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WO2000068427A1 - yphC - Google Patents

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Publication number
WO2000068427A1
WO2000068427A1 PCT/US2000/011894 US0011894W WO0068427A1 WO 2000068427 A1 WO2000068427 A1 WO 2000068427A1 US 0011894 W US0011894 W US 0011894W WO 0068427 A1 WO0068427 A1 WO 0068427A1
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WO
WIPO (PCT)
Prior art keywords
polypeptide
seq
polynucleotide
sequence
compnsmg
Prior art date
Application number
PCT/US2000/011894
Other languages
French (fr)
Inventor
Magdalena Zalacain
Sanjoy Biswas
Martin K. R. Burnham
Patrick V. Warren
Karen A. Ingraham
Alison F. Chalker
Chi Young So
David J. Holmes
Richard L. Warren
Stephanie Van Horn
Christopher M. Traini
Original Assignee
Smithkline Beecham Corporation
Smithkline Beecham Plc
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Filing date
Publication date
Application filed by Smithkline Beecham Corporation, Smithkline Beecham Plc filed Critical Smithkline Beecham Corporation
Publication of WO2000068427A1 publication Critical patent/WO2000068427A1/en

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/315—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Streptococcus (G), e.g. Enterococci
    • C07K14/3156—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Streptococcus (G), e.g. Enterococci from Streptococcus pneumoniae (Pneumococcus)

Definitions

  • This uwention relates to newh identified polynucleotides and pohpeptides. and their production and uses, as well as their variants, agonists and antagonists, and their uses
  • the invention relates to polynucleotides and pohpeptides of the yphC (GTP-binding proteins) family, as well as their va ⁇ ants. herem referred to as "yphC,” “yphC polynucleot ⁇ de(s),” and “yphC polypept ⁇ de(s)” as the case be
  • the Streptococci make up a medically important genera of microbes known to cause several types of disease in humans, mcludmg, 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 Smce its isolation more than 100 years ago.
  • Streptococcus pneumomae has been one of tlie more intensively studied microbes For example, much of our earlv understandmg that DNA is in fact tlie genetic mate ⁇ al was predicated on the work of G ⁇ ffith and of Avery, Macleod and McCartv us g this microbe Despite the vast amount of research with S pneumomae, many questions concerning tlie virulence of this microbe remain It is particularly preferred to employ Streptococcal genes and gene products as targets for tlie development of antibioUcs
  • Tlie frequency of Streptococcus pneumomae infections has ⁇ sen dramaticalh in tlie past few decades This has been att ⁇ ubbed to the emergence of multiply antibiotic resistant strains and an mcreasmg population of people with weakened immune systems It is no longer uncommon to isolate Streptococcus pneumomae strains that are resistant to some or all of tlie standard antibioUcs This phenomenon has created an unmet medical need and demand for new anti-microbial agents, vaccmes.
  • polynucleotides and pohpeptides such as the ⁇ phC embodiments of the invention, that have a present benefit of. among other things, bemg useful to screen compounds for antimicrobial activity Such factors are also useful to determine their role in pathogenesis of infection. dysfunction and disease There is also a need for identification and characterization of such factors and their antagonists and agonists to find ways to prevent, ameliorate or correct such infection. d ⁇ sfunction and disease
  • the present mvention relates to yphC, m particular yphC polypeptides and yphC polynucleotides recombinant mate ⁇ als and methods for their production
  • the mvention relates to methods for usmg such pohpeptides and polynucleotides.
  • the invention relates to methods for identifying agonists and antagonists using the mate ⁇ als provided by the invention, and for treatmg microbial infections and conditions associated ith such infections with the identified agomst or antagomst compounds
  • the mvention relates to diagnostic assays for detecting diseases associated w th microbial infections and conditions associated with such infections, such as assays for detectmg yphC expression or activity
  • the mvention relates to yphC polypeptides and polynucleotides as desc ⁇ bed in greater detail below
  • the mvention relates to polypeptides and polynucleotides of a yphC of Streptococcus pneumomae, that is related by ammo acid sequence homology to B subtilis yphC pohpeptide
  • the mvention relates especially to yphC having a nucleotide and ammo acid sequences set out m Table 1 as SEQ ID NO 1 and SEQ ID NO 2 respectively
  • sequences recited in the Sequence Listmg below as "DNA” represent an exemplification of the mvention. smce those of ordmary skill will recogmze that such sequences can be usefully employed m polynucleotides m general, mcludmg ⁇ bopolynucleotides
  • a deposit compnsing a Streptococcus pneumomae 0100993 strain has been deposited with the National Collections of Industrial and Marine Bactena Ltd (herem “NCIMB”). 23 St Machar D ⁇ e Aberdeen AB2 1RY, Scotland on 11 April 1996 and assigned deposit number 40794 The deposit was desc ⁇ bed as Streptococcus pneumomae 0100993 on deposit On 17 Ap ⁇ l 1996 a Streptococcus pneumomae 0100993 DNA hbraiy m E coli was similarh deposited with the NCIMB and assigned deposit number 40800 The Streptococcus pneumomae strain deposit is referred to herem as "the deposited strain” or as "the DNA of the deposited strain "
  • the deposited strain comp ⁇ ses a full length yphC gene
  • the sequence of the polynucleotides comp ⁇ sed m the deposited strain, as well as the ammo acid sequence of any pohpeptide encoded thereby, are controlling m the event of any conflict with any desc ⁇ ption of sequences herem
  • the deposit of the deposited strain has been made under the terms of the Budapest Treaty on the International Recognition of the Deposit of Micro-organisms for Purposes of Patent Procedure
  • the deposited strain will be irrevocably and without restnction or condition released to the public upon tlie issuance of a patent
  • the deposited strain is provided merely as convemence to those of skill m tlie art and is not an admission that a deposit is required for enablement, such as that required under 35 U S C ⁇ 112
  • a license may be required to make, use or sell the deposited strain, and compounds de ⁇ ved therefrom, and no such license is hereby granted
  • an isolated nucleic acid molecule encoding a mature polypeptide expressible by the Streptococcus pneumomae 0100993 strain, which polypeptide is comp ⁇ sed in the deposited strain
  • Furtlier provided by the mvention are yphC polynucleotide sequences m the deposited strain, such as DNA and RNA, and ammo acid sequences encoded thereby Also provided by the mvention are yphC polypeptide and polynucleotide sequences isolated from the deposited strain
  • YphC polypeptide of the mvention is substantially phylogenetically related to other proteins of the yphC (GTP-binding proteins) family
  • polypeptides of Streptococcus pneumomae referred to herem as "yphC” and “yphC polypeptides” as well as biologically, diagnostically . proplwlacticalh clinically or therapeutically useful variants thereof, and compositions compnsing the same
  • the present mvention further provides for an isolated polypeptide that (a) comp ⁇ ses or consists of an am o acid sequence that has at least 95% identity, most preferably at least 97-99% or exact identity to that of SEQ ID NO 2 over the entire length of SEQ ID NO 2.
  • polypeptides of the mvention mclude a polypeptide of Table 1 [SEQ ID NO 2] (in particular a mature polypeptide) as well as polypeptides and fragments, particularly those that has a biological activity of yphC.
  • R 1 X-(R 1 ) m -(R 2 )-(R 3 )n-Y
  • X is hydrogen, a metal or any other moiety descnbed herem for modified polypeptides, and at the carboxyl terminus
  • Y is hydrogen, a metal or any other moiety descnbed herem for modified polypeptides
  • Ri and R3 are any ammo acid residue or modified ammo acid residue
  • m is an mteger between 1 and 1000 or zero
  • n is an mteger between 1 and 1000 or zero
  • R 2 is an ammo acid sequence of the mvention, particularly an ammo acid sequence selected from Table 1 or modified forms thereof
  • R 2 is o ⁇ ented so that its am o terminal ammo acid residue is at the left, covalently bound to Ri and its carboxy terminal ammo acid residue is at the ⁇ ght, covalently bound to R3 Any stretch of ammo acid residues denoted by
  • a polypeptide of the mvention is denved from Streptococcus pneumomae. however, it may preferably be obtained from other organisms of the same taxonomic genus
  • a polypeptide of the mvention may also be obtained, for example, from organisms of the same taxonomic family or order
  • a fragment is a va ⁇ ant polypeptide havmg an ammo acid sequence that is entirely the same as part but not all of any ammo acid sequence of any polypeptide of the mvention
  • 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 m a smgle larger polypeptide Preferred fragments mclude.
  • truncation polypeptides havmg a portion of an am o acid sequence of Table 1 [SEQ ID NO 2], or of variants thereof, such as a continuous senes of residues that mcludes an ammo- and/or carboxyl-terminal ammo acid sequence Degradation forms of the polypeptides of the mvention produced by or m a host cell, particularly a Streptococcus pneumomae.
  • fragments characterized bv structural or functional att ⁇ butes such as fragments that compnse alpha-helix and alpha-hehx forming regions, beta-sheet and beta-sheet-forming regions, turn and tum-formmg regions, coil and coil-forming regions, hydrophihc regions, hydrophobic regions alpha amphipathic regions, beta amphipathic regions, flexible regions, surface-forming regions, substrate binding region, and high antigenic mdex regions
  • fragments m include an isolated polypeptide comprising an amino acid sequence havmg at least 15, 20, 30, 40, 50 or 100 contiguous amino acids trom the amino acid sequence of SEQ ID NO.2, or an isolated polypeptide comprising an amino acid sequence havmg at least 15, 20, 30, 40, 50 or 100 contiguous amino acids truncated or deleted trom the amino acid sequence ot SEQ ID NO.2 Fragments of the polypeptides of the mvention may be employed for producmg the
  • the polynucleotide compnses a region encoding yphC polypeptides comp ⁇ smg a sequence set out m Table 1 [SEQ ID NO 1] that mcludes a full length gene, or a variant thereof The Applicants beheve that this full length gene is essential to the growth and/or survival of an organism that possesses it, such as Streptococcus pneumomae
  • isolated nucleic acid molecules encoding and/or expressing yphC polypeptides and polynucleotides, particularly Streptococcus pneumomae yphC polypeptides and polynucleotides, mcludmg, for example, unprocessed RNAs, nbozyme RNAs, mRNAs, cDNAs, genomic DNAs, B- and Z-DNAs
  • Further embodiments of the mvention mclude biological
  • mcludmg at least one full length gene, that encodes a yphC polypeptide having a deduced ammo acid sequence of Table 1 [SEQ ID NO 2] and polynucleotides closely related thereto and variants thereof
  • yphC polypeptide from Streptococcus pneumomae compnsmg or consisting of an ammo acid sequence of Table 1 [SEQ ID NO 2], or a variant thereof
  • a polynucleotide of the mvention encoding yphC polypeptide may be obtained usmg standard cloning and screening methods, such as those for cloning and sequencmg chromosomal DNA fragments from bactena usmg Streptococcus pneumomae 0100993 cells as starting matenal.
  • a polynucleotide sequence of the invention such as a polynucleotide sequence given m Table 1 [SEQ ID NO 1]
  • a library of clones of chromosomal DNA of Streptococcus pneumomae 0100993 in E coh or some other suitable host is probed with a radiolabeled ohgonucleotide preferably a 17-mer or longer, denved from a partial sequence
  • Clones carrying DNA identical to that of the probe can then be distinguished usmg stringent hybndization conditions
  • sequencmg the individual clones thus identified by hybndization with sequencmg primers designed from the ongmal polypeptide or polynucleotide sequence it is then possible to extend the polynucleotide sequence in both directions to determine a full length gene sequence Convemently, such sequencmg is performed, for example,
  • each DNA sequence set out m Table 1 [SEQ ID NO 1] contains an open reading 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 to those skilled in the art
  • the present mvention provides for an isolated polynucleotide compnsmg or consistmg of (a) a polynucleotide sequence that has at least 95% identity, even more preferably at least 97%. still more preferably at least 99%, yet still more preferably at least 99 5% or exact identity to SEQ ID NO 1 over the entire length of SEQ ID NO 1, or the entire length of that portion of SEQ ID NO 1 which encodes SEQ ID NO 2, (b) a polynucleotide sequence encoding a polypeptide that has at least 95% identity, even more preferably at least 97-99% or 100% exact, to the ammo acid sequence of SEQ ID NO 2, over the entire length of SEQ ID NO 2
  • mcludmg homologs and orthologs from species other than Streptococcus pneumomae may be obtained by a process that compnses the steps of screening an approp ⁇ ate library under stringent hybndization conditions with a labeled or detectable probe consistmg of or compnsmg the sequence of SEQ ID NO 1 or a fragment thereof, and isolating a full-length gene and/or genomic clones compnsmg said polynucleotide sequence
  • the mvention provides a polynucleotide sequence identical over its entire length to a coding sequence (open reading frame) m Table 1 [SEQ ID NO 1] Also provided by the mvention is a coding sequence for a mature polypeptide or a fragment thereof, by itself as well as a coding sequence for a mature pohpeptide or a fragment in reading frame with another coding sequence, such as a sequence encoding a leader or secretory sequence, a pre-, or pro- or prepro-protein sequence
  • the polynucleotide of the mvention may also compnse at least one non-coding sequence, mcludmg for example, but not limited to at least one non-coding 5' and 3' sequence, such as the transcnbed but non-translated sequences, termination signals (such as rho-dependent and rho-mdependent termination signals), nbosome bmdmg sites, Kozak sequences, sequences that stabilize mRNA, introns, and
  • the marker sequence is a hexa-histidine peptide, as provided m the pQE vector (Qiagen, Inc ) and descnbed m Gentz et al , Proc Natl Acacl Set , USA 86 821-824 (1989), or an HA peptide tag (Wdson et al . Cell 37 767 (1984). both of that may be useful m purifying polypeptide sequence fused to them
  • Polynucleotides of the mvention also mclude. but are not limited to, polynucleotides compnsmg a structural gene and its naturally associated sequences that control gene expression
  • a prefened embodiment of the mvention is a polynucleotide of consistmg of or compnsmg nucleotide 1 to the nucleotide immediately upstream of or mcludmg nucleotide 1309 set forth m SEQ ID NO 1 of Table 1, both of that encode a yphC polypeptide
  • the mvention also mcludes a polynucleotide consisting of or compnsmg a polynucleotide of the formula
  • Ri and R3 is independently any nucleic acid residue or modified nucleic acid residue
  • m is an mteger between 1 and 3000 or zero
  • n is an mteger between 1 and 3000 or zero
  • R 2 is a nucleic acid sequence or modified nucleic acid sequence of the mvention.
  • R 2 is oriented so that its 5' end nucleic acid residue is at the left, bound to Ri and its 3' end nucleic acid residue is at the nght. bound to R3 Any stretch of nucleic acid residues denoted by either Rj and/or R . where m and/or n is greater than 1. may be either a heteropolymer or a homopolymer, preferably a heteropolymer Where, m a prefened embodiment.
  • the polynucleotide of the above formula is a closed, circular polynucleotide, that can be a double-stranded polynucleotide wherem the formula show s a first strand to which the second strand is complementary
  • m and/or n is an mteger between 1 and 1000.
  • Other prefened embodiments of the mvention are provided where m is an mteger between 1 and 50. 100 or 500, and n is an mteger between 1 and 50, 100, or 500
  • polynucleotide of the mvention is denved from Streptococcus pneumomae, however, it may preferably be obtained from other organisms of the same taxonomic genus
  • a polynucleotide of tlie mvention may also be obtained, for example, from organisms of the same taxonomic family or order
  • polynucleotide encoding a polypeptide encompasses polynucleotides that mclude a sequence encoding a polypeptide of the mvention, particularly a bactenal polypeptide and more particularly a polypeptide of the Streptococcus pneumomae yphC havmg an ammo acid sequence set out in Table 1 [SEQ ID NO.2]
  • the term also encompasses polynucleotides that mclude a smgle contmuous region or discontinuous regions encoding the polypeptide (for example, polynu).
  • the mvention further relates to variants of the polynucleotides descnbed herem that encode variants of a polypeptide having a deduced ammo acid sequence of Table 1 [SEQ ID NO 2] Fragments of polynucleotides of the mvention may be used, for example, to synthesize full-length polynucleotides of the mvention
  • prefened embodiments are polynucleotides encoding yphC variants, that have the ammo acid sequence of yphC polypeptide of Table 1 [SEQ ID NO.2] m which several, a few, 5 to 10, 1 to 5, 1 to 3, 2, 1 or no ammo acid residues are substituted, modified, deleted and/or added, in any combmation Especially prefened among these are silent substitutions, additions and deletions, that do not alter the properties and activities of yphC polypeptide
  • Prefened isolated polynucleotide embodiments also mclude polynucleotide fragments, such as a polynucleotide comprising a nuclic acid sequence having at least 15, 20, 30, 40, 50 or 100 contiguous nucleic acids from the polynucleotide sequence of SEQ ID NO: l, or an polynucleotide comprising a nucleic acid sequence havmg at least 15, 20, 30, 40, 50 or 100 contiguous nucleic acids truncated or deleted from the 5' and/or 3' end of the polynucleotide sequence of SEQ ID NO. l
  • prefened embodiments of the mvention are polynucleotides that are at least 95% or 97% identical over their entire length to a polynucleotide encoding yphC polypeptide havmg an am o acid sequence set out m Table 1 [SEQ ID NO 2], and polynucleotides that are complementary to such polynucleotides
  • Most highly prefened are polynucleotides that compnse a region that is at least 95% are especially prefened
  • 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 preferred, with at least 99% bemg the more prefened
  • Prefened embodiments are polynucleotides encoding polypeptides that retain substantialh the same biological function or activity as a mature polypeptide encoded by a DNA of Table 1 [SEQ ID NO 1]
  • polynucleotides that hybndize, particularly under strmgent conditions to yphC polynucleotide sequences, such as those polynucleotides in Table 1
  • the mvention further relates to polynucleotides that hybndize to the polynucleotide sequences provided herem
  • the mvention especially relates to polynucleotides that hybndize under strmgent conditions to the polynucleotides descnbed herem
  • strmgent conditions and “strmgent hybndization conditions” mean hybndization occurring only if there is at least 95% and preferably at least 97% identity between the sequences
  • strmgent hvbridization conditions is overnight incubation at 42°C m a solution compnsmg 50% formamide, 5x SSC (150mM NaCl, 15mM t ⁇ sodium citrate), 50 M sodium phosphate (pH7 6), 5x Denhardt's solution, 10% dextran sulfate, and 20 micrograms/ml of denatured, sheared salmon sperm DNA.
  • the mvention also provides a polynucleotide consistmg of or compnsmg a polynucleotide sequence obtained by screening an appropnate library compnsmg a complete gene for a polynucleotide sequence set forth m SEQ ID NO 1 under strmgent hybndization conditions with a probe having the sequence of said polynucleotide sequence set forth in SEQ ID NO 1 or a fragment thereof, and isolating said polynucleotide sequence Fragments useful for obtaining such a polynucleotide mclude. for example, probes and pnmers fully descnbed elsewhere herem As discussed elsewhere herem regarding polynucleotide assays of the mvention.
  • the polynucleotides of the mvention. may be used as a hybndization probe for RNA, cDNA and genomic DNA to isolate full-length cDNAs and genomic clones encoding yphC and to isolate cDNA and genomic clones of other genes that have a high identity, particularly high sequence identity, to a yphC gene
  • Such probes generally will compnse at least 15 nucleotide residues or base pairs
  • such probes will at least 30 nucleotide residues or base pairs and may have at least 50 nucleotide residues or base pairs
  • Particularh prefened probes will have at least 20 nucleotide residues or base pairs and will have lee than 30 nucleotide residues or base pairs
  • a coding region of a yphC gene may be isolated by screening usmg a DNA sequence provided in Table 1 [SEQ ID NO 1] to synthesize an ohgonucleotide probe
  • a labeled ohgonucleotide having a sequence complementary to that of a gene of the mvention is then used to screen a librarv of cDNA, genomic DNA or mRNA to determine which members of the library the probe hybndizes to
  • polynucleotides and polypeptides of the mvention may be employed, for example, as research reagents and matenals for discovery of treatments of and diagnostics for diseases, particularly human diseases, as further discussed herem relating to polynucleotide assays
  • SEQ ID NOS 1 or 2 may be used m the processes herem as described, but preferably for PCR, to determine whether or not the polynucleotides identified herem in whole or m part are transcnbed m bactena m infected tissue It is recognized that such sequences will also have utility m diagnosis of the stage of infection and type of mfection the pathogen has attained
  • the mvention also provides polynucleotides that encode a polypeptide that is a mature protem plus additional ammo or carboxyl-terminal ammo acids, or ammo acids intenor to a mature pohpeptide (when a mature form has more than one polypeptide chain, for instance) Such sequences may play a role in processing of a protem from precursor to a mature form, may allow protem transport, may lengthen or shorten protem half-life or may facilitate manipulation of a protem for assay or production, among other things As generally is the case in vivo, the additional ammo acids may be processed
  • a precursor protein, havmg a mature form of the polypeptide fused to one or more prosequences may be an inactive form of the polypeptide When prosequences are removed such inactive precursors generally are activated Some or all of the prosequences may be removed before activation Generally, such precursors are called proproteins As will be recognized, the entire polypeptide encoded by an open reading frame is often not required for activity Accordingly, it has become routine m molecular biology to map the boundanes of the primary structure required for activity with N-terrninal and C-terminal deletion experiments These experiments utilize exonuclease digestion or convement restriction sites to cleave coding nucleic acid sequence For example,
  • nucleic acid of SEQ ED NO 1 readily provides contiguous fragments of SEQ ID NO 2 sufficient to provide an activity, such as an enzymatic, bmdmg or antibody-inducing activity Nucleic acid sequences encoding such fragments of SEQ ID NO 2 and variants thereof as descnbed herem are within the mvention. as are polypeptides so encoded
  • a polynucleotide of the mvention may encode a mature protein, a mature protem plus a leader sequence (which may be refened 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. that is a precursor to a proprotein. havmg a leader sequence and one or more prosequences, that generally are removed du ⁇ ng processing steps that produce active and mature forms of the polypeptide
  • the mvention also relates to vectors that comp ⁇ se a polynucleotide or polynucleotides of tlie mvention, host cells that are genetically engmeered with vectors of the mvention and the production of polypeptides of the mvention by recombinant techniques Cell-free translation systems can also be employed to produce such proteins using RNAs denved from the DNA constructs of the mvention
  • Recombinant polypeptides of the present mvention may be prepared by processes well known m those skilled m the art from genetically engmeered host cells compnsmg expression sy stems Accordingly .
  • the present mvention relates to expression systems that compnse a polynucleotide or polvnucleotides of the present mvention, to host cells that are genetically engmeered w th such expression systems, and to the production of polypeptides of the mvention by recombinant techniques
  • host cells can be genetically engmeered to incorporate expression systems or portions thereof or polynucleotides of the mvention
  • Introduction of a polynucleotide mto the host cell can be effected by methods descnbed in mans standard laboratory manuals, such as Davis, et al . BASIC METHODS IN MOLECULAR BIOLOGY, (1986) and Sambrook. et al , MOLECULAR CLONING A LABORATORY MANUAL. 2nd Ed . Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N Y (1989), such as, calcium phosphate transfection, DEAE-dextran mediated transfection. transvection, microinjection, catiomc hpid-mediated transfection. electroporation transduction, scrape loading, ballistic introduction and infection
  • bactenal cells such as cells of streptococci, staphylococci, enterococci E colt, streptomyces, cyanobactena, Bacillus subtilis, and Streptococcus pneumomae
  • fungal cells such as cells of a yeast, Kluveromyce , Saccharomyces , a basidiomycete, Candida a ⁇ bicans and Aspergillus
  • insect cells such as cells of Drosoph ⁇ a S2 and Spodoptera Sf9.
  • animal cells such as CHO, COS, HeLa, C 127, 3T3, BHK, 293, CV-1 and Bowes melanoma cells
  • plant cells such as cells of a gymnosperm or angiosperm
  • vectors include, among others, chromosomal-, episomal- and virus-denved vectors, for example, vectors denved from bactenal plasmids, from bacte ⁇ ophage. from transposons, from yeast episomes.
  • the expression system constructs ma ⁇ comp ⁇ se control regions that regulate as well as engender expression
  • any system or vector suitable to maintain, propagate or express polynucleotides and/or to express a polypeptide m a host may be used for expression in this regard
  • the appropnate DNA sequence may be inserted mto the expression system by any of a vanety of well-known and routine techniques, such as, for example, those set forth in Sambrook et al , MOLECULAR CLONING, A LABORATORY MANUAL,
  • appropnate secretion signals may be incorporated mto the expressed polypeptide
  • These signals may be endogenous to the polypeptide or they may be heterologous signals
  • Polypeptides of the invention can be recovered and purified from recombinant cell cultures bv well- known methods mcludmg ammomum sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography. phosphocellulose chromatography , hydrophobic interaction chromatographv affinity chromatography. hydroxylapatite chromatography . and lectin chromatography Most preferably , high performance hquid 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
  • This mvention is also related to the use of yphC polynucleotides and polypeptides of the mvention for use as diagnostic reagents Detection of yphC polynucleotides and/or polypeptides in a eukaryote particularly a mammal, and especially a human, will provide a diagnostic method for diagnosis of disease.
  • Eukaryotes, particularly mammals, and especially humans, particularly those infected or suspected to be infected with an orgamsm comp ⁇ smg the yphC gene or protein may be detected at the nucleic acid or ammo acid level by a vanety of ell known techniques as well as by methods provided herem
  • Polypeptides and polynucleotides for prognosis, diagnosis or other analysis may be obtained from a putatively infected and/or infected individual's bodily matenals
  • Polynucleotides from any of these sources, particularly DNA or RNA may be used directly for detection or may be amplified enzymatically by usmg PCR or any other amplification technique p ⁇ or to analysis RNA, particularly mRNA.
  • cDNA and genomic DNA may also be used m the same ways Usmg amplification, characterization of the species and stram of infectious or resident orgamsm present m an mdividual, may be made by an analysis of the genotype of a selected polynucleotide of the organism Deletions and insertions can be detected by a change m size of the amplified product m comparison to a genotype of a reference sequence selected from a related orgamsm, preferably a different species of the same genus or a different strain of the same species Pomt mutations can be identified by hybndizmg amplified DNA to labeled yphC polynucleotide sequences Perfectly or significantly matched sequences can be distinguished from imperfectly or more significantly mismatched duplexes by DNase or RNase digestion, for DNA or RNA respectively, or by detecting differences m meltmg temperatures or renaturation kinetics Polynucleotide sequence differences may also be detected by alterations
  • an array of ohgonucleotides probes comp ⁇ smg yphC nucleotide sequence or fragments thereof can be constructed to conduct efficient screening of. for example, genetic mutations serotype.
  • the present mvention relates to a diagnostic kit that compnses
  • kits (a) a polynucleotide of the present mvention, preferably the nucleotide sequence of SEQ ID NO 1, or a fragment thereof, (b) a nucleotide sequence complementary to that of (a), (c) a polypeptide of the present mvention, preferably the polypeptide of SEQ ID NO 2 or a fragment thereof, or (d) an antibodv to a polypeptide of the present mvention, preferably to the polypeptide of SEQ ID NO 2
  • any such kit may compnse a substantial component
  • Such a kit will be of use m diagnosing a disease or susceptibility to a Disease, among others
  • This mvention also relates to the use of polynucleotides of the present mvention as diagnostic reagents Detection of a mutated form of a polynucleotide of the mvention, preferable. SEQ ED NO 1.
  • Organisms particularly infectious organisms, carrymg mutations m such polynucleotide may be detected at the polynucleotide level by a vanety of techniques, such as those descnbed elsewhere herem
  • the differences in a polynucleotide and/or polypeptide sequence between organisms possessing a first phenotype and organisms possessmg a different, second different phenotype can also be determined If a mutation is observed m some or all organisms possessmg the first phenotype but not in any organisms possessmg the second phenotype, then the mutation is likely to be the causative agent of the first phenotype
  • Cells from an organism carrymg mutations or polymorphisms (allehc variations) m a polynucleotide and/or polypeptide of the mvention may also be detected at the polynucleotide or polypeptide level bv a vanety of techniques, to allow for serotyping, for example For example.
  • RT-PCR can be used to detect mutations in the RNA It is particularly prefened to use RT-PCR m conjunction with automated detection systems, such as, for example, GeneScan RNA, cDNA or genomic DNA may also be used for the same purpose PCR
  • PCR primers complementary to a polynucleotide encoding yphC polypeptide can be used to identify and analyze mutations
  • the mvention further provides these printers 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 yphC DNA and/or RNA isolated from a sample de ⁇ v ed from an mdividual.
  • the primers may be used to amplify a polynucleotide isolated from an infected mdividual, such that the polynucleotide may then be subject to vanous techmques for elucidation of the polynucleotide sequence In this way . mutations in the polynucleotide sequence may be detected and used to diagnose and/or prognose the infection or its stage or course, or to serotype and/or classify' the infectious agent
  • the mvention further provides a process for diagnosing, disease, preferably bactenal infections more preferably infections caused by Streptococcus pneumomae. comprising determining from a sample derived from an individual, such as a bodily material an increased level of expression of poly nucleotide having a sequence of Table 1 [SEQ ID NO 1] Increased or decreased expression of a yphC polynucleotide can be measured usmg any on of the methods well known m the art for the quantitation of polynucleotides. such as. for example, amplification.
  • a diagnostic assay m accordance with the mvention for detecting over-expression of yphC polypeptide compared to normal control tissue samples may be used to detect the presence of an infection, for example Assay techmques that can be used to determine levels of a yphC polypeptide, m a sample denved from a host, such as a bodily matenal, are well-known to those of skill m the art
  • Assay techmques that can be used to determine levels of a yphC polypeptide, m a sample denved from a host, such as a bodily matenal, are well-known to those of skill m the art
  • Such assay methods mclude radioimmunoassays, competitive-binding assays.
  • Polypeptides and polynucleotides of the mvention may also be used to assess the bmdmg of small molecule substrates and hgands in, for example, cells, cell-free preparations, chemical hbranes. and natural product mixtures
  • substrates and hgands may be natural substrates and hgands or may be structural or functional rnimetics See, e g , Cohgan et al , Current Protocols in Immunology 1(2) Chapter 5 (1991)
  • Polypeptides and polynucleotides of the present mvention are responsible for many biological functions, mcludmg many disease states, in particular the Diseases herem mentioned It is therefore desirable to devise screenmg methods to identify compounds that agonize (e g , stimulate) or that antagonize (e g , ⁇ nl ⁇ b ⁇ t) the function of the polypeptide or polynucleotide Accordingly, m a further aspect the present mvention provides for a method of
  • Compounds may be employed for therapeutic and prophylactic purposes for such Diseases as herem mentioned
  • Compounds may be identified from a vanety of sources, for example, cells, cell-free preparations, chemical hbranes. and natural product mixtures
  • Such agonists and antagonists so-identified may be natural or modified substrates, hgands. receptors, enzymes, etc as the case may be. of yphC polypeptides and polynucleotides. or may be structural or functional mimetics thereof (see Cohgan et al , Current Protocols in Immunology 1(2) Chapter 5 (1991))
  • the screenmg methods mav simply measure the bmdmg of a candidate compound to the polypeptide or polynucleotide, or to cells or membranes bearing the polypeptide or polynucleotide. or a fusion protem of the polypeptide by means of a label directly or indirectly associated with the candidate compound Alternatively, the screenmg method may involve competition with a labeled competitor Further, these screening methods may test whether the candidate compound results m a signal generated by activation or inhibition of the polypeptide or polynucleotide usmg detection systems appropriate to die cells compnsmg the polypeptide or polynucleotide Inhibitors of activation are generally assayed in the presence of a known agomst and the effect on activation bv the agonist by the presence of the candidate compound is observed Constitutively active polypeptide and/or constitutiv ely expressed polypeptides and polynucleotides may be employed m screenmg methods for inverse agonists, in the absence of an
  • polypeptides and antibodies that bmd to and/or mteract with a polypeptide of the present mvention may also be used to configure screenmg methods for detectmg the effect of added compounds on the production of mRNA and/or polypeptide in cells
  • an ELISA assay may be constructed for measurmg secreted or cell associated levels of polypeptide usmg monoclonal and polyclonal antibodies by standard methods known in the art This can be used to discover agents that may inhibit or enhance the production of polypeptide (also called antagomst or agomst, respectively) from suitably manipulated cells or tissues
  • the mvention also provides a method of screenmg compounds to identify those that enhance (agomst) or block (antagomst) the action of yphC polypeptides or polynucleotides, particularly those compounds that are bacte ⁇ static and/or bactencidal
  • the method of screenmg may mvolve high-throughput techmques
  • a synthetic reaction mix to screen for agonists or antagonists, a synthetic reaction mix, a cellular compartment, such as a membrane, cell envelope or cell wall, or a preparation of any thereof, compnsmg yphC polypeptide and a labeled substrate or hgand of such polypeptide is incubated m the absence or the presence of a candidate molecule that may be a yphC agomst or antagomst
  • the ability of the candidate molecule to agonize or antagonize the yphC polypeptide is reflected in decreased bmdmg of the label
  • Molecules that bmd ell and. as the case mav be increase the rate of product production from substrate, mcrease signal transduction. or mcrease chemical channel activity are agonists Detection of the rate or level of, as the case may be, production of product from substrate, signal transduction, or chemical channel activity may be enhanced by usmg a reporter system Reporter systems that may be useful m this regard mclude but are not limited to colonmetnc. labeled substrate converted mto product, a reporter gene that is responsive to changes m yphC polynucleotide or pohpeptide activity, and bmdmg assays known in the art
  • Polypeptides of the mvention may be used to identify membrane bound or soluble receptors, if any, for such polypeptide, through standard receptor bmding techmques known m the art These techmques mclude, but are not limited to, hgand binding and crosslinking assays m which the polypeptide is labeled with a radioactive isotope (for instance, * ⁇ I), chemically modified (for instance, biotinylated), or fused to a peptide sequence suitable for detection or punfication, and mcubated with a source of the putative receptor (e g , cells, cell membranes, cell supernatants, tissue extracts, bodily matenals) Other methods mclude biophysical techmques such as surface plasmon resonance and spectroscopy These screenmg methods may also be used to identify agomsts and antagonists of the polypeptide that compete with the bindmg of the polypeptide to its receptor(s), if any Standard methods for conducting such assays are well
  • the fluorescence polarization value for a fluorescently-tagged molecule depends on the rotational correlation time or tumblmg rate Protem complexes, such as formed by yphC polypeptide associating vvrth another yphC polypeptide or other polypeptide, labeled to comprise a fluorescently- labeled molecule will have higher polarization values than a fluorescently labeled monome ⁇ c protem It is preferred that this method be used to characte ⁇ ze small molecules that disrupt polypeptide complexes
  • Fluorescence energy transfer may also be used charactenze small molecules that interfere with the formation of yphC polypeptide dimers, tnmers, tetramers or higher order structures, or structures formed by yphC polypeptide bound to another polypeptide
  • YphC polypeptide can be labeled with both a donor and acceptor fluorophore Upon mixing of the two labeled species and excitation of the donor fluorophore, fluorescence energy transfer can be detected by observing
  • YphC polypeptide can be coupled to a sensor chip at low site density such that covalently bound molecules will be monome ⁇ c Solution protem can then passed over the yphC polypeptide -coated surface and specific bmding can be detected in real-time by monitoring the change in resonance angle caused by a change in local refractive index
  • This technique can be used to characterize the effect of small molecules on kinetic rates and equilibrium bmdmg constants for yphC polypeptide self-association as well as an association of yphC polypeptide and another polypeptide or small molecule
  • a scintillation proximity assay may be used to characterize the interaction between an association of yphC polypeptide ith another yphC polypeptide or a different polypeptide YphC polypeptide can be coupled to a scintillation-filled bead Addition of radio-labeled yphC polypeptide results in bmding where the radioactive source molecule is in close proximity to the scintillation fluid Thus, signal is emitted upon yphC polypeptide bmdmg and compounds that prevent yphC polypeptide self-association or an association of yphC polypeptide and another polypeptide or small molecule will dimmish signal
  • bmdmg or mteraction preferably bemg associated with a second component capable of providing a detectable signal m response to the bmdmg or mteraction of the polypeptide and/or polynucleotide with the compound, and determining whether the compound bmds to or otherwise interacts with and activates or inhibits an activity or expression of the polypeptide and/or polynucleot
  • a polypeptide and/or polynucleotide of the present mvention may also be used m a method for the structure-based design of an agomst or antagomst of the polypeptide and/or polynucleotide, by (a) determinmg m the first mstance the three- dimensional structure of the polypeptide and/or polynucleotide.
  • the present mvention provides methods of treating abnormal conditions such as for instance, a Disease, related to either an excess of. an under-expression of, an elevated activity of, or a decreased activity of yphC polypeptide and/or polynucleotide
  • the invention also provides the use of the polypeptide. polynucleotide, agonist or antagonist of the invention to interfere with the initial physical mteraction between a pathogen or pathogens and a eukaryotic. preferably mammalian, host responsible for sequelae of infection
  • the molecules of the invention may be used m the prevention of adhesion of bacteria in particular gram positive and/or gram negative bactena, to eukaryotic, preferably mammalian, extracellular matrix protems on in-dwelling devices or to extracellular matnx protems in wounds, to block bacterial adhesion between eukaryotic, preferably mammalian, extracellular matnx protems and bacterial yphC protems that mediate tissue damage and/or, to block the normal progression of pathogenesis m infections initiated other than by the implantation of in-dwelling devices or by other surgical techniques
  • yphC agonists and antagonists to interfere with the initial physical mteraction between a
  • the antagonists and agonists of the mvention may be employed, for instance, to prevent, inhibit and/or treat diseases Hehcobacter pylori (herein "H pylori”) bacteria infect the stomachs of over one-third of the world's population causing stomach cancer, ulcers, and gastntis (International Agency for Research on Cancer (1994) Schistosomes, Liver Flukes and Hehcobacter Pylori (International Agency for Research on Cancer, Lyon.
  • H pylori diseases Hehcobacter pylori
  • Bodily mate ⁇ al(s) means any matenal denved from an mdividual or from an orgamsm infecting, infesting or inhabiting an mdividual, mcludmg but not limited to, cells, tissues and waste, such as. bone, blood, serum, cerebrospinal fluid, semen, saliva, muscle, cartilage, organ tissue, skm, urine, stool or autopsy mate ⁇ als
  • D ⁇ sease(s) means any disease caused by or related to infection by a bacte ⁇ a, mcludmg , for example, otitis media, conjunctivitis, pneumonia, bacteremia. meningitis, sinusitis, pleura! empyema and endocarditis, and most particularly meningitis, such as for example infection of cerebrospmal fluid
  • “Host cell(s)” is a cell that has been introduced (e g , transformed or transfected) or is capable of mtroduction (e g , transformation or transfection) by an exogenous polynucleotide sequence
  • Identity is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as the case may be, as determined by comparing the sequences
  • identity also means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as the case may be, as determmed by the match between strings of such sequences "Identit " can be readily calculated by known methods, mcludmg but not limited to those described m
  • Polynucleotide embodiments further mclude an isolated polynucleotide compnsing a polynucleotide sequence having at least a 95, 97, 99, 99 5 or 100% identity to the reference sequence of SEQ ID NO 1.
  • said polynucleotide sequence may be identical to the reference sequence of SEQ ID NO 1 or may mclude up to a certam mteger number of nucleotide alterations as compared to the reference sequence, wherem said alterations are selected from the group consistmg of at least one nucleotide deletion, substitution, mcludmg transition and transversion, or insertion, and wherem said alterations may occur at the 5' or 3' terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, mterspersed either individually among the nucleotides m the reference sequence or m one or more contiguous groups within the reference sequence, and wherem said number of nucleotide alterations is determmed by multiplying the total number of nucleotides in SEQ ID NO 1 by the integer defining the percent identity divided by 100 and then subtractmg that product from said total number of nucleotides in SEQ ID NO 1, or
  • n n is the number of nucleotide alterations
  • x n is the total number of nucleotides m SEQ ID NO 1
  • y is 0 95 for 95%.
  • any non-mteger product of x n and y is rounded down to the nearest mteger prior to subtractmg it from x n
  • Alterations of a polynucleotide sequence encodmg the polypeptide of SEQ ID NO 2 may create nonsense, rmssense or frameshift mutations in this coding sequence and thereby alter the polypeptide encoded by the polynucleotide following such alterations
  • Polypeptide embodiments further include an isolated polypeptide comprising a polypeptide having at least a 95, 97 or 100% identity to a polypeptide reference sequence of SEQ ID NO 2.
  • said polypeptide sequence may be identical to the reference sequence of SEQ ID NO 2 or may include up to a certain integer number of amino acid alterations as compared to the reference sequence, wherem said alterations are selected from the group consisting of at least one amino acid deletion, substitution, mcludmg conservative and non-conservative substitution, or insertion, and wherem said alterations may occur at the ammo- or carboxy-terminal positions of the reference polypeptide sequence or anywhere between those terminal positions, mterspersed either individually among the ammo acids m the reference sequence or m one or more contiguous groups within the reference sequence, and wherein said number of ammo acid alterations is determmed by multiplying the total number of ammo acids in SEQ ID NO 2 by the integer defining the percent identity divided by 100 and then subtractmg that product from said total number of am
  • n a is the number of amino acid alterations
  • x a is the total number of ammo acids in SEQ ID NO 2
  • y is 0 95 for 95%, 0 97 for 97% or 1 00 for 100%
  • • is the symbol for the multiplication operator, and wherem any non-integer product of x a and y is rounded down to the nearest integer pnor to subtractmg it from x a
  • Ind ⁇ v ⁇ dual(s) means a multicellular eukaryote, mcludmg, but not limited to a metazoan. a mammal, an ov ⁇ d. a bov ⁇ d, a simian, a primate, and a human
  • Isolated means altered “by the hand of man” from its natural state, / e , if it occurs m nature, it has been changed or removed from its onginal environment, or both
  • a polvnucleotide or a polypeptide naturally present m a living organism is not “isolated,” but the same polynucleotide or polypeptide separated from the coexisting matenals of its natural state is “isolated", as the term is employed herem
  • a polynucleotide or polypeptide that is introduced mto an orgamsm by transformation, genetic manipulation or by any other recombinant method is "isolated” even if it is still present in said orgamsm which orgamsm may be living or non-living
  • Organ ⁇ sm(s) means a (1) prokaryote. mcludmg but not limited to, a member of the genus Streptococcus, Staphylococcus, Bordetella, Corynebactenum Mycobactenum, Neissena, Haemoph ⁇ us Actinomycetes, Streptomycetes, Nocardia, Enter obacter, Yersima, Fancisella, Pasturella, Moraxella, Acmetobacter Erysipelothnx, Branhamella, Actinobacillus, Streptobacillus, Listena Calymmatobactenum, Brucella Bacillus, Clostndium, Treponema, Eschenchia, Salmonella, Kleibsiella Vibrio, Proteus, Erwinia, Borre a, Leptospira, Spirillum, Campylobacter, Shigella, Legtonella Pseudomonas, Aero
  • Streptococcus faecium a member of the species or group, Group A Streptococcus, Group B Streptococcus, Group C Streptococcus, Group D Streptococcus, Group G Streptococcus, Streptococcus pneumomae, Streptococcus pyogenes, Streptococcus agalactiae, Streptococcus faecahs. Streptococcus faecium.
  • Streptococcus duram Neissena gonorrheae, Neissena memngitidis, Staphylococcus aureus Staphylococcus epidermidis Corynebactenum d ⁇ thenae Gardnerella vagina s, Mycobactenum tuberculosis, Mycobactenum bovis Mycobactenum ulcerans, Mycobactenum leprae, Actinomyctes israelu, Listena monocytogenes, Bordetella pertusis, Bordatella parapertusis, Bordetella bronchiseptica, Eschenchia co , Shigella dysentenae, Haemoph ⁇ us influenzae, Haemoph ⁇ us aegyphus, Haemophilus parainfluenzae, Haemop lus ducreyi, Bordetella, Salmonella typhi, Citrobacter freundn, Proteus mirabi s, Proteus vulgans
  • Polynucleotide(s) generally refers to any poly ⁇ bonucleotide or polydeoxynbonucleotide, that may be unmodified RNA or DNA or modified RNA or DNA
  • Polynucleot ⁇ de(s)" mclude, without limitation, smgle- and double-stranded DNA, DNA that is a mixture of smgle- and double-stranded regions or smgle-, double- and triple-stranded regions, smgle- and double-stranded RNA, and RNA that is mixture of smgle- and double-stranded regions, hybnd molecules compnsing DNA and RNA that may be smgle-stranded or.
  • polynucleotide refers to triple-stranded regions compnsmg RNA or DNA or bodi 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 t ⁇ ple-hehcal region often is an ohgonucleotide
  • the term "polynucleotide(s)” also mcludes DNAs or RNAs as descnbed above that compnse one or more modified bases
  • DNAs or RNAs with backbones modified for stability- or for other reasons are "polynucleot ⁇ de(s)" as that term is mtended herem Moreover.
  • DNAs or RNAs compnsmg unusual bases such as inosine. or modified bases, such as t ⁇ tylated 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
  • polynucleot ⁇ de(s) as it is employed herem embraces such chemically, enzymatically or metabo cally modified forms of polynucleotides, as well as the chemical forms of DNA and RNA charactenstic of viruses and cells, including for example, simple and complex cells
  • Polynucleo ⁇ de(s) also embraces short polynucleotides often refened to as ohgonucleotide(s)
  • Polypept ⁇ de(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, commonh refened to as peptides, ohgopeptides and o gomers and to longer chains generally refened to as protems
  • Polypeptides may compnse ammo acids other than the 20 gene encoded ammo acids
  • Polypept ⁇ de(s)” mclude those modified either by natural processes, such as processmg and other post-transla ⁇ onal modifications, but also by chemical modification techmques 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 in the same or varymg degree at several sites m a given polypeptide Also, a given polypeptide
  • acetylation 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, cyclization. disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine.
  • Polypeptides may be branched or cyclic, with or without branching Cyclic, branched and branched circular polypeptides may result from posttranslational natural processes and may be made by entirely synthetic methods, as ell "Recombinant expression system(s)" refers to expression systems or portions thereof or polynucleotides of the mvention introduced or transformed mto a host cell or host cell lysate for the production of the polynucleotides and polypeptides of the mvention
  • 'Nanant(s) is a polynucleotide or polypeptide that differs from a reference polynucleotide or polypeptide respectively, but retains essential properties
  • a typical va ⁇ ant of a polynucleotide differs in nucleotide sequence from another, reference polynucleotide Changes m the nucleotide sequence of the vanant may or may not alter the ammo acid sequence of a pohpeptide encoded by the reference polynucleotide Nucleotide changes may result in ammo acid substitutions additions, deletions, fusion proteins and truncations in the polypeptide encoded by the reference sequence, as discussed below
  • a typical variant of a polypeptide differs m ammo acid sequence from another, reference polypeptide Generally, differences are limited so that the sequences of the reference polypeptide and the vanant are closely similar overall and, m many regions, identical A vanant and reference polypeptide may differ in ammo acid sequence
  • a variant of a polynucleotide or polypeptide may be a naturally occurring such as an alle c 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 techmques, by direct synthesis, and by other recombinant methods known to skilled artisans
  • Example 1 Strain selection, Library Production and Sequencing
  • the polynucleotide havmg a DNA sequence given m Table 1 [SEQ ID NO 1] was obtained from a library of clones of chromosomal DNA of Streptococcus pneumomae in E coli
  • the sequencmg data from two or more clones compnsmg overlappmg Streptococcus pneumomae DNAs w as used to construct the contiguous DNA sequence m SEQ ID NO 1 Libraries may be prepared by routme methods, for example Methods 1 and 2 below
  • Total cellular DNA is isolated from Streptococcus pneumomae 0100993 according to standard procedures and size-fractionated by either of two methods
  • Method 1 Total cellular DNA is mechanically sheared by passage through a needle 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 ligated mto the vector Lambda Zapll that has been cut with EcoRI, the library packaged by standard procedures and E coli mfected with the packaged library
  • the library is amplified by standard procedures
  • Total cellular DNA is partially hydrolyzed with a one or a combination of restriction enzymes appropriate to generate a series of fragments for clonmg mto library vectors (e g . Rsal. Pall, Alul. Bshl235I), and such fragments are size-fractionated accordmg to standard procedures EcoRI linkers are ligated to the DNA and the fragments then ligated into the vector Lambda Zapll that have been cut with EcoRI, the library packaged by standard procedures, and E coli infected with the packaged library The library is amplified by standard procedures Example 2 yphC Characterization
  • the S. pneumoniae yphC gene is expressed during infection in a respiratory tract infection model
  • RNAase free, DNAase free, DNA and protein free preparations of RNA obtained are suitable for Reverse Transcription PCR (RT-PCR) usmg unique primer pairs designed from the sequence of each gene of Streptococcus pneumomae 0100993 a) Isolation of tissue infected with Streptococcus pneumomae 0100993 from a mouse animal model of mfection (lungs)
  • Streptococcus pneumomae 0100993 is seeded onto TSA (Tryptic Soy Agar BBL) plates contaimng 5% horse blood and allowed to grow overnight at 37°C in a C02 incubator Bacterial growth is scraped into 5 ml of phosphate-buffered salme (PBS) and adjusted to an A600 ⁇ 0 6 (4 x 106/ml) Mice (male CBA/J-1 mice, approximately 20g) were anaesthetized with isoflurane and 50 microhters of the prepared bacterial inoculum is delivered by mtranasal instillation Animals are allowed to recover and observed twice daily for signs of mo ⁇ bundancy Forty-eight hours after infection the animals are euthanized by carbon dioxide overdose and their torsos swabbed ith ethanol and then RNAZap The torso is then opened, and the lungs are aseptically removed Half of each pair of lungs is placed m a cry
  • RNA preparations are stored at -80 oC for up to one month
  • the RNA precipitate can be stored at the wash stage of the protocol m 75% ethanol for at least one year at -20 oC
  • RNA isolation is assessed by running samples on 1% agarose gels 1 x TBE gels stamed with ethidium bromide are used to visualise total RNA yields
  • 2 2M formaldehyde gels are run and vacuum blotted to Hybond-N (Amersham)
  • the blot is then hybndised with a 32P-labelled ohgonucletide probe, of sequence 5' AACTGAGACTGGCTTTAAGAGATTA 3' [SEQ ID NO 3], specific to 16S rRNA of Streptococcus pneumomae
  • the size of the hybridising band is compared to that of control RNA isolated from m vitro grown Streptococcus pneumomae 0100993 m the Northern blot Correct sized bacterial 16S rRNA bands can be detected m total RNA samples which show degradation of the mammalian RNA when visualised on TBE gel
  • PCR reactions are set up on ice m 0 2ml tubes by adding the following components 43 microhtres PCR Master Mix (Advanced Biotechnologies Ltd ), 1 micro tre PCR primers (optimally 18- 25 basepairs m length and designed to possess similar annealing temperatures), each pnmer at 1 OmM initial concentration, and 5 microhtres cDNA
  • PCR reactions are run on a Perkin Elmer GeneAmp PCR System 9600 as follows 2 minutes at 94 oC, then 50 cycles of 30 seconds each at 94 oC, 50 oC and 72 oC followed by 7 minutes at 72 oC and then a hold temperature of 20 oC (the number of cycles is optimally 30-50 to determine the appearance or lack of a PCR product and optimally 8-30 cycles if an estimation of the starting quantity of cDNA from the RT reaction is to be made), 10 microhtre aliquots are then run out on 1% 1 x TBE gels stained with ethidium bromide, with PCR product, if present, sizes estimated by comparison to a 100 bp DNA Ladder (Gibco BRL, Life Technologies) Alternatively if the PCR products are convemently labelled by the use of a labelled PCR pnmer (e g labelled at the 5'end with a dye) a smtable aliquot of the PCR product is run out on
  • Primer pairs which fail to give the predicted sized product in either DNA PCR or RT/PCR are PCR failures and as such are uninformative Of those which give the correct size product widi DNA PCR two classes are distinguished m RT/PCR 1 Genes which are not transcribed m vivo reproducibh fail to give a product m RT/PCR. and 2 Genes which are transcribed m vivo reproducibh giv e the correct size product m RT/PCR and show a stronger signal in the +RT samples than the signal (if at all present) m -RT controls
  • the yphC gene is essential for S. pneumoniae in vitro growth.
  • allelic replacement cassette was generated usmg PCR technology
  • the cassette consisted of a pair of 500bp chromosomal DNA fragments flanking an erythromycm resistance gene
  • the chromosomal DNA sequences are the 500bp preceding and following the DNA sequence encodmg the yphC gene contained m Seq ID NO 1
  • the allelic replacement cassette was mtroduced mto S pneumomae R6 by transformation Competent cells were prepared according to published protocols
  • DNA was mtroduced mto the cells by mcubation of ng quantities of allelic replacement cassette with 10" cells at 30°C for 30 minutes The cells were transferred to 37°C for 90 minutes to allow expression of the erythromycm resistance gene
  • Cells were plated in agar containmg lug erythromycm per ml Following mcubation at 37°C for 36 hours, colonies are picked and grown overnight m Todd-Hewitt broth supplemented with 0 5% yeast extract Typically 1000 transformants containmg the appropnate allelic replacement are obtained If no transformants are obtained m three separate transformation experiments as w as the case for this gene yphC, then the gene is considered as bemg essential in vitro

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Abstract

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

Description

yphC
FIELD OF THE INVENTION
This uwention relates to newh identified polynucleotides and pohpeptides. and their production and uses, as well as their variants, agonists and antagonists, and their uses In particular, the invention relates to polynucleotides and pohpeptides of the yphC (GTP-binding proteins) family, as well as their vaπants. herem referred to as "yphC," "yphC polynucleotιde(s)," and "yphC polypeptιde(s)" as the case
Figure imgf000003_0001
be
BACKGROUND OF THE INVENTION The Streptococci make up a medically important genera of microbes known to cause several types of disease in humans, mcludmg, 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 Smce its isolation more than 100 years ago. Streptococcus pneumomae has been one of tlie more intensively studied microbes For example, much of our earlv understandmg that DNA is in fact tlie genetic mateπal was predicated on the work of Gπffith and of Avery, Macleod and McCartv us g this microbe Despite the vast amount of research with S pneumomae, many questions concerning tlie virulence of this microbe remain It is particularly preferred to employ Streptococcal genes and gene products as targets for tlie development of antibioUcs
Tlie frequency of Streptococcus pneumomae infections has πsen dramaticalh in tlie past few decades This has been attπbuted to the emergence of multiply antibiotic resistant strains and an mcreasmg population of people with weakened immune systems It is no longer uncommon to isolate Streptococcus pneumomae strains that are resistant to some or all of tlie standard antibioUcs This phenomenon has created an unmet medical need and demand for new anti-microbial agents, vaccmes. drug screening methods, and diagnostic tests for this organism Moreover, the drug discover}' process is currently undergoing a fundamental revolution as it embraces "functional genomics," that is, high throughput genome- or gene-based biolog} This approach is rapidly superseding earlier approaches based on "positional cloning" and other methods Functional genomics relies heavily on the various tools of bioinformatics to identify gene sequences of potential mterest from the many molecular biology databases now available as well as from other sources There is a continuing and significant need to identify and characterize further genes and other polynucleotides sequences and their related polypepUdes, as targets for drug discovery
Clearly, there exists a need for polynucleotides and pohpeptides, such as the }phC embodiments of the invention, that have a present benefit of. among other things, bemg useful to screen compounds for antimicrobial activity Such factors are also useful to determine their role in pathogenesis of infection. dysfunction and disease There is also a need for identification and characterization of such factors and their antagonists and agonists to find ways to prevent, ameliorate or correct such infection. d\ sfunction and disease
SUMMARY OF THE INVENTION The present mvention relates to yphC, m particular yphC polypeptides and yphC polynucleotides recombinant mateπals and methods for their production In another aspect, the mvention relates to methods for usmg such pohpeptides and polynucleotides. mcludmg treatment of microbial diseases, amongst others In a further aspect, the invention relates to methods for identifying agonists and antagonists using the mateπals provided by the invention, and for treatmg microbial infections and conditions associated ith such infections with the identified agomst or antagomst compounds In a still further aspect, the mvention relates to diagnostic assays for detecting diseases associated w th microbial infections and conditions associated with such infections, such as assays for detectmg yphC expression or activity
Vaπous changes and modifications within the spirit and scope of the disclosed mvention will become readily apparent to those skilled m the art from reading the following descπptions and from reading the other parts of the present disclosure
DESCRIPTION OF THE INVENTION
The mvention relates to yphC polypeptides and polynucleotides as descπbed in greater detail below In particular, the mvention relates to polypeptides and polynucleotides of a yphC of Streptococcus pneumomae, that is related by ammo acid sequence homology to B subtilis yphC pohpeptide The mvention relates especially to yphC having a nucleotide and ammo acid sequences set out m Table 1 as SEQ ID NO 1 and SEQ ID NO 2 respectively Note that sequences recited in the Sequence Listmg below as "DNA" represent an exemplification of the mvention. smce those of ordmary skill will recogmze that such sequences can be usefully employed m polynucleotides m general, mcludmg πbopolynucleotides
TABLE 1 yphC Polynucleotide and Polypeptide Sequences
(A) Streptococcus pneumomae yphC polynucleotide sequence [SEQ ID NO 1] 5 ' -
ATGGCCCTACCAACTATTGCCATTGTAGGACGTCCCAATGTTGGGAAATCAACCCTATTTAATCGGATCGCTGGT GAGCG
AATCTCCATTGTAGAAGATGTCGAAGGAGTGACACGTGACCGTATTTATGCAACGGGTGAGTGGCTCAATCGTTC TTTTA GCATGATTGATACAGGAGGAATTGATGATGTCGATGCTCCTTTCATGGAACAAATCAAGCACCAGGCAGAAATTG
CCATG
GAAGAAGCAGATGTTATCGTTTTTGTCGTGTCTGGTAAGGAAGGAATTACTGATGCAGACGAATACGTAGCTCGT
AAGCT TTATAAGACCCACAAACCAGTTATCCTCGCAGTCAACAAGGTGGACAACCCTGAGATGCGAAATGATATCTATGA
TTTCT
ATGCCCTCGGTTTGGGTGAACCACTGCCTATCTCATCTGTCCATGGTATCGGTACAGGGGATGTACTAGATGCGA
TTGTG
GAAAACCTTCCAAATGAATATGAAGAAGAAAATCCAGATGTCATTAAGTTTAGCTTGATTGGTCGTCCTAACGTT GGAAA
ATCAAGCTTGATTAATGCTATCTTGGGAGAAGACCGTGTCATTGCCAGTCCTGTTGCTGGAACAACTCGTGACGC
TATTG
ATACCCACTTTACAGATACAGATGGTCAAGAGTTTACCATGATTGATACGGCTGGTATGCGTAAGTCTGGTAAGG
TTTAT GAAAATACTGAGAAGTACTCTGTCATGCGTGCCATGCGTGCTATTGACCGTTCAGATGTGGTCTTAATGGTCATC
AATGC
GGAAGAGGGGATTCGTGAATACGACAAACGTATCGCTGGATTTGCTCATGAAGCTGGTAAAGGGATGATTATCGT
GGTCA
ACAAGTGGGATACGCTTGAAAAAGATAACCACACTATGAAAAACTGGGAAGAAGATATCCGTGAGCAGTTCCAAT ACCTG
CCTTACGCACCGATTATCTTTGTATCAGCTTTAACCAAGCAACGTCTCCACAAACTTCCTGAGATGATTAAGCAA
ATCAG
CGAAAGTCAAAATACACGTATTCCATCAGCTGTCTTGAACGATGTCATCATGGATGCCATTGCCATCAACCCAAC
ACCGA CAGACAAAGGAAAACGTCTCAAGATTTTCTATGCGACCCAAGTGGCAACCAAACCACCAACCTTTGTCATCTTTG
TCAAT
GAAGAAGAACTCATGCACTTTTCTTACCTGCGTTTCTTGGAAAATCAAATCCGCAAGGCCTTTGTTTTTGAGGGA
ACACC
GATTCATCTCATCGCAAGAAAACGCAGATAA-3 '
(B) Streptococcus pneumoniae yphC polypeptide sequence deduced from a polynucleotide sequence in this table [SEQ ID NO:2].
NH2-
MALPTIAIVGRPNVGKSTLFNRIAGERISIVEDVEGλ/TRDRIYATGEWLNRSFSMIDTGGIDDVDAPFMEQIKHQ AEIAM
EEADVIVFvVSGKEGITDADEYVARKLYKTHKPVI AVIKVDNPEMRNDIYDFYALGLGEPLPISSVHGIGTGDV
LDAIV
ENLPNEYEEENPDVIKFSLIGRPNVGKSSLINAILGEDRVIASPVAGTTRDAIDTHFTDTDGQEFTMIDTAGMRK
SGKVY ENTEKYSv^_RAMR IDRSDVVL^^v^INAEEGIREYDKRIAGFAH__.GKGMIIVv^^KWDTLEKDNHTMKN EEDIRE
QFQYL PYAPI I FVSALTKQRLHKLPEMI KQI SESQNTRI PSAVLNDVIMDAIAINPTPTDKGKRLKI FYATQVATKPPTF
VI FVN
EEELMHFSY RFLENQI RKAFVFEGTPIHLIARKRR-COOH
Deposited materials
A deposit compnsing a Streptococcus pneumomae 0100993 strain has been deposited with the National Collections of Industrial and Marine Bactena Ltd (herem "NCIMB"). 23 St Machar Dπ\e Aberdeen AB2 1RY, Scotland on 11 April 1996 and assigned deposit number 40794 The deposit was descπbed as Streptococcus pneumomae 0100993 on deposit On 17 Apπl 1996 a Streptococcus pneumomae 0100993 DNA hbraiy m E coli was similarh deposited with the NCIMB and assigned deposit number 40800 The Streptococcus pneumomae strain deposit is referred to herem as "the deposited strain" or as "the DNA of the deposited strain "
The deposited strain compπses a full length yphC gene The sequence of the polynucleotides compπsed m the deposited strain, as well as the ammo acid sequence of any pohpeptide encoded thereby, are controlling m the event of any conflict with any descπption of sequences herem
The deposit of the deposited strain has been made under the terms of the Budapest Treaty on the International Recognition of the Deposit of Micro-organisms for Purposes of Patent Procedure The deposited strain will be irrevocably and without restnction or condition released to the public upon tlie issuance of a patent The deposited strain is provided merely as convemence to those of skill m tlie art and is not an admission that a deposit is required for enablement, such as that required under 35 U S C §112 A license may be required to make, use or sell the deposited strain, and compounds deπved therefrom, and no such license is hereby granted
In one aspect of the mvention there is provided an isolated nucleic acid molecule encoding a mature polypeptide expressible by the Streptococcus pneumomae 0100993 strain, which polypeptide is compπsed in the deposited strain Furtlier provided by the mvention are yphC polynucleotide sequences m the deposited strain, such as DNA and RNA, and ammo acid sequences encoded thereby Also provided by the mvention are yphC polypeptide and polynucleotide sequences isolated from the deposited strain
Polypeptides
YphC polypeptide of the mvention is substantially phylogenetically related to other proteins of the yphC (GTP-binding proteins) family
In one aspect of the mvention there are provided polypeptides of Streptococcus pneumomae referred to herem as "yphC" and "yphC polypeptides" as well as biologically, diagnostically . proplwlacticalh clinically or therapeutically useful variants thereof, and compositions compnsing the same
Among the particularly preferred embodiments of the mvention are variants of yphC polypeptide encoded by naturally occurring alleles of a yphC gene The present mvention further provides for an isolated polypeptide that (a) compπses or consists of an am o acid sequence that has at least 95% identity, most preferably at least 97-99% or exact identity to that of SEQ ID NO 2 over the entire length of SEQ ID NO 2. (b) a polypeptide encoded by an isolated polynucleotide compπsmg or consistmg of a polynucleotide sequence that has at least 95% identity, even more preferably at least 97-99% or exact identity to SEQ ID NO 1
Figure imgf000007_0001
entire length of SEQ ID NO 1, (c) a polypeptide encoded by an isolated polynucleotide compπsmg or consisting of a polynucleotide sequence encoding a polypeptide that has at least 95% identity, even more preferably at least 97-99% or exact identity, to the ammo acid sequence of SEQ ID NO 2, over the entire length of SEQ ID NO 2 The polypeptides of the mvention mclude a polypeptide of Table 1 [SEQ ID NO 2] (in particular a mature polypeptide) as well as polypeptides and fragments, particularly those that has a biological activity of yphC. and also those that have at least 95% identity to a polypeptide of Table 1 [SEQ ED NO 2] and also mclude portions of such polypeptides with such portion of the polypeptide generally compπsmg at least 30 ammo acids and more preferably at least 50 ammo acids The mvention also mcludes a polypeptide consistmg of or compπsmg a polypeptide of the formula
X-(R1)m-(R2)-(R3)n-Y wherem, at the ammo terminus, X is hydrogen, a metal or any other moiety descnbed herem for modified polypeptides, and at the carboxyl terminus, Y is hydrogen, a metal or any other moiety descnbed herem for modified polypeptides, Ri and R3 are any ammo acid residue or modified ammo acid residue, m is an mteger between 1 and 1000 or zero, n is an mteger between 1 and 1000 or zero, and R2 is an ammo acid sequence of the mvention, particularly an ammo acid sequence selected from Table 1 or modified forms thereof In the formula above, R2 is oπented so that its am o terminal ammo acid residue is at the left, covalently bound to Ri and its carboxy terminal ammo acid residue is at the πght, covalently bound to R3 Any stretch of ammo acid residues denoted by either Ri or R3, where m and/or n is greater than 1, may be either a heteropolymer or a homopolymer, preferably a heteropolymer Other preferred embodiments of the mvention are provided where m is an mteger between 1 and 50, 100 or 500, and n is an mteger between 1 and 50. 100, or 500
It is most preferred that a polypeptide of the mvention is denved from Streptococcus pneumomae. however, it may preferably be obtained from other organisms of the same taxonomic genus A polypeptide of the mvention may also be obtained, for example, from organisms of the same taxonomic family or order A fragment is a vaπant polypeptide havmg an ammo acid sequence that is entirely the same as part but not all of any ammo acid sequence of any polypeptide of the mvention As with yphC 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 m a smgle larger polypeptide Preferred fragments mclude. for example, truncation polypeptides havmg a portion of an am o acid sequence of Table 1 [SEQ ID NO 2], or of variants thereof, such as a continuous senes of residues that mcludes an ammo- and/or carboxyl-terminal ammo acid sequence Degradation forms of the polypeptides of the mvention produced by or m a host cell, particularly a Streptococcus pneumomae. are also prefened Further prefened are fragments characterized bv structural or functional attπbutes such as fragments that compnse alpha-helix and alpha-hehx forming regions, beta-sheet and beta-sheet-forming regions, turn and tum-formmg regions, coil and coil-forming regions, hydrophihc regions, hydrophobic regions alpha amphipathic regions, beta amphipathic regions, flexible regions, surface-forming regions, substrate binding region, and high antigenic mdex regions Further prefened fragments mclude an isolated polypeptide comprising an amino acid sequence havmg at least 15, 20, 30, 40, 50 or 100 contiguous amino acids trom the amino acid sequence of SEQ ID NO.2, or an isolated polypeptide comprising an amino acid sequence havmg at least 15, 20, 30, 40, 50 or 100 contiguous amino acids truncated or deleted trom the amino acid sequence ot SEQ ID NO.2 Fragments of the polypeptides of the mvention may be employed for producmg the conesponding full-length polypeptide by peptide synthesis, therefore, these variants may be employed as intermediates for producmg the full-length polypeptides of the mvention Polynucleotides It is an object of the mvention to provide polynucleotides that encode yphC polypeptides, particularly polynucleotides that encode a polypeptide herem designated yphC
In a particularly prefened embodiment of the mvention the polynucleotide compnses a region encoding yphC polypeptides compπsmg a sequence set out m Table 1 [SEQ ID NO 1] that mcludes a full length gene, or a variant thereof The Applicants beheve that this full length gene is essential to the growth and/or survival of an organism that possesses it, such as Streptococcus pneumomae As a further aspect of the mvention there are provided isolated nucleic acid molecules encoding and/or expressing yphC polypeptides and polynucleotides, particularly Streptococcus pneumomae yphC polypeptides and polynucleotides, mcludmg, for example, unprocessed RNAs, nbozyme RNAs, mRNAs, cDNAs, genomic DNAs, B- and Z-DNAs Further embodiments of the mvention mclude biologically, diagnostically, prophylactically, clinically or therapeutically useful polynucleotides and polypeptides and variants thereof, and compositions compnsing the same
Another aspect of the mvention relates to isolated polynucleotides. mcludmg at least one full length gene, that encodes a yphC polypeptide having a deduced ammo acid sequence of Table 1 [SEQ ID NO 2] and polynucleotides closely related thereto and variants thereof In another particularly preferred embodiment of the mvention there is a yphC polypeptide from Streptococcus pneumomae compnsmg or consisting of an ammo acid sequence of Table 1 [SEQ ID NO 2], or a variant thereof
Usmg the information provided herein, such as a polynucleotide sequence set out in Table 1 [SEQ ID NO 1]. a polynucleotide of the mvention encoding yphC polypeptide may be obtained usmg standard cloning and screening methods, such as those for cloning and sequencmg chromosomal DNA fragments from bactena usmg Streptococcus pneumomae 0100993 cells as starting matenal. followed by obtaining a full length clone For example, to obtam a polynucleotide sequence of the invention, such as a polynucleotide sequence given m Table 1 [SEQ ID NO 1], typically a library of clones of chromosomal DNA of Streptococcus pneumomae 0100993 in E coh or some other suitable host is probed with a radiolabeled ohgonucleotide preferably a 17-mer or longer, denved from a partial sequence Clones carrying DNA identical to that of the probe can then be distinguished usmg stringent hybndization conditions By sequencmg the individual clones thus identified by hybndization with sequencmg primers designed from the ongmal polypeptide or polynucleotide sequence it is then possible to extend the polynucleotide sequence in both directions to determine a full length gene sequence Convemently, such sequencmg is performed, for example, usmg denatured double stranded DNA prepared from a plasmid clone Suitable techniques are described by Mamatis, 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 Screemng By Hybridization 1 90 and Sequencmg Denatured Double-Stranded DNA Templates 13 70) Direct genomic DNA sequencmg may also be performed to obtam a full length gene sequence Illustrative of the mvention, each polynucleotide set out in Table 1 [SEQ ID NO 1] was discovered m a DNA library denved from Streptococcus pneumomae 0100993
Moreover, each DNA sequence set out m Table 1 [SEQ ID NO 1] contains an open reading 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 to those skilled in the art The polynucleotide of SEQ ID NO 1, between nucleotide number 1 and the stop codon that begins at nucleotide number 1309 of SEQ ID NO 1, encodes the polypeptide of SEQ ID NO 2
In a further aspect, the present mvention provides for an isolated polynucleotide compnsmg or consistmg of (a) a polynucleotide sequence that has at least 95% identity, even more preferably at least 97%. still more preferably at least 99%, yet still more preferably at least 99 5% or exact identity to SEQ ID NO 1 over the entire length of SEQ ID NO 1, or the entire length of that portion of SEQ ID NO 1 which encodes SEQ ID NO 2, (b) a polynucleotide sequence encoding a polypeptide that has at least 95% identity, even more preferably at least 97-99% or 100% exact, to the ammo acid sequence of SEQ ID NO 2, over the entire length of SEQ ID NO 2
A polynucleotide encoding a polypeptide of the present mvention. mcludmg homologs and orthologs from species other than Streptococcus pneumomae, may be obtained by a process that compnses the steps of screening an appropπate library under stringent hybndization conditions with a labeled or detectable probe consistmg of or compnsmg the sequence of SEQ ID NO 1 or a fragment thereof, and isolating a full-length gene and/or genomic clones compnsmg said polynucleotide sequence
The mvention provides a polynucleotide sequence identical over its entire length to a coding sequence (open reading frame) m Table 1 [SEQ ID NO 1] Also provided by the mvention is a coding sequence for a mature polypeptide or a fragment thereof, by itself as well as a coding sequence for a mature pohpeptide or a fragment in reading frame with another coding sequence, such as a sequence encoding a leader or secretory sequence, a pre-, or pro- or prepro-protein sequence The polynucleotide of the mvention may also compnse at least one non-coding sequence, mcludmg for example, but not limited to at least one non-coding 5' and 3' sequence, such as the transcnbed but non-translated sequences, termination signals (such as rho-dependent and rho-mdependent termination signals), nbosome bmdmg sites, Kozak sequences, sequences that stabilize mRNA, introns, and polyadenylation signals The polynucleotide sequence may also compnse additional coding sequence encoding additional ammo acids For example, a marker sequence that facilitates purification of a 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 m Gentz et al , Proc Natl Acacl Set , USA 86 821-824 (1989), or an HA peptide tag (Wdson et al . Cell 37 767 (1984). both of that may be useful m purifying polypeptide sequence fused to them Polynucleotides of the mvention also mclude. but are not limited to, polynucleotides compnsmg a structural gene and its naturally associated sequences that control gene expression
A prefened embodiment of the mvention is a polynucleotide of consistmg of or compnsmg nucleotide 1 to the nucleotide immediately upstream of or mcludmg nucleotide 1309 set forth m SEQ ID NO 1 of Table 1, both of that encode a yphC polypeptide
The mvention also mcludes a polynucleotide consisting of or compnsmg a polynucleotide of the formula
X-(R1)m-(R2)-(R3)n-Y wherem, at the 5' end of the molecule, X is hydrogen, a metal or a modified nucleotide residue, or together with Y defines a covalent bond, and at the 3' end of the molecule, Y is hydrogen, a metal, or a modified nucleotide residue, or together with X defines the covalent bond, each occurrence of Ri and R3 is independently any nucleic acid residue or modified nucleic acid residue, m is an mteger between 1 and 3000 or zero , n is an mteger between 1 and 3000 or zero, and R2 is a nucleic acid sequence or modified nucleic acid sequence of the mvention. particularly a nucleic acid sequence selected from Table 1 or a modified nucleic acid sequence thereof In the polynucleotide formula above. R2 is oriented so that its 5' end nucleic acid residue is at the left, bound to Ri and its 3' end nucleic acid residue is at the nght. bound to R3 Any stretch of nucleic acid residues denoted by either Rj and/or R . where m and/or n is greater than 1. may be either a heteropolymer or a homopolymer, preferably a heteropolymer Where, m a prefened embodiment. X and Y together define a covalent bond, the polynucleotide of the above formula is a closed, circular polynucleotide, that can be a double-stranded polynucleotide wherem the formula show s a first strand to which the second strand is complementary In another prefened embodiment m and/or n is an mteger between 1 and 1000. Other prefened embodiments of the mvention are provided where m is an mteger between 1 and 50. 100 or 500, and n is an mteger between 1 and 50, 100, or 500
It is most preferred that a polynucleotide of the mvention is denved from Streptococcus pneumomae, however, it may preferably be obtained from other organisms of the same taxonomic genus A polynucleotide of tlie mvention may also be obtained, for example, from organisms of the same taxonomic family or order The term "polynucleotide encoding a polypeptide" as used herem encompasses polynucleotides that mclude a sequence encoding a polypeptide of the mvention, particularly a bactenal polypeptide and more particularly a polypeptide of the Streptococcus pneumomae yphC havmg an ammo acid sequence set out in Table 1 [SEQ ID NO.2] The term also encompasses polynucleotides that mclude a smgle contmuous region or discontinuous regions encoding the polypeptide (for example, polynucleotides interrupted by mtegrated phage, an mtegrated insertion sequence, an mtegrated vector sequence, an mtegrated transposon sequence, or due to RNA editing or genomic DNA reorganization) together with additional regions, that also may compnse cooing and/or non-coding sequences
The mvention further relates to variants of the polynucleotides descnbed herem that encode variants of a polypeptide having a deduced ammo acid sequence of Table 1 [SEQ ID NO 2] Fragments of polynucleotides of the mvention may be used, for example, to synthesize full-length polynucleotides of the mvention
Further particularly prefened embodiments are polynucleotides encoding yphC variants, that have the ammo acid sequence of yphC polypeptide of Table 1 [SEQ ID NO.2] m which several, a few, 5 to 10, 1 to 5, 1 to 3, 2, 1 or no ammo acid residues are substituted, modified, deleted and/or added, in any combmation Especially prefened among these are silent substitutions, additions and deletions, that do not alter the properties and activities of yphC polypeptide
Prefened isolated polynucleotide embodiments also mclude polynucleotide fragments, such as a polynucleotide comprising a nuclic acid sequence having at least 15, 20, 30, 40, 50 or 100 contiguous nucleic acids from the polynucleotide sequence of SEQ ID NO: l, or an polynucleotide comprising a nucleic acid sequence havmg at least 15, 20, 30, 40, 50 or 100 contiguous nucleic acids truncated or deleted from the 5' and/or 3' end of the polynucleotide sequence of SEQ ID NO. l
Further prefened embodiments of the mvention are polynucleotides that are at least 95% or 97% identical over their entire length to a polynucleotide encoding yphC polypeptide havmg an am o acid sequence set out m Table 1 [SEQ ID NO 2], and polynucleotides that are complementary to such polynucleotides Most highly prefened are polynucleotides that compnse a region that is at least 95% are especially prefened Furthermore, those with at least 97% are highly prefened among those with at least 95% and among these those with at least 98% and at least 99% are particularly highly preferred, with at least 99% bemg the more prefened
Prefened embodiments are polynucleotides encoding polypeptides that retain substantialh the same biological function or activity as a mature polypeptide encoded by a DNA of Table 1 [SEQ ID NO 1]
In accordance with certam prefened embodiments of this mvention there are provided polynucleotides that hybndize, particularly under strmgent conditions to yphC polynucleotide sequences, such as those polynucleotides in Table 1
The mvention further relates to polynucleotides that hybndize to the polynucleotide sequences provided herem In this regard, the mvention especially relates to polynucleotides that hybndize under strmgent conditions to the polynucleotides descnbed herem As herem used, the terms "strmgent conditions" and "strmgent hybndization conditions" mean hybndization occurring only if there is at least 95% and preferably at least 97% identity between the sequences A specific example of strmgent hvbridization conditions is overnight incubation at 42°C m a solution compnsmg 50% formamide, 5x SSC (150mM NaCl, 15mM tπsodium citrate), 50 M sodium phosphate (pH7 6), 5x Denhardt's solution, 10% dextran sulfate, and 20 micrograms/ml of denatured, sheared salmon sperm DNA. followed by washing the hybridization support in 0 lx SSC at about 65°C Hybridization and wash conditions are well known and exemplified in Sambrook, et al , Molecular Clonmg A Laboratory Manual, Second Edition, Cold Spring Harbor, N Y , (1989), particularly Chapter 11 therein Solution hybndization may also be used with the polynucleotide sequences provided by the mvention
The mvention also provides a polynucleotide consistmg of or compnsmg a polynucleotide sequence obtained by screening an appropnate library compnsmg a complete gene for a polynucleotide sequence set forth m SEQ ID NO 1 under strmgent hybndization conditions with a probe having the sequence of said polynucleotide sequence set forth in SEQ ID NO 1 or a fragment thereof, and isolating said polynucleotide sequence Fragments useful for obtaining such a polynucleotide mclude. for example, probes and pnmers fully descnbed elsewhere herem As discussed elsewhere herem regarding polynucleotide assays of the mvention. for instance, the polynucleotides of the mvention. may be used as a hybndization probe for RNA, cDNA and genomic DNA to isolate full-length cDNAs and genomic clones encoding yphC and to isolate cDNA and genomic clones of other genes that have a high identity, particularly high sequence identity, to a yphC gene Such probes generally will compnse at least 15 nucleotide residues or base pairs Preferably, such probes will
Figure imgf000013_0001
at least 30 nucleotide residues or base pairs and may have at least 50 nucleotide residues or base pairs Particularh prefened probes will have at least 20 nucleotide residues or base pairs and will have lee than 30 nucleotide residues or base pairs
A coding region of a yphC gene may be isolated by screening usmg a DNA sequence provided in Table 1 [SEQ ID NO 1] to synthesize an ohgonucleotide probe A labeled ohgonucleotide having a sequence complementary to that of a gene of the mvention is then used to screen a librarv of cDNA, genomic DNA or mRNA to determine which members of the library the probe hybndizes to
There are several methods available and well known to those skilled m the art to obtam full- length DNAs. or extend short DNAs, for example those based on the method of Rapid Amplification of cDNA ends (RACE) (see, for example, Frohman, et al , PNAS USA 85 8998-9002, 1988) Recent modifications of the technique, exemplified by the Marathon™ technology (Clontech Laboratones Inc ) for example, have significantly simplified the search for longer cDNAs In the Marathon™ technology , cDNAs have been prepared from mRNA extracted from a chosen tissue and an 'adaptor' sequence hgated onto each end Nucleic acid amplification (PCR) is then carried out to amplify the "missing" 5' end of the DNA usmg a combination of gene specific and adaptor specific ohgonucleotide primers The PCR reaction is then repeated usmg "nested" primers, that is, primers designed to anneal within the amplified product (typically an adaptor specific primer that anneals further 3' m the adaptor sequence and a gene specific primer that anneals further 5' m the selected gene sequence) The products of this reaction can then be analyzed by DNA sequencing and a full-length DNA constructed either by joining the product directly to the existmg DNA to give a complete sequence, or carrymg out a separate full- length PCR usmg the new sequence information for the design of the 5' primer
The polynucleotides and polypeptides of the mvention may be employed, for example, as research reagents and matenals for discovery of treatments of and diagnostics for diseases, particularly human diseases, as further discussed herem relating to polynucleotide assays The polynucleotides of the mvention that are ohgonucleotides derived from a sequence of Table
1 [SEQ ID NOS 1 or 2] may be used m the processes herem as described, but preferably for PCR, to determine whether or not the polynucleotides identified herem in whole or m part are transcnbed m bactena m infected tissue It is recognized that such sequences will also have utility m diagnosis of the stage of infection and type of mfection the pathogen has attained The mvention also provides polynucleotides that encode a polypeptide that is a mature protem plus additional ammo or carboxyl-terminal ammo acids, or ammo acids intenor to a mature pohpeptide (when a mature form has more than one polypeptide chain, for instance) Such sequences may play a role in processing of a protem from precursor to a mature form, may allow protem transport, may lengthen or shorten protem half-life or may facilitate manipulation of a protem for assay or production, among other things As generally is the case in vivo, the additional ammo acids may be processed away from a mature protem by cellular enzymes
For each and every polynucleotide of the mvention there is provided a polynucleotide complementary to it It is prefened that these complementary polynucleotides are fully complementary to each polynucleotide with which they are complementary
A precursor protein, havmg a mature form of the polypeptide fused to one or more prosequences may be an inactive form of the polypeptide When prosequences are removed such inactive precursors generally are activated Some or all of the prosequences may be removed before activation Generally, such precursors are called proproteins As will be recognized, the entire polypeptide encoded by an open reading frame is often not required for activity Accordingly, it has become routine m molecular biology to map the boundanes of the primary structure required for activity with N-terrninal and C-terminal deletion experiments These experiments utilize exonuclease digestion or convement restriction sites to cleave coding nucleic acid sequence For example,
Promega (Madison, WI) sell an Erase-a-base™ system that uses Exonuclease HI designed to facilitate analysis of the deletion products (protocol available at www promega com) The digested endpomts can be repaired (e g , by hgation to synthetic linkers) to the extent necessary to preserve an open reading frame hi this way, the nucleic acid of SEQ ED NO 1 readily provides contiguous fragments of SEQ ID NO 2 sufficient to provide an activity, such as an enzymatic, bmdmg or antibody-inducing activity Nucleic acid sequences encoding such fragments of SEQ ID NO 2 and variants thereof as descnbed herem are within the mvention. as are polypeptides so encoded
In sum, a polynucleotide of the mvention may encode a mature protein, a mature protem plus a leader sequence (which may be refened 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. that is a precursor to a proprotein. havmg a leader sequence and one or more prosequences, that generally are removed duπng processing steps that produce active and mature forms of the polypeptide
Vectors, Host Cells, Expression Systems
The mvention also relates to vectors that compπse a polynucleotide or polynucleotides of tlie mvention, host cells that are genetically engmeered with vectors of the mvention and the production of polypeptides of the mvention by recombinant techniques Cell-free translation systems can also be employed to produce such proteins using RNAs denved from the DNA constructs of the mvention
Recombinant polypeptides of the present mvention may be prepared by processes well known m those skilled m the art from genetically engmeered host cells compnsmg expression sy stems Accordingly . in a further aspect, the present mvention relates to expression systems that compnse a polynucleotide or polvnucleotides of the present mvention, to host cells that are genetically engmeered w th such expression systems, and to the production of polypeptides of the mvention by recombinant techniques
For recombinant production of the polypeptides of the mvention, host cells can be genetically engmeered to incorporate expression systems or portions thereof or polynucleotides of the mvention Introduction of a polynucleotide mto the host cell can be effected by methods descnbed in mans standard laboratory manuals, such as Davis, et al . BASIC METHODS IN MOLECULAR BIOLOGY, (1986) and Sambrook. et al , MOLECULAR CLONING A LABORATORY MANUAL. 2nd Ed . Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N Y (1989), such as, calcium phosphate transfection, DEAE-dextran mediated transfection. transvection, microinjection, catiomc hpid-mediated transfection. electroporation transduction, scrape loading, ballistic introduction and infection
Representative examples of appropπate hosts mclude bactenal cells, such as cells of streptococci, staphylococci, enterococci E colt, streptomyces, cyanobactena, Bacillus subtilis, and Streptococcus pneumomae, fungal cells, such as cells of a yeast, Kluveromyce , Saccharomyces , a basidiomycete, Candida aϊbicans and Aspergillus, insect cells such as cells of Drosophύa S2 and Spodoptera Sf9. animal cells such as CHO, COS, HeLa, C 127, 3T3, BHK, 293, CV-1 and Bowes melanoma cells, and plant cells, such as cells of a gymnosperm or angiosperm
A great vanety of expression systems can be used to produce the polypeptides of the mvention Such vectors mclude, among others, chromosomal-, episomal- and virus-denved vectors, for example, vectors denved from bactenal plasmids, from bacteπophage. from transposons, from yeast episomes. from insertion elements, from yeast chromosomal elements, from viruses such as baculoviruses, papova viruses, such as SV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabies viruses, picornaviruses and retrovrruses, and vectors denved from combinations thereof, such as those denved from plasroid and bactenophage genetic elements, such as cosmids and phagemids The expression system constructs ma\ compπse control regions that regulate as well as engender expression Generally, any system or vector suitable to maintain, propagate or express polynucleotides and/or to express a polypeptide m a host may be used for expression in this regard The appropnate DNA sequence may be inserted mto the expression system by any of a vanety of well-known and routine techniques, such as, for example, those set forth in Sambrook et al , MOLECULAR CLONING, A LABORATORY MANUAL, (supra) In recombinant expression systems m eukary otes, for secretion of a translated protem mto the lumen of the endoplasmic reticulum. mto the peπplasmic space or mto the extracellular environment, appropnate secretion signals may be incorporated mto the expressed polypeptide These signals may be endogenous to the polypeptide or they may be heterologous signals Polypeptides of the invention can be recovered and purified from recombinant cell cultures bv well- known methods mcludmg ammomum sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography. phosphocellulose chromatography , hydrophobic interaction chromatographv affinity chromatography. hydroxylapatite chromatography . and lectin chromatography Most preferably , high performance hquid 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 yphC polynucleotides and polypeptides of the mvention for use as diagnostic reagents Detection of yphC polynucleotides and/or polypeptides in a eukaryote particularly a mammal, and especially a human, will provide a diagnostic method for diagnosis of disease. staging of disease or response of an infectious organism to drugs Eukaryotes, particularly mammals, and especially humans, particularly those infected or suspected to be infected with an orgamsm compπsmg the yphC gene or protein, may be detected at the nucleic acid or ammo acid level by a vanety of ell known techniques as well as by methods provided herem Polypeptides and polynucleotides for prognosis, diagnosis or other analysis may be obtained from a putatively infected and/or infected individual's bodily matenals Polynucleotides from any of these sources, particularly DNA or RNA, may be used directly for detection or may be amplified enzymatically by usmg PCR or any other amplification technique pπor to analysis RNA, particularly mRNA. cDNA and genomic DNA may also be used m the same ways Usmg amplification, characterization of the species and stram of infectious or resident orgamsm present m an mdividual, may be made by an analysis of the genotype of a selected polynucleotide of the organism Deletions and insertions can be detected by a change m size of the amplified product m comparison to a genotype of a reference sequence selected from a related orgamsm, preferably a different species of the same genus or a different strain of the same species Pomt mutations can be identified by hybndizmg amplified DNA to labeled yphC polynucleotide sequences Perfectly or significantly matched sequences can be distinguished from imperfectly or more significantly mismatched duplexes by DNase or RNase digestion, for DNA or RNA respectively, or by detecting differences m meltmg temperatures or renaturation kinetics Polynucleotide sequence differences may also be detected by alterations in the electrophoretic mobility of polynucleotide fragments in gels as compared to a reference sequence This may be earned out with or without denatunng agents Polynucleotide differences may also be detected by direct DNA or RNA sequencing See. for example. My ers et al . Science 230 1242 (1985) Sequence changes at specific locations also may be revealed by nuclease protection assays, such as RNase. λ;l and SI protection assay or a chemical cleavage method See, for example, Cotton et al . Proc Natl Acad Sci USA 85 4397-4401 (1985) In another embodiment, an array of ohgonucleotides probes compπsmg yphC nucleotide sequence or fragments thereof can be constructed to conduct efficient screening of. for example, genetic mutations serotype. taxonomic classification or identification Anay technology methods are ell known and hav e general applicability and can be used to address a vanety of questions in molecular genetics mcludmg gene expression, genetic linkage, and genetic variability (see, for example, Chee et al . Science, 274 610 (1996)) Thus in another aspect, the present mvention relates to a diagnostic kit that compnses
(a) a polynucleotide of the present mvention, preferably the nucleotide sequence of SEQ ID NO 1, or a fragment thereof, (b) a nucleotide sequence complementary to that of (a), (c) a polypeptide of the present mvention, preferably the polypeptide of SEQ ID NO 2 or a fragment thereof, or (d) an antibodv to a polypeptide of the present mvention, preferably to the polypeptide of SEQ ID NO 2 It will be appreciated that m any such kit, (a), (b), (c) or (d) may compnse a substantial component Such a kit will be of use m diagnosing a disease or susceptibility to a Disease, among others
This mvention also relates to the use of polynucleotides of the present mvention as diagnostic reagents Detection of a mutated form of a polynucleotide of the mvention, preferable. SEQ ED NO 1. that is associated with a disease or pathogenicity will provide a diagnostic tool that can add to, or define, a diagnosis of a disease, a prognosis of a course of disease, a determination of a stage of disease, or a susceptibilrtv to a disease, that results from under-expression, over-expression or altered expression of the polynucleotide Organisms, particularly infectious organisms, carrymg mutations m such polynucleotide may be detected at the polynucleotide level by a vanety of techniques, such as those descnbed elsewhere herem
The differences in a polynucleotide and/or polypeptide sequence between organisms possessing a first phenotype and organisms possessmg a different, second different phenotype can also be determined If a mutation is observed m some or all organisms possessmg the first phenotype but not in any organisms possessmg the second phenotype, then the mutation is likely to be the causative agent of the first phenotype
Cells from an organism carrymg mutations or polymorphisms (allehc variations) m a polynucleotide and/or polypeptide of the mvention may also be detected at the polynucleotide or polypeptide level bv a vanety of techniques, to allow for serotyping, for example For example. RT-PCR can be used to detect mutations in the RNA It is particularly prefened to use RT-PCR m conjunction with automated detection systems, such as, for example, GeneScan RNA, cDNA or genomic DNA may also be used for the same purpose PCR As an example, PCR primers complementary to a polynucleotide encoding yphC polypeptide can be used to identify and analyze mutations The mvention further provides these printers 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 yphC DNA and/or RNA isolated from a sample deπv ed from an mdividual. such as a bodily matenal The primers may be used to amplify a polynucleotide isolated from an infected mdividual, such that the polynucleotide may then be subject to vanous techmques for elucidation of the polynucleotide sequence In this way . mutations in the polynucleotide sequence may be detected and used to diagnose and/or prognose the infection or its stage or course, or to serotype and/or classify' the infectious agent
The mvention further provides a process for diagnosing, disease, preferably bactenal infections more preferably infections caused by Streptococcus pneumomae. comprising determining from a sample derived from an individual, such as a bodily material an increased level of expression of poly nucleotide having a sequence of Table 1 [SEQ ID NO 1] Increased or decreased expression of a yphC polynucleotide can be measured usmg any on of the methods well known m the art for the quantitation of polynucleotides. such as. for example, amplification. PCR, RT-PCR, RNase protection, Northern blotting, spectrometry and other hy bπdization methods In addition, a diagnostic assay m accordance with the mvention for detecting over-expression of yphC polypeptide compared to normal control tissue samples may be used to detect the presence of an infection, for example Assay techmques that can be used to determine levels of a yphC polypeptide, m a sample denved from a host, such as a bodily matenal, are well-known to those of skill m the art Such assay methods mclude radioimmunoassays, competitive-binding assays. Western Blot analysis, antibody sandwich assays, antibody detection and ELISA assays
Antagonists and Agonists - Assays and Molecules
Polypeptides and polynucleotides of the mvention may also be used to assess the bmdmg of small molecule substrates and hgands in, for example, cells, cell-free preparations, chemical hbranes. and natural product mixtures These substrates and hgands may be natural substrates and hgands or may be structural or functional rnimetics See, e g , Cohgan et al , Current Protocols in Immunology 1(2) Chapter 5 (1991) Polypeptides and polynucleotides of the present mvention are responsible for many biological functions, mcludmg many disease states, in particular the Diseases herem mentioned It is therefore desirable to devise screenmg methods to identify compounds that agonize (e g , stimulate) or that antagonize (e g ,ιnlιιbιt) the function of the polypeptide or polynucleotide Accordingly, m a further aspect the present mvention provides for a method of screenmg compounds to identify those that agonize or that antagonize the function of a polypeptide or polynucleotide of the mvention, as well as related polypeptides and polynucleotides In general, agonists or antagonists (e g . inhibitors) may be employed for therapeutic and prophylactic purposes for such Diseases as herem mentioned Compounds may be identified from a vanety of sources, for example, cells, cell-free preparations, chemical hbranes. and natural product mixtures Such agonists and antagonists so-identified may be natural or modified substrates, hgands. receptors, enzymes, etc as the case may be. of yphC polypeptides and polynucleotides. or may be structural or functional mimetics thereof (see Cohgan et al , Current Protocols in Immunology 1(2) Chapter 5 (1991))
The screenmg methods mav simply measure the bmdmg of a candidate compound to the polypeptide or polynucleotide, or to cells or membranes bearing the polypeptide or polynucleotide. or a fusion protem of the polypeptide by means of a label directly or indirectly associated with the candidate compound Alternatively, the screenmg method may involve competition with a labeled competitor Further, these screening methods may test whether the candidate compound results m a signal generated by activation or inhibition of the polypeptide or polynucleotide usmg detection systems appropriate to die cells compnsmg the polypeptide or polynucleotide Inhibitors of activation are generally assayed in the presence of a known agomst and the effect on activation bv the agonist by the presence of the candidate compound is observed Constitutively active polypeptide and/or constitutiv ely expressed polypeptides and polynucleotides may be employed m screenmg methods for inverse agonists, in the absence of an agonist or antagonist, by testmg whether the candidate compound results in inhibition of activation of the polypeptide or polynucleotide, as the case may be Further, the screenmg methods may simply comprise the steps of mixing a candidate compound with a solution compnsmg a polypeptide or polynucleotide of the present invention, to form a mixture, measurmg yphC polypeptide and/or polynucleotide activity in the mixture, and comparing the yphC polypeptide and/or polynucleotide activity of the mixture to a standard Fusion protems, such as those made from Fc portion and yphC polypeptide, as herem described, can also be used for high-throughput screening assays to identify antagonists of the polypeptide of the present invention, as well as of phylogenetically and and/or functionally related polypeptides (see D Bennett et al , J Mol Recognition, 8 52-58 (1995), and K Johanson et al , J Biol Chem, 270(16) 9459-9471 (1995))
The polynucleotides, polypeptides and antibodies that bmd to and/or mteract with a polypeptide of the present mvention may also be used to configure screenmg methods for detectmg the effect of added compounds on the production of mRNA and/or polypeptide in cells For example, an ELISA assay may be constructed for measurmg secreted or cell associated levels of polypeptide usmg monoclonal and polyclonal antibodies by standard methods known in the art This can be used to discover agents that may inhibit or enhance the production of polypeptide (also called antagomst or agomst, respectively) from suitably manipulated cells or tissues
The mvention also provides a method of screenmg compounds to identify those that enhance (agomst) or block (antagomst) the action of yphC polypeptides or polynucleotides, particularly those compounds that are bacteπstatic and/or bactencidal The method of screenmg may mvolve high-throughput techmques For example, to screen for agonists or antagonists, a synthetic reaction mix, a cellular compartment, such as a membrane, cell envelope or cell wall, or a preparation of any thereof, compnsmg yphC polypeptide and a labeled substrate or hgand of such polypeptide is incubated m the absence or the presence of a candidate molecule that may be a yphC agomst or antagomst The ability of the candidate molecule to agonize or antagonize the yphC polypeptide is reflected in decreased bmdmg of the labeled hgand or decreased production of product from such substrate Molecules that bmd gratuitously, / e . without inducing the effects of yphC polypeptide are most likely to be good antagonists Molecules that bmd ell and. as the case mav be increase the rate of product production from substrate, mcrease signal transduction. or mcrease chemical channel activity are agonists Detection of the rate or level of, as the case may be, production of product from substrate, signal transduction, or chemical channel activity may be enhanced by usmg a reporter system Reporter systems that may be useful m this regard mclude but are not limited to colonmetnc. labeled substrate converted mto product, a reporter gene that is responsive to changes m yphC polynucleotide or pohpeptide activity, and bmdmg assays known in the art
Polypeptides of the mvention may be used to identify membrane bound or soluble receptors, if any, for such polypeptide, through standard receptor bmding techmques known m the art These techmques mclude, but are not limited to, hgand binding and crosslinking assays m which the polypeptide is labeled with a radioactive isotope (for instance, *^I), chemically modified (for instance, biotinylated), or fused to a peptide sequence suitable for detection or punfication, and mcubated with a source of the putative receptor (e g , cells, cell membranes, cell supernatants, tissue extracts, bodily matenals) Other methods mclude biophysical techmques such as surface plasmon resonance and spectroscopy These screenmg methods may also be used to identify agomsts and antagonists of the polypeptide that compete with the bindmg of the polypeptide to its receptor(s), if any Standard methods for conducting such assays are well understood m the art
The fluorescence polarization value for a fluorescently-tagged molecule depends on the rotational correlation time or tumblmg rate Protem complexes, such as formed by yphC polypeptide associating vvrth another yphC polypeptide or other polypeptide, labeled to comprise a fluorescently- labeled molecule will have higher polarization values than a fluorescently labeled monomeπc protem It is preferred that this method be used to characteπze small molecules that disrupt polypeptide complexes
Fluorescence energy transfer may also be used charactenze small molecules that interfere with the formation of yphC polypeptide dimers, tnmers, tetramers or higher order structures, or structures formed by yphC polypeptide bound to another polypeptide YphC polypeptide can be labeled with both a donor and acceptor fluorophore Upon mixing of the two labeled species and excitation of the donor fluorophore, fluorescence energy transfer can be detected by observing
- l i fluorescence of the acceptor Compounds that block dimenzation will inhibit fluorescence energv transfer
Surface plasmon resonance can be used to monitor the effect of small molecules on yphC polypeptide self-association as well as an association of yphC polypeptide and another polypeptide or small molecule YphC polypeptide can be coupled to a sensor chip at low site density such that covalently bound molecules will be monomeπc Solution protem can then passed over the yphC polypeptide -coated surface and specific bmding can be detected in real-time by monitoring the change in resonance angle caused by a change in local refractive index This technique can be used to characterize the effect of small molecules on kinetic rates and equilibrium bmdmg constants for yphC polypeptide self-association as well as an association of yphC polypeptide and another polypeptide or small molecule
A scintillation proximity assay may be used to characterize the interaction between an association of yphC polypeptide ith another yphC polypeptide or a different polypeptide YphC polypeptide can be coupled to a scintillation-filled bead Addition of radio-labeled yphC polypeptide results in bmding where the radioactive source molecule is in close proximity to the scintillation fluid Thus, signal is emitted upon yphC polypeptide bmdmg and compounds that prevent yphC polypeptide self-association or an association of yphC polypeptide and another polypeptide or small molecule will dimmish signal
In other embodiments of the mvention there are provided methods for identifying compounds that bmd to or otherwise mteract with and inhibit or activate an activity or expression of a polypeptide and/or polynucleotide of the mvention compnsmg contacting a polypeptide and/or polynucleotide of the mv ention with a compound to be screened under conditions to permit bmdmg to or other interaction between the compound and the polypeptide and/or polynucleotide to assess the bmding to or other mteraction with the compound, such bmdmg or mteraction preferably bemg associated with a second component capable of providing a detectable signal m response to the bmdmg or mteraction of the polypeptide and/or polynucleotide with the compound, and determining whether the compound bmds to or otherwise interacts with and activates or inhibits an activity or expression of the polypeptide and/or polynucleotide by detectmg the presence or absence of a signal generated from the bmdmg or mteraction of the compound with the polypeptide and/or polynucleotide Another example of an assay for yphC agonists is a competitive assay that combmes yphC and a potential agomst with yphC-binding molecules, recombinant yphC bmding molecules, natural substrates or hgands, or substrate or hgand numerics, under appropπate conditions for a competitive inhibition assay YphC can be labeled, such as by radioactivity or a colonmetnc compound, such that the number of yphC molecules bound to a bmdmg molecule or converted to product can be determmed accurately to assess tlie effectiveness of the potential antagomst
It will be readily appreciated by the skilled artisan that a polypeptide and/or polynucleotide of the present mvention may also be used m a method for the structure-based design of an agomst or antagomst of the polypeptide and/or polynucleotide, by (a) determinmg m the first mstance the three- dimensional structure of the polypeptide and/or polynucleotide. or complexes thereof, (b) deducing the three-dimensional structure for the likely reactive sιte(s), bindmg sιte(s) or motιf(s) of an agonist or antagonist, (c) synthesizing candidate compounds that are predicted to bmd to or react with the deduced bmding sιte(s), reactive sιte(s), and/or motιf(s). and (d) testmg whether the candidate compounds are indeed agonists or antagonists
It will be further appreciated that this will normally be an iterative process, and this iterative process may be performed usmg automated and computer-controlled steps
In a further aspect, the present mvention provides methods of treating abnormal conditions such as for instance, a Disease, related to either an excess of. an under-expression of, an elevated activity of, or a decreased activity of yphC polypeptide and/or polynucleotide
If the expression and/or activity of the polypeptide and/or polynucleotide is in excess, several approaches are available One approach compnses administering to an mdividual m need thereof an inhibitor compound (antagomst) as herem descnbed, optionally m combination with a pharmaceutically acceptable earner, m an amount effective to inhibit the function and/or expression of the polypeptide and/or polynucleotide, such as, for example, by blockmg the bmding of hgands, substrates, receptors, enzymes, etc , or by inhibiting a second signal, and thereby alleviating the abnormal condition In another approach, soluble forms of the polypeptides still capable of bmding the hgand, substrate, enzymes, receptors, etc in competition with endogenous polypeptide and/or polynucleotide may be administered Typical examples of such competitors mclude fragments of the yphC polypeptide and/or polypeptide In still another approach, expression of the gene encodmg endogenous yphC polypeptide can be inhibited usmg expression blocking techniques This blockmg may be targeted against any step in gene expression, but is preferably targeted against transcnption and/or translation An examples of a known technique of this sort mvolve the use of antisense sequences, either internally generated or separately administered (see, for example, O'Connor, J Neurochem (1991) 56 560 in Ohgodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, FL (1988)) Alternatively, ohgonucleotides that form tnple helices with the gene can be supplied (see, for example, Lee et al , Nucleic Acids Res (1979) 6 3073, Cooney et al , Science (1988) 241 456, Dervan et al , Science (1991) 251 1360) These oligomers can be administered per se or the relevant ohgomers can be expressed in vivo Each of the polynucleotide sequences provided herein may be used m the discoverv and development of antibactenal compounds The encoded protem, upon expression, can be used as a target for the screemng of antibactenal drugs Additionally, the polynucleotide sequences encodmg the ammo terminal regions of the encoded protem 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 coding sequence of mterest
The invention also provides the use of the polypeptide. polynucleotide, agonist or antagonist of the invention to interfere with the initial physical mteraction between a pathogen or pathogens and a eukaryotic. preferably mammalian, host responsible for sequelae of infection In particular the molecules of the invention may be used m the prevention of adhesion of bacteria in particular gram positive and/or gram negative bactena, to eukaryotic, preferably mammalian, extracellular matrix protems on in-dwelling devices or to extracellular matnx protems in wounds, to block bacterial adhesion between eukaryotic, preferably mammalian, extracellular matnx protems and bacterial yphC protems that mediate tissue damage and/or, to block the normal progression of pathogenesis m infections initiated other than by the implantation of in-dwelling devices or by other surgical techniques In accordance with yet another aspect of the mvention, there are provided yphC agonists and antagonists, preferably bacteπstatic or bactencidal agonists and antagonists
The antagonists and agonists of the mvention may be employed, for instance, to prevent, inhibit and/or treat diseases Hehcobacter pylori (herein "H pylori") bacteria infect the stomachs of over one-third of the world's population causing stomach cancer, ulcers, and gastntis (International Agency for Research on Cancer (1994) Schistosomes, Liver Flukes and Hehcobacter Pylori (International Agency for Research on Cancer, Lyon. France, http //www uicc ch/ecp/ecp2904 htm) Moreover, the International Agencv for Research on Cancer recently recognized a cause-and-effect relationship between H pylon and gastric adenocarcmoma, classifymg the bactenum as a Group I (defimte) carcmogen Preferred antimicrobial compounds of the mvention (agonists and antagonists of yphC polypeptides and/or polynucleotides) found usmg screens provided by the mvention, or known in the art, particularly narrow-spectrum antibiotics, should be useful m the treatment of H pylori infection Such treatment should decrease the advent of H τy/or7-ιnduced cancers, such as gastrointestinal carcmoma Such treatment should also prevent, inhibit and/or cure gastnc ulcers and gastntis
All publications and references, mcludmg but not limited to patents and patent applications cited m this specification are herem incorporated by reference in their entirety as if each individual publication or reference were specifically and individually mdicated to be incorporated by reference herein as bemg fully set forth Any patent application to which this application claims priority is also incorporated by reference herem m its entirety in the manner descnbed above for publications and references
GLOSSARY The following definitions are provided to facilitate understanding of certam terms used frequently herem
"Bodily mateπal(s) means any matenal denved from an mdividual or from an orgamsm infecting, infesting or inhabiting an mdividual, mcludmg but not limited to, cells, tissues and waste, such as. bone, blood, serum, cerebrospinal fluid, semen, saliva, muscle, cartilage, organ tissue, skm, urine, stool or autopsy mateπals
"Dιsease(s)" means any disease caused by or related to infection by a bacteπa, mcludmg , for example, otitis media, conjunctivitis, pneumonia, bacteremia. meningitis, sinusitis, pleura! empyema and endocarditis, and most particularly meningitis, such as for example infection of cerebrospmal fluid
"Host cell(s)" is a cell that has been introduced (e g , transformed or transfected) or is capable of mtroduction (e g , transformation or transfection) by an exogenous polynucleotide sequence
"Identity," as known in the art, is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as the case may be, as determined by comparing the sequences In the art, "identity" also means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as the case may be, as determmed by the match between strings of such sequences "Identit " can be readily calculated by known methods, mcludmg but not limited to those described m
(Computational Molecular Biology, Lesk, A M , ed , Oxford University Press, New York, 1988, Biocomputing Informatics and Genome Projects, Smith, D W , ed , Academic Press, New York, 1993, Computer Analysis of Sequence Data, Part I, Gnffin, A M . and Griffin, H G , eds . Humana Press, New Jersey, 1994, Sequence Analysis in Molecular Biology, von Hemje, 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) 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 mclude, but are not limited to, the GCG program package (Devereux, J . et al , Nucleic Acids Research 12(1) 387 (1984)), BLASTP, BLASTN. and FASTA (Altschul, S F et al , J Molec Bwl 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 Bwl 215 403-410 (1990) The well known Smith Waterman algoπthm may also be used to determine identity Parameters for polypeptide sequence companson mclude the following Algonthm Needleman and Wunsch, J Mol Biol 48 443-453 (1970)
Comparison matrix BLOSSUM62 from Hentikoff and Hentikoff. Proc Natl Acad Sci USA 89 10915-10919 (1992) Gap Penalty 12
Gap Length Penalty 4
A program useful with these parameters is publich available as the "gap" program from Genetics Computer Group, Madison WI The aforementioned parameters are the default parameters for peptide comparisons (along with no penalty for end gaps) Parameters for polynucleotide comparison include the follow mg Algonthm 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 preferred meaning for "identity" for polynucleotides and polypeptides. as the case may be, are provided in (1) and (2) below
(1) Polynucleotide embodiments further mclude an isolated polynucleotide compnsing a polynucleotide sequence having at least a 95, 97, 99, 99 5 or 100% identity to the reference sequence of SEQ ID NO 1. wherem said polynucleotide sequence may be identical to the reference sequence of SEQ ID NO 1 or may mclude up to a certam mteger number of nucleotide alterations as compared to the reference sequence, wherem said alterations are selected from the group consistmg of at least one nucleotide deletion, substitution, mcludmg transition and transversion, or insertion, and wherem said alterations may occur at the 5' or 3' terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, mterspersed either individually among the nucleotides m the reference sequence or m one or more contiguous groups within the reference sequence, and wherem said number of nucleotide alterations is determmed by multiplying the total number of nucleotides in SEQ ID NO 1 by the integer defining the percent identity divided by 100 and then subtractmg that product from said total number of nucleotides in SEQ ID NO 1, or
nn ≤ xn " (xn * )> wherein nn is the number of nucleotide alterations, xn is the total number of nucleotides m SEQ ID NO 1, y is 0 95 for 95%. 0 97 for 97%, 0 99 for 99%, 0 995 for 99 5% or 1 00 for 100%, and • is the symbol for the multiplication operator, and wherem any non-mteger product of xn and y is rounded down to the nearest mteger prior to subtractmg it from xn Alterations of a polynucleotide sequence encodmg the polypeptide of SEQ ID NO 2 may create nonsense, rmssense or frameshift mutations in this coding sequence and thereby alter the polypeptide encoded by the polynucleotide following such alterations
(2) Polypeptide embodiments further include an isolated polypeptide comprising a polypeptide having at least a 95, 97 or 100% identity to a polypeptide reference sequence of SEQ ID NO 2. 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 amino acid alterations as compared to the reference sequence, wherem said alterations are selected from the group consisting of at least one amino acid deletion, substitution, mcludmg conservative and non-conservative substitution, or insertion, and wherem said alterations may occur at the ammo- or carboxy-terminal positions of the reference polypeptide sequence or anywhere between those terminal positions, mterspersed either individually among the ammo acids m the reference sequence or m one or more contiguous groups within the reference sequence, and wherein said number of ammo acid alterations is determmed by multiplying the total number of ammo acids in SEQ ID NO 2 by the integer defining the percent identity divided by 100 and then subtractmg that product from said total number of ammo acids in SEQ ID NO 2, or
na < xa " (xa • )>
wherein na is the number of amino acid alterations, xa is the total number of ammo acids in SEQ ID NO 2, y is 0 95 for 95%, 0 97 for 97% or 1 00 for 100%, and • is the symbol for the multiplication operator, and wherem any non-integer product of xa and y is rounded down to the nearest integer pnor to subtractmg it from xa
"Indιvιdual(s)" means a multicellular eukaryote, mcludmg, but not limited to a metazoan. a mammal, an ovαd. a bovαd, a simian, a primate, and a human
"Isolated" means altered "by the hand of man" from its natural state, / e , if it occurs m nature, it has been changed or removed from its onginal environment, or both For example, a polvnucleotide or a polypeptide naturally present m a living organism is not "isolated," but the same polynucleotide or polypeptide separated from the coexisting matenals of its natural state is "isolated", as the term is employed herem Moreover, a polynucleotide or polypeptide that is introduced mto an orgamsm by transformation, genetic manipulation or by any other recombinant method is "isolated" even if it is still present in said orgamsm which orgamsm may be living or non-living
"Organιsm(s)" means a (1) prokaryote. mcludmg but not limited to, a member of the genus Streptococcus, Staphylococcus, Bordetella, Corynebactenum Mycobactenum, Neissena, Haemophύus Actinomycetes, Streptomycetes, Nocardia, Enter obacter, Yersima, Fancisella, Pasturella, Moraxella, Acmetobacter Erysipelothnx, Branhamella, Actinobacillus, Streptobacillus, Listena Calymmatobactenum, Brucella Bacillus, Clostndium, Treponema, Eschenchia, Salmonella, Kleibsiella Vibrio, Proteus, Erwinia, Borre a, Leptospira, Spirillum, Campylobacter, Shigella, Legtonella Pseudomonas, Aeromonas, Rickettsia, Chlamydia, Borreha and Mycoplasma, and further mcludmg. but not limited to. a member of the species or group, Group A Streptococcus, Group B Streptococcus, Group C Streptococcus, Group D Streptococcus, Group G Streptococcus, Streptococcus pneumomae, Streptococcus pyogenes, Streptococcus agalactiae, Streptococcus faecahs. Streptococcus faecium. Streptococcus duram Neissena gonorrheae, Neissena memngitidis, Staphylococcus aureus Staphylococcus epidermidis Corynebactenum dψthenae Gardnerella vagina s, Mycobactenum tuberculosis, Mycobactenum bovis Mycobactenum ulcerans, Mycobactenum leprae, Actinomyctes israelu, Listena monocytogenes, Bordetella pertusis, Bordatella parapertusis, Bordetella bronchiseptica, Eschenchia co , Shigella dysentenae, Haemophύus influenzae, Haemophύus aegyphus, Haemophilus parainfluenzae, Haemop lus ducreyi, Bordetella, Salmonella typhi, Citrobacter freundn, Proteus mirabi s, Proteus vulgans, Yersima pestis, Kleibsiella pneumomae, Serratia marcessens, Serratia quefaciens, Vibno cholera, Shigella dysenteni, Shigella flexnen, Pseudomonas aeruginosa, Franscisella tularensis, Bmcella abortis, Bacillus anthracis, Bacillus cereus, Clostndium perjhngens, Clostndium tetani, Clostndium botuhnum, Treponema pallidum, Rickettsia nckettsii and Chlamydia trachomitis, (u) an archaeon, mcludmg but not limited to Archaebacter, and (in) a unicellular or filamentous eukaryote, mcludmg but not limited to, a protozoan, a fungus, a member of the genus Saccharomyces, Kluveromyces, or Candida, and a member of the species Saccharomyces cenviseae, Kluveromyces lactis, or Candida albicans
"Polynucleotide(s)" generally refers to any polyπbonucleotide or polydeoxynbonucleotide, that may be unmodified RNA or DNA or modified RNA or DNA "Polynucleotιde(s)" mclude, without limitation, smgle- and double-stranded DNA, DNA that is a mixture of smgle- and double-stranded regions or smgle-, double- and triple-stranded regions, smgle- and double-stranded RNA, and RNA that is mixture of smgle- and double-stranded regions, hybnd molecules compnsing DNA and RNA that may be smgle-stranded or. more typically, double-stranded, or triple-stranded regions, or a mixture of smgle- and double-stranded regions hi addition, "polynucleotide" as used herem refers to triple-stranded regions compnsmg RNA or DNA or bodi 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 tπple-hehcal region often is an ohgonucleotide As used herem the term "polynucleotide(s)" also mcludes DNAs or RNAs as descnbed above that compnse one or more modified bases Thus, DNAs or RNAs with backbones modified for stability- or for other reasons are "polynucleotιde(s)" as that term is mtended herem Moreover. DNAs or RNAs compnsmg unusual bases such as inosine. or modified bases, such as tπtylated bases, to name just two examples, are polynucleotides as the term is used herem It will be appreciated that a great vanety of modifications have been made to DNA and RNA that serve many useful purposes known to those of skill m the art The term "polynucleotιde(s)" as it is employed herem embraces such chemically, enzymatically or metabo cally modified forms of polynucleotides, as well as the chemical forms of DNA and RNA charactenstic of viruses and cells, including for example, simple and complex cells "Polynucleoϋde(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, commonh refened to as peptides, ohgopeptides and o gomers and to longer chains generally refened to as protems Polypeptides may compnse ammo acids other than the 20 gene encoded ammo acids "Polypeptιde(s)" mclude those modified either by natural processes, such as processmg and other post-translaϋonal modifications, but also by chemical modification techmques 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 in the same or varymg degree at several sites m a given polypeptide Also, a given polypeptide may compnse many types of modifications Modifications can occur anywhere m a polypeptide, mcludmg the peptide backbone, the ammo acid side-chains, and the ammo or carboxyl temuru 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, cyclization. disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine. formation of pyroglutamate, formylation, gamma-carboxylation, GPI anchor formation, hydroxylation, lodination, methylation, mynstoylation, oxidation, proteolytic processmg, phosphorylation. prenylation. racemization, glycosylation, hpid attachment, sulfation, gamma-carboxylation of glutamic acid residues, hydroxylation and ADP-nbosylation, selenoylation, sulfation, transfer-RNA mediated addition of ammo acids to proteins, such as argmylation, and ubiquitination See, for instance, PROTEINS - STRUCTURE AND MOLECULAR PROPERTIES, 2nd Ed , T E Creighton, W H Freeman and Company, New York (1993) and Wold. F Posttranslational Protem Modifications Perspectives and Prospects, pgs 1-12 m POSTTRANSLATIONAL COVALENT MODIFICATION OF PROTEINS, B C Johnson, Ed , Academic Press, New York (1983). Serfter et al . Meth Enzymol 182 626-646 (1990) and Rattan et al . Protem Synthesis Posttra slational 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 posttranslational natural processes and may be made by entirely synthetic methods, as ell "Recombinant expression system(s)" refers to expression systems or portions thereof or polynucleotides of the mvention introduced or transformed mto a host cell or host cell lysate for the production of the polynucleotides and polypeptides of the mvention
'Nanant(s)" as the term is used herem, is a polynucleotide or polypeptide that differs from a reference polynucleotide or polypeptide respectively, but retains essential properties A typical vaπant of a polynucleotide differs in nucleotide sequence from another, reference polynucleotide Changes m the nucleotide sequence of the vanant may or may not alter the ammo acid sequence of a pohpeptide encoded by the reference polynucleotide Nucleotide changes may result in ammo acid substitutions additions, deletions, fusion proteins and truncations in the polypeptide encoded by the reference sequence, as discussed below A typical variant of a polypeptide differs m ammo acid sequence from another, reference polypeptide Generally, differences are limited so that the sequences of the reference polypeptide and the vanant are closely similar overall and, m many regions, identical A vanant and reference polypeptide may differ in ammo acid sequence by one or more substitutions, additions, deletions in any combmation A substituted or inserted ammo acid residue may or may not be one encoded by the genetic code The present mvention also mcludes mclude variants of each of tlie polypeptides of the mvention. that is polypeptides that vary from the referents by conservative am o acid substitutions, whereby a residue is substituted by another with like charactenstics Typical such substitutions are among Ala, Val, I_eu and lie, among Ser and Thr. among the acidic residues Asp and Glu. among Asn and Gin, and among the basic residues Lys and Arg, or aromatic residues Phe and Tyr Particularly prefened are vanants m which several, 5-10, 1-5, 1-3. 1-2 or 1 ammo acids are substituted, deleted, or added m any combmation A variant of a polynucleotide or polypeptide may be a naturally occurring such as an alle c 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 techmques, by direct synthesis, and by other recombinant methods known to skilled artisans
EXAMPLES
The examples below are earned out usmg standard techmques, that are well known and routme to those of skill m the art. except where otherwise descnbed in detail The examples are illustrative, but do not limit die mvention Example 1 Strain selection, Library Production and Sequencing The polynucleotide havmg a DNA sequence given m Table 1 [SEQ ID NO 1] was obtained from a library of clones of chromosomal DNA of Streptococcus pneumomae in E coli The sequencmg data from two or more clones compnsmg overlappmg Streptococcus pneumomae DNAs w as used to construct the contiguous DNA sequence m SEQ ID NO 1 Libraries may be prepared by routme methods, for example Methods 1 and 2 below
Total cellular DNA is isolated from Streptococcus pneumomae 0100993 according to standard procedures and size-fractionated by either of two methods
Method 1 Total cellular DNA is mechanically sheared by passage through a needle 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 ligated mto the vector Lambda Zapll that has been cut with EcoRI, the library packaged by standard procedures and E coli mfected with the packaged library The library is amplified by standard procedures
Method 2
Total cellular DNA is partially hydrolyzed with a one or a combination of restriction enzymes appropriate to generate a series of fragments for clonmg mto library vectors (e g . Rsal. Pall, Alul. Bshl235I), and such fragments are size-fractionated accordmg to standard procedures EcoRI linkers are ligated to the DNA and the fragments then ligated into the vector Lambda Zapll that have been cut with EcoRI, the library packaged by standard procedures, and E coli infected with the packaged library The library is amplified by standard procedures Example 2 yphC Characterization
The S. pneumoniae yphC gene is expressed during infection in a respiratory tract infection model
The determination of expression durmg infection of a gene from Streptococcus pneumoniae
Excised lungs from a 48 hour respiratory tract infection of Streptococcus pneumomae 0100993 in the mouse is efficiently disrupted and processed in the presence of chaotropic agents and RNAase inhibitor to provide a mixture of animal and bacterial RNA The optimal conditions for disruption and processing to give stable preparations and high yields of bacterial RNA are followed by the use of hybridisation to a radiolabelled ohgonucleotide specific to Streptococcus pneumomae 16S RNA on Northern blots The RNAase free, DNAase free, DNA and protein free preparations of RNA obtained are suitable for Reverse Transcription PCR (RT-PCR) usmg unique primer pairs designed from the sequence of each gene of Streptococcus pneumomae 0100993 a) Isolation of tissue infected with Streptococcus pneumomae 0100993 from a mouse animal model of mfection (lungs)
Streptococcus pneumomae 0100993 is seeded onto TSA (Tryptic Soy Agar BBL) plates contaimng 5% horse blood and allowed to grow overnight at 37°C in a C02 incubator Bacterial growth is scraped into 5 ml of phosphate-buffered salme (PBS) and adjusted to an A600 ~ 0 6 (4 x 106/ml) Mice (male CBA/J-1 mice, approximately 20g) were anaesthetized with isoflurane and 50 microhters of the prepared bacterial inoculum is delivered by mtranasal instillation Animals are allowed to recover and observed twice daily for signs of moπbundancy Forty-eight hours after infection the animals are euthanized by carbon dioxide overdose and their torsos swabbed ith ethanol and then RNAZap The torso is then opened, and the lungs are aseptically removed Half of each pair of lungs is placed m a cry ovial and immediately frozen in liquid nitrogen, the other half is used for bacterial enumeration after homogenization of the tissue m 1 ml of PBS b) Isolation of Streptococcus pneumoniae 0100993 RNA from mfected tissue samples Infected tissue samples, in 2-ml cryo-strorage tubes, are removed from -80°C storage mto a dn ice ethanol bath In a microbiological safety cabmet the samples are disrupted up to eight at a time while the remammg samples are kept frozen m the dry ice ethanol badi To disrupt the bactena within the tissue sample, 50-100 nig of the tissue is transfered to a FastRNA tube containing a silica/ceramic matrix (BIO 101) Immediately, 1 ml of extraction reagents (FastRNA reagents, BIO 101) are added to give a sample to reagent volume ratio of approximately 1 to 20 The tubes are shaken m a reciprocatmg shaker (FastPrep FP120, BIOIOI) at 6000 rpm for 20-120 sec The crude RNA preparation is extracted with chloroform/isoamyl alcohol, and precipitated with DEPC-treated/Isopropanol Precipitation Solution (BIOIOI) RNA preparations are stored m this isopropanol solution at -80°C if necessary The RNA is pelleted (12,000g for 10 mm ), washed with 75% ethanol (v/v m DEPC-treated water), air-dried for 5-10 mm, and resuspended m 0 1 ml of DEPC-treated water followed by 5-10 minutes at 55 oC Finally, after at least 1 mmute on ice, 200 units of Rnasin (Promega) is added
RNA preparations are stored at -80 oC for up to one month For longer term storage the RNA precipitate can be stored at the wash stage of the protocol m 75% ethanol for at least one year at -20 oC
Quality of the RNA isolated is assessed by running samples on 1% agarose gels 1 x TBE gels stamed with ethidium bromide are used to visualise total RNA yields To demonstrate the isolation of bacterial RNA from the infected tissue 1 x MOPS, 2 2M formaldehyde gels are run and vacuum blotted to Hybond-N (Amersham) The blot is then hybndised with a 32P-labelled ohgonucletide probe, of sequence 5' AACTGAGACTGGCTTTAAGAGATTA 3' [SEQ ID NO 3], specific to 16S rRNA of Streptococcus pneumomae The size of the hybridising band is compared to that of control RNA isolated from m vitro grown Streptococcus pneumomae 0100993 m the Northern blot Correct sized bacterial 16S rRNA bands can be detected m total RNA samples which show degradation of the mammalian RNA when visualised on TBE gels c) The removal of DNA from Streptococcus pneumoniae-deπved RNA DNA was removed from 50 microgram samples of RNA by a 30 minute treatment at 37°C with
20 umts of RNAase-free DNAasel (GenHunter) m the buffer supplied m a final volume of 57 microhters
The DNAase as inactivated and removed by treatment with TRIzol LS Reagent (Gibco BRL. Life Technologies) accordmg to the manufacturers protocol DNAase treated RNA was resuspended in 100 microhtres of DEPC treated water with the addition of Rnasin as descnbed before d) The preparation of cDNA from RNA samples derived from infected tissue
3 microgram samples of DNAase treated RNA are reverse transcnbed usmg a Superscript
Preamphfication System for First Strand cDNA Synthesis kit (Gibco BRL. Life Technologies) accordmg to the manufacturers instructions 150 nanogram of random hexamers is used to prime each reaction Controls without the addition of SuperScnptll reverse transcriptase are also run Both +/-RT samples are treated with RNaseH before proceeding to the PCR reaction e) The use of PCR to determine the presence of a bactenal cDNA species
PCR reactions are set up on ice m 0 2ml tubes by adding the following components 43 microhtres PCR Master Mix (Advanced Biotechnologies Ltd ), 1 micro tre PCR primers (optimally 18- 25 basepairs m length and designed to possess similar annealing temperatures), each pnmer at 1 OmM initial concentration, and 5 microhtres cDNA
PCR reactions are run on a Perkin Elmer GeneAmp PCR System 9600 as follows 2 minutes at 94 oC, then 50 cycles of 30 seconds each at 94 oC, 50 oC and 72 oC followed by 7 minutes at 72 oC and then a hold temperature of 20 oC (the number of cycles is optimally 30-50 to determine the appearance or lack of a PCR product and optimally 8-30 cycles if an estimation of the starting quantity of cDNA from the RT reaction is to be made), 10 microhtre aliquots are then run out on 1% 1 x TBE gels stained with ethidium bromide, with PCR product, if present, sizes estimated by comparison to a 100 bp DNA Ladder (Gibco BRL, Life Technologies) Alternatively if the PCR products are convemently labelled by the use of a labelled PCR pnmer (e g labelled at the 5'end with a dye) a smtable aliquot of the PCR product is run out on a polyacrylamide sequencing gel and its presence and quantity detected usmg a suitable gel scanning system (e g ABI PπsmTM 377 Sequencer using GeneScanTM software as supplied by Perkin Elmer) RT/PCR controls may mclude +/- reverse transcπptase reactions. 16S rRNA primers or DNA specific pnmer pairs designed to produce PCR products from non-transcnbed Streptococcus pneumomae 0100993 genomic sequences
To test the efficiency of the primer pairs they are used m DNA PCR with Streptococcus pneumomae 0100993 total DNA PCR reactions are set up and run as descnbed above usmg approx 1 microgram of DNA m place of the cDNA
Primer pairs which fail to give the predicted sized product in either DNA PCR or RT/PCR are PCR failures and as such are uninformative Of those which give the correct size product widi DNA PCR two classes are distinguished m RT/PCR 1 Genes which are not transcribed m vivo reproducibh fail to give a product m RT/PCR. and 2 Genes which are transcribed m vivo reproducibh giv e the correct size product m RT/PCR and show a stronger signal in the +RT samples than the signal (if at all present) m -RT controls Example 3 The yphC gene is essential for S. pneumoniae in vitro growth.
Demonstration of gene essentiality to bacterial viability An allelic replacement cassette was generated usmg PCR technology The cassette consisted of a pair of 500bp chromosomal DNA fragments flanking an erythromycm resistance gene The chromosomal DNA sequences are the 500bp preceding and following the DNA sequence encodmg the yphC gene contained m Seq ID NO 1
The allelic replacement cassette was mtroduced mto S pneumomae R6 by transformation Competent cells were prepared according to published protocols DNA was mtroduced mto the cells by mcubation of ng quantities of allelic replacement cassette with 10" cells at 30°C for 30 minutes The cells were transferred to 37°C for 90 minutes to allow expression of the erythromycm resistance gene Cells were plated in agar containmg lug erythromycm per ml Following mcubation at 37°C for 36 hours, colonies are picked and grown overnight m Todd-Hewitt broth supplemented with 0 5% yeast extract Typically 1000 transformants containmg the appropnate allelic replacement are obtained If no transformants are obtained m three separate transformation experiments as w as the case for this gene yphC, then the gene is considered as bemg essential in vitro

Claims

What is claimed is:
1 An isolated polypeptide selected from the group consistmg of
(I) an isolated polypeptide compnsmg an ammo acid havmg at least 95% identity to the amino acid sequence of SEQ ID NO 2 over the entire length of SEQ ID NO 2.
(π) an isolated polypeptide comprising the ammo acid sequence of SEQ ID NO 2.
(in) an isolated polypeptide that is the ammo acid sequence of SEQ ID NO 2, and
(IV) a polypeptide that is encoded by a recombinant polynucleotide compnsmg the polyncleotide sequence of SEQ ID NO 1
2 An isolated polynucleotide selected from the group consistmg of
(I) an isolated polynucleotide compnsmg a polynucleotide sequence encodmg a polypeptide that has at least 95% identity to the ammo acid sequence of SEQ ED NO 2, over the entire length of SEQ ID NO 2,
(n) an isolated polynucleotide compnsmg a polynucleotide sequence that has at least 95% identity over its entire length to a polynucleotide sequence encoding the polypeptide of SEQ ID NO 2,
(m) an isolated polynucleotide compnsmg a nucleotide sequence that has at least 95% identity to that of SEQ ID NO 1 over the entire length of SEQ ID NO 1 ,
(iv) an isolated polynucleotide compnsmg a nucleotide sequence encodmg the polypeptide of SEQ ED NO 2,
(v) an isolated polynucleotide that is the polynucleotide of SEQ ID NO 1 ,
(vi) an isolated polynucleotide of at least 30 nucleotides in length obtainable by screening an appropπate library under strmgent hybndization conditions with a probe having the sequence of SEQ ED NO 1 or a fragment thereof of of at least 30 nucleotides in length,
(vn) an isolated polynucleotide encoding a mature polypeptide expressed by the yphC gene compnsed m the Streptococcus pneumoniae, and
(vm) a polynucleotide sequence complementary to said isolated polynucleotide of (I), (n), (in), (iv), (v), (vi) or (vn)
3 A method for the treatment of an mdividual
(I) in need of enhanced activity or expression of or immunological response to the polypeptide of claim 1 compπsmg the step of admimstermg to the mdividual a therapeutically effective amount of an antagomst to said polypeptide, or
(n) having need to inhibit activity or expression of the polypeptide of claim 1 compnsmg (a) admimstermg to the mdividual a therapeutically effective amount of an antagomst to said polypeptide, or
(b) admmistermg to the mdividual a nucleic acid molecule that inhibits the expression of a polynucleotide sequence encodmg said polypeptide,
(c) admimstermg to the mdividual a therapeutically effective amount of a polypeptide that competes with said polypeptide for its hgand, substrate, or receptor, or
(d) administenng to the individual an amount of a polypeptide that mduces an immunological response to said polypeptide m said mdividual
4 A process for diagnosmg or prognosrng a disease or a susceptibility to a disease in an individual related to expression or activity of the polypeptide of claim 1 m an mdividual compnsmg the step of
(a) determinmg the presence or absence of a mutation m the nucleotide sequence encoding said polypeptide m an orgamsm in said individual, or
(b) analyzing for the presence or amount of said polypeptide expression in a sample denved from said mdividual
5 A process for producmg a polypeptide selected from the group consistmg of
(I) an isolated polypeptide compnsmg an ammo acid sequence selected from the group having at least 95% identity to the ammo acid sequence of SEQ ID NO 2 over the entire length of SEQ ID
NO 2,
(n) an isolated polypeptide compnsmg the ammo acid sequence of SEQ ID NO 2, (in) an isolated polypeptide that is the ammo acid sequence of SEQ ID NO 2, and (iv) a polypeptide that is encoded by a recombinant polynucleotide compπsmg the polynucleotide sequence of SEQ ID NO 1, compnsmg the step of cultunng a host cell under conditions sufficient for the production of the polypeptide
6 A process for producmg a host cell compπsmg an expression system or a membrane thereof expressmg a polypeptide selected from the group consistmg of
(I) an isolated polypeptide compnsmg an ammo acid sequence selected from the group havmg at least 95% identity to the amino acid sequence of SEQ ID NO 2 over the entire length of SEQ ID NO 2,
(π) an isolated polypeptide compnsmg the ammo acid sequence of SEQ ID NO 2, (in) an isolated polypeptide that is the ammo acid sequence of SEQ ID NO 2. and (iv) a polypeptide that is encoded bv a recombinant polynucleotide comprising the polynucleotide sequence of SEQ ID NO 1, said process compnsmg the step of transforming or transfectmg a cell ith an expression system compπsmg a polynucleotide capable of producing said polypeptide of (I). (n), (m) or (iv) when said expression system is present m a compatible host cell such the host cell, under appropnate culture conditions, produces said polypeptide of (I), (11), (m) or (iv)
7 A host cell or a membrane expressing a polypeptide selected from the group consisting of (I) an isolated polypeptide compnsmg an ammo acid sequence selected from the group having at least 95% identity to the amino acid sequence of SEQ ID NO 2 over the entire length of SEQ ID
NO 2,
(n) an isolated polypeptide compnsmg the amino acid sequence of SEQ ID NO 2, (in) an isolated polypeptide that is the ammo acid sequence of SEQ ID NO 2, and (iv) a polypeptide that is encoded by a recombinant polynucleotide comprising the polynucleotide sequence of SEQ ID NO 1
8 An antibody lmmunospecific for the polypeptide of claim 1
9 A method for screenmg to identify compounds that agonize or that inhibit the function of the polypeptide of claim 1 that compnses a method selected from the group consisting of
(a) measurmg the bmdmg of a candidate compound to the polypeptide (or to the cells or membranes beanng the polypeptide) or a fusion protein thereof by means of a label directly or mdirectly associated with the candidate compound,
(b) measurmg the bmdmg of a candidate compound to the polypeptide (or to the cells or membranes beanng the polypeptide) or a fusion protem thereof m the presence of a labeled competitor,
(c) testmg whether the candidate compound results m a signal generated by activation or inhibition of the polypeptide, usmg detection systems appropnate to the cells or cell membranes bearmg the polypeptide,
(d) mixing a candidate compound with a solution compnsmg a polypeptide of claim 1, to form a mixture, measurmg activity of the polypeptide m the mixture, and comparing the activity of the mixture to a standard, or
(e) detectmg the effect of a candidate compound on the production of mRNA encoding said polypeptide and said polypeptide m cells, usmg for instance, an ELISA assay
10 An agomst or antagomst to the polypeptide of claim 1
PCT/US2000/011894 1999-05-07 2000-05-02 yphC WO2000068427A1 (en)

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Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2000014200A2 (en) * 1998-09-09 2000-03-16 Millennium Pharmaceuticals, Inc. Essential bacterial genes and their use

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2000014200A2 (en) * 1998-09-09 2000-03-16 Millennium Pharmaceuticals, Inc. Essential bacterial genes and their use

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
DATABASE CAPLUS ON STN FRITZ C. ET AL.: "Two genes of steptococcus pneumoniae essential for bacterial survival and widely distributed among eubacteria as potential targets for antibiotics", XP002953091 *
KUNST F. ET AL.: "The complete genome sequence of the gram-positive bacterium bacillus subtilis", vol. 390, no. 20, 20 November 1997 (1997-11-20), pages 249 - 256, XP002929157 *

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