
 from an infected individual such that the gene may then be subject to
 various techniques for elucidation of the DNA sequence. In this way,
 mutations in the DNA sequence may be detected and used to diagnose
 infection and to serotype and/or classify the infectious agent.
 The invention further provides a process for diagnosing, disease,
 preferably bacterial infections, more preferably infections by
 Streptococcus pneumoniae, and most preferably otitis media,
 conjunctivitis, pneumonia, bacteremia, meningitis, sinusitis, pleural
 empyema and endocarditis, and most particularly meningitis, such as for
 example infection of cerebrospinal fluid, comprising determining from a
 sample derived from an individual a increased level of expression of
 polynucleotide having the sequence of Table 1 [SEQ ID NO: 1]. Increased or
 decreased expression of ileS polynucleotide can be measured using any on
 of the methods well known in the art for the quantation of
 polynucleotides, such as, for example, amplification, PCR, RT-PCR, RNase
 protection, Northern blotting and other hybridization methods.
 In addition, a diagnostic assay in accordance with the invention for
 detecting over-expression of ileS protein compared to normal control
 tissue samples may be used to detect the presence of an infection, for
 example. Assay techniques that can be used to determine levels of a ileS
 protein, in a sample derived from a host are well-known to those of skill
 in the art. Such assay methods include radioimmunoassays,
 competitive-binding assays, Western Blot analysis and ELISA assays.
 Antibodies
 The polypeptides of the invention or variants thereof, or cells expressing
 them can be used as an immunogen to produce antibodies immunospecific for
 such polypeptides. "Antibodies" as used herein includes monoclonal and
 polyclonal antibodies, chimeric, single chain, simianized antibodies and
 humanized antibodies, as well as Fab fragments, including the products of
 an Fab immunolglobulin expression library.
 Antibodies generated against the polypeptides of the invention can be
 obtained by administering the polypeptides or epitope-bearing fragments,
 analogues or cells to an animal, preferably a nonhuman, using routine
 protocols. For preparation of monoclonal antibodies, any technique known
 in the art that provides antibodies produced by continuous cell line
 cultures can be used. Examples include various techniques, such as those
 in Kohler, G. and Milstein, C., Nature 256: 495-497 (1975); Kozbor et al.,
 Immunology Today 4: 72 (1983); Cole et al., pg. 77-96 in MONOCLONAL
 ANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc. (1985).
 Techniques for the production of single chain antibodies (U.S. Pat. No.
 4,946,778) can be adapted to produce single chain antibodies to
 polypeptides of this invention. Also, transgenic mice, or other organisms
 such as other mammals, may be used to express humanized antibodies.
 Alternatively phage display technology may be utilized to select antibody
 genes with binding activities towards the polypeptide either from
 repertoires of PCR amplified v-genes of lymphocytes from humans screened
 for possessing anti-ileS or from naive libraries (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 by chain
 shuffling (Clackson, T. et al., (1991) Nature 352, 624-628).
 If two antigen binding domains are present each domain may be directed
 against a different epitope--termed `bispecific` antibodies.
 The above-described antibodies may be employed to isolate or to identify
 clones expressing the polypeptides to purify the polypeptides by affinity
 chromatography.
 Thus, among others, antibodies against ileS- polypeptide may be employed to
 treat infections, particularly bacterial infections and especially otitis
 media, conjunctivitis, pneumonia, bacteremia, meningitis, sinusitis,
 pleural empyema and endocarditis, and most particularly meningitis, such
 as for example infection of cerebrospinal fluid.
 Polypeptide variants include antigenically, epitopically or immunologically
 equivalent variants that form a particular aspect of this invention. The
 term "antigenically equivalent derivative" as used herein encompasses a
 polypeptide or its equivalent which will be specifically recognized by
 certain antibodies which, when raised to the protein or polypeptide
 according to the invention, interfere with the immediate physical
 interaction between pathogen and mammalian host. The term "immunologically
 equivalent derivative" as used herein encompasses a peptide or its
 equivalent which when used in a suitable formulation to raise antibodies
 in a vertebrate, the antibodies act to interfere with the immediate
 physical interaction between pathogen and mammalian host.
 The polypeptide, such as an antigenically or immunologically equivalent
 derivative 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 immunogenic carrier protein for example
 bovine serum albumin (BSA) or keyhole limpet haemocyanin (KLH).
 Alternatively a multiple antigenic peptide comprising multiple copies of
 the protein or polypeptide, or an antigenically or immunologically
 equivalent polypeptide thereof may be sufficiently antigenic to improve
 immunogenicity so as to obviate the use of a carrier.
 Preferably, the antibody or variant thereof is modified to make it less
 immunogenic in the individual. For example, if the individual is human the
 antibody may most preferably be "humanized"; where the complimentarity
 determining region(s) of the hybridoma-derived antibody has been
 transplanted into a human monoclonal antibody , for example as described
 in 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 invention in genetic immunization will
 preferably employ a suitable delivery method such as direct injection of
 plasmid DNA into muscles (Wolff et al., Hum Mol Genet 1992, 1:363,
 Manthorpe et al., Hum. Gene Ther. 1963:4, 419), delivery of DNA complexed
 with specific protein carriers (Wu et al., J. Biol Chem. 1989: 264,16985),
 coprecipitation of DNA with calcium phosphate (Benvenisty & Reshef, PNAS
 USA, 1986:83,9551), encapsulation of DNA in various forms of liposomes
 (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 invention may also be used to assess the binding of
 small molecule substrates and ligands in, for example, cells, cell-free
 preparations, chemical libraries, and natural product mixtures. These
 substrates and ligands may be natural substrates and ligands or may be
 structural or functional mimetics. See, e.g., Coligan et al., Current
 Protocols in Immunology 1(2): Chapter 5 (1991).
 The invention also provides a method of screening compounds to identify
 those which enhance (agonist) or block (antagonist) the action of ileS
 polypeptides or polynucleotides, particularly those compounds that are
 bacteriostatic and/or bactericidal. The method of screening may involve
 high-throughput techniques. For example, to screen for agonists or
 antogonists, a synthetic reaction mix, a cellular compartment, such as a
 membrane, cell envelope or cell wall, or a preparation of any thereof,
 comprising ileS polypeptide and a labeled substrate or ligand of such
 polypeptide is incubated in the absence or the presence of a candidate
 molecule that may be a ileS agonist or antagonist. The ability of the
 candidate molecule to agonize or antagonize the ileS polypeptide is
 reflected in decreased binding of the labeled ligand or decreased
 production of product from such substrate. Molecules that bind
 gratuitously, i.e., without inducing the effects of ileS polypeptide are
 most likely to be good antagonists. Molecules that bind well and increase
 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 using a reporter system. Reporter systems that may be useful in this
 regard include but are not limited to colorimetric labeled substrate
 converted into product, a reporter gene that is responsive to changes in
 ileS polynucleotide or polypeptide activity, and binding assays known in
 the art.
 Another example of an assay for ileS antagonists is a competitive assay
 that combines ileS and a potential antagonist with ileS-binding molecules,
 recombinant ileS binding molecules, natural substrates or ligands, or
 substrate or ligand mimetics, under appropriate conditions for a
 competitive inhibition assay. ileS can be labeled, such as by
 radioactivity or a colorimetric compound, such that the number of ileS
 molecules bound to a binding molecule or converted to product can be
 determined accurately to assess the effectiveness of the potential
 antagonist.
 Potential antagonists include small organic molecules, peptides,
 polypeptides and antibodies that bind to a polynucleotide or polypeptide
 of the invention and thereby inhibit or extinguish its activity. Potential
 antagonists also may be small organic molecules, a peptide, a polypeptide
 such as a closely related protein or antibody that binds the same sites on
 a binding molecule, such as a binding molecule, without inducing
 ileS-induced activities, thereby preventing the action of ileS by
 excluding ileS from binding.
 Potential antagonists include a small molecule that binds to and occupies
 the binding site of the polypeptide thereby preventing binding to cellular
 binding molecules, such that normal biological activity is prevented.
 Examples of small molecules include but are not limited to small organic
 molecules, peptides or peptide-like molecules. Other potential antagonists
 include antisense molecules (see Okano, J. Neurochem. 56: 560 (1991);
 OLIGODEOXYNUCLEOTIDES AS ANTISENSE INHIBITORS OF GENE EXPRESSION, CRC
 Press, Boca Raton, Fla. (1988), for a description of these molecules).
 Preferred potential antagonists include compounds related to and variants
 of ileS.
 Each of the DNA sequences provided herein may be used in the discovery and
 development of antibacterial compounds. The encoded protein, upon
 expression, can be used as a target for the screening of antibacterial
 drugs. Additionally, the DNA sequences encoding the amino terminal regions
 of the encoded protein or Shine-Delgarno or other translation facilitating
 sequences of the respective mRNA can be used to construct antisense
 sequences to control the expression of the coding sequence of interest.
 The invention also provides the use of the polypeptide, polynucleotide 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 matrix proteins on in-dwelling
 devices or to extracellular matrix proteins in wounds; to block ileS
 protein-mediated mammalian cell invasion by, for example, initiating
 phosphorylation of mammalian tyrosine kinases (Rosenshine et al., Infect.
 Immun. 60:2211 (1992); to block bacterial adhesion between mammalian
 extracellular matrix proteins and bacterial ileS 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.
 The antagonists and agonists of the invention may be employed, for
 instance, to inhibit and treat otitis media, conjunctivitis, pneumonia,
 bacteremia, meningitis, sinusitis, pleural empyema and endocarditis, and
 most particularly meningitis, such as for example infection of
 cerebrospinal fluid.
 Helicobacter pylori (herein H. pylori) bacteria infect the stomachs of over
 one-third of the world's population causing stomach cancer, ulcers, and
 gastritis (International Agency for Research on Cancer (1994)
 Schistosomes, Liver Flukes and Helicobacter Pylori (International Agency
 for Research on Cancer, Lyon, France; http://www.uicc.ch/ecp/ecp2904.htm).
 Moreover, the international Agency for Research on Cancer recently
 recognized a cause-and-effect relationship between H. pylori and gastric
 adenocarcinoma, classifying the bacterium as a Group I (definite)
 carcinogen. Preferred antimicrobial compounds of the invention (agonists
 and antagonists of ileS) found using screens provided by the invention,
 particularly broad-spectrum antibiotics, should be useful in the treatment
 of H. pylori infection. Such treatment should decrease the advent of H.
 pylori-induced cancers, such as gastrointestinal carcinoma. Such treatment
 should also cure gastric ulcers and gastritis.
 Vaccines
 Another aspect of the invention relates to a method for inducing an
 immunological response in an individual, particularly a mammal which
 comprises inoculating the individual with ileS, or a fragment or variant
 thereof, adequate to produce antibody and/or T cell immune response to
 protect said individual from infection, particularly bacterial infection
 and most particularly Streptococcus pneumoniae 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 ileS, or a fragment or a variant thereof, for expressing ileS, or a
 fragment or a variant thereof in vivo in order to induce an immunological
 response, such as, to produce antibody and/or T cell immune response,
 including, for example, cytokine-producing T cells or cytotoxic T cells,
 to protect said individual from disease, whether that disease is already
 established within the individual or not. One way of administering the
 gene is by accelerating it into the desired cells as a coating on
 particles or otherwise. Such nucleic acid vector may comprise DNA, RNA, a
 modified nucleic acid, or a DNA/RNA hybrid.
 A further aspect of the invention relates to an immunological composition
 which, when introduced into an individual capable or having induced within
 it an immunological response, induces an immunological response in such
 individual to a ileS or protein coded therefrom, wherein the composition
 comprises a recombinant ileS or protein coded therefrom comprising DNA
 which codes for and expresses an antigen of said ileS or protein 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 arising from CTL or CD4+ T cells.
 A ileS 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 protein and producing a fused protein which will have immunogenic
 and protective properties. Thus fused recombinant protein, preferably
 further comprises an antigenic co-protein, such as lipoprotein D from
 Hemophilus influenzae, Glutathione-S-transferase (GST) or
 beta-galactosidase, relatively large co-proteins which solubilize the
 protein and facilitate production and purification thereof. Moreover, the
 co-protein may act as an adjuvant in the sense of providing a generalized
 stimulation of the immune system. The co-protein may be attached to either
 the amino or carboxy terminus of the first protein.
 Provided by this invention are compositions, particularly vaccine
 compositions, and methods comprising the polypeptides or polynucleotides
 of the invention and immunostimulatory DNA sequences, such as those
 described in Sato, Y. et al. Science 273: 352 (1996).
 Also, provided by this invention are methods using the described
 polynucleotide or particular fragments thereof which have been shown to
 encode non-variable regions of bacterial cell surface proteins in DNA
 constructs used in such genetic immunization experiments in animal models
 of infection with Streptococcus pneumoniae will be particularly useful for
 identifying protein epitopes able to provoke a prophylactic or therapeutic
 immune response. It is believed that this approach will allow for the
 subsequent preparation of monoclonal antibodies of particular value from
 the requisite organ of the animal successfully resisting or clearing
 infection for the development of prophylactic agents or therapeutic
 treatments of bacterial infection, particularly Streptococcus pneumoniae
 infection, in mammals, particularly humans.
 The polypeptide may be used as an antigen for vaccination of a host to
 produce specific antibodies which protect against invasion of bacteria,
 for example by 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, mammary
 glands, urethra or vagina.
 The invention also includes a vaccine formulation which comprises an
 immunogenic recombinant protein of the invention together with a suitable
 carrier. Since the protein may be broken down in the stomach, it is
 preferably administered parenterally, including, for example,
 administration that is subcutaneous, intramuscular, intravenous, or
 intradermal. Formulations suitable for parenteral administration include
 aqueous and non-aqueous sterile injection solutions which may contain
 anti-oxidants, buffers, bacteriostats and solutes which render the
 formulation isotonic with the bodily fluid, preferably the blood, of the
 individual; and aqueous and non-aqueous sterile suspensions which may
 include suspending agents or thickening agents. The formulations may be
 presented in unit-dose or multi-dose containers, for example, sealed
 ampules and vials and may be stored in a freeze-dried condition requiring
 only the addition of the sterile liquid carrier immediately prior to use.
 The vaccine formulation 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 routine
 experimentation.
 While the invention has been described with reference to certain ileS
 protein, 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 substantially affect the immunogenic
 properties of the recombinant protein.
 Compositions, kits and administration
 The invention also relates to compositions comprising the polynucleotide or
 the polypeptides discussed above or their agonists or antagonists. The
 polypeptides of the invention may be employed in combination with a
 non-sterile or sterile carrier or carriers for use with cells, tissues or
 organisms, such as a pharmaceutical carrier suitable for administration to
 a subject. Such compositions comprise, for instance, a media additive or a
 therapeutically effective amount of a polypeptide of the invention and a
 pharmaceutically acceptable carrier or excipient. Such carriers may
 include, but are not limited to, saline, buffered saline, dextrose, water,
 glycerol, ethanol and combinations thereof. The formulation should suit
 the mode of administration. The invention further relates to diagnostic
 and pharmaceutical packs and kits comprising one or more containers filled
 with one or more of the ingredients of the aforementioned compositions of
 the invention.
 Polypeptides and other compounds of the invention may be employed alone or
 in conjunction with other compounds, such as therapeutic compounds.
 The pharmaceutical compositions may be administered in any effective,
 convenient manner including, for instance, administration by topical,
 oral, anal, vaginal, intravenous, intraperitoneal, intramuscular,
 subcutaneous, intranasal or intradermal routes among others.
 In therapy or as a prophylactic, the active agent may be administered to an
 individual as an injectable composition, for example as a sterile aqueous
 dispersion, preferably isotonic.
 Alternatively the composition may be formulated for topical application for
 example in the form of ointments, creams, lotions, eye ointments, eye
 drops, ear drops, mouthwash, impregnated dressings and sutures and
 aerosols, and may contain appropriate 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
 mg/kg, typically around 1 mg/kg. The physician in any event will determine
 the actual dosage which will be most suitable for an individual and will
 vary with the age, weight and response of the particular individual. The
 above dosages are exemplary of the average case. There can, of course, be
 individual instances where higher or lower dosage ranges are merited, and
 such are 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, cerebrospinal fluid shunts, urinary catheters,
 continuous ambulatory peritoneal dialysis (CAPD) catheters.
 The composition of the invention may be administered by injection to
 achieve a systemic effect against relevant bacteria shortly before
 insertion of an in-dwelling device. Treatment may be continued after
 surgery during the in-body time of the device. In addition, the
 composition could also be used to broaden perioperative cover for any
 surgical technique to prevent bacterial wound infections, especially
 Streptococcus pneumoniae wound infections.
 Many orthopaedic surgeons consider that humans with prosthetic joints
 should be considered for antibiotic prophylaxis before dental treatment
 that could produce a bacteremia. Late deep infection is a serious
 complication sometimes leading to loss of the prosthetic joint and is
 accompanied by significant morbidity and mortality. It 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 described above, the compositions of this
 invention may be used generally as a wound treatment agent to prevent
 adhesion of bacteria to matrix proteins exposed in wound tissue and for
 prophylactic use in dental treatment as an alternative to, or in
 conjunction with, antibiotic prophylaxis.
 Alternatively, the composition of the invention may be used to bathe an
 indwelling device immediately before insertion. The active agent will
 preferably be present at a concentration of 1 .mu.g/ml to 10 mg/ml for
 bathing of wounds or indwelling devices.
 A vaccine composition is conveniently in injectable form. Conventional
 adjuvants may be employed to enhance the immune response. A suitable unit
 dose for vaccination is 0.5-5 microgram/kg of antigen, and such dose is
 preferably administered 1-3 times and with an interval of 1-3 weeks. With
 the indicated dose range, no adverse toxicological effects will be
 observed with the compounds of the invention which would preclude their
 administration to suitable individuals.
 Each reference disclosed herein is incorporated by reference herein in its
 entirety. Any patent application to which this application claims priority
 is also incorporated by reference herein in its entirety.