WO2000009541A1 - nrdE - Google Patents

nrdE Download PDF

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Publication number
WO2000009541A1
WO2000009541A1 PCT/US1999/017545 US9917545W WO0009541A1 WO 2000009541 A1 WO2000009541 A1 WO 2000009541A1 US 9917545 W US9917545 W US 9917545W WO 0009541 A1 WO0009541 A1 WO 0009541A1
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Prior art keywords
polypeptide
sequence
polynucleotide
seq
identity
Prior art date
Application number
PCT/US1999/017545
Other languages
French (fr)
Inventor
Edwina I. Wilding
Michael T. Black
Christopher M. Traini
Original Assignee
Smithkline Beecham Corporation
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Smithkline Beecham Corporation filed Critical Smithkline Beecham Corporation
Priority to JP2000564991A priority Critical patent/JP2002522059A/en
Priority to EP99939673A priority patent/EP1105411A1/en
Publication of WO2000009541A1 publication Critical patent/WO2000009541A1/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
    • C07K14/305—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Micrococcaceae (F)
    • C07K14/31—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Micrococcaceae (F) from Staphylococcus (G)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/04—Antibacterial agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/10—Antimycotics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P33/00—Antiparasitic agents
    • A61P33/02—Antiprotozoals, e.g. for leishmaniasis, trichomoniasis, toxoplasmosis
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/573—Immunoassay; Biospecific binding assay; Materials therefor for enzymes or isoenzymes
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/94—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving narcotics or drugs or pharmaceuticals, neurotransmitters or associated receptors
    • G01N33/9446—Antibacterials
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10S530/00—Chemistry: natural resins or derivatives; peptides or proteins; lignins or reaction products thereof
    • Y10S530/808—Materials and products related to genetic engineering or hybrid or fused cell technology, e.g. hybridoma, monoclonal products
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10S530/00—Chemistry: natural resins or derivatives; peptides or proteins; lignins or reaction products thereof
    • Y10S530/82—Proteins from microorganisms
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10S—TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10S530/00—Chemistry: natural resins or derivatives; peptides or proteins; lignins or reaction products thereof
    • Y10S530/82—Proteins from microorganisms
    • Y10S530/825—Bacteria

Definitions

  • This u ention relates to newly identified polynucleotides and polypeptides. and their production and uses, as well as their vanants, agonists and antagonists, and their uses
  • the invention relates to polynucleotides and polypeptides of the nbonucleotide diphosphate reductase family, as well as their vanants, hereinafter referred to as "nrdE,” “nrdE pofynucleot ⁇ de(s),” and “nrdE polypept ⁇ de(s)" as tlie case may be
  • Staphylococcal genes and gene products are particularly preferred to employ Staphylococcal genes and gene products as targets for the development of antibiotics
  • the Staphylococci make up a medically important genera of microbes They are known to produce two types of disease, invasive and toxigenic Invasive infections are charactenzed generally by abscess formation effectmg both skin surfaces and deep tissues Staphylococcus aureus is the second leading cause of bacteremia in cancer patients Osteomyelitis, septic arthntis, septic thrombophlebitis and acute bactenal endocarditis are also relatively common
  • Osteomyelitis, septic arthntis, septic thrombophlebitis and acute bactenal endocarditis are also relatively common
  • There are at least three clinical conditions resulting from the toxigenic properties of Staphylococci Tlie manifestation of these diseases result from the actions of exotoxins as opposed to tissue invasion and bacteremia These
  • Staphylococcus aureus infections has nsen dramatically in the past few decades This has been attributed to tlie emergence of multiply antibiotic resistant strains and an increasing population of people with weakened immune systems It is no longer uncommon to isolate Staphylococcus aureus strains which are resistant to some or all of the standard antibiotics This phenomenon has created an unmet medical need and demand for new anti-microbial agents, vaccines, drug screening methods, and diagnostic tests for tins organism
  • polynucleotides and pohpeptides such as the nrdE embodiments of the invention, that have a present benefit of, among other things, being useful to screen compounds for antimicrobial activity
  • Such factors are also useful to determine their role in pathogenesis of infection. dysfunction and disease
  • identification and charactenzation of such factors and their antagonists and agonists to find ways to prevent, ameliorate or correct such infection, dysfunction and disease
  • the present invention relates to nrdE. in particular nrdE polypeptides and nrdE polynucleotides. recombinant matenals and methods for their production
  • the mvention relates to methods for using such polypeptides and polynucleotides, including treatment of microbial diseases, amongst others
  • the invention relates to methods for identifying agonists and antagonists using the materials provided by the invention, and for treating microbial infections and conditions associated with such infections with tlie identified agonist or antagonist compounds
  • the mvention relates to diagnostic assays for detectmg diseases associated with microbial infections and conditions associated with such infections, such as assays for detecting nrdE expression or activity
  • Tlie mvention relates to nrdE pohpeptides and polynucleotides as descnbed m greater detail below
  • the mvention relates to polypeptides and polynucleotides of a nrdE of Staphylococcus aureus.
  • nrdE which is related by ammo acid sequence homology to nrdE pohpeptide
  • the mvention relates especialh to nrdE havmg the nucleotide and ammo acid sequences set out in Table 1 as SEQ ID NO 1 and SEQ ID NO 2 respectively
  • sequences recited m the Sequence Listing below as "DNA "" represent an exemplification of the invention, since those of ordinary skill w ill recognize that such sequences can be usefully employed in polynucleotides in general, including ⁇ bopolynucleotides
  • a deposit containing a Staphylococcus aureus WCUH 29 stram has been deposited with the
  • NCIMB National Collections of Industrial and Marine Bactena Ltd
  • Staphylococcus aureus WCUH29 on deposit
  • the Staphylococcus aureus stram deposit is referred to herem as "the deposited stram” or as "the DNA of the deposited stram"
  • the deposited stram contains a full length nrdE gene
  • Tlie deposit of tlie deposited stram has been made under the terms of tlie 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 tlie public upon the issuance of a patent Tlie deposited stram is provided merely as convenience 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 stram. and compounds denved therefrom, and no such license is hereby granted
  • an isolated nucleic acid molecule encodmg a mature polypeptide expressible by the Staphylococcus aureus WCUH 29 stram, which polypeptide is contamed m the deposited stram
  • nrdE polypeptide of the mvention is substantially phylogenetically related to other proteins of the nbonucleotide diphosphate reductase family
  • nrdE polypeptides of Staphylococcus aureus referred to herem as "nrdE” and “nrdE polypeptides” as well as biologically, diagnostically, prophylactically, clinically or therapeutically useful vanants thereof, and compositions compnsmg the same Among the particularly preferred embodiments of the mvention are vanants of nrdE polypeptide encoded by naturally occurring alleles of the nrdE gene
  • the present mvention further provides for an isolated polypeptide which (a) comprises or consists of an ammo acid sequence which has at least 70% identity, preferably at least 80% identity, more preferably at least 90% identity, yet more preferably 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 comprising or consisting of a polynucleotide sequence which has at least 70% identity preferably at least 80% identity, more preferably at least 90% identity, yet more preferably at least 95% identity, even more preferably at least 97-99% or exact identity to SEQ ID NO 1 over the entire length of SEQ ID NO 1 , (c) a polypeptide encoded by an isolated polynucleotide comprising or consisting of a polynucleotide sequence encodmg a polypeptide which has at least 70% identity, preferably at least 80% identity,
  • polypeptides of the mvention mclude a polypeptide of Table 1 [SEQ ID NO 2] (m particular the mature polypeptide) as well as polypeptides and fragments, particularly those which have the biological activity of nrdE. and also those which have at least 70% identity to a polypeptide of Table 1 [SEQ ID NO l]or the relevant portion, preferably at least 80% identity to a polypeptide of Table 1 [SEQ ID NO 2and more preferabh at least 90% identity to a polypeptide of Table 1 [SEQ ID NO 2] and still more preferabh at least 95% identity to a polypeptide of Table 1 [SEQ ID NO 2] and also mclude portions of such polypeptides with such portion of tlie polypeptide generally containing at least 30 ammo acids and more preferably at least 50 ammo acids
  • Tlie mvention also mcludes a polypeptide consisting of or compnsmg a polypeptide of the formula X-(R 1 ) m -(R 2 )-(R3)n-Y wherein, at the ammo terminus, X is hydrogen, a metal or any other moiety descnbed herem for modified polypeptides, and at tlie carboxyl terminus.
  • Y is hydrogen, a metal or any other moiety descnbed herem for modified polypeptides
  • R j 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 In the formula above.
  • R is onented so that its ammo terminal ammo acid residue is at the left, covalently bound to Ri and its carboxy terminal ammo acid residue is at the nght, covalently bound to R3 Any stretch of ammo acid residues denoted b either Ri or R3.
  • m and/or 11 is greater than 1, may be either a heteropolymer or a homopolymer, preferably a heteropolymer
  • n is an mteger between 1 and 50, 100, or 500
  • a polypeptide of the mvention is denved from Staphylococcus aureus, 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 tlie same taxonomic family or order
  • a fragment is a vanant polypeptide havmg an ammo acid sequence that is entirely the same as part but not all of any ammo acid sequence of any polypeptide of the mvention
  • fragments may be "free-standing.” or compnsed within a larger polypeptide of which they fonn a part or region most preferably as a smgle contmuous region m a smgle larger polypeptide
  • Preferred fragments m include. for example, truncation polypeptides havmg a portion of an amino acid sequence of Table 1 [SEQ ID NO 2], or of vanants thereof, such as a contmuous senes of residues that mcludes an ammo- and/or carboxyl-termmal ammo acid sequence
  • Degradation forms of the polypeptides of the mvention produced by or m a host cell, particularly a Staphylococcus aureus are also preferred
  • fragments charactenzed by structural or functional attributes such as fragments that compnse alpha-helix and alpha-helix forming regions beta-sheet and beta-sheet-formmg regions, turn and turn-forming regions coil and coil-forming regions, hydrophilic regions, hydrophobic regions, alpha amphipathic regions, beta amphipathic regions, flexible regions surface-forming regions, substrate bmdmg region, and high antigenic mdex regions
  • fragments include an isolated polypeptide comprising an ammo acid sequence having at least 15, 20, 30, 40, 50 or 100 contiguous amino acids from the amino acid sequence of SEQ ID NO.2, or an isolated polypeptide comprising an amino acid sequence having at least 15, 20, 30, 40, 50 or 100 contiguous amino acids truncated or deleted from the amino acid sequence of SEQ ID NO:2.
  • biologically active fragments which are those fragments that mediate activities of nrdE. mcludmg those with a similar activity or an improved activity, or with a decreased undesirable activity
  • those fragments that are antigeruc or lmmunogenic m an animal especially in a human
  • fragments compnsmg receptors or domains of enzymes that confer a function essential for viability of Staphylococcus aureus or the ability to initiate, or maintain cause Disease m an individual particularly a human Fragments of the polypeptides of the mvention may be employed for producmg tlie corresponding full-length polypeptide by peptide synthesis, therefore, these vanants may be employed as intermediates for producmg the full-length polypeptides of the mvention
  • X or "Xaa” may also be used m describing certain polypeptides of the invention "X” and “Xaa” mean that any of the twenty naturally occurring amino acids may appear at such a designated position in the polypeptide sequence
  • nrdE polypeptides particularly polynucleotides that encode the polypeptide herem designated nrdE
  • tlie polynucleotide compnses a region encodmg nrdE polypeptides compnsmg a sequence set out m Table 1 [SEQ ID NO 1] which mcludes a full length gene, or a variant thereof
  • SEQ ID NO 1 mcludes a full length gene, or a variant thereof
  • isolated nucleic acid molecules encodmg and/or expressmg nrdE polypeptides and polynucleotides. particularly Staphylococcus aureus nrdE polypeptides and polynucleotides.
  • mcludmg for example, unprocessed RNAs. nbozyme RNAs, niRNAs. cDNAs, genomic DNAs, B- and Z-DNAs
  • Further embodiments of the mvention mclude biologically, diagnostically. prophylactically. clinically or therapeutically useful polynucleotides and polypeptides.
  • nrdE polypeptide from Staphylococcus aureus comprising or consisting of an ammo acid sequence of Table 1 [SEQ ID NO 2], or a variant thereof
  • a polynucleotide of the mvention encoding nrdE polypeptide may be obtained usmg standard cloning and screening methods, such as those for cloning and sequencmg chromosomal DNA fragments from bactena usmg Staphylococcus aureus WCUH 29 cells as starting matenal, followed by obtaining a full length clone
  • a polynucleotide sequence of the invention such as a polynucleotide sequence given in Table 1 [SEQ ID NO 1] typically a library of clones of chromosomal DNA of Staphylococcus aureus WCUH 29 in E coh or some other suitable host is probed with a radiolabeled ohgonucleotide, preferably a 17-mer or longer, derived from
  • each DNA sequence set out m Table 1 [SEQ ID NO 1] contains an open rearing frame encodmg a protein having about the numbei of amino 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 m the art Tlie polynucleotide of SEQ ID NO 1.
  • the present mvention provides for an isolated polynucleotide comprising or consisting of (a) a polynucleotide sequence which has at least 70% identity, preferably at least 80% identity, more preferably at least 90% identity, yet more preferably at least 95% identity, even more preferably at least 97-99% or exact identity to SEQ ID NO 1 over the entire length of SEQ ID NO 1, (b) a polynucleotide sequence encodmg a polypeptide which has at least 70% identity, preferably at least 80% identity, more preferably at least 90% identity, yet more preferably 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 encodmg a polypeptide of the present mvention, mcludmg homologs and orthologs from species other than Staphylococcus aureus may be obtained by a process which compnses the steps of screening an appropnate library under stringent hybndization conditions with a labeled or detectable probe consisting of or compnsmg the sequence of SEQ ID NO 1 or a fragment thereof, and isolating a full-length gene and/or genomic clones containing said polynucleotide sequence
  • the mvention provides a polynucleotide sequence identical over its entire length to a codmg sequence (open readmg frame) in Table 1 [SEQ ID NO 1] Also provided by the mvention is a codmg 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 readmg frame with another codmg sequence, such as a sequence encodmg a leader or secretory sequence, a pre-, or pro- or prepro-protem sequence
  • the polynucleotide of the mvention may also contain at least one non-coding sequence, mcludmg for example, but not limited to at least one non-coding 5 " and 3' sequence, such as tlie transcnbed but non-translated sequences, termmation signals (such as rho-dependent and rho-independent termmation signals), nbosome bmdmg sites.
  • the polynucleotide sequence may also compnse additional coding sequence encoding additional ammo acids
  • a marker sequence that facilitates punfication of the fused polypeptide can be encoded in certain embodiments of the mvention.
  • the marker sequence is a hexa-histidine peptide, as provided m tlie pQE vector (Qiagen. Inc ) and descnbed in Gentz et al . Proc Natl Acad Su , USA 86 821-824 (1989). or an HA peptide tag (Wilson et a! . Cell 37 767 (1984).
  • both of winch may be useful m punfymg polypeptide sequence fused to them
  • Polynucleotides of the mvention also mclude. but are not lmuted to, polynucleotides compnsmg a structural gene and its naturally associated sequences that control gene expression
  • a preferred embodiment of tlie mvention is a polynucleotide of consisting of or compnsmg nucleotide
  • the mvention also mcludes a polynucleotide consisting of or compnsmg a polynucleotide of the formula X-(R 1 ) m -(R 2 )-(R 3 ) n -Y wherein 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 R j and R3 is independently any nucleic acid residue or modified nucleic acid residue
  • m is an integer between 1 and 3000 or zero .
  • n is an integer between 1 and 3000 or zero
  • R 2 is a nucleic acid sequence or modified nucleic acid sequence of the invention, particularly a nucleic acid sequence selected from Table 1 or a modified nucleic acid sequence thereof
  • R 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 right, bound to R3 Any stretch of nucleic acid residues denoted by either Ri and/or R 2 .
  • m and/or 11 may be either a heteropolymer or a homopolymer, preferably a heteropolymer
  • the polynucleotide of the above formula is a closed, circular polynucleotide, which can be a double-stranded polynucleotide wherein the formula shows a first strand to which the second strand is complementary
  • m and/or n is an integer between 1 and 1000.
  • 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
  • a polynucleotide of the mvention is denved from Staphylococcus aureus, however, it may preferably be obtamed from other organisms of the same taxonomic genus A polynucleotide of the mvention may also be obtamed. 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 Staphylococcus aureus nrdE havmg an ammo acid sequence set out m Table 1 [SEQ ID NO 2]
  • Tlie term also encompasses polynucleotides that mclude a smgle contmuous region or discontinuous regions encodmg tlie 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 genonnc DNA reorganization) together with additional regions, that also may contain coding and/or non-coding sequences
  • the mvention may contain coding and/
  • polynucleotides encodmg nrdE vanants that have the am o acid sequence of nrdE polypeptide of Table 1 [SEQ ID NO 2] m which several, a few. 5 to 10, 1 to 5, 1 to 3. 2.
  • polynucleotides that are at least 70% identical over their entire length to a polynucleotide encodmg nrdE polypeptide havmg an ammo acid sequence set out in Table 1 [SEQ ID NO 2], and polynucleotides that are complementary to such polynucleotides
  • polynucleotides that compnse a region that is at least 80% identical over its entire length to a polynucleotide encoding nrdE polypeptide and polynucleotides complementary thereto
  • polynucleotides at least 90% identical over their entire length to the same are particularly preferred, and among these particularly preferred polynucleot
  • Preferred embodiments are polynucleotides encodmg polypeptides that retain substantially the same biological function or activity as the mature polypeptide encoded by a DNA of Table 1 [SEQ ID NO 1] hi accordance with certain preferred embodiments of this mvention there are provided polynucleotides that hybndize. particularly under stringent conditions, to nrdE polynucleotide sequences, such as those polynucleotides m Table 1
  • Tlie mvention further relates to polynucleotides that hybndize to the polynucleotide sequences provided herem
  • tlie mvention especially relates to polynucleotides that hybndize under stringent conditions to the polynucleotides descnbed herem
  • stringent conditions and “stringent 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 stringent hybridization conditions is overnight incubation at 42°C in a solution comprising 50% formamide, 5x SSC (150mM NaCl.
  • the invention also provides a polynucleotide consisting of or comprising a polynucleotide sequence obtained by screening an appropriate library containing the complete gene for a polynucleotide sequence set forth in SEQ ID NO 1 under stringent hybridization conditions with a probe having the sequence of said polynucleotide sequence set forth m SEQ ID NO 1 or a fragment thereof, and isolating said polynucleotide sequence Fragments useful for obtaining such a polynucleotide include, for example, probes and primers fully described elsewhere herein As discussed elsewhere herem regarding polynucleotide assays of the mvention, for instance, the polynucleotides of tlie mvention.
  • probes may be used as a hybndization probe for RNA, cDNA and genomic DNA to isolate full-length cDNAs and genomic clones encoding nrdE and to isolate cDNA and genomic clones of other genes that have a high identity, particularly high sequence identity, to the nrdE gene
  • Such probes generally will compnse at least 15 nucleotide residues or base pairs
  • such probes will have at least 30 nucleotide residues or base pairs and may have at least 50 nucleotide residues or base pairs
  • Particularly preferred 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 nrdE gene may be isolated by screening usmg a DNA sequence provided m Table 1 [SEQ ID NO 1] to synthesize an ohgonucleotide probe
  • a labeled ohgonucleotide havmg a sequence complementary to that of a gene of the mvention is then used to screen a library of cDNA, genomic DNA or mRNA to determine which members of the library the probe hybndizes to
  • primers designed to anneal within the amplified product typically an adaptor specific primer that anneals further 3' in the adaptor sequence and a gene specific primer that anneals further 5' 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 existing DNA to give a complete sequence, or carrying out a separate full- length PCR using the new sequence information for the design of the 5' pnmer
  • polynucleotides and polypeptides of tlie 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
  • polynucleotides of the invention that are ohgonucleotides derived from a sequence of Table
  • SEQ ID NOS 1 or 2 may be used m the processes herein as described, but preferably for PCR, to determine whether or not the polynucleotides identified herein in whole or in part are transcribed in bacteria in infected tissue It is recognized that such sequences will also have utility in diagnosis of the stage of infection and type of infection the pathogen has attained
  • Tlie mvention also provides polynucleotides that encode a polypeptide that is the mature protem plus additional ammo or carboxyl-terminal ammo acids, or ammo acids mtenor to the mature polypeptide (when the mature form has more than one polypeptide cham.
  • Such sequences may a role m processmg of a protem from precursor to a mature form, may allow protem transport, may lengthen or shorten protem half-life or may facilitate manipulation of a protem for assay or production, among other things
  • the additional ammo acids may be processed away from the mature protem by cellular enzymes
  • a polynucleotide complementary to it it is preferred that these complementary polynucleotides are fully complementary to each po nucleotide with which they are complementary
  • a precursor protem, havmg a mature form of the polypeptide fused to one or more prosequences may be an inactive fonn 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
  • N means that any of the four DNA or RNA nucleotides ma> appear at such a designated position in the DNA or RNA sequence, except it is preferred that N is not a nucleic acid that when taken m combination with adjacent nucleotide positions, when read in the correct reading frame, would have the effect of generating a premature termination codon in such reading frame
  • a pohnucleotide of the mvention may encode a mature protem.
  • a mature protem plus a leader sequence (which may be referred to as a preprotem).
  • a precursor of a mature protem havmg one or more prosequences that are not the leader sequences of a preprotem, or a preproprotem, which is a precursor to a proprotein.
  • havmg a leader sequence and one or more prosequences which generally are removed during processmg steps that produce active and mature forms of tl e polypeptide
  • Tlie mvention also relates to vectors that compnse a polynucleotide or polynucleotides of the mvention.
  • host cells that are genetically engmeered with vectors of the mvention and the production of polypeptides of the mvention by recombinant techniques
  • Cell-free translation systems can also be employed to produce such proteins usmg RNAs denved from tlie DNA constructs of the mvention
  • Recombinant polypeptides of the present mvention may be prepared by processes well known in those skilled m tlie art from genetically engmeered host cells compnsmg expression systems
  • the present mvention relates to expression systems which compnse a polynucleotide or polynucleotides of the present mvention, to host cells which are genetically engmeered with 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 tlie host cell can be effected by methods descnbed m many standard laboratory manuals, such as Davis, et al . BASIC METHODS IN MOLECULAR BIOLOGY, (1986) and Sambrook. et al , MOLECULAR CLONING A LABORATORY MANUAL, 2nd Ed . Cold Spring Harbor Laboratory Press. Cold Spring Harbor, N Y (1989), such as. calcium phosphate transfection, DEAE-dextran mediated transfection. transvection. microinjection, catiomc pid-mediated transfection. electroporation, transduction. scrape loading, ballistic mtroduction and infection
  • bactenal cells such as cells of streptococci, staphylococci. enterococci E cob, streptomyces, cyanobactena.
  • Bacillus subtibs, and Staphylococcus aureus fungal cells such as cells of a yeast. Kluveromyces, Saccharomyce . a basidiomycete, Candida albicans and Aspergillus, msect cells such as cells of Drosoph ⁇ a S2 and Spodoptera Sf9, animal cells such as CHO. COS.
  • Such vectors mclude. among others, chromosomal-, episomal- and virus-denved vectors, for example, vectors denved from bactenal plasmids. from bactenophage. from transposons. from yeast episomes. from insertion elements, from yeast chromosomal elements, from viruses such as baculoviruses. papova vimses. such as SV40. vaccinia viruses, adenoviruses.
  • the expression system constructs may contain control regions that regulate as well as engender expression Generally, any system or vector suitable to maintain, propagate or express polynucleotides and/or to express a polypeptide m a host may be used for expression m this regard
  • the appropnate DNA sequence may be inserted mto the expression system by any of a vanety of well-known and routme techniques, such as.
  • Polypeptides of the mvention can be recovered and punfied from recombinant cell cultures by well-known methods mcludmg ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography. phosphocellulose chromatography, hydrophobic mteraction chromatography, affinity chromatography. hydroxylapatite chromatography. and lectm chromatography Most preferably, high performance liquid chromatography is employed for punficatioii Well known techniques for refolding protem may be employed to regenerate active conformation when the polypeptide is denatured during isolation and or punfication Diagnostic, Prognostic, Serotyping and Mutation Assays
  • This mvention is also related to the use of nrdE polynucleotides and polypeptides of the mvention for use as diagnostic reagents Detection of nrdE polynucleotides and/or polypeptides m 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 organism compnsmg tlie nrdE gene or protem may be detected at the nucleic acid or ammo acid level by a vanety of well known techniques as well as by methods provided herem
  • Polypeptides and polynucleotides for prognosis, diagnosis or other analysis may be obtamed from a putatively infected and/or infected individual's bodily matenals
  • Polynucleotides from am of these sources, particularly DNA or RNA. may be used directly for detection or may be amplified enzymatically by usmg PCR or any other amplification technique pnor to analysis RNA, particularly mRNA.
  • cDNA and genonnc DNA may also be used m the same ways Usmg amplification, charactenzation of the species and stram of infectious or resident organism present m an individual, 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 in companson to a genotype of a reference sequence selected from a related organism, preferably a different species of the same genus or a different stram of the same species Pomt mutations can be identified by hybndizing amplified DNA to labeled nrdE 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 detectmg differences m meltmg temperatures or renaturation kinetics Polynucleotide sequence differences may also be detected by alterations m
  • an array of o gonucleotides probes compnsmg nrdE nucleotide sequence or fragments tliereof can be constructed to conduct efficient screenmg of, for example, genetic mutations, serotype.
  • taxonomic classification or identification Array technology methods are well known and have general applicability and can be used to address a vanety of questions m molecular genetics mcludmg gene expression, genetic linkage and genetic vanabi ty (see. for example, Chee et al . Science, 274 610 (1996))
  • the present invention relates to a diagnostic kit which comprises (a) a polynucleotide of the present invention, preferably the nucleotide sequence of SEQ ID NO 1, or a fragment thereof , (b) a nucleotide sequence complementary to that of (a), (c) a polypeptide of the present invention, preferably the polypeptide of SEQ ID NO 2 or a fragment thereof, or (d) an antibody to a polypeptide of the present invention, preferably to the polypeptide of SEQ ID NO 2
  • kits may comprise a substantial component
  • Such a kit will be of use in 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.
  • SEQ ID NO 1. which is associated with a disease or pathogemcity will provide a diagnostic tool that can add to, or define, a diagnosis of a disease, a prognosis of a course of disease, a determination of a stage of disease, or a susceptibility to a disease, which results from under-expression.
  • Organisms, particularly infectious organisms, carrying mutations m such polynucleotide may be detected at the polynucleotide level by a vanety of techniques, such as those described elsewhere herem
  • Tlie nucleotide sequences of the present mvention are also valuable for orgamsm chromosome identification
  • the sequence is specifically targeted to, and can hybndize with, a particular location on an organism's chromosome, particularly to a Staphylococcus aureus chromosome
  • the mapping of relevant sequences to chromosomes according to the present mvention may be an important step m correlating those sequences with pathogenic potential and/or an ecological mche of an orgamsm and/or drug resistance of an orgamsm.
  • tlie essentiality of tlie gene to the organism Once a sequence has been mapped to a precise chromosomal location, the physical position of the sequence on the chromosome can be correlated with genetic map data Such data may be found on-lme m a sequence database The relationship between genes and diseases that have been mapped to the same chromosomal region are then identified through known genetic methods, for example, through linkage analysis (coinhentance of physically adjacent genes) or matmg studies, such as by conjugation
  • the differences in a polynucleotide and/or polypeptide sequence between organisms possessing a first phenotype and organisms possessing a different, second different phenotype can also be determined If a mutation is observed in some or all organisms possessing the first phenotype but not in any organisms possessing the second phenotype, then the mutation is likely to be the causative agent of the first phenotype
  • a polynucleotide and/or polypeptide of tlie mvention may also be detected at the pohnucleotide or polypeptide level by a vanety of techniques, to allow for serotypmg. for example
  • RT-PCR can be used to detect mutations m the RNA It is particularly preferred 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 tlie same purpose, PCR As an example.
  • PCR primers complementary to a polynucleotide encoding nrdE polypeptide can be used to identify and analyze mutations Examples of representative primers are shown below in Table 2
  • the mvention also mcludes primers of the formula
  • X is hydrogen, a metal or a modified nucleotide residue, and at the 3' end of tlie molecule.
  • Y is hydrogen, a metal or a modified nucleotide residue.
  • Ri and R3 are any nucleic acid residue or modified nucleotide residue, m is an mteger between 1 and 20 or zero . n is an mteger between 1 and 20 or zero, and R2 is a primer sequence of the mvention.
  • R 2 is onented so that its 5' end nucleotide residue is at the left, bound to Ri and its 3' end nucleotide residue is at the nght. bound to R3
  • Any stretch of nucleic acid residues denoted by either R group, where m and/or 11 is greater than 1. may be either a heteropolymer or a homopolymer, preferably a heteropolymer being complementary to a region of a polynucleotide of Table 1
  • m and/or n is an mteger between 1 and 10.
  • the mvention further provides these primers with 1, 2, 3 or 4 nucleotides removed from the 5' and/or tlie 3' end These primers may be used for. among other things, amplifying nrdE DNA and/or RNA isolated from a sample denved from an individual, such as a bodily matenal
  • the primers may be used to amplify a polynucleotide isolated from an mfected individual, such that tlie polynucleotide may then be subject to vanous techniques for elucidation of the pohnucleotide sequence In this way, mutations in tlie 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 bacterial infections, more preferably mfections caused by Staphylococcus aureus.
  • Increased or decreased expression of a nrdE polynucleotide can be measured using 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 hybridization methods
  • a diagnostic assay m accordance with the mvention for detectmg over-expression of nrdE polypeptide compared to normal control tissue samples be used to detect the presence of an infection, for example Assay teclnnques that can be used to determine levels of a nrdE polypeptide, in 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
  • the polynucleotides and polynucleotides of the mvention may be used as reagents for differential screenmg methods
  • differential screening and differential display methods There are many differential screening and differential display methods known m the art in which tlie polynucleotides and polypeptides of the mvention may be used
  • the differential displaj technique is described by Chuang et al . J Bactenol 175 2026-2036 (1993) This method identifies those genes which are expressed in an organism by identifying mRNA present using randomly-primed RT-PCR By comparing pre-infection and post infection profiles, genes up and down regulated during infection can be identified and the RT-PCR product sequenced and matched to ORF "unknowns"
  • IVET In Vivo Expression Technology (IVET) is described by Camilh et al , Proc Nat 'I Acad Sci USA 91 2634-2638 (1994) IVET identifies genes up-regulated during infection when compared to laboratory cultivation, implying an important role in infection ORFs identified by this technique are implied to have a significant role in infection establishment and/or maintenance
  • random chromosomal fragments of target organism are cloned upstream of a promoter-less recombinase gene in a plasmid vector
  • This construct is introduced into the target organism which carries an antibiotic resistance gene flanked by resolvase sites Growth in the presence of the antibiotic removes from the population those fragments cloned into the plasmid vector capable of supporting transcription of the recombinase gene and therefore have caused loss of antibiotic resistance
  • the resistant pool is introduced into a host and at various times after infection bacteria may be recovered and assessed for the presence of antibiotic resistance
  • RT-PCR may also be used to analyze gene expression patterns
  • messenger RNA is isolated from bacterial infected tissue, e g . 48 hour murine lung infections, and the amount of each mRNA species assessed by reverse transcription of the RNA sample primed with random hexanucleotides followed by PCR with gene specific primer pairs
  • the determination of the presence and amount of a particular mRNA species by quantification of the resultant PCR product provides information on the bacterial genes which are transcribed in the infected tissue Analysis of gene transcription can be carried out at different times of infection to gain a detailed knowledge of gene regulation m bacterial pathogenesis allowing for a clearer understanding of which gene products represent targets for screens for antibacterials
  • the bacterial mRNA preparation need not be free of mammalian RNA This allows the investigator to carry out a simple and quick RNA preparation from infected tissue to obtain bacterial mRNA species which are
  • polynucleotides of the invention may be used as components of polynucleotide arrays, preferabh' high density arrays or grids These high density arrays are particularly useful for diagnostic and prognostic purposes
  • a set of spots each comprising a different gene, and further comprising a polynucleotide or polynucleotides of the invention may be used for probing, such as using hybridization or nucleic acid amplification, using a probes obtained or derived from a bodily sample, to determine the presence of a particular polynucleotide sequence or related sequence in an individual
  • Such a presence may indicate the presence of a pathogen, particularly Staphylococcus aureus, and may be useful in diagnosing and/or prognosing disease or a course of disease
  • a grid comprising a number of variants of the polynucle
  • Tlie pohpeptides and polynucleotides of the mvention or vanants tliereof, or cells expressmg the same can be used as lmmunogens to produce antibodies rmmunospecific for such polypeptides or polynucleotides respectively hi certain preferred embodiments of tlie mvention there are provided antibodies agamst nrdE polypeptides or polynucleotides
  • Antibodies generated agamst the polypeptides or polynucleotides of the mvention can be obtamed by administering the polypeptides and/or polynucleotides of the mvention. or epitope-beanng fragments of either or both, analogues of either or both, or cells expressmg either or both, to an animal, preferably a nonhuman.
  • usmg routine protocols For preparation of monoclonal antibodies am technique known m the art that provides antibodies produced by contmuous cell line cultures can be used Examples mclude vanous techniques, such as those m Koliler. G and Milstem, C , Nature 256 495-497 (1975). Kozbor et al . Immunology Today 4 72 (1983). Cole et al . pg 77-96 m MONOCLONAL ANTIBODIES AND CANCER THERAPY. Alan R Liss. Inc (1985)
  • phage display technology may be utilized to select antibody genes w ith binding activities towards a polypeptide of the invention either from repertoires of PCR amplified v-genes of lymphocytes from humans screened for possessing anti-nrdE or from naive libraries (McCafferty. et al , (1990). Nature 348, 552-554, Marks, et al , (1992) Biotechnology 10, 779-783)
  • the affinity of these antibodies can also be improved by, for example, chain shuffling (Clackson et al , (1991) Nature 352 628)
  • the above-descnbed antibodies may be employed to isolate or to identify clones expressmg the polypeptides or polynucleotides of the mvention to punfy tlie polypeptides or polynucleotides by. for example. affinity chromatography
  • antibodies against nrdE-polypeptide or nrdE-polynucleotide may be employed to treat infections, particularly bactenal infections
  • Polypeptide variants include antigemcally. epitopicalh or lmmunologically equivalent variants form a particular aspect of this invention
  • a polypeptide or polynucleotide of the invention such as an antigemcally or linmunologically equivalent derivative or a fusion protem of the polypeptide is used as an antigen to immunize a mouse or other animal such as a rat or chicken
  • the fusion protein may provide stability to the polypeptide
  • the antigen may be associated, for example by conjugation, with an lmmunogemc carrier protein for example bovine serum albumin, keyhole limpet haemocyanm or tetanus toxoid
  • an lmmunogemc carrier protein for example bovine serum albumin, keyhole limpet haemocyanm or tetanus toxoid
  • a multiple antigenic polypeptide comprising multiple copies of the polypeptide. or an antigemcally or lmmunological
  • the antibody or variant thereof is modified to make it less lmmunogemc in the individual
  • the antibody may most preferably be "humanized.” where the comphmentarity detenninmg region or regions of the hybridoma-derived antibody has been transplanted into a human monoclonal antibody, for example as described in Jones et al (1986). Nature
  • a polynucleotide of the invention for therapeutic or prophylactic purposes, in particular genetic immunization
  • genetic immunization Among the particularly preferred embodiments of the mvention are naturally occurring allehc vanants of nrdE polynucleotides and polypeptides encoded thereby
  • the use of a polynucleotide of the invention in genetic immunization will preferably employ a suitable delivery method such as direct injection of plasmid DNA mto muscles (Wolff et al , Hum Mol Genet (1992) 1 363.
  • Polypeptides and polynucleotides of the mvention may also be used to assess the bmdmg of small molecule substrates and ligands m, for example, cells, cell-free preparations, chemical hbranes, and natural product mixtures
  • substrates and ligands may be natural substrates and ligands or may be structural or functional mimetics See. e g . Coligan et al . Current Protocols in Immunology 1(2) Chapter 5 (1991)
  • Polypeptides and polynucleotides of the present mvention are responsible for many biological functions, mcludmg many disease states, m particular the Diseases herembefore mentioned It is therefore desirable to devise screenmg methods to identify compounds which stimulate or which inhibit the function of tlie polypeptide or polynucleotide Accordingly, m a further aspect, the present mvention provides for a method of screening compounds to identify those which stimulate or which inhibit the function of a polypeptide or polynucleotide of the mvention.
  • agomsts or antagonists may be employed for therapeutic and prophylactic purposes for such Diseases as hereinbefore mentioned
  • Compounds may be identified from a vanety of sources, for example, cells, cell-free preparations, chemical hbranes, and natural product mixtures
  • agomsts, antagonists or inhibitors so- identified may be natural or modified substrates, ligands. receptors, enzymes, etc , as the case may be. of nrdE polypeptides and polynucleotides, or may be structural or functional mimetics thereof (see Coligan et al .
  • the screening methods may simply measure the bmdmg of a candidate compound to the polypeptide or polynucleotide. or to cells or membranes bearing the polypeptide or polynucleotide.
  • the screening 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, using detection systems appropriate to the cells comprising the polypeptide or polynucleotide Inhibitors of activation are generally assayed m the presence of a known agonist and the effect on activation by the agonist by the presence of the candidate compound is observed Constitutively active polypeptide and/or constitutively expressed polypeptides and polynucleotides may be employed m screening methods for inverse agonists or inhibitors, m the absence of an agonist or inhibitor, by testing whether the candidate compound results in inhibition of activation of the polypeptide or polynucleotide.
  • the screening methods may simply comprise the steps of mixing a candidate compound with a solution containing a polypeptide or polynucleotide of the present invention, to form a mixture, measuring nrdE polypeptide and/or polynucleotide activity m the mixture, and comparing the nrdE polypeptide and/or polynucleotide activity of the mixture to a standard Fusion proteins, such as those made from Fc portion and nrdE polypeptide.
  • polypeptides and antibodies that bind to and/or interact with a polypeptide of the present invention may also be used to configure screening methods for detecting the effect of added compounds on the production of mRNA and/or polypeptide in cells
  • an ELISA assay may be constructed for measuring secreted or cell associated levels of polypeptide using monoclonal and polyclonal antibodies by standard methods known in the art This can be used to discover agents which may inhibit or enhance the production of polypeptide (also called antagonist or agonist respectively) from suitably manipulated cells or tissues
  • the mvention also provides a method of screenmg compounds to identify those which enhance (agomst) or block (antagomst) tlie action of nrdE polypeptides or polynucleotides, particularly those compounds that are bactenstatic and/or bactencidal
  • the method of screeiung may mvolve high-throughput techniques
  • a synthetic reaction mix for agomsts 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 nrdE polypeptide and a labeled substrate or hgand of such polypeptide is mcubated m the absence or the presence of a candidate molecule that mav be a nrdE agomst or antagomst
  • the abihtv of the candidate molecule to agomze or antagonize tlie nrdE polypeptide is reflected m decreased
  • nrdE polypeptide are most likely to be good antagonists Molecules that bmd well and, as the case may be. increase tlie rate of product production from substrate, mcrease signal transduetion.
  • chemical channel activity are agomsts Detection of the rate or level of, as the case may be, production of product from substrate, signal transduetion, or chemical channel activity may be enhanced by usmg a reporter system Reporter systems that may be useful in this regard mclude but are not limited to colonmetnc, labeled substrate converted mto product, a reporter gene that is responsive to changes m nrdE polynucleotide or polypeptide activity, and bmdmg assays known m the art
  • Polypeptides of the invention may be used to identify membrane bound or soluble receptors, if any for such poly peptide. through standard receptor binding techniques known in the art These techniques include but are not limited to. hgand binding and crosslinking assays in 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 purification, and incubated with a source of the putative receptor (e g , cells, cell membranes, cell supernatants, tissue extracts, bodily materials) Other methods include biophy sical techniques such as surface plasmon resonance and spectroscopy These screening methods may also be used to identify agonists and antagonists of the polypeptide which compete with the binding of the polypeptide to its receptor(s), if any Standard methods for conducting such assays are well understood in the art
  • a radioactive isotope for instance, ⁇ I
  • chemically modified for instance
  • the fluorescence polarization value for a fluorescently -tagged molecule depends on the rotational correlation time or tumbling rate Protem complexes, such as formed by nrdE polypeptide associating with another nrdE polypeptide or other polypeptide.
  • labeled to comprise a fluorescently- labeled molecule will have higher polarization values than a fluorescently labeled monomeric protein It is preferred that this method be used to characterize small molecules that disrupt polypeptide complexes
  • Fluorescence energy transfer ma ⁇ also be used characterize small molecules that interfere with the formation of nrdE polypeptide dimers, t ⁇ mers. tetramers or higher order structures, or structures formed by nrdE polypeptide bound to another polypeptide nrdE polypeptide can be labeled with both a donor and acceptor fluorophore Upon mixing of the two labeled species and excitation of the donor fluorophore, fluorescence energy transfer can be detected by observing fluorescence of the acceptor Compounds that block dime ⁇ zation will inhibit fluorescence energy transfer
  • Surface plasmon resonance can be used to monitor the effect of small molecules on nrdE polypeptide self-association as well as an association of nrdE polypeptide and another polypeptide or small molecule nrdE polypeptide can be coupled to a sensor chip at low site density such that covalently bound molecules will be monomeric Solution protein can then passed over the nrdE polypeptide -coated surface and specific binding can
  • a scintillation proximity assay may be used to characterize the interaction between an association of nrdE polypeptide with another nrdE polypeptide or a different polypeptide nrdE polypeptide can be coupled to a scintillation-filled bead Addition of radio-labeled nrdE polypeptide results in binding where the radioactive source molecule is in close proximity to the scintillation fluid Thus, signal is emitted upon nrdE polypeptide binding and compounds that prevent nrdE polypeptide self-association or an association of nrdE polypeptide and another polypeptide or small molecule will diminish signal
  • ICS biosensors have been described by AMBRI (Australian Membrane Biotechnology Research Institute) They couple the self-association of macromolecules to the closing of gramacidin- facilitated ion channels in suspended membrane bilayers and hence to a measurable change in the admittance (similar to impedence) of the biosensor This approach is linear over six decades of admittance change and is ideally suited for large scale, high through-put screening of small molecule combinatorial libraries
  • a polypeptide and/or polynucleotide of tlie mvention compnsmg contacting a polypeptide and/or polynucleotide of the mvention with a compound to be screened under conditions to permit bmdmg to or other mteraction between the compound and tlie polypeptide and/or polynucleotide to assess the bmdmg to or other mteraction with the compound
  • such bmdmg or mteraction preferably bemg associated with a second component capable of providmg a detectable signal m response to the bmdmg or mteraction of the polypeptide and/or pohnucleotide with tlie compound, and determining whether the compound bmds to or otherwise mteracts with and activates or inhibits an
  • nrdE molecule can be labeled, such as by radioactivity or a colonmetnc compound, such that the number of nrdE molecules bound to a bmdmg molecule or converted to product can be determined accurately to assess tlie effectiveness of the potential antagomst
  • Potential antagonists mclude, among others, small orgamc molecules, peptides, polypeptides and antibodies that bmd to a polynucleotide and/or polypeptide of the mvention and thereby inhibit or extinguish its activity or expression
  • Potential antagorasts also may be small orgamc molecules, a peptide, a polypeptide such as a closely related protem or antibody that binds the same sites on a bmdmg molecule, such as a bmdmg molecule, without mducmg nrdE-induced activities, thereby preventmg the action or expression of nrdE polypeptides and/or polynucleotides by excluding nrdE polypeptides and/or polynucleotides from bmdmg
  • Potential antagonists m clude a small molecule that bmds to and occupies the bmdmg site of the polypeptide thereby preventmg bmdmg to cellular bmdmg molecules, such that normal biological activity is prevented
  • small molecules mclude but are not lmnted to small organic molecules, peptides or peptide-like molecules
  • Other potential antagonists m clude antisense molecules (see Okano, J Neurochem 56 560 (1991).
  • Preferred potential antagorasts m include compounds related to and vanants of nrdE
  • polypeptide antagonists include antibodies or, m some cases. ohgonucleotides or proteins which are closely related to the ligands. substrates, receptors, enzymes, etc . as the case may be, of tlie polypeptide, e g . a fragment of the ligands. substrates, receptors, enzymes, etc . or small molecules which bmd to the polypeptide of tlie present mvention but do not elicit a response, so that the activity of the polypeptide is prevented
  • polypeptides of the mvention are biomimetics.
  • functional mimetics of tlie natural nrdE polypeptide These functional mimetics may be used for. among other things, antagonizing the activity of nrdE polypeptide or as a antigen or lmmunogen m a manner described elsewhere herem
  • Functional mimetics of the polypeptides of the mvention m clude but are not limited to truncated polypeptides
  • preferred functional mimetics mclude. a polypeptide compnsmg the polypeptide sequence set forth m SEQ ID NO 2 lacking 20, 30. 40. 50.
  • polynucleotides encodmg each of these functional mimetics may be used as expression cassettes to express each mimetic polypeptide It is preferred that these cassettes compnse 5' and 3' restnction sites to allow for a convenient means to hgate the cassettes together when desired It is further preferred that these cassettes compnse gene expression signals known m the art or descnbed elsewhere herem
  • the present invention relates to a screening kit for identifying agonists antagonists, ligands. receptors, substrates, enzymes, etc for a polypeptide and/or polynucleotide of the present invention, or compounds which decrease or enhance the production of such polypeptides and/or polynucleotides which comprises (a) a polypeptide and/or a polynucleotide of the present invention, (b) a recombinant cell expressing a polypeptide and/or polynucleotide of the present invention, (c) a cell membrane expressing a polypeptide and/or polynucleotide of the present invention, or (d) antibody to a polypeptide and/or polynucleotide of the present invention, which polypeptide is preferably that of SEQ ID NO 2. and which polynucleotide is preferably that of SEQ ID NO 1
  • kits may comprise a substantial component
  • a polypeptide and/or polynucleotide of the present invention may also be used m a method for the structure-based design of an agonist, antagonist or inhibitor of the polypeptide and/or polynucleotide.
  • tlie present mvention provides methods of treatmg abnormal conditions such as. for mstance, a Disease, related to either an excess of. an under-expression of, an elevated activity of, or a decreased activity of nrdE polypeptide and/or polynucleotide
  • tlie expression and/or activity of the polypeptide and/or polynucleotide is m excess
  • several approaches are available
  • One approach composes administering to an mdividual in need tliereof an inhibitor compound (antagomst) as herem descnbed, optionally m combmation with a pharmaceutically acceptable earner, in an amount effective to inhibit the function and/or expression of tlie polypeptide and/or polynucleotide.
  • an inhibitor compound as herem descnbed
  • optionally m combmation with a pharmaceutically acceptable earner in an amount effective to inhibit the function and/or expression of tlie polypeptide and/or polynucleotide.
  • tlie polypeptide and/or polynucleotide such as. for example, by blocking tlie bmdmg of ligands.
  • soluble forms of the polypeptides still capable of binding the hgand. substrate, enzymes, receptors, etc in competition with endogenous polypeptide and/or polynucleotide may be administered Typical examples of such competitors include fragments of the nrdE polypeptide and/or polypeptide
  • the present invention relates to genetically engineered soluble fusion proteins comprising a polypeptide of the present invention, or a fragment thereof, and various portions of the constant regions of heavy or light chains of immunoglobuhns of various subclasses (IgG, IgM. IgA. IgE) Preferred as an lmmunoglobuhn is the constant part of the heavy chain of human IgG, particularly IgG 1.
  • the Fc part can be removed simply by incorporation of a cleavage sequence which can be cleaved with blood clotting factor Xa
  • this invention relates to processes for the preparation of these fusion proteins by genetic engineering, and to the use thereof for drug screening, diagnosis and therapy
  • a further aspect of the invention also relates to polynucleotides encoding such fusion proteins Examples of fusion protem technology can be found in International Patent Application Nos W094/29458 and W094/22914
  • expression of the gene encoding endogenous nrdE polypeptide can be inhibited using expression blocking techniques This blocking may be targeted agamst any step m gene expression, but is preferably targeted agamst transcription and/or translation
  • An examples of a known technique of this sort involve the use of antisense sequences, either internally generated or separately administered (see.
  • each of the polynucleotide sequences provided herein may be used in the discovery and clopment of antibacterial compounds
  • the encoded protein upon expression, can be used as a target for the screening of antibacterial drugs
  • the polynucleotide sequences encoding the amino terminal regions of the encoded protem or Shine-Delgarno or other translation facilitating sequences of the respective mRNA can be used to construct antisense sequences to control the expression of the coding sequence of interest
  • the invention also provides the use of the polypeptide, polynucleotide. agonist or antagonist of the invention to interfere with the initial physical interaction between a pathogen or pathogens and a cukary otic preferably mammalian, host responsible for sequelae of infection
  • the molecules of the invention may be used in the prevention of adhesion of bacteria, in particular gram positive and/or gram negative bacteria, to eukarvotic.
  • eukarvotic preferably mammalian, extracellular matrix proteins on in-dwelling devices or to extracellular matrix proteins m wounds, to block bacterial adhesion between eukarvotic.
  • mammalian, extracellular matrix proteins and bacterial nrdE proteins that mediate tissue damage and/or, to block the normal progression of pathogenesis in infections initiated other than by the implantation of in-dwelling devices or by other surgical techniques
  • nrdE agonists and antagonists preferably bactenstatic or bactencidal agonists and antagorasts
  • the antagonists and agomsts of the mvention may be employed, for instance, to prevent, inhibit and/or treat diseases
  • H pylori Helicobacter pylori bacteria infect the stomachs of over one-third of the world's population causing stomach cancer, ulcers, and gastritis (International Agency for Research on Cancer (1994) Schistosomes Liver Flukes and Helicobacter Pylori (International Agency for Research on Cancer. Lyon.
  • H pylori infection should decrease the advent of H pylori - ⁇ uce ⁇ cancers, such as gastrointestinal carcinoma
  • Such treatment should also prevent, inhibit and/or cure gastric ulcers and gastritis
  • Another aspect of the invention relates to a method for inducing an immunological response in an individual, particularly a mammal which comprises inoculating the individual with nrdE polynucleotide and/or polypeptide, or a fragment or variant thereof, adequate to produce antibody and/ or T cell immune response to protect said individual from infection, particularly bacterial infection and most particularly Staphylococcus aureus infection Also provided are methods whereby such immunological response slows bacterial replication
  • Yet another aspect of the invention relates to a method of inducing immunological response in an individual which comprises delivering to such individual a nucleic acid vector, sequence or ribozyme to direct expression of nrdE polynucleotide and/or polypeptide, or a fragment or a variant thereof, for expressing nrdE polynucleotide and/or polypeptide.
  • nucleic acid vector may comprise DNA.
  • a further aspect of the invention relates to an immunological composition that when introduced into an individual, preferably a human, capable of having induced within it an immunological response, induces an immunological response m such individual to a nrdE polynucleotide and/or polypeptide encoded therefrom, wherein the composition comprises a recombinant nrdE polynucleotide and/or polypeptide encoded therefrom and/or comprises DNA and/or RNA which encodes and expresses an antigen of said nrdE polynucleotide polypeptide encoded therefrom, or other polypeptide of the invention
  • the immunological response may be used therapeutically or prophylactically and may take the form of antibody immunity and/or cellular immunity, such as cellular immunity arising from CTL or CD4+ T cells
  • a nrdE polypeptide or a fragment thereof may be fused with co-protein or chemical moiety which ma ⁇ or not bv itself produce antibodies but which is capable of stabilizing the first protein
  • the co-protein may act as an adjuvant in the sense of providing a generalized stimulation of the immune system of the organism receiving the protein Th co-protem be attached to either the amino- or carbow -terminus of the first protein
  • compositions particularly vaccine compositions, and methods comprising the polypeptides and or polynucleotides of the invention and immunostimulatory DNA sequences, such as those described in Sato. Y et al Science 273 352 (1996)
  • polynucleotide constructs used m such genetic immunization experiments in animal models of infection with Staphylococcus aureus Such experiments will be particularly useful for identifying protein epitopes able to provoke a prophylactic or therapeutic immune response It is believed that this approach will allow for the subsequent preparation of monoclonal antibodies of particular value, derived from the requisite organ of the animal successfully resisting or clearing infection, for the development of prophylactic agents or therapeutic treatments of bacterial infection, particularly Staphylococcus aureus infection, in mammals, particularly humans
  • a poly peptide of the invention may be used as an antigen for vaccination of a host to produce specific antibodies which protect against invasion of bacteria, for example by blocking adherence of bacteria to damaged tissue
  • tissue damage include wounds in skm or connective tissue caused, for example, by mechanical, chemical, thermal or radiation damage or by implantation of indwelling devices, or wounds in the mucous membranes, such as the mouth, throat, mammary glands, urethra or vagina
  • the invention also includes a vaccine formulation which comprises an lmmunogemc recombinant polypeptide and/or polynucleotide of the invention together with a suitable carrier, such as a pharmaceutically acceptable carrier Since the polypeptides and polynucleotides may be broken down m the stomach, each is preferably administered parenterally, including, for example, administration that is subcutaneous, intramuscular, intravenous, or mtradermal
  • Formulations suitable for parenteral administration include aqueous and non-aqueous sterile injection solutions which may contain anti- oxidants buffers bacteristatic compounds and solutes which render the formulation isotomc with the bodily fluid, preferably the blood, of the individual, and aqueous and non-aqueous sterile suspensions which may include suspending agents or thickening agents
  • the formulations may be presented in unit- dose or multi-dose containers, for example, sealed ampoules and vials and may be stored in a freeze- d ⁇ ed condition requiring
  • compositions for purposes of compositions, kits and administration
  • compositions compnsmg a nrdE polynucleotide and or a nrdE polypeptide for administration to a cell or to a multicellular orgamsm
  • Tlie mvention also relates to compositions compnsmg a polynucleotide and/or a polypeptides discussed herem or their agonists or antagorasts
  • Tlie polypeptides and polynucleotides of the mvention may be employed m combmation with a non-stenle or stenle earner or carriers for use with cells, tissues or organisms, such as a pharmaceutical earner suitable for administration to an individual
  • Such earners may mclude but are not limited to. salme. buffered salme.
  • the mvention further relates to diagnostic and pharmaceutical packs and kits compnsmg one or more containers filled with one or more of the ingredients of the aforementioned compositions of the mvention
  • Polypeptides polynucleotides and other compounds of tlie mvention may be employed alone or m conjunction with other compounds, such as therapeutic compounds
  • the pharmaceutical compositions may be administered in any effective, convenient manner mcludmg, for instance, administration by topical, oral. anal, vagmal. mtravenous. mtrapentoneal. intramuscular, subcutaneous, mtranasal or lntradermal routes among others
  • the active agent may be administered to an individual as an liijectable composition, for example as a sterile aqueous dispersion, preferably isotomc
  • the composition may be formulated for topical application for example in the form of ointments, creams, lotions, eye ointments, eye drops, ear drops, mouthwash, impregnated dressings and sutures and aerosols, and may contain appropriate conventional additives, including, for example, preservatives, solvents to assist drug penetration, and emollients m ointments and creams
  • Such topical formulations may also contain compatible conventional carriers, for example cream or ointment bases, and ethanol or oleyl alcohol for lotions
  • Such carriers may constitute from about 1% to about 98% by weight of the formulation, more usually they will constitute up to about 80% by weight of the formulation hi a further aspect, the present mvention provides for pharmaceutical compositions compnsmg a therapeutically effective amount of a polypeptid
  • tlie soluble fonn of a polypeptide and/or polynucleotide of the present mvention agomst or antagonist peptide or small molecule compound, m combination with a pharmaceutically acceptable earner or excipient
  • earners mclude, but are not limited to. saline, buffered salme. dextrose, water, glycerol, ethanol, and combmations thereof
  • the mvention further relates to pharmaceutical packs and kits compnsmg one or more containers filled with one or more of tlie ingredients of the aforementioned compositions of tlie mvention Polypeptides, polynucleotides and other compounds of the present mvention may be employed alone or m conjunction with other compounds, such as therapeutic compounds
  • Tlie composition will be adapted to the route of administration, for instance by a systemic or an oral route
  • Preferred forms of systemic administration mclude mjection, typically by mtravenous injection
  • Other injection routes such as subcutaneous, mtramuscular. or mtrapentoneal.
  • transmucosal and transdermal administration usmg penetrants such as bile salts or fusidic acids or other detergents
  • oral administration may also be possible
  • Administration of these compounds may also be topical and or localized, m the form of salves, pastes, gels, and the like
  • the daily dosage level of the active agent will be from 0 01 mg/kg to 10 mg/kg, typically around 1 mg/kg
  • the physician in any event will determine the actual dosage which will be most suitable for an individual and will vary with the age, weight and response of the particular individual
  • the above dosages are exemplary of the average case There can, of course, be individual instances where higher or lower dosage ranges are merited, and such are within the scope of this invention
  • In-dwelling devices include surgical implants, prosthetic devices and catheters. 1 e . devices that are introduced to the body of an individual and remain in position for an extended time Such devices include, for example, artificial joints, heart valves, pacemakers, vascular grafts, vascular catheters. cerebrospmal fluid shunts, urinary catheters, continuous ambulatory peritoneal dialysis (CAPD) catheters
  • composition of the invention may be administered by injection to achieve a systemic effect against relevant bacteria shortly before insertion of an m-dwelhng device Treatment may be continued after surgery during the m-body time of the device
  • composition could also be used to broaden pe ⁇ operative cover for any surgical technique to prevent bacterial wound infections, especially
  • compositions of this invention may be used generally as a wound treatment agent to prevent adhesion of bacteria to matrix proteins exposed m wound tissue and for prophylactic use in dental treatment as an alternative to. or in conjunction with, antibiotic prophylaxis
  • the composition of the invention may be used to bathe an indwelling device immediately before insertion
  • the active agent will preferably be present at a concentration of l ⁇ g/ml to lOmg/ml for bathing of wounds or indwelling devices
  • a vaccine composition is conveniently in injectable form
  • Conventional adjuvants may be employed to enhance the immune response
  • a suitable unit dose for vaccination is 0 5-5 microgram/kg of antigen, and such dose is preferably administered 1 -3 times and with an interval of 1 -3 weeks With the indicated dose range, no adverse toxicological effects will be observed with the compounds of the invention which would preclude their administration to suitable individuals Sequence Databases, Sequences in a Tangible Medium, and Algorithms
  • Polynucleotide and polypeptide sequences form a valuable information resource with which to determine their 2- and 3 -dimensional structures as well as to identify further sequences of similar homology
  • These approaches are most easily facilitated by storing tlie sequence m a computer readable medium and then usmg tlie stored data m a known macromolecular structure program or to search a sequence database usmg well known searching tools, such as GCC
  • polynucleotide and polypeptide sequences of the invention are particularly useful as components in databases useful for search analyses as well as m sequence analysis algorithms
  • sequence databases Sequences in a Tangible Medium, and Algorithms As used in this section entitled "Sequence Databases Sequences in a Tangible Medium, and Algorithms.” and in claims related to this section, the terms “polynucleotide of the invention” and “polynucleotide sequence of the invention” mean any detectable chemical or physical characteristic of a polynucleotide of the invention that is or may be reduced to or stored in a tangible medium, preferably a computer readable form For example, chromatographic scan data or peak data, photographic data or scan data therefrom, called bases, and mass spectrographic data
  • polypeptide of the invention and polypeptide sequence of the invention mean any detectable chemical or physical characteristic of a polypeptide of the invention that is or may be reduced to or stored in a tangible medium, preferably
  • methods for the analy sis of character sequences or strings particularly genetic sequences or encoded genetic sequences
  • Preferred methods of sequence analysis include, for example, methods of sequence homology analysis, such as identity and similarity analysis, RNA structure analysis, sequence assembly, cladistic analysis, sequence motif analysis, open reading frame determination, nucleic acid base calling, nucleic acid base trimming, and sequencing chromatogram peak analysis
  • a computer based method for performing homology identification This method comprises the steps of providing a first polynucleotide sequence comprising the sequence a polynucleotide of the invention in a computer readable medium, and comparing said first polynucleotide sequence to at least one second polynucleotide or polypeptide sequence to identify homology
  • a computer based method for performing homology identification, said method comprising the steps of providing a first polypeptide sequence comprising the sequence of a polypeptide of the invention in a computer readable medium, and comparing said first polypeptide sequence to at least one second polynucleotide or polypeptide sequence to identify homology
  • a computer based method is still further provided for polynucleotide assembly, said method comprising the steps of providing a first polynucleotide sequence comprising the sequence of a polynucleotide of the invention in a computer readable medium, and screening for at least one overlapping region between said first polynucleotide sequence and at least one second polynucleotide or polypeptide sequence
  • a computer based method is still further provided for polynucleotide assembly, said method comprising the steps of providing a first polypeptide sequence comprising a polypeptide of the invention in a computer readable medium, and screening for at least one overlapping region between said first polypeptide sequence and at least one second polynucleotide or polypeptide sequence hi another preferred embodiment of die mvention there is provided a computer readable medium having stored thereon a member selected from the group consisting of a polynucleotide comprising the sequence of SEQ ID NO 1, a polypeptide comprising the sequence of SEQ ID NO 2, a set of polynucleotide sequences wherein at least one of said sequences comprises the sequence of SEQ ID NO 1 , a set of polypeptide sequences wherein at least one of said sequences comprises the sequence of SEQ ID NO 2, a data set representing a polynucleotide sequence comprising the sequence of SEQ ID NO 1 , a data set representing a polynucleotide sequence
  • a polynucleotide comprising the sequence of SEQ ID NO 1, a polypeptide comprising the sequence of SEQ ID NO 2.
  • a set of polynucleotide sequences wherein at least one of said sequences comprises the sequence of SEQ ID NO 1
  • a set of polypeptide sequences wherein at least one of said sequences comprises the sequence of SEQ ID NO 2.
  • a further preferred embodiment of the invention provides a computer based method for performing homology identification, said method comprising the steps of providing a polynucleotide sequence comprising the sequence of SEQ ID NO 1 a computer readable medium, and comparing said polynucleotide sequence to at least one polynucleotide or polypeptide sequence to identify homology
  • a still further preferred embodiment of the invention provides a computer based method for performing homolog ⁇ identification, said method comprising the steps of providing a polypeptide sequence comprising the sequence of SEQ ID NO 2 in a computer readable medium, and comparing said poly peptide sequence to at least one polynucleotide or polypeptide sequence to identify homology
  • a further embodiment of the invention provides a computer based method for polynucleotide assembly, said method comprising the steps of providing a first polynucleotide sequence comprising the sequence of SEQ ID NO 1 in a computer readable medium, and screening for at least one overlapping region between said first polynucleotide sequence and a second polynucleotide sequence
  • a further embodiment of the invention provides a computer based method for performing homology identification, said method comprising the steps of providing a polynucleotide sequence comprising the sequence of SEQ ID NO 1 in a computer readable medium, and comparing said polynucleotide sequence to at least one polynucleotide or polypeptide sequence to identify homology
  • ant ⁇ body( ⁇ es) as used herein includes polyclonal and monoclonal antibodies, chime ⁇ c. single chain, and humanized antibodies, as well as Fab fragments, including the products of an Fab or other lmmunoglobuhn expression library
  • Antigemcally equivalent de ⁇ vat ⁇ ve(s) encompasses a polypeptide, polynucleotide. or the equivalent of either which will be specifically recognized by certain antibodies which, when raised to the protem, polypeptide or polynucleotide according to the invention, interferes with the immediate physical interaction between pathogen and mammalian host
  • Bispecific ant ⁇ body( ⁇ es) means an antibody comprising at least two antigen binding domains, each domain directed against a different epitope
  • Bodily mate ⁇ al(s) means any matenal denved from an individual or from an orgamsm infecting, infesting or inhabiting an individual, mcludmg but not limited to, cells, tissues and waste, such as. bone, blood, serum, cerebrospmal fluid, semen, saliva, muscle, cartilage, organ tissue, skin, urine, stool or autopsy matenals
  • D ⁇ sease(s) means any disease caused by or related to infection by a bactena. mcludmg , for example, disease, such as. infections of the upper respiratory tract (e g , otitis media, bactenal tracheitis. acute epiglottitis, thyroiditis). lower respiratory (e g . empyema. lung abscess), cardiac (e g . infective endocarditis), gastromtestmal (e g . secretory diarrhoea, splemc absces, retropentoneal abscess), CNS (e g . cerebral abscess), eye (e g . blephantis.
  • infections of the upper respiratory tract e g , otitis media, bactenal tracheitis. acute epiglottitis, thyroiditis.
  • lower respiratory e g . empyema. lung abscess
  • cardiac e g . infective end
  • kidney and urinary tract e g . epididymitis. mtrarenal and pennephnc absces, toxic shock syndrome
  • skin e g . impetigo, follicuhtis. cutaneous abscesses, cellulitis. wound infection, bactenal myositis
  • bone and joint e g . septic arthntis. osteomyelitis
  • Fusion prote ⁇ n(s) refers to a protein encoded by two. often unrelated, fused genes or fragments thereof
  • EP-A-0464 discloses fusion proteins comprising various portions of constant region of lmmunoglobu n molecules together with another human protein or part thereof
  • employing an lmmunoglobuhn Fc region as a part of a fusion protein is advantageous for use in therapy and diagnosis resulting in, for example, improved pharmacokinetic properties [see, e g , EP-A 0232262]
  • “Host cell(s)” is a cell which has been transformed or transfected, or is capable of transformation or transfection by an exogenous polynucleotide sequence
  • Identity as known m tlie 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
  • identity also means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as the case may be, as determined by the match between strings of such sequences
  • Identity can be readily calculated by known methods, including but not limited to those described in (Computational Molecular Biology. Lesk. A M , ed . Oxford University Press, New York. 1988. Biocomputing Informatics and Genome Projects. Smith, D W , ed . Academic Press. New York, 1993.
  • Parameters for polypeptide sequence comparison include the following Algorithm Needleman and Wunsch, J Mol Biol 48 443-453 (1970) Comparison matrix BLOSSUM62 from Hentikoff and Hentikoff. Proc Natl Acad Sci USA 89 10915-10919 (1992) Gap Penalty 12 Gap Length Penalty 4 A program useful with these parameters is publicly available as the "gap" program from Genetics Computer Group. Madison WI The aforementioned parameters are the default parameters for peptide comparisons (along with no penalty for end gaps)
  • Polynucleotide embodiments further include an isolated polynucleotide comprising a polynucleotide sequence having at least a 50. 60, 70. 80, 85, 90, 95. 97 or 100% identity to the reference sequence of SEQ ID NO 1. wherein said polynucleotide sequence may be identical to the reference sequence of SEQ ID NO 1 or may include up to a certain integer number of nucleotide alterations as compared to the reference sequence, wherein said alterations are selected from the group consisting of at least one nucleotide deletion, substitution, including transition and transversion.
  • alterations may occur at the 5' or 3' terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among the nucleotides in the reference sequence or m one or more contiguous groups withm the reference sequence, and wherein said number of nucleotide alterations is determined by multiplying the total number of nucleotides in SEQ ID NO 1 by the integer defining the percent identity divided by 100 and then subtracting 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 50 for 50% 0 60 for 60%. 0 70 for 70%. 0 80 for 80%. 0 85 for 85%. 0 90 for 90%. 0 95 for 95%. 0 97 for 97% or 1 00 for 100%.
  • any non-integer product of x n and y is rounded down to the nearest integer prior to subtracting it from x n
  • Alterations of a pohnucleotide sequence encoding the polypeptide of SEQ ID NO 2 may create nonsense, nnssense or frameshift mutations in this coding sequence and thereby alter the polypeptide encoded by the polynucleotide following such alterations
  • a polynucleotide sequence of the present invention may be identical to the reference sequence of SEQ ID NO 1. that is it may be 100% identical, or it may include up to a certain integer number of nucleic acid alterations as compared to the reference sequence such that the percent identity is less than 100% identity
  • Such alterations are selected from the group consisting of at least one nucleic acid deletion, substitution, including transition and transversion, or insertion, and wherein said alterations may occur at the 5' or 3' terminal positions of the reference polynucleotide sequence or anywhere between those ten nal positions, interspersed either individually among the nucleic acids in the reference sequence or in one or more contiguous groups within the reference sequence
  • the number of nucleic acid alterations for a given percent identity is deten ned by multiplying the total number of nucleic acids in SEQ ID NO 1 by the integer defining the percent identity divided by 100 and then subtracting that product from said total number of nucleic acids m SEQ ID NO 1, or
  • n n is the number of nucleic acid alterations.
  • x n is the total number of nucleic acids in SEQ ID NO 1
  • y is, for instance 0 70 for 70%. 0 80 for 80%. 0 85 for 85% etc .
  • • is the symbol for the multiplication operator, and wherein any non-integer product of x n and y is rounded down to the nearest integer prior to subtracting it from x n
  • Polypeptide embodiments further include an isolated polypeptide comprising a polypeptide having at least a 50,60, 70. 80. 85, 90, 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 ammo acid alterations as compared to the reference sequence, wherein said alterations are selected from the group consisting of at least one amino acid deletion, substitution, including conservative and non-conservative substitution, or insertion, and wherein said alterations may occur at the amino- or carboxy-terminal positions of the reference polypeptide sequence or anywhere between those terminal positions, interspersed either individually among the ammo acids in the reference sequence or in one or more contiguous groups withm the reference sequence, and wherein said number of ammo acid alterations is determined by multiplying the total number of ammo acids in SEQ ID NO 2 b ⁇ the integer defining the percent identity divided by 100 and then subtracting that product from said total
  • n a is the number of amino acid alterations
  • x a is the total number of amino acids m SEQ ID NO 2
  • y is 0 50 for 50%, 0 60 for 60%. 0 70 for 70%, 0 80 for 80%, 0 85 for 85%, 0 90 for 90%, 0 95 for 95%, 0 97 for 97% or 1 00 for 100%
  • • is the symbol for the multiplication operator, and wherein any non-integer product of x a and y is rounded down to the nearest integer prior to subtracting
  • a polypeptide sequence of the present invention may be identical to the reference sequence of SEQ ID NO 2, that is it may be 100% identical, or it may include up to a certain integer number of amino acid alterations as compared to the reference sequence such that the percent identity is less than 100% identity
  • Such alterations are selected from the group consisting of at least one ammo acid deletion, substitution, including conservative and non-conservative substitution, or insertion, and wherein said alterations may occur at the amino- or carboxy-terminal positions of the reference polypeptide sequence or anywhere between those terminal positions, interspersed either individually among the ammo acids in the reference sequence or m one or more contiguous groups within the reference sequence
  • the number of amino acid alterations for a given % identity is determined by multiplying the total number of ammo acids m SEQ ID NO 2 by the integer defining the percent identity divided by 100 and then subtracting that product from said total number of amino acids in SEQ ID NO 2, or
  • n a is the number of amino acid alterations.
  • x a is the total number of ammo acids in SEQ ID NO 2
  • y is. for instance 0 70 for 70%. 0 80 for 80%. 0 85 for 85% etc
  • • is the symbol for the multiplication operator and wherein any non-mteger product of x a and y is rounded down to the nearest integer prior to subtracting it from x a
  • “lmmunologically equivalent de ⁇ vat ⁇ ve(s)” as used herein encompasses a polypeptide polynucleotide. or the equivalent of either which when used in a suitable formulation to raise antibodies in a vertebrate, the antibodies act to interfere with the immediate physical interaction between pathogen and mammalian host "Immunospecific' " means that characteristic of an antibody whereby it possesses substantially greater affinity for the polypeptides of the mvention or the polynucleotides of the invention than its affinity for other related polypeptides or polynucleotides respectively, particularly those polypeptides and polynucleotides in the pnor art.
  • “Individual(s)” means a multicellular eukaryote. mcludmg. but not limited to a metazoan, a mammal, an ovid. a bovid. a simian, a primate, and a human.
  • Isolated means altered “by the hand of man” from its natural state, ; e., if it occurs m nature, it has been changed or removed from its original environment, or both
  • a polynucleotide or a polypeptide naturally present in a livmg organism is not “isolated,” but the same polynucleotide or polypeptide separated from the coexistmg materials of its natural state is “isolated", as the term is employed herem.
  • a polynucleotide or polypeptide that is introduced into an organism by transformation, genetic manipulation or by any other recombinant method is "isolated” even if it is still present in said organism, which organism may be living or non-living.
  • Organism(s) means a (I) prokaryote.
  • mcludmg but not limited to, a member of the genus Streptococcus, Staphylococcus, Bordetella, Corynebacterium, Mycobacterium, Neissena, Haemophilus, Actinomycetes, Streptomycetes, Nocardia, Enterobacter, Yersinia, Fancisella, Pasturella, Moraxella, Acinetobacter, Erysipelothnx, Branhamella, Actinobacillus, Streptobacillus, Listeria, Calymmatobactenum, Brucella, Bacillus, Clostndium, Treponema, Eschenchia, Salmonella, Kleibsiella, Vibrio, Proteus.
  • Group A Streptococcus Group B Streptococcus, Group C Streptococcus, Group D Streptococcus, Group G Streptococcus, Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus agalactiae, Streptococcus faecabs, Streptococcus faecium, Streptococcus durans.
  • Neissena gonorrheae Neissena menmgitidis, Staphylococcus aureus, Staphylococcus ep dermidis, Corynebacterium diptheriae, Gardnerella vaginabs, Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium ulcerans, Mycobacterium leprae, Actinomyctes israelu, Listeria monocytogenes, Bordetella pertusis, Bordatella parapertusis, Bordetella bronchiseptica, Eschenchia cob, Shigella dysentenae, Haemophilus mfluenzae, Haemophilus aegypt us, Haemophilus parainfluenzae, Haemophilus ducrey , Bordetella, Salmonella typhi, Citrobacter freundn.
  • Proteus mirabibs Proteus vulga ⁇ s, Yersinia pestis, Kleibsiella pneumoniae, Serratia marcessens, Serratia bquefaciens, Vibrio cholera, Shigella dysenterii, Shigella flexnen, Pseudomonas aeruginosa, Franscisella tularensis, Brucella aborbs, Bacillus anthracis, Bacillus cereus Clostndium perfrmgens.
  • Polynucleot ⁇ de(s) generally refers to any polynbonucleotide or polydeoxynbonucleotide, which 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 tnple-stranded regions, smgle- and double-stranded RNA, and RNA that is mixture of smgle- and double-stranded regions, hybnd molecules compnsmg DNA and RNA that may be single-stranded or, more typically, double-stranded, or tnple-stranded regions, or a mixture of smgle- and double-stranded regions
  • polynucleotide as used herem refers to tnple-stranded regions compn
  • Polynucleot ⁇ de(s) also embraces short polynucleotides often referred to as ohgonucleot ⁇ de(s)
  • Polypept ⁇ de(s) refers to any peptide or protem compnsmg two or more amino acids jomed to each other by peptide bonds or modified peptide bonds
  • Polypept ⁇ de(s) refers to both short chams, commonly referred to as peptides, ohgopeptides and ohgomers and to longer chams generally referred to as protems
  • Polypeptides may contain ammo acids other than the 20 gene encoded amino acids
  • Polypept ⁇ de(s)” mclude those modified either by natural processes, such as processmg and oilier post-translational modifications, but also by chemical modification techniques Such modifications are well descnbed m basic texts and m more detailed monographs, as well as m a volummous research literature, and they are well known to those of skill m the art It will be appreciated that the same type of modification may be present m the same or varying degree at several sites m a given polypeptide Also, a given polypeptide may contain
  • mcludmg the peptide backbone, the ammo acid side-chams. and tlie ammo or carboxyl termini Modifications mclude. for example, acetylation. acvlation. 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 de ⁇ vative covalent attachment of phosphotidylinositol, cross-linking, cychzation, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, fonnylation, gamma-carboxylation, GPI anchor formation, hydroxylation, lodination. methylation, mynstoylation, oxidation, proteolytic processmg. phosphorylation. prenylation, racemization, glycosylation.
  • 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 well
  • Recombinant expression system(s) refers to expression systems or portions thereof or polynucleotides of tlie mvention mtroduced or transformed mto a host cell or host cell lysate for the production of tlie polynucleotides and polypeptides of the mvention
  • “Subtraction set” is one or more, but preferably less than 100, polynucleotides comprising at least one polynucleotide of the invention
  • 'Na ⁇ ant(s) ' as the tenn is a polynucleotide or polypeptide that differs from a reference polynucleotide or polypeptide respectively, but retains essential properties
  • a typical vanant of a polynucleotide differs in nucleotide sequence from another, reference polynucleotide Changes m the nucleotide sequence of the variant may or may not alter the amino acid sequence of a polypeptide encoded by the reference polynucleotide Nucleotide changes may result in amino acid substitutions, additions, deletions, fusion protems and truncations in the polypeptide encoded by the reference sequence, as discussed below
  • a typical variant of a polypeptide differs in ammo acid sequence from another reference polypeptide Generally, differences are limited so that the sequences of the reference polypeptide and the variant are closely similar overall and.
  • a variant and reference polypeptide may differ in ammo acid sequence by one or more substitutions, additions, deletions m any combination A substituted or inserted amino acid residue may or may not be one encoded by the genetic code
  • the present mvention also mcludes mclude vanants of each of the polypeptides of the mvention. that is polypeptides that vary from the referents by conservative ammo acid substitutions, whereby a residue is substituted by another with like charactenstics Typical such substitutions are among Ala. Val. Leu and He. among Ser and Thr.
  • a variant of a polynucleotide or polypeptide may be a naturally occurring such as an allehc variant, or it may be a variant that is not known to occur naturally
  • Non-naturally occurring variants of polynucleotides and polypeptides may be made by mutagenesis techniques, by direct synthesis, and by other recombinant methods known to skilled artisans EXAMPLES
  • the polynucleotide having a DNA sequence given in Table 1 [SEQ ID NO 1] was obtained from a library of clones of chromosomal DNA of Staphylococcus aureus m E cob
  • the sequencing data from two or more clones containing overlapping Staphylococcus aureus DNAs was used to construct the contiguous DNA sequence in SEQ ID NO 1 Libraries may be prepared by routine methods, for example
  • Total cellular DNA is isolated from Staphylococcus aureus WCUH 29 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 according to standard procedures
  • DNA fragments of up to 1 lkbp in size are rendered blunt by treatment with exonuclease and DNA polymerase. and EcoRI linkers added Fragments are hgated into the vector Lambda ZapII that has been cut with EcoRI.
  • the library 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 cloning into library vectors (e g , Rsal. Pall. Alul, Bshl235I), and such fragments are size-fractionated according to standard procedures EcoRI linkers are ligated to the DNA and the fragments then ligated into the vector Lambda ZapII 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

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Abstract

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

Description

nrdE
FIELD OF THE INVENTION
This u ention relates to newly identified polynucleotides and polypeptides. and their production and uses, as well as their vanants, agonists and antagonists, and their uses In particular, the invention relates to polynucleotides and polypeptides of the nbonucleotide diphosphate reductase family, as well as their vanants, hereinafter referred to as "nrdE," "nrdE pofynucleotιde(s)," and "nrdE polypeptιde(s)" as tlie case may be
BACKGROUND OF THE INVENTION
It is particularly preferred to employ Staphylococcal genes and gene products as targets for the development of antibiotics The Staphylococci make up a medically important genera of microbes They are known to produce two types of disease, invasive and toxigenic Invasive infections are charactenzed generally by abscess formation effectmg both skin surfaces and deep tissues Staphylococcus aureus is the second leading cause of bacteremia in cancer patients Osteomyelitis, septic arthntis, septic thrombophlebitis and acute bactenal endocarditis are also relatively common There are at least three clinical conditions resulting from the toxigenic properties of Staphylococci Tlie manifestation of these diseases result from the actions of exotoxins as opposed to tissue invasion and bacteremia These conditions include Staphylococcal food poisoning, scalded skin syndrome and toxic shock syndrome
The frequency of Staphylococcus aureus infections has nsen dramatically in the past few decades This has been attributed to tlie emergence of multiply antibiotic resistant strains and an increasing population of people with weakened immune systems It is no longer uncommon to isolate Staphylococcus aureus strains which are resistant to some or all of the standard antibiotics This phenomenon has created an unmet medical need and demand for new anti-microbial agents, vaccines, drug screening methods, and diagnostic tests for tins organism
Moreover, the drug discovery process is currently undergoing a fundamental revolution as it embraces "functional genomics." that is, high throughput genome- or gene-based biology This approach is rapidly superseding earlier approaches based on "positional cloning" and other methods Functional genomics relies heavily on tlie vanous tools of bioinfonnatics to identify' gene sequences of potential interest from tlie mam molecular biologλ databases now available as well as from other sources There is a continuing and significant need to identify' and charactenze further genes and other polynucleotides sequences and their related polypeptides. as targets for drug discovery Clearly, there exists a need for polynucleotides and pohpeptides, such as the nrdE embodiments of the invention, that have a present benefit of, among other things, being 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 charactenzation of such factors and their antagonists and agonists to find ways to prevent, ameliorate or correct such infection, dysfunction and disease
SUMMARY OF THE INVENTION
The present invention relates to nrdE. in particular nrdE polypeptides and nrdE polynucleotides. recombinant matenals and methods for their production In another aspect, the mvention relates to methods for using such polypeptides and polynucleotides, including treatment of microbial diseases, amongst others In a further aspect, the invention relates to methods for identifying agonists and antagonists using the materials provided by the invention, and for treating microbial infections and conditions associated with such infections with tlie identified agonist or antagonist compounds In a still further aspect, the mvention relates to diagnostic assays for detectmg diseases associated with microbial infections and conditions associated with such infections, such as assays for detecting nrdE expression or activity
Vanous changes and modifications ithin the spmt and scope of tlie disclosed mvention will become readily apparent to those skilled m tlie art from reading tlie follow mg descnptions and from reading the other parts of tlie present disclosure
DESCRIPTION OF THE INVENTION
Tlie mvention relates to nrdE pohpeptides and polynucleotides as descnbed m greater detail below In particular, the mvention relates to polypeptides and polynucleotides of a nrdE of Staphylococcus aureus. which is related by ammo acid sequence homology to nrdE pohpeptide The mvention relates especialh to nrdE havmg the nucleotide and ammo acid sequences set out in Table 1 as SEQ ID NO 1 and SEQ ID NO 2 respectively Note that sequences recited m the Sequence Listing below as "DNA"" represent an exemplification of the invention, since those of ordinary skill w ill recognize that such sequences can be usefully employed in polynucleotides in general, including πbopolynucleotides
TABLE 1 nrdE Polynucleotide and Polypeptide Sequences (A) Staphylococcus aureus nrdE polynucleotide sequence [SEQ ID NO: 1],
5 ' -ATGAAAACCATGGAAGAGAAAAAGTACAATCATATTGAATTAAATAATGA
GGTCACTAAACGAAGAGAAGATGGATTCTTTAGTTTAGAAAAAGACCAAG
AAGCTTTAGTAGCTTATTTAGAAGAAGTAAAAGACAAAACAATCTTCTTC GATACTGAAATCGAGCGTTTACGTTATTTAGTAGACAACGATTTTTATTT
CAATGTGTTTGATATTTATAGTGAAGCGGATCTAATTGAAATCACTGATT
ATGCAAAATCAATCTCGTTTAATTTTGCAAGTTATATGTCAGCTAGTAAA
TTTTTCAAAGATTACGCTTTGAAAACAAATGATAAAAGTCAATACTTAGA
AGACTATAATCAACACGTTGCCATTGTTGCTTTATACCTAGCAAATGGTA ATAAAGCACAAGCTAAACAATTTATTTCTGCTATGGTTGAACAAAGATAT
CAACCAGCGACACCAACATTTTTAAACGCAGGCCGTGCGCGTCGTGGTGA
GCTAGTGTCATGTTTCTTATTAGAAGTGGATGACAGCTTAAATTCAATTA
ACTTTATTGATTCAACTGCAAAACAATTAAGTAAAATTGGGGGCGGCGTT
GCAATTAACTTATCTAAATTGCGTGCACGTGGTGAAGCAATTAAAGGAAT TAAAGGCGTAGCGAAAGGCGTTTTACCTATTGCTAAGTCACTTGAAGGTG
GCTTTAGCTATGCAGATCAACTTGGTCAACGCCCTGGTGCTGGTGCTGTG
TACTTAAATATCTTCCATTATGATGTAGAAGAATTTTTAGATACTAAAAA
AGTAAATGCGGATGAAGATTTACGTTTATCTACAATATCAACTGGTTTAA
TTGTTCCATCTAAATTCTTCGATTTAGCTAAAGAAGGTAAGGACTTTTAT ATGTTTGCACCTCATACAGTTAAAGAAGAATATGGTGTGACATTAGACGA
TATCGATTTAGAAAAATATTATGATGACATGGTTGCAAACCCAAATGTTG
AGAAAAAGAAAAAGAA GCGCGTGAAA GT GAAT ATTGCGCAAACA
CAATTACAATCAGGTTATCCATATTTAATGTTTAAAGATAATGCTAACAG
AGTGCATCCGAATTCAAACATTGGACAAATTAAAATGAGTAACTTATGTA CGGAAATTTTCCAACTACAAGAAACTTCAATTATTAATGACTATGGTATT
GAAGACGAAATTAAACGTGATATTTCTTGTAACTTGGGCTCATTAAATAT
TGTTAATGTAATGGAAAGCGGAAAATTCAGAGATTCAGTTCACTCTGGTA
TGGACGCATTAACTGTTGTGAGTGATGTAGCAAATATTCAAAATGCACCA
GGAGTTAGAAAAGCTAACAGTGAATTACATTCAGTTGGTCTTGGTGTGAT GAATTTACACGGTTACCTAGCAAAAAATAAAATTGGTTATGAGTCAGAAG
AAGCAAAAGATTTTGCAAATATCTTCTTTATGATGATGAATTTCTACTCA
ATCGAACGTTCAATGGAAATCGCTAAAGAGCGTGGTATCAAATATCAAGA
CTTTGAAAAGTCTGATTATGCTAATGGCAAATATTTCGAGTTCTATACAA
CTCAAGAATTTGAACCTCAATTCGAAAAAGTACGTGAATTATTCGATGGT ATGGCTATTCCTACTTCTGAGGATTGGAAGAAACTACAACAAGATGTTGA
ACAATATGGTTTATATCATGCATATAGATTAGCAATTGCTCCAACACAAA
GTATTTCTTATGTTCAAAATGCAACAAGTTCTGTAATGCCAATCGTTGAC
CAAATTGAACGTCGTACTTATGGTAATGCGGAAACATTTTACCCTATGCC
ATTCTTATCACCACAAACAATGTGGTACTACAAATCAGCATTCAATACTG ATCAGATGAAATTAATCGATTTAATTGCGACAATTCAAACGCATATTGAC CAAGGTATCTCAACGATCCTTTATGTTAATTCTGAAATTTCTACACGTGA GTTAGCAAGATTATATGTATATGCGCACTATAAAGGATTAAAATCACTTT ACTATACTAGAAATAAATTATTAAGTGTAGAAGAATGTACAAGTTGTTCT ATCTAA-3 '
(B) Staphylococcus aureus nrdE polypeptide sequence deduced from a polynucleotide sequence in this table [SEQ ID NO 2]
NH -MKTMEEKKYNHIELNNEVTKRREDGFFSLEKDQEALVAYLEEVKDKTIFF
DTEIERLRYLVDNDFYFNVFDIYSEADLIEITDYAKSISFNFASYMSASK FFKDYALKTNDKSQYLEDYNQHVAIVALYLANGNKAQAKQFISAMVEQRY
QPATPTFLNAGRARRGELVSCFLLEVDDSLNSINFIDSTAKQLSKIGGGV
AINLSK RARGEAIKGIKGVAKGVLPIAKSLEGGFSYADQLGQRPGAGAV
YLNIFHYDVEEFLDTKKVNADEDLRLSTISTGLIVPSKFFDLAKEGKDFY
MFAPHTVKEEYGVTLDDIDLEKYYDDMVANPNVEKKKKNAREMLNLIAQT QLQSGYPYLMFKDNANRVHPNSNIGQIKMSNLCTEIFQLQETSIINDYGI
EDEIKRDISCNLGSLNI VMESGKFRDSVHSGMDALTWSDVANIQNAP
GVRKANSELHSVGLGλ/MNLHGYLAKNKIGYESEEAKDFANIFFMMMNFYS
IERSMEIAKERGIKYQDFEKSDYA GKYFEFYTTQEFEPQFEKVRELFDG
MAIPTSEDWKKLQQDVEQYGLYHAYRLAIAPTQSISYVQNATSSVMPIVD QIERRTYGNAETFYPMPFLSPQTMWYYKSAFNTDQMKLID IATIQTHID
QGISTILYVNSEISTRELARLYVYAHYKGLKSLYYTRNKLLSVEECTSCS
I-COOH
Deposited materials
A deposit containing a Staphylococcus aureus WCUH 29 stram has been deposited with the
National Collections of Industrial and Marine Bactena Ltd (herein "NCIMB"), 23 St Machar Dnve.
Aberdeen AB2 IRY, Scotland on 11 September 1995 and assigned NCIMB Deposit No 40771, and referred to as Staphylococcus aureus WCUH29 on deposit The Staphylococcus aureus stram deposit is referred to herem as "the deposited stram" or as "the DNA of the deposited stram "
The deposited stram contains a full length nrdE gene The sequence of the polynucleotides contained m the deposited stram, as well as the ammo acid sequence of any polypeptide encoded thereby, are controlling m the event of am conflict with any descnption of sequences herem
Tlie deposit of tlie deposited stram has been made under the terms of tlie 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 tlie public upon the issuance of a patent Tlie deposited stram is provided merely as convenience 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 stram. and compounds denved therefrom, and no such license is hereby granted
In one aspect of the mvention there is provided an isolated nucleic acid molecule encodmg a mature polypeptide expressible by the Staphylococcus aureus WCUH 29 stram, which polypeptide is contamed m the deposited stram Further provided by the mvention are nrdE polynucleotide sequences m tlie deposited stram, such as DNA and RNA, and ammo acid sequences encoded thereb} Also provided by the mvention are nrdE polypeptide and polynucleotide sequences isolated from the deposited stram
Polypeptides The nrdE polypeptide of the mvention is substantially phylogenetically related to other proteins of the nbonucleotide diphosphate reductase family
In one aspect of tlie mvention there are provided polypeptides of Staphylococcus aureus referred to herem as "nrdE" and "nrdE polypeptides" as well as biologically, diagnostically, prophylactically, clinically or therapeutically useful vanants thereof, and compositions compnsmg the same Among the particularly preferred embodiments of the mvention are vanants of nrdE polypeptide encoded by naturally occurring alleles of the nrdE gene
The present mvention further provides for an isolated polypeptide which (a) comprises or consists of an ammo acid sequence which has at least 70% identity, preferably at least 80% identity, more preferably at least 90% identity, yet more preferably 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 comprising or consisting of a polynucleotide sequence which has at least 70% identity preferably at least 80% identity, more preferably at least 90% identity, yet more preferably at least 95% identity, even more preferably at least 97-99% or exact identity to SEQ ID NO 1 over the entire length of SEQ ID NO 1 , (c) a polypeptide encoded by an isolated polynucleotide comprising or consisting of a polynucleotide sequence encodmg a polypeptide which has at least 70% identity, preferably at least 80% identity, more preferably at least 90% identity, yet more preferably at least 95% identity, even more preferably at least 97-99% or exact identity, to the ammo acid sequence of SEQ ID NO 2. over the entire length of SEQ ID NO 2
The polypeptides of the mvention mclude a polypeptide of Table 1 [SEQ ID NO 2] (m particular the mature polypeptide) as well as polypeptides and fragments, particularly those which have the biological activity of nrdE. and also those which have at least 70% identity to a polypeptide of Table 1 [SEQ ID NO l]or the relevant portion, preferably at least 80% identity to a polypeptide of Table 1 [SEQ ID NO 2and more preferabh at least 90% identity to a polypeptide of Table 1 [SEQ ID NO 2] and still more preferabh at least 95% identity to a polypeptide of Table 1 [SEQ ID NO 2] and also mclude portions of such polypeptides with such portion of tlie polypeptide generally containing at least 30 ammo acids and more preferably at least 50 ammo acids
Tlie mvention also mcludes a polypeptide consisting of or compnsmg a polypeptide of the formula X-(R1)m-(R2)-(R3)n-Y wherein, at the ammo terminus, X is hydrogen, a metal or any other moiety descnbed herem for modified polypeptides, and at tlie carboxyl terminus. Y is hydrogen, a metal or any other moiety descnbed herem for modified polypeptides, Rj 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. R is onented so that its ammo terminal ammo acid residue is at the left, covalently bound to Ri and its carboxy terminal ammo acid residue is at the nght, covalently bound to R3 Any stretch of ammo acid residues denoted b either Ri or R3. where m and/or 11 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 Staphylococcus aureus, 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 tlie same taxonomic family or order
A fragment is a vanant polypeptide havmg an ammo acid sequence that is entirely the same as part but not all of any ammo acid sequence of any polypeptide of the mvention As with nrdE polypeptides fragments may be "free-standing." or compnsed within a larger polypeptide of which they fonn a part or region most preferably as a smgle contmuous region m a smgle larger polypeptide
Preferred fragments mclude. for example, truncation polypeptides havmg a portion of an amino acid sequence of Table 1 [SEQ ID NO 2], or of vanants thereof, such as a contmuous senes of residues that mcludes an ammo- and/or carboxyl-termmal ammo acid sequence Degradation forms of the polypeptides of the mvention produced by or m a host cell, particularly a Staphylococcus aureus, are also preferred Further preferred are fragments charactenzed by structural or functional attributes such as fragments that compnse alpha-helix and alpha-helix forming regions beta-sheet and beta-sheet-formmg regions, turn and turn-forming regions coil and coil-forming regions, hydrophilic regions, hydrophobic regions, alpha amphipathic regions, beta amphipathic regions, flexible regions surface-forming regions, substrate bmdmg region, and high antigenic mdex regions
Further preferred fragments mclude an isolated polypeptide comprising an ammo acid sequence having at least 15, 20, 30, 40, 50 or 100 contiguous amino acids from the amino acid sequence of SEQ ID NO.2, or an isolated polypeptide comprising an amino acid sequence having at least 15, 20, 30, 40, 50 or 100 contiguous amino acids truncated or deleted from the amino acid sequence of SEQ ID NO:2.
Also preferred are biologically active fragments which are those fragments that mediate activities of nrdE. mcludmg those with a similar activity or an improved activity, or with a decreased undesirable activity Also included are those fragments that are antigeruc or lmmunogenic m an animal, especially in a human Particularly preferred are fragments compnsmg receptors or domains of enzymes that confer a function essential for viability of Staphylococcus aureus or the ability to initiate, or maintain cause Disease m an individual, particularly a human Fragments of the polypeptides of the mvention may be employed for producmg tlie corresponding full-length polypeptide by peptide synthesis, therefore, these vanants may be employed as intermediates for producmg the full-length polypeptides of the mvention
In addition to the standard single and triple letter representations for amino acids, the term "X" or "Xaa" may also be used m describing certain polypeptides of the invention "X" and "Xaa" mean that any of the twenty naturally occurring amino acids may appear at such a designated position in the polypeptide sequence
Polynucleotides
It is an object of the mvention to provide polynucleotides that encode nrdE polypeptides, particularly polynucleotides that encode the polypeptide herem designated nrdE In a particularly preferred embodiment of the mvention tlie polynucleotide compnses a region encodmg nrdE polypeptides compnsmg a sequence set out m Table 1 [SEQ ID NO 1] which mcludes a full length gene, or a variant thereof The Applicants believe that tins full length gene is essential to the growth and/or survival of an organism winch possesses it. such as Staphylococcus aureus
As a further aspect of the mvention there are provided isolated nucleic acid molecules encodmg and/or expressmg nrdE polypeptides and polynucleotides. particularly Staphylococcus aureus nrdE polypeptides and polynucleotides. mcludmg. for example, unprocessed RNAs. nbozyme RNAs, niRNAs. cDNAs, genomic DNAs, B- and Z-DNAs Further embodiments of the mvention mclude biologically, diagnostically. prophylactically. clinically or therapeutically useful polynucleotides and polypeptides. and vanants thereof, and compositions compnsmg tlie same Another aspect of the mvention relates to isolated polynucleotides. mcludmg at least one full length gene, that encodes a nrdE polypeptide havmg a deduced ammo acid sequence of Table 1 [SEQ ID NO 2] and polynucleotides closely related thereto and vanants thereof In another particularly preferred embodiment of the invention there is a nrdE polypeptide from Staphylococcus aureus comprising or consisting of an ammo acid sequence of Table 1 [SEQ ID NO 2], or a variant thereof
Usmg the lnfonnation provided herem. such as a polynucleotide sequence set out in Table 1 [SEQ ID NO 1]. a polynucleotide of the mvention encoding nrdE polypeptide may be obtained usmg standard cloning and screening methods, such as those for cloning and sequencmg chromosomal DNA fragments from bactena usmg Staphylococcus aureus WCUH 29 cells as starting matenal, followed by obtaining a full length clone For example, to obtain a polynucleotide sequence of the invention, such as a polynucleotide sequence given in Table 1 [SEQ ID NO 1] typically a library of clones of chromosomal DNA of Staphylococcus aureus WCUH 29 in E coh or some other suitable host is probed with a radiolabeled ohgonucleotide, preferably a 17-mer or longer, derived from a partial sequence Clones carrying DNA identical to that of the probe can then be distinguished using stringent hybridization conditions By sequencing the individual clones thus identified by hybridization with sequencing primers designed from the original polypeptide or polynucleotide sequence it is then possible to extend the polynucleotide sequence in both directions to determine a full length gene sequence Conveniently, such sequencing is performed, for example, using denatured double stranded DNA prepared from a plasmid clone Suitable techniques are described b\ Mamatis, T Fπtsch. E F and Sambrook et al . MOLECULAR CLONING, A LABORATORY MANUAL, 2nd Ed , Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York (1989) (see in particular Screening By Hybridization 1 90 and Sequencing Denatured Double-Stranded DNA Templates 13 70) Direct genomic DNA sequencing may also be performed to obtain a full length gene sequence Illustrative of the mvention. each polynucleotide set out m Table 1 [SEQ ID NO 1] was discovered m a DNA library denved from Staphylococcus aureus WCUH 29
Moreover, each DNA sequence set out m Table 1 [SEQ ID NO 1] contains an open rearing frame encodmg a protein having about the numbei of amino 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 m the art Tlie polynucleotide of SEQ ID NO 1. between nucleotide number 1 and the stop codon which begms at nucleotide number 2104 of SEQ ID NO 1, encodes the polypeptide of SEQ ID NO 2 hi a further aspect, the present mvention provides for an isolated polynucleotide comprising or consisting of (a) a polynucleotide sequence which has at least 70% identity, preferably at least 80% identity, more preferably at least 90% identity, yet more preferably at least 95% identity, even more preferably at least 97-99% or exact identity to SEQ ID NO 1 over the entire length of SEQ ID NO 1, (b) a polynucleotide sequence encodmg a polypeptide which has at least 70% identity, preferably at least 80% identity, more preferably at least 90% identity, yet more preferably 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 encodmg a polypeptide of the present mvention, mcludmg homologs and orthologs from species other than Staphylococcus aureus, may be obtained by a process which compnses the steps of screening an appropnate library under stringent hybndization conditions with a labeled or detectable probe consisting of or compnsmg the sequence of SEQ ID NO 1 or a fragment thereof, and isolating a full-length gene and/or genomic clones containing said polynucleotide sequence
The mvention provides a polynucleotide sequence identical over its entire length to a codmg sequence (open readmg frame) in Table 1 [SEQ ID NO 1] Also provided by the mvention is a codmg 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 readmg frame with another codmg sequence, such as a sequence encodmg a leader or secretory sequence, a pre-, or pro- or prepro-protem sequence The polynucleotide of the mvention may also contain at least one non-coding sequence, mcludmg for example, but not limited to at least one non-coding 5" and 3' sequence, such as tlie transcnbed but non-translated sequences, termmation signals (such as rho-dependent and rho-independent termmation signals), nbosome bmdmg sites. Kozak sequences, sequences that stabilize mRNA. mtrons. and polyadenylation signals The polynucleotide sequence may also compnse additional coding sequence encoding additional ammo acids For example, a marker sequence that facilitates punfication of the fused polypeptide can be encoded In certain embodiments of the mvention. the marker sequence is a hexa-histidine peptide, as provided m tlie pQE vector (Qiagen. Inc ) and descnbed in Gentz et al . Proc Natl Acad Su , USA 86 821-824 (1989). or an HA peptide tag (Wilson et a! . Cell 37 767 (1984). both of winch may be useful m punfymg polypeptide sequence fused to them Polynucleotides of the mvention also mclude. but are not lmuted to, polynucleotides compnsmg a structural gene and its naturally associated sequences that control gene expression A preferred embodiment of tlie mvention is a polynucleotide of consisting of or compnsmg nucleotide
1 to the nucleotide immediately upstream of or mcludmg nucleotide 2104 set forth m SEQ ID NO 1 of Table 1. both of winch encode the nrdE polypeptide
The mvention also mcludes a polynucleotide consisting of or compnsmg a polynucleotide of the formula X-(R1)m-(R2)-(R3)n-Y wherein 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 Rj and R3 is independently any nucleic acid residue or modified nucleic acid residue, m is an integer between 1 and 3000 or zero . n is an integer between 1 and 3000 or zero, and R2 is a nucleic acid sequence or modified nucleic acid sequence of the invention, particularly a nucleic acid sequence selected from Table 1 or a modified nucleic acid sequence thereof In the polynucleotide formula above, R 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 right, bound to R3 Any stretch of nucleic acid residues denoted by either Ri and/or R2. where m and/or 11 is greater than 1 , may be either a heteropolymer or a homopolymer, preferably a heteropolymer Where, m a preferred embodiment, X and Y together define a covalent bond, the polynucleotide of the above formula is a closed, circular polynucleotide, which can be a double-stranded polynucleotide wherein the formula shows a first strand to which the second strand is complementary In another preferred embodiment m and/or n is an integer between 1 and 1000. 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 polynucleotide of the mvention is denved from Staphylococcus aureus, however, it may preferably be obtamed from other organisms of the same taxonomic genus A polynucleotide of the mvention may also be obtamed. for example, from organisms of the same taxonomic family or order
The tenn "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 Staphylococcus aureus nrdE havmg an ammo acid sequence set out m Table 1 [SEQ ID NO 2] Tlie term also encompasses polynucleotides that mclude a smgle contmuous region or discontinuous regions encodmg tlie 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 genonnc DNA reorganization) together with additional regions, that also may contain coding and/or non-coding sequences The mvention further relates to vanants of the polynucleotides descnbed herem that encode vanants of a polypeptide havmg a deduced amino acid sequence of Table 1 [SEQ ID NO 2] Fragments of a polynucleotides of tlie mvention ma}' be used, for example, to synthesize full-length polynucleotides of the mvention
Further particularly preferred embodiments are polynucleotides encodmg nrdE vanants, that have the am o acid sequence of nrdE 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 amino acid residues are substituted, modified, deleted and/or added, m any combmation Especially preferred among these are silent substitutions, additions and deletions, that do not alter the properties and activities of nrdE pohpeptide Further preferred embodiments of the mvention are polynucleotides that are at least 70% identical over their entire length to a polynucleotide encodmg nrdE polypeptide havmg an ammo acid sequence set out in Table 1 [SEQ ID NO 2], and polynucleotides that are complementary to such polynucleotides Alternatively, most highly preferred are polynucleotides that compnse a region that is at least 80% identical over its entire length to a polynucleotide encoding nrdE polypeptide and polynucleotides complementary thereto In this regard, polynucleotides at least 90% identical over their entire length to the same are particularly preferred, and among these particularly preferred polynucleotides, those with at least 95% are especially preferred Furthermore, those with at least 97% are highly preferred among those with at least 95%. and among these those with at least 98% and at least 99% are particularly highly preferred, with at least 99% bemg the more preferred
Preferred embodiments are polynucleotides encodmg polypeptides that retain substantially the same biological function or activity as the mature polypeptide encoded by a DNA of Table 1 [SEQ ID NO 1] hi accordance with certain preferred embodiments of this mvention there are provided polynucleotides that hybndize. particularly under stringent conditions, to nrdE polynucleotide sequences, such as those polynucleotides m Table 1
Tlie mvention further relates to polynucleotides that hybndize to the polynucleotide sequences provided herem In tins regard, tlie mvention especially relates to polynucleotides that hybndize under stringent conditions to the polynucleotides descnbed herem As herem used, tlie terms "stringent conditions" and "stringent 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 stringent hybridization conditions is overnight incubation at 42°C in a solution comprising 50% formamide, 5x SSC (150mM NaCl. 15mM tπsodium citrate). 50 mM sodium phosphate (pH7 6). 5x Denhardt's solution, 10% dextran sulfate. and 20 micrograms/ml of denatured, sheared salmon sperm DNA. followed by washing the hybridization support in 0 lx SSC at about 65°C Hybridization and wash conditions are well known and exemplified in Sambrook. el al . Molecular Cloning A Laboratory Manual. Second Edition, Cold Spring Harbor, N Y , (1989). particularly Chapter 11 therein Solution hybridization may also be used with the polynucleotide sequences provided by the invention
The invention also provides a polynucleotide consisting of or comprising a polynucleotide sequence obtained by screening an appropriate library containing the complete gene for a polynucleotide sequence set forth in SEQ ID NO 1 under stringent hybridization conditions with a probe having the sequence of said polynucleotide sequence set forth m SEQ ID NO 1 or a fragment thereof, and isolating said polynucleotide sequence Fragments useful for obtaining such a polynucleotide include, for example, probes and primers fully described elsewhere herein As discussed elsewhere herem regarding polynucleotide assays of the mvention, for instance, the polynucleotides of tlie mvention. may be used as a hybndization probe for RNA, cDNA and genomic DNA to isolate full-length cDNAs and genomic clones encoding nrdE and to isolate cDNA and genomic clones of other genes that have a high identity, particularly high sequence identity, to the nrdE gene Such probes generally will compnse at least 15 nucleotide residues or base pairs Preferably, such probes will have at least 30 nucleotide residues or base pairs and may have at least 50 nucleotide residues or base pairs Particularly preferred 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 nrdE gene may be isolated by screening usmg a DNA sequence provided m Table 1 [SEQ ID NO 1] to synthesize an ohgonucleotide probe A labeled ohgonucleotide havmg a sequence complementary to that of a gene of the mvention is then used to screen a library of cDNA, genomic DNA or mRNA to determine which members of the library the probe hybndizes to
There are several methods available and well known to those skilled in the art to obtain full- length DNAs or extend short DNAs, for example those based on the method of Rapid Amplification of cDNA ends (RACE) (see. for example, Frohman. et al . PNAS USA 85 8998-9002. 1988) Recent modifications of the technique, exemplified by the Marathon™ technology (Clontech Laboratories Inc ) for example, have significantly simplified the search for longer cDNAs In the Marathon™ technology, cDNAs have been prepared from mRNA extracted from a chosen tissue and an 'adaptor' sequence gated 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 using "nested" primers, that is. primers designed to anneal within the amplified product (typically an adaptor specific primer that anneals further 3' in the adaptor sequence and a gene specific primer that anneals further 5' 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 existing DNA to give a complete sequence, or carrying out a separate full- length PCR using the new sequence information for the design of the 5' pnmer
The polynucleotides and polypeptides of tlie mvention may be employed, for example, as research reagents and matenals for discovery of treatments of and diagnostics for diseases, particularly human diseases as further discussed herem relating to polynucleotide assays The polynucleotides of the invention that are ohgonucleotides derived from a sequence of Table
1 [SEQ ID NOS 1 or 2] may be used m the processes herein as described, but preferably for PCR, to determine whether or not the polynucleotides identified herein in whole or in part are transcribed in bacteria in infected tissue It is recognized that such sequences will also have utility in diagnosis of the stage of infection and type of infection the pathogen has attained
Tlie mvention also provides polynucleotides that encode a polypeptide that is the mature protem plus additional ammo or carboxyl-terminal ammo acids, or ammo acids mtenor to the mature polypeptide (when the mature form has more than one polypeptide cham. for instance) Such sequences may
Figure imgf000015_0001
a role m processmg of a protem from precursor to a mature form, may allow protem transport, may lengthen or shorten protem half-life or may facilitate manipulation of a protem for assay or production, among other things As generally is the case in vivo, the additional ammo acids may be processed away from the mature protem by cellular enzymes For each and every polynucleotide of the mvention there is provided a polynucleotide complementary to it It is preferred that these complementary polynucleotides are fully complementary to each po nucleotide with which they are complementary
A precursor protem, havmg a mature form of the polypeptide fused to one or more prosequences may be an inactive fonn of the polypeptide When prosequences are removed such inactive precursors generally are activated Some or all of the prosequences may be removed before activation Generally, such precursors are called proproteins
In addition to the standard A, G, C, T/U representations for nucleotides. the term "N" may also be used in describing certain polynucleotides of the invention "N" means that any of the four DNA or RNA nucleotides ma> appear at such a designated position in the DNA or RNA sequence, except it is preferred that N is not a nucleic acid that when taken m combination with adjacent nucleotide positions, when read in the correct reading frame, would have the effect of generating a premature termination codon in such reading frame
In sum. a pohnucleotide of the mvention may encode a mature protem. a mature protem plus a leader sequence (which may be referred to as a preprotem). a precursor of a mature protem havmg one or more prosequences that are not the leader sequences of a preprotem, or a preproprotem, which is a precursor to a proprotein. havmg a leader sequence and one or more prosequences, which generally are removed during processmg steps that produce active and mature forms of tl e polypeptide
Vectors, Host Cells, Expression Systems
Tlie mvention also relates to vectors that compnse a polynucleotide or polynucleotides of the mvention. host cells that are genetically engmeered with vectors of the mvention and the production of polypeptides of the mvention by recombinant techniques Cell-free translation systems can also be employed to produce such proteins usmg RNAs denved from tlie DNA constructs of the mvention Recombinant polypeptides of the present mvention may be prepared by processes well known in those skilled m tlie art from genetically engmeered host cells compnsmg expression systems Accordingly, m a further aspect, the present mvention relates to expression systems which compnse a polynucleotide or polynucleotides of the present mvention, to host cells which are genetically engmeered with 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 tlie host cell can be effected by methods descnbed m many standard laboratory manuals, such as Davis, et al . BASIC METHODS IN MOLECULAR BIOLOGY, (1986) and Sambrook. et al , MOLECULAR CLONING A LABORATORY MANUAL, 2nd Ed . Cold Spring Harbor Laboratory Press. Cold Spring Harbor, N Y (1989), such as. calcium phosphate transfection, DEAE-dextran mediated transfection. transvection. microinjection, catiomc pid-mediated transfection. electroporation, transduction. scrape loading, ballistic mtroduction and infection
Representative examples of appropnate hosts mclude bactenal cells, such as cells of streptococci, staphylococci. enterococci E cob, streptomyces, cyanobactena. Bacillus subtibs, and Staphylococcus aureus fungal cells, such as cells of a yeast. Kluveromyces, Saccharomyce . a basidiomycete, Candida albicans and Aspergillus, msect cells such as cells of Drosophύa S2 and Spodoptera Sf9, animal cells such as CHO. COS. HeLa, C127, 3T3, BHK, 293, CV-1 and Bowes melanoma cells, and plant cells, such as cells of a gymnosperm or angiosperm A great vanety of expression systems can be used to produce the polypeptides of the mvention Such vectors mclude. among others, chromosomal-, episomal- and virus-denved vectors, for example, vectors denved from bactenal plasmids. from bactenophage. from transposons. from yeast episomes. from insertion elements, from yeast chromosomal elements, from viruses such as baculoviruses. papova vimses. such as SV40. vaccinia viruses, adenoviruses. fowl pox viruses, pseudorabies viruses, picornaviruses and retroviruses. and vectors denved from combmations thereof, such as those denved from plasmid and bactenophage genetic elements, such as cosmids and phagemids The expression system constructs may contain control regions that regulate as well as engender expression Generally, any system or vector suitable to maintain, propagate or express polynucleotides and/or to express a polypeptide m a host may be used for expression m this regard The appropnate DNA sequence may be inserted mto the expression system by any of a vanety of well-known and routme techniques, such as. for example, those set forth m Sambrook et al , MOLECULAR CLONING, A LABORATORY MANUAL, (supra) hi recombinant expression systems m eukaryotes. for secretion of a translated protem mto the lumen of tlie endoplasmic reticulum, mto the penplasmic space or mto the extracellular environment, appropnate secretion signals may be incorporated mto the expressed polypeptide These signals may be endogenous to the polypeptide or they may be heterologous signals
Polypeptides of the mvention can be recovered and punfied from recombinant cell cultures by well- known methods mcludmg ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography. phosphocellulose chromatography, hydrophobic mteraction chromatography, affinity chromatography. hydroxylapatite chromatography. and lectm chromatography Most preferably, high performance liquid chromatography is employed for punficatioii Well known techniques for refolding protem may be employed to regenerate active conformation when the polypeptide is denatured during isolation and or punfication Diagnostic, Prognostic, Serotyping and Mutation Assays
This mvention is also related to the use of nrdE polynucleotides and polypeptides of the mvention for use as diagnostic reagents Detection of nrdE polynucleotides and/or polypeptides m 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 organism compnsmg tlie nrdE gene or protem may be detected at the nucleic acid or ammo acid level by a vanety of well known techniques as well as by methods provided herem
Polypeptides and polynucleotides for prognosis, diagnosis or other analysis may be obtamed from a putatively infected and/or infected individual's bodily matenals Polynucleotides from am of these sources, particularly DNA or RNA. may be used directly for detection or may be amplified enzymatically by usmg PCR or any other amplification technique pnor to analysis RNA, particularly mRNA. cDNA and genonnc DNA may also be used m the same ways Usmg amplification, charactenzation of the species and stram of infectious or resident organism present m an individual, 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 in companson to a genotype of a reference sequence selected from a related organism, preferably a different species of the same genus or a different stram of the same species Pomt mutations can be identified by hybndizing amplified DNA to labeled nrdE 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 detectmg differences m meltmg temperatures or renaturation kinetics Polynucleotide sequence differences may also be detected by alterations m the electrophoretic mobility of polynucleotide fragments m gels as compared to a reference sequence This may be earned out with or without denaturing agents Polynucleotide differences may also be detected by direct DNA or RNA sequencmg See. for example. Myers et al . Science, 230 1242 (1985) Sequence changes at specific locations also may be revealed by nuclease protection assays, such as RNase, VI and SI protection assay or a chemical cleavage method See. for example, Cotton et al , Proc Nail Acad Sci , USA, 85 4397-4401 (1985)
In another embodiment, an array of o gonucleotides probes compnsmg nrdE nucleotide sequence or fragments tliereof can be constructed to conduct efficient screenmg of, for example, genetic mutations, serotype. taxonomic classification or identification Array technology methods are well known and have general applicability and can be used to address a vanety of questions m molecular genetics mcludmg gene expression, genetic linkage and genetic vanabi ty (see. for example, Chee et al . Science, 274 610 (1996))
Thus in another aspect, the present invention relates to a diagnostic kit which comprises (a) a polynucleotide of the present invention, preferably the nucleotide sequence of SEQ ID NO 1, or a fragment thereof , (b) a nucleotide sequence complementary to that of (a), (c) a polypeptide of the present invention, preferably the polypeptide of SEQ ID NO 2 or a fragment thereof, or (d) an antibody to a polypeptide of the present invention, preferably to the polypeptide of SEQ ID NO 2
It will be appreciated that in any such kit. (a), (b), (c) or (d) may comprise a substantial component Such a kit will be of use in 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 ID NO 1. which is associated with a disease or pathogemcity will provide a diagnostic tool that can add to, or define, a diagnosis of a disease, a prognosis of a course of disease, a determination of a stage of disease, or a susceptibility to a disease, which results from under-expression. over-expression or altered expression of the polynucleotide Organisms, particularly infectious organisms, carrying mutations m such polynucleotide may be detected at the polynucleotide level by a vanety of techniques, such as those described elsewhere herem
Tlie nucleotide sequences of the present mvention are also valuable for orgamsm chromosome identification The sequence is specifically targeted to, and can hybndize with, a particular location on an organism's chromosome, particularly to a Staphylococcus aureus chromosome The mapping of relevant sequences to chromosomes according to the present mvention may be an important step m correlating those sequences with pathogenic potential and/or an ecological mche of an orgamsm and/or drug resistance of an orgamsm. as well as tlie essentiality of tlie gene to the organism Once a sequence has been mapped to a precise chromosomal location, the physical position of the sequence on the chromosome can be correlated with genetic map data Such data may be found on-lme m a sequence database The relationship between genes and diseases that have been mapped to the same chromosomal region are then identified through known genetic methods, for example, through linkage analysis (coinhentance of physically adjacent genes) or matmg studies, such as by conjugation
The differences in a polynucleotide and/or polypeptide sequence between organisms possessing a first phenotype and organisms possessing a different, second different phenotype can also be determined If a mutation is observed in some or all organisms possessing the first phenotype but not in any organisms possessing the second phenotype, then the mutation is likely to be the causative agent of the first phenotype
Cells from an orgamsm carrying mutations or polymorphisms (allehc vanations) m a polynucleotide and/or polypeptide of tlie mvention may also be detected at the pohnucleotide or polypeptide level by a vanety of techniques, to allow for serotypmg. for example For example. RT-PCR can be used to detect mutations m the RNA It is particularly preferred 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 tlie same purpose, PCR As an example. PCR primers complementary to a polynucleotide encoding nrdE polypeptide can be used to identify and analyze mutations Examples of representative primers are shown below in Table 2
Table 2 Primers for amplification of nrdE polynucleotides SEQ ID NO PRIMER SEQUENCE
3 5 ' -ATGAAAACCATGGAAGAGAA- 3 '
4 5 ' -TTAGATAGAACAACTTGTAC-3 '
The mvention also mcludes primers of the formula
X-(R1)m-(R2)-(R3)n-Y wherem. at the 5' end of tlie molecule. X is hydrogen, a metal or a modified nucleotide residue, and at the 3' end of tlie molecule. Y is hydrogen, a metal or a modified nucleotide residue. Ri and R3 are any nucleic acid residue or modified nucleotide residue, m is an mteger between 1 and 20 or zero . n is an mteger between 1 and 20 or zero, and R2 is a primer sequence of the mvention. particularly a primer sequence selected from Table 2 In the polynucleotide formula above R2 is onented so that its 5' end nucleotide residue is at the left, bound to Ri and its 3' end nucleotide residue is at the nght. bound to R3 Any stretch of nucleic acid residues denoted by either R group, where m and/or 11 is greater than 1. may be either a heteropolymer or a homopolymer, preferably a heteropolymer being complementary to a region of a polynucleotide of Table 1 In a preferred embodiment m and/or n is an mteger between 1 and 10.
The mvention further provides these primers with 1, 2, 3 or 4 nucleotides removed from the 5' and/or tlie 3' end These primers may be used for. among other things, amplifying nrdE DNA and/or RNA isolated from a sample denved from an individual, such as a bodily matenal The primers may be used to amplify a polynucleotide isolated from an mfected individual, such that tlie polynucleotide may then be subject to vanous techniques for elucidation of the pohnucleotide sequence In this way, mutations in tlie 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 bacterial infections, more preferably mfections caused by Staphylococcus aureus. comprising determining from a sample derived from an individual, such as a bodily material, an increased level of expression of polynucleotide having a sequence of Table 1 [SEQ ID NO 1] Increased or decreased expression of a nrdE polynucleotide can be measured using 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 hybridization methods
In addition, a diagnostic assay m accordance with the mvention for detectmg over-expression of nrdE polypeptide compared to normal control tissue samples
Figure imgf000020_0001
be used to detect the presence of an infection, for example Assay teclnnques that can be used to determine levels of a nrdE polypeptide, in 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
Differential Expression
The polynucleotides and polynucleotides of the mvention may be used as reagents for differential screenmg methods There are many differential screening and differential display methods known m the art in which tlie polynucleotides and polypeptides of the mvention may be used For example, the differential displaj technique is described by Chuang et al . J Bactenol 175 2026-2036 (1993) This method identifies those genes which are expressed in an organism by identifying mRNA present using randomly-primed RT-PCR By comparing pre-infection and post infection profiles, genes up and down regulated during infection can be identified and the RT-PCR product sequenced and matched to ORF "unknowns "
In Vivo Expression Technology (IVET) is described by Camilh et al , Proc Nat 'I Acad Sci USA 91 2634-2638 (1994) IVET identifies genes up-regulated during infection when compared to laboratory cultivation, implying an important role in infection ORFs identified by this technique are implied to have a significant role in infection establishment and/or maintenance In this technique random chromosomal fragments of target organism are cloned upstream of a promoter-less recombinase gene in a plasmid vector This construct is introduced into the target organism which carries an antibiotic resistance gene flanked by resolvase sites Growth in the presence of the antibiotic removes from the population those fragments cloned into the plasmid vector capable of supporting transcription of the recombinase gene and therefore have caused loss of antibiotic resistance The resistant pool is introduced into a host and at various times after infection bacteria may be recovered and assessed for the presence of antibiotic resistance The chromosomal fragment carried by each antibiotic sensitive bacterium should carr a promoter or portion of a gene normally upregulated during infection Sequencing upstream of the recombinase gene allows identification of the up regulated gene
RT-PCR may also be used to analyze gene expression patterns For RT PCR using the polynucleotides of the invention, messenger RNA is isolated from bacterial infected tissue, e g . 48 hour murine lung infections, and the amount of each mRNA species assessed by reverse transcription of the RNA sample primed with random hexanucleotides followed by PCR with gene specific primer pairs The determination of the presence and amount of a particular mRNA species by quantification of the resultant PCR product provides information on the bacterial genes which are transcribed in the infected tissue Analysis of gene transcription can be carried out at different times of infection to gain a detailed knowledge of gene regulation m bacterial pathogenesis allowing for a clearer understanding of which gene products represent targets for screens for antibacterials Because of the gene specific nature of the PCR primers employed it should be understood that the bacterial mRNA preparation need not be free of mammalian RNA This allows the investigator to carry out a simple and quick RNA preparation from infected tissue to obtain bacterial mRNA species which are very short lived in the bacterium (in the order of 2 minute halflives) Optimally the bacterial mRNA is prepared from infected murine lung tissue by mechanical disruption in the presence of TRJzole (GIBCO-BRL) for very short periods of time, subsequent processing according to the manufacturers of TRIzole reagent and DNAase treatment to remove contaminating DNA Preferably the process is optimized by finding those conditions which give a maximum amount of Staphylococcus aureus 16S πbosomal RNA as detected by probing Northerns with a suitably labeled sequence specific ohgonucleotide probe Typically a 5' dye labeled primer is used in each PCR primer pair m a PCR reaction which is terminated optimally between 8 and 25 cycles The PCR products are separated on 6% polyacrylamide gels with detection and quantification using GeneScanner (manufactured by ABI) Gridding and Polynucleotide Subtraction Methods have been described for obtaining information about gene expression and identity using so called "high density DNA arrays" or grids See, e g , M Chee et al , Science, 274 610-614 ( 1996) and other references cited therein Such gπdding assays have been employed to identify certain novel gene sequences, referred to as Expressed Sequence Tags (EST) (Adams et a , Science, 252 1651-1656 (1991)) A variety of techniques have also been described for identifying particular gene sequences on the basis of their gene products For example, see International Patent Application No WO91/07087. published May 30, 1991 In addition, methods have been described for the amplification of desired sequences For example, see International Patent Application No W091/17271, published November 14, 1991 The polynucleotides of the invention may be used as components of polynucleotide arrays, preferabh' high density arrays or grids These high density arrays are particularly useful for diagnostic and prognostic purposes For example, a set of spots each comprising a different gene, and further comprising a polynucleotide or polynucleotides of the invention, may be used for probing, such as using hybridization or nucleic acid amplification, using a probes obtained or derived from a bodily sample, to determine the presence of a particular polynucleotide sequence or related sequence in an individual Such a presence may indicate the presence of a pathogen, particularly Staphylococcus aureus, and may be useful in diagnosing and/or prognosing disease or a course of disease A grid comprising a number of variants of the polynucleotide sequence of SEQ ID NO 1 are preferred Also preferred is a comprising a number of variants of a polynucleotide sequence encoding the polypeptide sequence of SEQ ID NO 2 Antibodies
Tlie pohpeptides and polynucleotides of the mvention or vanants tliereof, or cells expressmg the same can be used as lmmunogens to produce antibodies rmmunospecific for such polypeptides or polynucleotides respectively hi certain preferred embodiments of tlie mvention there are provided antibodies agamst nrdE polypeptides or polynucleotides
Antibodies generated agamst the polypeptides or polynucleotides of the mvention can be obtamed by administering the polypeptides and/or polynucleotides of the mvention. or epitope-beanng fragments of either or both, analogues of either or both, or cells expressmg either or both, to an animal, preferably a nonhuman. usmg routine protocols For preparation of monoclonal antibodies, am technique known m the art that provides antibodies produced by contmuous cell line cultures can be used Examples mclude vanous techniques, such as those m Koliler. G and Milstem, C , Nature 256 495-497 (1975). Kozbor et al . Immunology Today 4 72 (1983). Cole et al . pg 77-96 m MONOCLONAL ANTIBODIES AND CANCER THERAPY. Alan R Liss. Inc (1985)
Techniques for tlie production of smgle cham antibodies (U S Patent No 4.946,778) can be adapted to produce smgle cham antibodies to polypeptides or polynucleotides of this mvention Also, transgenic mice. or other organisms such as other mammals, may be used to express humanized antibodies lmmunospecific to the polypeptides or polynucleotides of tlie mvention
Alternatively phage display technology may be utilized to select antibody genes w ith binding activities towards a polypeptide of the invention either from repertoires of PCR amplified v-genes of lymphocytes from humans screened for possessing anti-nrdE or from naive libraries (McCafferty. et al , (1990). Nature 348, 552-554, Marks, et al , (1992) Biotechnology 10, 779-783) The affinity of these antibodies can also be improved by, for example, chain shuffling (Clackson et al , (1991) Nature 352 628)
The above-descnbed antibodies may be employed to isolate or to identify clones expressmg the polypeptides or polynucleotides of the mvention to punfy tlie polypeptides or polynucleotides by. for example. affinity chromatography
Thus, among others, antibodies against nrdE-polypeptide or nrdE-polynucleotide may be employed to treat infections, particularly bactenal infections
Polypeptide variants include antigemcally. epitopicalh or lmmunologically equivalent variants form a particular aspect of this invention A polypeptide or polynucleotide of the invention, such as an antigemcally or linmunologically equivalent derivative or a fusion protem of the polypeptide is used as an antigen to immunize a mouse or other animal such as a rat or chicken The fusion protein may provide stability to the polypeptide The antigen may be associated, for example by conjugation, with an lmmunogemc carrier protein for example bovine serum albumin, keyhole limpet haemocyanm or tetanus toxoid Alternatively, a multiple antigenic polypeptide comprising multiple copies of the polypeptide. or an antigemcally or lmmunologically equivalent polypeptide thereof may be sufficiently antigenic to improve lmmunogenicity so as to obviate the use of a carrier
Preferably, the antibody or variant thereof is modified to make it less lmmunogemc in the individual For example, if the individual is human the antibody may most preferably be "humanized." where the comphmentarity detenninmg region or regions of the hybridoma-derived antibody has been transplanted into a human monoclonal antibody, for example as described in Jones et al (1986). Nature
321, 522-525 or Tempest et al , (1991) Biotechnology 9, 266-273 In accordance with an aspect of the invention, there is provided the use of a polynucleotide of the invention for therapeutic or prophylactic purposes, in particular genetic immunization Among the particularly preferred embodiments of the mvention are naturally occurring allehc vanants of nrdE polynucleotides and polypeptides encoded thereby The use of a polynucleotide of the invention in genetic immunization will preferably employ a suitable delivery method such as direct injection of plasmid DNA mto muscles (Wolff et al , Hum Mol Genet (1992) 1 363. Manthorpe et al , Hum Gene Ther (1983) 4 419), delivery of DNA complexed with specific protem carriers (Wu et a! . J Bwl Chem (1989) 264 16985). coprecipitation of DNA with calcium phosphate (Benvemsty & Reshef, PNAS USA. (1986) 83 9551), encapsulation of DNA m various forms of hposomes (Kaneda et al Science (1989) 243 375), particle bombardment (Tang et al . Nature (1992) 356 152. Eisenbraun et al , DNA Cell Bio! (1993) 12 791) and in vivo infection using cloned retroviral vectors (Seeger et al . PNAS USA (1984) 81 5849) Antagonists and Agonists - Assays and Molecules Polypeptides and polynucleotides of the mvention may also be used to assess the bmdmg of small molecule substrates and ligands m, for example, cells, cell-free preparations, chemical hbranes, and natural product mixtures These substrates and ligands may be natural substrates and ligands or may be structural or functional mimetics See. e g . Coligan et al . Current Protocols in Immunology 1(2) Chapter 5 (1991)
Polypeptides and polynucleotides of the present mvention are responsible for many biological functions, mcludmg many disease states, m particular the Diseases herembefore mentioned It is therefore desirable to devise screenmg methods to identify compounds which stimulate or which inhibit the function of tlie polypeptide or polynucleotide Accordingly, m a further aspect, the present mvention provides for a method of screening compounds to identify those which stimulate or which inhibit the function of a polypeptide or polynucleotide of the mvention. as well as related polypeptides and polynucleotides hi general, agomsts or antagonists may be employed for therapeutic and prophylactic purposes for such Diseases as hereinbefore mentioned Compounds may be identified from a vanety of sources, for example, cells, cell-free preparations, chemical hbranes, and natural product mixtures Such agomsts, antagonists or inhibitors so- identified may be natural or modified substrates, ligands. receptors, enzymes, etc , as the case may be. of nrdE polypeptides and polynucleotides, or may be structural or functional mimetics thereof (see Coligan et al . Current Protocols in Immunology 1(2) Chapter 5 (1991)) The screening methods may simply measure the bmdmg of a candidate compound to the polypeptide or polynucleotide. or to cells or membranes bearing the polypeptide or polynucleotide. or a fusion protein of the polypeptide by means of a label directly or indirectly associated with the candidate compound Alternatively, the screening 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, using detection systems appropriate to the cells comprising the polypeptide or polynucleotide Inhibitors of activation are generally assayed m the presence of a known agonist and the effect on activation by the agonist by the presence of the candidate compound is observed Constitutively active polypeptide and/or constitutively expressed polypeptides and polynucleotides may be employed m screening methods for inverse agonists or inhibitors, m the absence of an agonist or inhibitor, by testing whether the candidate compound results in inhibition of activation of the polypeptide or polynucleotide. as the case may be Further, the screening methods may simply comprise the steps of mixing a candidate compound with a solution containing a polypeptide or polynucleotide of the present invention, to form a mixture, measuring nrdE polypeptide and/or polynucleotide activity m the mixture, and comparing the nrdE polypeptide and/or polynucleotide activity of the mixture to a standard Fusion proteins, such as those made from Fc portion and nrdE polypeptide. as herembefoie 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 , 1 Mol Recognition, 8 52-58 (1995), and K Johanson et al . 1 Biol Chem, 270(16) 9459-9471 (1995))
The polynucleotides. polypeptides and antibodies that bind to and/or interact with a polypeptide of the present invention may also be used to configure screening methods for detecting the effect of added compounds on the production of mRNA and/or polypeptide in cells For example, an ELISA assay may be constructed for measuring secreted or cell associated levels of polypeptide using monoclonal and polyclonal antibodies by standard methods known in the art This can be used to discover agents which may inhibit or enhance the production of polypeptide (also called antagonist or agonist respectively) from suitably manipulated cells or tissues
The mvention also provides a method of screenmg compounds to identify those which enhance (agomst) or block (antagomst) tlie action of nrdE polypeptides or polynucleotides, particularly those compounds that are bactenstatic and/or bactencidal The method of screeiung may mvolve high-throughput techniques For example, to screen for agomsts 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 nrdE polypeptide and a labeled substrate or hgand of such polypeptide is mcubated m the absence or the presence of a candidate molecule that mav be a nrdE agomst or antagomst The abihtv of the candidate molecule to agomze or antagonize tlie nrdE polypeptide is reflected m decreased bmdmg of tlie labeled hgand or decreased production of product from such substrate Molecules that bind gratuitously. / e . without mducmg the effects of nrdE polypeptide are most likely to be good antagonists Molecules that bmd well and, as the case may be. increase tlie rate of product production from substrate, mcrease signal transduetion. or mcrease chemical channel activity are agomsts Detection of the rate or level of, as the case may be, production of product from substrate, signal transduetion, or chemical channel activity may be enhanced by usmg a reporter system Reporter systems that may be useful in this regard mclude but are not limited to colonmetnc, labeled substrate converted mto product, a reporter gene that is responsive to changes m nrdE polynucleotide or polypeptide activity, and bmdmg assays known m the art
Polypeptides of the invention may be used to identify membrane bound or soluble receptors, if any for such poly peptide. through standard receptor binding techniques known in the art These techniques include but are not limited to. hgand binding and crosslinking assays in 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 purification, and incubated with a source of the putative receptor (e g , cells, cell membranes, cell supernatants, tissue extracts, bodily materials) Other methods include biophy sical techniques such as surface plasmon resonance and spectroscopy These screening methods may also be used to identify agonists and antagonists of the polypeptide which compete with the binding of the polypeptide to its receptor(s), if any Standard methods for conducting such assays are well understood in the art
The fluorescence polarization value for a fluorescently -tagged molecule depends on the rotational correlation time or tumbling rate Protem complexes, such as formed by nrdE polypeptide associating with another nrdE polypeptide or other polypeptide. labeled to comprise a fluorescently- labeled molecule will have higher polarization values than a fluorescently labeled monomeric protein It is preferred that this method be used to characterize small molecules that disrupt polypeptide complexes
Fluorescence energy transfer ma\ also be used characterize small molecules that interfere with the formation of nrdE polypeptide dimers, tπmers. tetramers or higher order structures, or structures formed by nrdE polypeptide bound to another polypeptide nrdE polypeptide can be labeled with both a donor and acceptor fluorophore Upon mixing of the two labeled species and excitation of the donor fluorophore, fluorescence energy transfer can be detected by observing fluorescence of the acceptor Compounds that block dimeπzation will inhibit fluorescence energy transfer Surface plasmon resonance can be used to monitor the effect of small molecules on nrdE polypeptide self-association as well as an association of nrdE polypeptide and another polypeptide or small molecule nrdE polypeptide can be coupled to a sensor chip at low site density such that covalently bound molecules will be monomeric Solution protein can then passed over the nrdE polypeptide -coated surface and specific binding can be detected m 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 binding constants for nrdE polypeptide self-association as well as an association of nrdE polypeptide and another polypeptide or small molecule
A scintillation proximity assay may be used to characterize the interaction between an association of nrdE polypeptide with another nrdE polypeptide or a different polypeptide nrdE polypeptide can be coupled to a scintillation-filled bead Addition of radio-labeled nrdE polypeptide results in binding where the radioactive source molecule is in close proximity to the scintillation fluid Thus, signal is emitted upon nrdE polypeptide binding and compounds that prevent nrdE polypeptide self-association or an association of nrdE polypeptide and another polypeptide or small molecule will diminish signal
ICS biosensors have been described by AMBRI (Australian Membrane Biotechnology Research Institute) They couple the self-association of macromolecules to the closing of gramacidin- facilitated ion channels in suspended membrane bilayers and hence to a measurable change in the admittance (similar to impedence) of the biosensor This approach is linear over six decades of admittance change and is ideally suited for large scale, high through-put screening of small molecule combinatorial libraries
In other embodiments of the mvention there are provided methods for identifying compounds which bmd to or otherwise mteract with and mhibit or activate an activity or expression of a polypeptide and/or polynucleotide of tlie mvention compnsmg contacting a polypeptide and/or polynucleotide of the mvention with a compound to be screened under conditions to permit bmdmg to or other mteraction between the compound and tlie polypeptide and/or polynucleotide to assess the bmdmg to or other mteraction with the compound, such bmdmg or mteraction preferably bemg associated with a second component capable of providmg a detectable signal m response to the bmdmg or mteraction of the polypeptide and/or pohnucleotide with tlie compound, and determining whether the compound bmds to or otherwise mteracts with and activates or inhibits an activity or expression of tlie 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 nrdE agomsts is a competitive assay that combmes nrdE and a potential agomst with mdE-bmdmg molecules, recombinant nrdE bmdmg molecules, natural substrates or ligands, or substrate or hgand mimetics. under appropnate conditions for a competitive inhibition assay The nrdE molecule can be labeled, such as by radioactivity or a colonmetnc compound, such that the number of nrdE molecules bound to a bmdmg molecule or converted to product can be determined accurately to assess tlie effectiveness of the potential antagomst
Potential antagonists mclude, among others, small orgamc molecules, peptides, polypeptides and antibodies that bmd to a polynucleotide and/or polypeptide of the mvention and thereby inhibit or extinguish its activity or expression Potential antagorasts also may be small orgamc molecules, a peptide, a polypeptide such as a closely related protem or antibody that binds the same sites on a bmdmg molecule, such as a bmdmg molecule, without mducmg nrdE-induced activities, thereby preventmg the action or expression of nrdE polypeptides and/or polynucleotides by excluding nrdE polypeptides and/or polynucleotides from bmdmg
Potential antagonists mclude a small molecule that bmds to and occupies the bmdmg site of the polypeptide thereby preventmg bmdmg to cellular bmdmg molecules, such that normal biological activity is prevented Examples of small molecules mclude but are not lmnted to small organic molecules, peptides or peptide-like molecules Other potential antagonists mclude antisense molecules (see Okano, J Neurochem 56 560 (1991). OLIGODEOXYNUCLEOTIDES AS ANTISENSE INHIBITORS OF GENE EXPRESSION, CRC Press, Boca Raton. FL (1988), for a descnption of these molecules) Preferred potential antagorasts mclude compounds related to and vanants of nrdE
Other examples of potential polypeptide antagonists mclude antibodies or, m some cases. ohgonucleotides or proteins which are closely related to the ligands. substrates, receptors, enzymes, etc . as the case may be, of tlie polypeptide, e g . a fragment of the ligands. substrates, receptors, enzymes, etc . or small molecules which bmd to the polypeptide of tlie present mvention but do not elicit a response, so that the activity of the polypeptide is prevented
Certain of the polypeptides of the mvention are biomimetics. functional mimetics of tlie natural nrdE polypeptide These functional mimetics may be used for. among other things, antagonizing the activity of nrdE polypeptide or as a antigen or lmmunogen m a manner described elsewhere herem Functional mimetics of the polypeptides of the mvention mclude but are not limited to truncated polypeptides For example, preferred functional mimetics mclude. a polypeptide compnsmg the polypeptide sequence set forth m SEQ ID NO 2 lacking 20, 30. 40. 50. 60, 70 or 80 ammo- or carboxy-terminal ammo acid residues, mcludmg fusion proteins composing one or more of these truncated sequences Polynucleotides encodmg each of these functional mimetics may be used as expression cassettes to express each mimetic polypeptide It is preferred that these cassettes compnse 5' and 3' restnction sites to allow for a convenient means to hgate the cassettes together when desired It is further preferred that these cassettes compnse gene expression signals known m the art or descnbed elsewhere herem
Thus, in another aspect, the present invention relates to a screening kit for identifying agonists antagonists, ligands. receptors, substrates, enzymes, etc for a polypeptide and/or polynucleotide of the present invention, or compounds which decrease or enhance the production of such polypeptides and/or polynucleotides which comprises (a) a polypeptide and/or a polynucleotide of the present invention, (b) a recombinant cell expressing a polypeptide and/or polynucleotide of the present invention, (c) a cell membrane expressing a polypeptide and/or polynucleotide of the present invention, or (d) antibody to a polypeptide and/or polynucleotide of the present invention, which polypeptide is preferably that of SEQ ID NO 2. and which polynucleotide is preferably that of SEQ ID NO 1
It will be appreciated that in any such kit, (a), (b), (c) or (d) may comprise a substantial component It will be readily appreciated by the skilled artisan that a polypeptide and/or polynucleotide of the present invention may also be used m a method for the structure-based design of an agonist, antagonist or inhibitor of the polypeptide and/or polynucleotide. by (a) determining in the first instance the three-dimensional structure of the polypeptide and/or polynucleotide, or complexes thereof, (b) deducing the three-dimensional structure for the likely reactive sιte(s), binding sιte(s) or motιf(s) of an agonist, antagonist or inhibitor, (c) synthesizing candidate compounds that are predicted to bind to or react with the deduced binding sιte(s), reactive sιte(s). and/or motifis), and (d) testing whether the candidate compounds are indeed agonists, antagonists or inhibitors It will be further appreciated that this will normally be an iterative process, and this iterative process may be performed using automated and computer-controlled steps hi a further aspect, tlie present mvention provides methods of treatmg abnormal conditions such as. for mstance, a Disease, related to either an excess of. an under-expression of, an elevated activity of, or a decreased activity of nrdE polypeptide and/or polynucleotide
If tlie expression and/or activity of the polypeptide and/or polynucleotide is m excess, several approaches are available One approach composes administering to an mdividual in need tliereof an inhibitor compound (antagomst) as herem descnbed, optionally m combmation with a pharmaceutically acceptable earner, in an amount effective to inhibit the function and/or expression of tlie polypeptide and/or polynucleotide. such as. for example, by blocking tlie bmdmg of ligands. 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 binding the hgand. substrate, enzymes, receptors, etc in competition with endogenous polypeptide and/or polynucleotide may be administered Typical examples of such competitors include fragments of the nrdE polypeptide and/or polypeptide
In a further aspect, the present invention relates to genetically engineered soluble fusion proteins comprising a polypeptide of the present invention, or a fragment thereof, and various portions of the constant regions of heavy or light chains of immunoglobuhns of various subclasses (IgG, IgM. IgA. IgE) Preferred as an lmmunoglobuhn is the constant part of the heavy chain of human IgG, particularly IgG 1. where fusion takes place at the hinge region In a particular embodiment, the Fc part can be removed simply by incorporation of a cleavage sequence which can be cleaved with blood clotting factor Xa Furthermore, this invention relates to processes for the preparation of these fusion proteins by genetic engineering, and to the use thereof for drug screening, diagnosis and therapy A further aspect of the invention also relates to polynucleotides encoding such fusion proteins Examples of fusion protem technology can be found in International Patent Application Nos W094/29458 and W094/22914 In still another approach, expression of the gene encoding endogenous nrdE polypeptide can be inhibited using expression blocking techniques This blocking may be targeted agamst any step m gene expression, but is preferably targeted agamst transcription and/or translation An examples of a known technique of this sort involve 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 which form triple helices with the gene can be supplied (see, for example, Lee et al , Nucleic Acids Res ( 1979) 6 3073, Cooney et al , Science (1988) 241 456. Dervan et al Science (1991) 251 1360) These ohgomers can be administered per se or the relevant ohgomers can be expressed in vivo Each of the polynucleotide sequences provided herein may be used in the discovery and clopment of antibacterial compounds The encoded protein, upon expression, can be used as a target for the screening of antibacterial drugs Additionally, the polynucleotide sequences encoding the amino terminal regions of the encoded protem or Shine-Delgarno or other translation facilitating sequences of the respective mRNA can be used to construct antisense sequences to control the expression of the coding sequence of interest
The invention also provides the use of the polypeptide, polynucleotide. agonist or antagonist of the invention to interfere with the initial physical interaction between a pathogen or pathogens and a cukary otic preferably mammalian, host responsible for sequelae of infection In particular the molecules of the invention may be used in the prevention of adhesion of bacteria, in particular gram positive and/or gram negative bacteria, to eukarvotic. preferably mammalian, extracellular matrix proteins on in-dwelling devices or to extracellular matrix proteins m wounds, to block bacterial adhesion between eukarvotic. preferably mammalian, extracellular matrix proteins and bacterial nrdE proteins that mediate tissue damage and/or, to block the normal progression of pathogenesis in infections initiated other than by the implantation of in-dwelling devices or by other surgical techniques
In accordance with yet another aspect of tlie mvention, there are provided nrdE agonists and antagonists, preferably bactenstatic or bactencidal agonists and antagorasts The antagonists and agomsts of the mvention may be employed, for instance, to prevent, inhibit and/or treat diseases
Helicobacter pylori (herein "H pylori") bacteria infect the stomachs of over one-third of the world's population causing stomach cancer, ulcers, and gastritis (International Agency for Research on Cancer (1994) Schistosomes Liver Flukes and Helicobacter Pylori (International Agency for Research on Cancer. Lyon. France, http //www uicc ch/ecp/ecp2904 htm) Moreover, the International Agency for Research on Cancer recently recognized a cause-and-effect relationship between H pylori and gastric adenocarcinoma, classifying the bacterium as a Group I (definite) carcinogen Preferred antimicrobial compounds of the invention (agonists and antagonists of nrdE polypeptides and/or polynucleotides) found using screens provided by the invention, or known in the art. particularly narrow-spectrum antibiotics, should be useful in the treatment of H pylori infection Such treatment should decrease the advent of H pylori - άuceά cancers, such as gastrointestinal carcinoma Such treatment should also prevent, inhibit and/or cure gastric ulcers and gastritis
Vaccines
There are provided by the mvention. products, compositions and methods for assessmg nrdE expression, treatmg disease, assaymg genetic vanation. and administering a nrdE polypeptide and/or polynucleotide to an orgamsm to raise an immunological response agamst a bacteπa. especially a Staphylococcus aureus bactena
Another aspect of the invention relates to a method for inducing an immunological response in an individual, particularly a mammal which comprises inoculating the individual with nrdE polynucleotide and/or polypeptide, or a fragment or variant thereof, adequate to produce antibody and/ or T cell immune response to protect said individual from infection, particularly bacterial infection and most particularly Staphylococcus aureus infection Also provided are methods whereby such immunological response slows bacterial replication Yet another aspect of the invention relates to a method of inducing immunological response in an individual which comprises delivering to such individual a nucleic acid vector, sequence or ribozyme to direct expression of nrdE polynucleotide and/or polypeptide, or a fragment or a variant thereof, for expressing nrdE polynucleotide and/or polypeptide. or a fragment or a variant thereof in vivo in order to induce an immunological response, such as. to produce antibody and/ or T cell immune response, including, for example, cytokine- producing T cells or cytotoxic T cells, to protect said individual, preferably a human, from disease, whether that disease is already established within the individual or not One example of administering the gene is by accelerating it into the desired cells as a coating on particles or otherwise Such nucleic acid vector may comprise DNA. RNA. a ribozyme. a modified nucleic acid, a DNA/RNA hybrid, a DNA-protem complex or an RNA-protem complex
A further aspect of the invention relates to an immunological composition that when introduced into an individual, preferably a human, capable of having induced within it an immunological response, induces an immunological response m such individual to a nrdE polynucleotide and/or polypeptide encoded therefrom, wherein the composition comprises a recombinant nrdE polynucleotide and/or polypeptide encoded therefrom and/or comprises DNA and/or RNA which encodes and expresses an antigen of said nrdE polynucleotide polypeptide encoded therefrom, or other polypeptide of the invention The immunological response may be used therapeutically or prophylactically and may take the form of antibody immunity and/or cellular immunity, such as cellular immunity arising from CTL or CD4+ T cells A nrdE polypeptide or a fragment thereof may be fused with co-protein or chemical moiety which ma\ or
Figure imgf000032_0001
not bv itself produce antibodies but which is capable of stabilizing the first protein and producing a fused or modified protein which will have antigenic and/or lmmunogemc properties, and preferably protective properties Thus fused recombinant protein, preferably further comprises an antigenic co-protein, such as hpoprotein D from Hemophilus influenzae, Glutathione-S-transferase (GST) or beta-galactosidase. or any other relatively large co-protem which solubihzes the protein and facilitates production and purification thereof Moreover, the co-protein may act as an adjuvant in the sense of providing a generalized stimulation of the immune system of the organism receiving the protein Th co-protem
Figure imgf000032_0002
be attached to either the amino- or carbow -terminus of the first protein
Provided by this invention are compositions particularly vaccine compositions, and methods comprising the polypeptides and or polynucleotides of the invention and immunostimulatory DNA sequences, such as those described in Sato. Y et al Science 273 352 (1996)
Also, provided by this invention are methods using the described polynucleotide or particular fragments thereof, which have been shown to encode non-variable regions of bacterial cell surface proteins, in polynucleotide constructs used m such genetic immunization experiments in animal models of infection with Staphylococcus aureus Such experiments will be particularly useful for identifying protein epitopes able to provoke a prophylactic or therapeutic immune response It is believed that this approach will allow for the subsequent preparation of monoclonal antibodies of particular value, derived from the requisite organ of the animal successfully resisting or clearing infection, for the development of prophylactic agents or therapeutic treatments of bacterial infection, particularly Staphylococcus aureus infection, in mammals, particularly humans
A poly peptide of the invention may be used as an antigen for vaccination of a host to produce specific antibodies which protect against invasion of bacteria, for example by blocking adherence of bacteria to damaged tissue Examples of tissue damage include wounds in skm or connective tissue caused, for example, by mechanical, chemical, thermal or radiation damage or by implantation of indwelling devices, or wounds in the mucous membranes, such as the mouth, throat, mammary glands, urethra or vagina
The invention also includes a vaccine formulation which comprises an lmmunogemc recombinant polypeptide and/or polynucleotide of the invention together with a suitable carrier, such as a pharmaceutically acceptable carrier Since the polypeptides and polynucleotides may be broken down m the stomach, each is preferably administered parenterally, including, for example, administration that is subcutaneous, intramuscular, intravenous, or mtradermal Formulations suitable for parenteral administration include aqueous and non-aqueous sterile injection solutions which may contain anti- oxidants buffers bacteristatic compounds and solutes which render the formulation isotomc with the bodily fluid, preferably the blood, of the individual, and aqueous and non-aqueous sterile suspensions which may include suspending agents or thickening agents The formulations may be presented in unit- dose or multi-dose containers, for example, sealed ampoules and vials and may be stored in a freeze- dπed condition requiring only the addition of the sterile liquid carrier immediately prior to use The vaccine formulation may also include adjuvant systems for enhancing the lmmunogenicity of the formulation, such as oil-in water systems and other systems known in the art The dosage will depend on the specific activity of the vaccine and can be readily detenmned by routine experimentation
While the invention has been described with reference to certain nrdE polypeptides and polynucleotides. it is to be understood that this covers fragments of the naturally occurring polypeptides and polynucleotides, and similar polypeptides and polynucleotides with additions, deletions or substitutions which do not substantially affect the lmniunogenic properties of the recombinant polypeptides or polynucleotides
Compositions, kits and administration
In a further aspect of tlie mvention there are provided compositions compnsmg a nrdE polynucleotide and or a nrdE polypeptide for administration to a cell or to a multicellular orgamsm
Tlie mvention also relates to compositions compnsmg a polynucleotide and/or a polypeptides discussed herem or their agonists or antagorasts Tlie polypeptides and polynucleotides of the mvention may be employed m combmation with a non-stenle or stenle earner or carriers for use with cells, tissues or organisms, such as a pharmaceutical earner suitable for administration to an individual Such compositions compnse. for instance, a media additive or a therapeutically effective amount of a polypeptide and/or polynucleotide of the invention and a pharmaceutically acceptable earner or excipient Such earners may mclude but are not limited to. salme. buffered salme. dextrose, water, glycerol, ethanol and combmations thereof The formulation should suit the mode of administration The mvention further relates to diagnostic and pharmaceutical packs and kits compnsmg one or more containers filled with one or more of the ingredients of the aforementioned compositions of the mvention
Polypeptides. polynucleotides and other compounds of tlie mvention may be employed alone or m conjunction with other compounds, such as therapeutic compounds The pharmaceutical compositions may be administered in any effective, convenient manner mcludmg, for instance, administration by topical, oral. anal, vagmal. mtravenous. mtrapentoneal. intramuscular, subcutaneous, mtranasal or lntradermal routes among others
In therapy or as a prophylactic, the active agent may be administered to an individual as an liijectable composition, for example as a sterile aqueous dispersion, preferably isotomc Alternatively the composition may be formulated for topical application for example in the form of ointments, creams, lotions, eye ointments, eye drops, ear drops, mouthwash, impregnated dressings and sutures and aerosols, and may contain appropriate conventional additives, including, for example, preservatives, solvents to assist drug penetration, and emollients m ointments and creams Such topical formulations may also contain compatible conventional carriers, for example cream or ointment bases, and ethanol or oleyl alcohol for lotions Such carriers may constitute from about 1% to about 98% by weight of the formulation, more usually they will constitute up to about 80% by weight of the formulation hi a further aspect, the present mvention provides for pharmaceutical compositions compnsmg a therapeutically effective amount of a polypeptide and/or polynucleotide. such as tlie soluble fonn of a polypeptide and/or polynucleotide of the present mvention, agomst or antagonist peptide or small molecule compound, m combination with a pharmaceutically acceptable earner or excipient Such earners mclude, but are not limited to. saline, buffered salme. dextrose, water, glycerol, ethanol, and combmations thereof The mvention further relates to pharmaceutical packs and kits compnsmg one or more containers filled with one or more of tlie ingredients of the aforementioned compositions of tlie mvention Polypeptides, polynucleotides and other compounds of the present mvention may be employed alone or m conjunction with other compounds, such as therapeutic compounds
Tlie composition will be adapted to the route of administration, for instance by a systemic or an oral route Preferred forms of systemic administration mclude mjection, typically by mtravenous injection Other injection routes, such as subcutaneous, mtramuscular. or mtrapentoneal. can be used Alternative means for systemic administration mclude transmucosal and transdermal administration usmg penetrants such as bile salts or fusidic acids or other detergents In addition, if a polypeptide or other compounds of the present mvention can be formulated m an entenc or an encapsulated formulation, oral administration may also be possible Administration of these compounds may also be topical and or localized, m the form of salves, pastes, gels, and the like
For administration to mammals, and particularly humans, it is expected that the daily dosage level of the active agent will be from 0 01 mg/kg to 10 mg/kg, typically around 1 mg/kg The physician in any event will determine the actual dosage which will be most suitable for an individual and will vary with the age, weight and response of the particular individual The above dosages are exemplary of the average case There can, of course, be individual instances where higher or lower dosage ranges are merited, and such are within the scope of this invention
In-dwelling devices include surgical implants, prosthetic devices and catheters. 1 e . devices that are introduced to the body of an individual and remain in position for an extended time Such devices include, for example, artificial joints, heart valves, pacemakers, vascular grafts, vascular catheters. cerebrospmal fluid shunts, urinary catheters, continuous ambulatory peritoneal dialysis (CAPD) catheters
The composition of the invention may be administered by injection to achieve a systemic effect against relevant bacteria shortly before insertion of an m-dwelhng device Treatment may be continued after surgery during the m-body time of the device In addition, the composition could also be used to broaden peπoperative cover for any surgical technique to prevent bacterial wound infections, especially
Staphylococcus aureus wound infections
Many orthopedic surgeons consider that humans with prosthetic joints should be considered for antibiotic prophylaxis before dental treatment that could produce a bacteremia Late deep infection is a serious complication sometimes leading to loss of the prosthetic joint and is accompanied by significant morbidity and mortality It may therefore be possible to extend the use of the active agent as a replacement for prophylactic antibiotics in this situation
In addition to the therapy described above, the compositions of this invention may be used generally as a wound treatment agent to prevent adhesion of bacteria to matrix proteins exposed m wound tissue and for prophylactic use in dental treatment as an alternative to. or in conjunction with, antibiotic prophylaxis Alternatively, the composition of the invention may be used to bathe an indwelling device immediately before insertion The active agent will preferably be present at a concentration of lμg/ml to lOmg/ml for bathing of wounds or indwelling devices A vaccine composition is conveniently in injectable form Conventional adjuvants may be employed to enhance the immune response A suitable unit dose for vaccination is 0 5-5 microgram/kg of antigen, and such dose is preferably administered 1 -3 times and with an interval of 1 -3 weeks With the indicated dose range, no adverse toxicological effects will be observed with the compounds of the invention which would preclude their administration to suitable individuals Sequence Databases, Sequences in a Tangible Medium, and Algorithms
Polynucleotide and polypeptide sequences form a valuable information resource with which to determine their 2- and 3 -dimensional structures as well as to identify further sequences of similar homology These approaches are most easily facilitated by storing tlie sequence m a computer readable medium and then usmg tlie stored data m a known macromolecular structure program or to search a sequence database usmg well known searching tools, such as GCC
The polynucleotide and polypeptide sequences of the invention are particularly useful as components in databases useful for search analyses as well as m sequence analysis algorithms As used in this section entitled "Sequence Databases Sequences in a Tangible Medium, and Algorithms." and in claims related to this section, the terms "polynucleotide of the invention" and "polynucleotide sequence of the invention" mean any detectable chemical or physical characteristic of a polynucleotide of the invention that is or may be reduced to or stored in a tangible medium, preferably a computer readable form For example, chromatographic scan data or peak data, photographic data or scan data therefrom, called bases, and mass spectrographic data As used in this section entitled Databases and Algorithms and in claims related thereto, the terms "polypeptide of the invention" and "polypeptide sequence of the invention" mean any detectable chemical or physical characteristic of a polypeptide of the invention that is or may be reduced to or stored in a tangible medium, preferably a computer readable form For example, chromatographic scan data or peak data, photographic data or scan data therefrom, and mass spectrographic data The mvention provides a computer readable medium having stored thereon polypeptide sequences of the invention and/or polynucleotide sequences of the invention For example, a computer readable medium is provided comprising and having stored thereon a member selected from the group consistmg of a polynucleotide comprising the sequence of a polynucleotide of the invention, a polypeptide comprising the sequence of a polypeptide sequence of the invention, a set of polynucleotide sequences wherein at least one of the sequences comprises the sequence of a polynucleotide sequence of the invention, a set of polypeptide sequences wherein at least one of the sequences comprises the sequence of a polypeptide sequence of the invention, a data set representing a polynucleotide sequence comprising the sequence of polynucleotide sequence of the invention, a data set representing a polynucleotide sequence encoding a polypeptide sequence comprising the sequence of a polypeptide sequence of the invention, a polynucleotide comprising the sequence of a polynucleotide sequence of the invention, a polypeptide comprising the sequence of a polypeptide sequence of the invention, a set of polynucleotide sequences wherein at least one of the sequences comprises the sequence of a polynucleotide sequence of the invention, a set of polypeptide sequences wherein at least one of said sequences comprises the sequence of a polypeptide sequence of the invention, a data set representing a polynucleotide sequence comprising the sequence of a polynucleotide sequence of the invention, a data set representing a polynucleotide sequence encoding a polypeptide sequence comprising the sequence of a polypeptide sequence of the invention The computer readable medium can be any composition of matter used to store information or data, including, for example, commercially available floppy disks, tapes, chips, hard drives, compact disks, and video disks
Also provided by the invention are methods for the analy sis of character sequences or strings, particularly genetic sequences or encoded genetic sequences Preferred methods of sequence analysis include, for example, methods of sequence homology analysis, such as identity and similarity analysis, RNA structure analysis, sequence assembly, cladistic analysis, sequence motif analysis, open reading frame determination, nucleic acid base calling, nucleic acid base trimming, and sequencing chromatogram peak analysis
A computer based method is provided for performing homology identification This method comprises the steps of providing a first polynucleotide sequence comprising the sequence a polynucleotide of the invention in a computer readable medium, and comparing said first polynucleotide sequence to at least one second polynucleotide or polypeptide sequence to identify homology
A computer based method is also provided for performing homology identification, said method comprising the steps of providing a first polypeptide sequence comprising the sequence of a polypeptide of the invention in a computer readable medium, and comparing said first polypeptide sequence to at least one second polynucleotide or polypeptide sequence to identify homology
A computer based method is still further provided for polynucleotide assembly, said method comprising the steps of providing a first polynucleotide sequence comprising the sequence of a polynucleotide of the invention in a computer readable medium, and screening for at least one overlapping region between said first polynucleotide sequence and at least one second polynucleotide or polypeptide sequence
A computer based method is still further provided for polynucleotide assembly, said method comprising the steps of providing a first polypeptide sequence comprising a polypeptide of the invention in a computer readable medium, and screening for at least one overlapping region between said first polypeptide sequence and at least one second polynucleotide or polypeptide sequence hi another preferred embodiment of die mvention there is provided a computer readable medium having stored thereon a member selected from the group consisting of a polynucleotide comprising the sequence of SEQ ID NO 1, a polypeptide comprising the sequence of SEQ ID NO 2, a set of polynucleotide sequences wherein at least one of said sequences comprises the sequence of SEQ ID NO 1 , a set of polypeptide sequences wherein at least one of said sequences comprises the sequence of SEQ ID NO 2, a data set representing a polynucleotide sequence comprising the sequence of SEQ ID NO 1 , a data set representing a polynucleotide sequence encoding a polypeptide sequence comprising the sequence of SEQ ID NO 2. a polynucleotide comprising the sequence of SEQ ID NO 1, a polypeptide comprising the sequence of SEQ ID NO 2. a set of polynucleotide sequences wherein at least one of said sequences comprises the sequence of SEQ ID NO 1 , a set of polypeptide sequences wherein at least one of said sequences comprises the sequence of SEQ ID NO 2. a data set representing a polynucleotide sequence comprising the sequence of SEQ ID NO 1. a data set representing a polynucleotide sequence encoding a polypeptide sequence comprising the sequence of SEQ ID NO 2 A further preferred embodiment of the invention provides a computer based method for performing homology identification, said method comprising the steps of providing a polynucleotide sequence comprising the sequence of SEQ ID NO 1 a computer readable medium, and comparing said polynucleotide sequence to at least one polynucleotide or polypeptide sequence to identify homology A still further preferred embodiment of the invention provides a computer based method for performing homolog\ identification, said method comprising the steps of providing a polypeptide sequence comprising the sequence of SEQ ID NO 2 in a computer readable medium, and comparing said poly peptide sequence to at least one polynucleotide or polypeptide sequence to identify homology
A further embodiment of the invention provides a computer based method for polynucleotide assembly, said method comprising the steps of providing a first polynucleotide sequence comprising the sequence of SEQ ID NO 1 in a computer readable medium, and screening for at least one overlapping region between said first polynucleotide sequence and a second polynucleotide sequence
A further embodiment of the invention provides a computer based method for performing homology identification, said method comprising the steps of providing a polynucleotide sequence comprising the sequence of SEQ ID NO 1 in a computer readable medium, and comparing said polynucleotide sequence to at least one polynucleotide or polypeptide sequence to identify homology All publications and references, including but not limited to patents and patent applications, cited in this specification are herein incorporated by reference in their entirety as if each individual publication or reference were specifically and individually indicated to be incorporated by reference herein as being fully set forth Any patent application to which this application claims prionty is also incorporated by reference herein in its entirety in the manner described above for publications and references
GLOSSARY
The following definitions are provided to facilitate understanding of certain terms used frequently herem
"Antιbody(ιes)" as used herein includes polyclonal and monoclonal antibodies, chimeπc. single chain, and humanized antibodies, as well as Fab fragments, including the products of an Fab or other lmmunoglobuhn expression library
"Antigemcally equivalent deπvatιve(s)" as used herein encompasses a polypeptide, polynucleotide. or the equivalent of either which will be specifically recognized by certain antibodies which, when raised to the protem, polypeptide or polynucleotide according to the invention, interferes with the immediate physical interaction between pathogen and mammalian host
"Bispecific antιbody(ιes)" means an antibody comprising at least two antigen binding domains, each domain directed against a different epitope "Bodily mateπal(s) means any matenal denved from an individual or from an orgamsm infecting, infesting or inhabiting an individual, mcludmg but not limited to, cells, tissues and waste, such as. bone, blood, serum, cerebrospmal fluid, semen, saliva, muscle, cartilage, organ tissue, skin, urine, stool or autopsy matenals
"Dιsease(s)" means any disease caused by or related to infection by a bactena. mcludmg , for example, disease, such as. infections of the upper respiratory tract (e g , otitis media, bactenal tracheitis. acute epiglottitis, thyroiditis). lower respiratory (e g . empyema. lung abscess), cardiac (e g . infective endocarditis), gastromtestmal (e g . secretory diarrhoea, splemc absces, retropentoneal abscess), CNS (e g . cerebral abscess), eye (e g . blephantis. conjunctivitis, keratitis. endophthalrratis, preseptal and orbital cellulitis. darcryocystitis). kidney and urinary tract (e g . epididymitis. mtrarenal and pennephnc absces, toxic shock syndrome), skin (e g . impetigo, follicuhtis. cutaneous abscesses, cellulitis. wound infection, bactenal myositis) bone and joint (e g . septic arthntis. osteomyelitis)
"Fusion proteιn(s)" refers to a protein encoded by two. often unrelated, fused genes or fragments thereof In one example, EP-A-0464 discloses fusion proteins comprising various portions of constant region of lmmunoglobu n molecules together with another human protein or part thereof In many cases, employing an lmmunoglobuhn Fc region as a part of a fusion protein is advantageous for use in therapy and diagnosis resulting in, for example, improved pharmacokinetic properties [see, e g , EP-A 0232262] On the other hand, for some uses it would be desirable to be able to delete the Fc part after the fusion protein has been expressed, detected and purified
"Host cell(s)" is a cell which has been transformed or transfected, or is capable of transformation or transfection by an exogenous polynucleotide sequence
"Identity." as known m tlie art. is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as the case may be, as determined by comparing the sequences In the art, "identity" also means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as the case may be, as determined by the match between strings of such sequences "Identity" can be readily calculated by known methods, including but not limited to those described in (Computational Molecular Biology. Lesk. A M , ed . Oxford University Press, New York. 1988. Biocomputing Informatics and Genome Projects. Smith, D W , ed . Academic Press. New York, 1993. Computer Analysis of Sequence Data, Part I, Griffin. A M . and Griffin, H G . eds , Humana Press, New Jersey, 1994, Sequence Analysis in Molecular Biology, von Heinje, G , Academic Press, 1987. and Sequence Analysis Primer, Gπbskov, M and Devereux, J , eds , M Stockton Press, New York. 1991, and Caπllo, 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 in publicly available computer programs Computer program methods to determine identity between two sequences include, but are not limited to. the GCG program package (Devereux, J , et al , Nucleic Acids Research 12(1) 387 (1984)). BLASTP. BLASTN, and FASTA (Altschul. S F et al , ./ Molec Biol 215 403-410 (1990) The BLAST X program is publicly available from NCBI and other sources (BLAST Manual . Altschul, S , et al . NCBI NLM NIH Bethesda. MD 20894, Altschul, S . et al . J Mol Biol 215 403-410 (1990) The well known Smith Watennan algorithm may also be used to determine identity
Parameters for polypeptide sequence comparison include the following Algorithm Needleman and Wunsch, J Mol Biol 48 443-453 (1970) Comparison matrix BLOSSUM62 from Hentikoff and Hentikoff. Proc Natl Acad Sci USA 89 10915-10919 (1992) Gap Penalty 12 Gap Length Penalty 4 A program useful with these parameters is publicly available as the "gap" program from Genetics Computer Group. Madison WI The aforementioned parameters are the default parameters for peptide comparisons (along with no penalty for end gaps)
Parameters for polynucleotide comparison include the following Algorithm Needleman and Wunsch. J Mol Biol 48 443-453 (1970)
Comparison matrix matches = +10, mismatch = 0 Gap Penalty 50 Gap Length Penalty 3
Available as The "gap" program from Genetics Computer Group. Madison WI These are the default parameters for nucleic acid comparisons
A preferred meaning for "identity" for polynucleotides and polypeptides, as the case may be, are provided in ( 1 ) and (2) below
(1) Polynucleotide embodiments further include an isolated polynucleotide comprising a polynucleotide sequence having at least a 50. 60, 70. 80, 85, 90, 95. 97 or 100% identity to the reference sequence of SEQ ID NO 1. wherein said polynucleotide sequence may be identical to the reference sequence of SEQ ID NO 1 or may include up to a certain integer number of nucleotide alterations as compared to the reference sequence, wherein said alterations are selected from the group consisting of at least one nucleotide deletion, substitution, including transition and transversion. or insertion, and wherein said alterations may occur at the 5' or 3' terminal positions of the reference nucleotide sequence or anywhere between those terminal positions, interspersed either individually among the nucleotides in the reference sequence or m one or more contiguous groups withm the reference sequence, and wherein said number of nucleotide alterations is determined by multiplying the total number of nucleotides in SEQ ID NO 1 by the integer defining the percent identity divided by 100 and then subtracting 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 50 for 50% 0 60 for 60%. 0 70 for 70%. 0 80 for 80%. 0 85 for 85%. 0 90 for 90%. 0 95 for 95%. 0 97 for 97% or 1 00 for 100%. and • is the symbol for the multiplication operator, and wherein any non-integer product of xn and y is rounded down to the nearest integer prior to subtracting it from xn Alterations of a pohnucleotide sequence encoding the polypeptide of SEQ ID NO 2 may create nonsense, nnssense or frameshift mutations in this coding sequence and thereby alter the polypeptide encoded by the polynucleotide following such alterations
By way of example, a polynucleotide sequence of the present invention may be identical to the reference sequence of SEQ ID NO 1. that is it may be 100% identical, or it may include up to a certain integer number of nucleic acid alterations as compared to the reference sequence such that the percent identity is less than 100% identity Such alterations are selected from the group consisting of at least one nucleic acid deletion, substitution, including transition and transversion, or insertion, and wherein said alterations may occur at the 5' or 3' terminal positions of the reference polynucleotide sequence or anywhere between those ten nal positions, interspersed either individually among the nucleic acids in the reference sequence or in one or more contiguous groups within the reference sequence The number of nucleic acid alterations for a given percent identity is deten ned by multiplying the total number of nucleic acids in SEQ ID NO 1 by the integer defining the percent identity divided by 100 and then subtracting that product from said total number of nucleic acids m SEQ ID NO 1, or
nn < xn - (xn • y),
wherein nn is the number of nucleic acid alterations. xn is the total number of nucleic acids in SEQ ID NO 1, y is, for instance 0 70 for 70%. 0 80 for 80%. 0 85 for 85% etc . • is the symbol for the multiplication operator, and wherein any non-integer product of xn and y is rounded down to the nearest integer prior to subtracting it from xn
(2) Polypeptide embodiments further include an isolated polypeptide comprising a polypeptide having at least a 50,60, 70. 80. 85, 90, 95. 97 or 100% identity to a polypeptide reference sequence of SEQ ID NO 2. wherein said polypeptide sequence may be identical to the reference sequence of SEQ ID NO 2 or may include up to a certain integer number of ammo acid alterations as compared to the reference sequence, wherein said alterations are selected from the group consisting of at least one amino acid deletion, substitution, including conservative and non-conservative substitution, or insertion, and wherein said alterations may occur at the amino- or carboxy-terminal positions of the reference polypeptide sequence or anywhere between those terminal positions, interspersed either individually among the ammo acids in the reference sequence or in one or more contiguous groups withm the reference sequence, and wherein said number of ammo acid alterations is determined by multiplying the total number of ammo acids in SEQ ID NO 2 b\ the integer defining the percent identity divided by 100 and then subtracting that product from said total number of ammo acids in SEQ ID NO 2. or na ≤ xa - (xa * Y)»
wherein na is the number of amino acid alterations, xa is the total number of amino acids m SEQ ID NO 2, y is 0 50 for 50%, 0 60 for 60%. 0 70 for 70%, 0 80 for 80%, 0 85 for 85%, 0 90 for 90%, 0 95 for 95%, 0 97 for 97% or 1 00 for 100%, and • is the symbol for the multiplication operator, and wherein any non-integer product of xa and y is rounded down to the nearest integer prior to subtracting
By way of example, a polypeptide sequence of the present invention may be identical to the reference sequence of SEQ ID NO 2, that is it may be 100% identical, or it may include up to a certain integer number of amino acid alterations as compared to the reference sequence such that the percent identity is less than 100% identity Such alterations are selected from the group consisting of at least one ammo acid deletion, substitution, including conservative and non-conservative substitution, or insertion, and wherein said alterations may occur at the amino- or carboxy-terminal positions of the reference polypeptide sequence or anywhere between those terminal positions, interspersed either individually among the ammo acids in the reference sequence or m one or more contiguous groups within the reference sequence The number of amino acid alterations for a given % identity is determined by multiplying the total number of ammo acids m SEQ ID NO 2 by the integer defining the percent identity divided by 100 and then subtracting that product from said total number of amino acids in SEQ ID NO 2, or
na ≤ xa " (xa * y)>
wherein na is the number of amino acid alterations. xa is the total number of ammo acids in SEQ ID NO 2, y is. for instance 0 70 for 70%. 0 80 for 80%. 0 85 for 85% etc , and • is the symbol for the multiplication operator and wherein any non-mteger product of xa and y is rounded down to the nearest integer prior to subtracting it from xa
"lmmunologically equivalent deπvatιve(s)" as used herein encompasses a polypeptide polynucleotide. or the equivalent of either which when used in a suitable formulation to raise antibodies in a vertebrate, the antibodies act to interfere with the immediate physical interaction between pathogen and mammalian host "Immunospecific'" means that characteristic of an antibody whereby it possesses substantially greater affinity for the polypeptides of the mvention or the polynucleotides of the invention than its affinity for other related polypeptides or polynucleotides respectively, particularly those polypeptides and polynucleotides in the pnor art. "Individual(s)" means a multicellular eukaryote. mcludmg. but not limited to a metazoan, a mammal, an ovid. a bovid. a simian, a primate, and a human.
"Isolated" means altered "by the hand of man" from its natural state, ; e., if it occurs m nature, it has been changed or removed from its original environment, or both For example, a polynucleotide or a polypeptide naturally present in a livmg organism is not "isolated," but the same polynucleotide or polypeptide separated from the coexistmg materials of its natural state is "isolated", as the term is employed herem. Moreover, a polynucleotide or polypeptide that is introduced into an organism by transformation, genetic manipulation or by any other recombinant method is "isolated" even if it is still present in said organism, which organism may be living or non-living.
"Organism(s)" means a (I) prokaryote. mcludmg but not limited to, a member of the genus Streptococcus, Staphylococcus, Bordetella, Corynebacterium, Mycobacterium, Neissena, Haemophilus, Actinomycetes, Streptomycetes, Nocardia, Enterobacter, Yersinia, Fancisella, Pasturella, Moraxella, Acinetobacter, Erysipelothnx, Branhamella, Actinobacillus, Streptobacillus, Listeria, Calymmatobactenum, Brucella, Bacillus, Clostndium, Treponema, Eschenchia, Salmonella, Kleibsiella, Vibrio, Proteus. Erwinia, Borreba, Leptospira, Spirillum, Campylobacter, Shigella, Legionella, Pseudomonas, Aeromonas, Rickettsia, Chlamydia, Borreba and Mycoplasma. and further mcludmg. but not limited to. a member of the species or group, Group A Streptococcus, Group B Streptococcus, Group C Streptococcus, Group D Streptococcus, Group G Streptococcus, Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus agalactiae, Streptococcus faecabs, Streptococcus faecium, Streptococcus durans. Neissena gonorrheae, Neissena menmgitidis, Staphylococcus aureus, Staphylococcus ep dermidis, Corynebacterium diptheriae, Gardnerella vaginabs, Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium ulcerans, Mycobacterium leprae, Actinomyctes israelu, Listeria monocytogenes, Bordetella pertusis, Bordatella parapertusis, Bordetella bronchiseptica, Eschenchia cob, Shigella dysentenae, Haemophilus mfluenzae, Haemophilus aegypt us, Haemophilus parainfluenzae, Haemophilus ducrey , Bordetella, Salmonella typhi, Citrobacter freundn. Proteus mirabibs, Proteus vulgaπs, Yersinia pestis, Kleibsiella pneumoniae, Serratia marcessens, Serratia bquefaciens, Vibrio cholera, Shigella dysenterii, Shigella flexnen, Pseudomonas aeruginosa, Franscisella tularensis, Brucella aborbs, Bacillus anthracis, Bacillus cereus Clostndium perfrmgens. Clostndium tetani Clostndium botubnum, Treponema palbdum Rickettsia rickettsu and Chlamydia trachomitis, (n) 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
"Polynucleotιde(s)" generally refers to any polynbonucleotide or polydeoxynbonucleotide, which 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 tnple-stranded regions, smgle- and double-stranded RNA, and RNA that is mixture of smgle- and double-stranded regions, hybnd molecules compnsmg DNA and RNA that may be single-stranded or, more typically, double-stranded, or tnple-stranded regions, or a mixture of smgle- and double-stranded regions In addition, "polynucleotide" as used herem refers to tnple-stranded regions compnsmg RNA or DNA or both RNA and DNA The strands in 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 triple-helical region often is an ohgonucleotide As used herem, the term "polynucleotιde(s)" also mcludes DNAs or RNAs as descnbed above that contain one or more modified bases Thus, DNAs or RNAs with backbones modified for stability or for other reasons are "polynucleotιde(s)" as that term is mtended herem Moreover, DNAs or RNAs compnsmg unusual bases, such as inosine, or modified bases, such as tntylated 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 in the art The term "polynucleotιde(s)" as it is employed herem embraces such chemically, enzymatically or metabolically modified forms of polynucleotides. as well as tlie chemical forms of DNA and RNA charactenstic of viruses and cells, mcludmg, for example, simple and complex cells "Polynucleotιde(s)" also embraces short polynucleotides often referred to as ohgonucleotιde(s)
"Polypeptιde(s)" refers to any peptide or protem compnsmg two or more amino acids jomed to each other by peptide bonds or modified peptide bonds "Polypeptιde(s)" refers to both short chams, commonly referred to as peptides, ohgopeptides and ohgomers and to longer chams generally referred to as protems Polypeptides may contain ammo acids other than the 20 gene encoded amino acids "Polypeptιde(s)" mclude those modified either by natural processes, such as processmg and oilier post-translational modifications, but also by chemical modification techniques Such modifications are well descnbed m basic texts and m more detailed monographs, as well as m a volummous research literature, and they are well known to those of skill m the art It will be appreciated that the same type of modification may be present m the same or varying degree at several sites m a given polypeptide Also, a given polypeptide may contain many types of modifications Modifications can occur anywhere in a polypeptide. mcludmg the peptide backbone, the ammo acid side-chams. and tlie ammo or carboxyl termini Modifications mclude. for example, acetylation. acvlation. 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 deπvative, covalent attachment of phosphotidylinositol, cross-linking, cychzation, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, fonnylation, 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 protems, 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), Seifter et al . Meth Enzymol 182 626-646 (1990) and Rattan et al , Protein Synthesis Posttranslational Modifications and Aging. Ann N Y Acad Sci 663 48-62 (1992) Polypeptides may be branched or cyclic, with or without branching Cyclic, branched and branched circular polypeptides may result from posttranslational natural processes and may be made by entirely synthetic methods, as well
"Recombinant expression system(s)" refers to expression systems or portions thereof or polynucleotides of tlie mvention mtroduced or transformed mto a host cell or host cell lysate for the production of tlie polynucleotides and polypeptides of the mvention
"Subtraction set" is one or more, but preferably less than 100, polynucleotides comprising at least one polynucleotide of the invention
'Naπant(s)' as the tenn is used herein, is a polynucleotide or polypeptide that differs from a reference polynucleotide or polypeptide respectively, but retains essential properties A typical vanant of a polynucleotide differs in nucleotide sequence from another, reference polynucleotide Changes m the nucleotide sequence of the variant may or may not alter the amino acid sequence of a polypeptide encoded by the reference polynucleotide Nucleotide changes may result in amino acid substitutions, additions, deletions, fusion protems and truncations in the polypeptide encoded by the reference sequence, as discussed below A typical variant of a polypeptide differs in ammo acid sequence from another reference polypeptide Generally, differences are limited so that the sequences of the reference polypeptide and the variant are closely similar overall and. in many regions, identical A variant and reference polypeptide may differ in ammo acid sequence by one or more substitutions, additions, deletions m any combination A substituted or inserted amino acid residue may or may not be one encoded by the genetic code The present mvention also mcludes mclude vanants of each of the polypeptides of the mvention. that is polypeptides that vary from the referents by conservative ammo acid substitutions, whereby a residue is substituted by another with like charactenstics Typical such substitutions are among Ala. Val. Leu and He. among Ser and Thr. among tlie acidic residues Asp and Glu, among Asn and Gin and among the basic residues Lvs and Arg, or aromatic residues Phe and Tyr Particularly preferred 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 allehc variant, or it may be a variant that is not known to occur naturally Non-naturally occurring variants of polynucleotides and polypeptides may be made by mutagenesis techniques, by direct synthesis, and by other recombinant methods known to skilled artisans EXAMPLES
The examples below are earned out usmg standard techniques, which are well known and routme to those of skill in the art. except where otherwise descnbed m detail The examples are illustrative but do not limit the mvention Example 1 Strain selection, Library Production and Sequencing
The polynucleotide having a DNA sequence given in Table 1 [SEQ ID NO 1] was obtained from a library of clones of chromosomal DNA of Staphylococcus aureus m E cob The sequencing data from two or more clones containing overlapping Staphylococcus aureus DNAs was used to construct the contiguous DNA sequence in SEQ ID NO 1 Libraries may be prepared by routine methods, for example
Methods 1 and 2 below
Total cellular DNA is isolated from Staphylococcus aureus WCUH 29 according to standard procedures and size-fractionated by either of two methods Method 1 Total cellular DNA is mechanically sheared by passage through a needle in order to size- fractionate according to standard procedures DNA fragments of up to 1 lkbp in size are rendered blunt by treatment with exonuclease and DNA polymerase. and EcoRI linkers added Fragments are hgated into the vector Lambda ZapII that has been cut with EcoRI. the library packaged b\ standard procedures and E cob infected with the packaged library The library is amplified by standard procedures
Method 2
Total cellular DNA is partially hydrolyzed with a one or a combination of restriction enzymes appropriate to generate a series of fragments for cloning into library vectors (e g , Rsal. Pall. Alul, Bshl235I), and such fragments are size-fractionated according to standard procedures EcoRI linkers are ligated to the DNA and the fragments then ligated into the vector Lambda ZapII 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

Claims

What is claimed is: 1 An isolated polypeptide selected from the group consisting of
(1) an isolated polypeptide comprising an ammo acid having at least
(a) 70% identity,
(b) 80% identity,
(c) 90% identity, or
(d) 95% identity to the ammo acid sequence of SEQ ID NO 2 over the entire length of SEQ ID NO 2, (u) an isolated polypeptide comprising the amino acid sequence of SEQ ID NO 2, (in) an isolated polypeptide which is the ammo acid sequence of SEQ ID NO 2, and (iv) a polypeptide which is encoded by a recombinant polynucleotide comprising the polynucleotide sequence of SEQ ID NO 1
2 An isolated polynucleotide selected from the group consisting of
(I) an isolated polynucleotide compnsmg a polynucleotide sequence encoding a polypeptide that has at least
(a) 70% identity,
(b) 80% identity,
(c) 90% identity, or
(d) 95% identity, to tlie amino acid sequence of SEQ ID NO 2, over the entire length of SEQ ID NO 2, (n) an isolated polynucleotide compnsmg a polynucleotide sequence that has at least
(a) 70% identity
(b) 80% identity,
(c) 90% identity, or
(d) 95% identity, over its entire length to a polynucleotide sequence encodmg the polypeptide of SEQ ID
NO 2.
(m) an isolated polynucleotide composing a nucleotide sequence which has at least
(a) 70% identity,
(b) 80% ιdentιt
(c) 90% identity, or
(d) 95% identity, to that of SEQ ID NO 1 over the entire length of SEQ ID NO 1 ,
(iv) an isolated polynucleotide composmg a nucleotide sequence encodmg the polypeptide of SEQ ID
NO 2,
(v) an isolated polynucleotide which is the polynucleotide of SEQ ID NO 1 ,
(vi) an isolated polynucleotide obtainable by screenmg an appropoate library under stringent hybodization conditions with a probe havmg the sequence of SEQ ID NO 1 or a fragment thereof, (vn) an isolated polynucleotide encodmg a mature polypeptide expressed by the nrdE gene contamed in the Staphylococcus aureus, and
(vin) a polynucleotide sequence complementary to said isolated polynucleotide of (l), (u), (in), (iv),
Figure imgf000050_0001
3 An antibody antigenic to or lmmunospecific for the polypeptide of claim 1
4 A method for the treatment of an individual
(l) in need of enhanced activity or expression of the polypeptide of claim 1 composing the step of
(a) administering to the individual a therapeutically effective amount of an agonist to said polypeptide, or
(b) providing to the individual an isolated polynucleotide composmg a polynucleotide sequence encodmg said polypeptide in a foπn so as to effect production of said polypeptide activity in vivo, or
(n) having need to inhibit activity or expression of the polypeptide of claim 1 comprising
(a) administering to the individual a therapeutically effective amount of an antagonist to said polypeptide, or
(b) administering to the individual a nucleic acid molecule that inhibits the expression of a polynucleotide sequence encoding said polypeptide, or
(c) administering to the individual a therapeutically effective amount of a polypeptide that competes with said polypeptide for its hgand. substrate . or receptor
5 A process for diagnosing or prognosing 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 comprising the step of
(a) determining the presence or absence of a mutation in the nucleotide sequence encoding said polypeptide m the genome of said individual, or (b) analyzing for the presence or amount of said polypeptide expression in a sample derived from said individual
6 A method for screening to identify compounds that activate or that inhibit the function of tlie polypeptide of claim 1 which composes a method selected from the group consisting of
(a) measuring the bmdmg of a candidate compound to the polypeptide or to the cells or membranes bearing the polypeptide or a fusion protein thereof by means of a label directly or indirectly associated with the candidate compound,
(b) measuring the bmdmg of a candidate compound to the polypeptide or to the cells or membranes bearing the polypeptide or a fusion protein thereof in the presence of a labeled competitor,
(c) testing whether the candidate compound results in a signal generated by activation or inhibition of the polypeptide. using detection systems appropriate to the cells or cell membranes bearing the polypeptide,
(d) mixing a candidate compound with a solution containing a polypeptide of claim 1. to form a mixture, measuring activity of the polypeptide m the mixture, and comparing the activity of the mixture to a standard,
(e) detecting the effect of a candidate compound on the production of mRNA encoding said polypeptide and said polypeptide in cells, using for instance, an ELISA assay, or
(f) (1) contacting a composition composmg the polypeptide with the compound to be screened under conditions to permit mteraction between the compound and the polypeptide to assess the mteraction of a compound, such mteraction bemg associated with a second component capable of providing a detectable signal in response to the mteraction of tlie polypeptide with the compound, and
(2) determining whether the compound mteracts with and activates or inhibits an activity of the polypeptide by detectmg the presence or absence of a signal generated from the mteraction of the compound with the polypeptide
7 An agonist or an antagonist of the activity or expression polypeptide of claim 1
8 An expression system composmg a polynucleotide capable of producing a polypeptide of claim 1 when said expression system is present m a compatible host cell
9 A host cell composing the expression system of claim 8 or a membrane thereof expressing a poly peptide selected from the group consisting of (1) an isolated polypeptide composing an amino acid sequence selected from the group having at least
(a) 70% identity,
(b) 80% identity,
(c) 90% identity, or
(d) 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 comprising the amino acid sequence of SEQ ID NO 2, (in) an isolated polypeptide which is the amino acid sequence of SEQ ID NO 2. and (iv) a polypeptide which is encoded by a recombinant polynucleotide comprising the polynucleotide sequence of SEQ ID NO 1
10 A process for producing a polypeptide selected from the group consisting of
(1) an isolated polypeptide comprising an amino acid sequence selected from the group having at least
(a) 70% identity,
(b) 80% identity.
(c) 90% identity, or
(d) 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 comprising the ammo acid sequence of SEQ ID NO 2, (in) an isolated polypeptide which is the ammo acid sequence of SEQ ID NO 2, and (iv) a polypeptide which is encoded by a recombinant polynucleotide comprising the polynucleotide sequence of SEQ ID NO 1. composing the step of cultuπng a host cell of claim 9 under conditions sufficient for the production of said polypeptide
1 1 A process for producing a host cell comprising the expression system of claim 8 or a membrane thereof expressing a polypeptide selected from the group consisting of
(I) an isolated polypeptide comprising an amino acid sequence selected from the group having at least
(a) 70% identity.
(b) 80% identity.
(c) 90% identity, or (d) 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 composing the ammo acid sequence of SEQ ID NO 2, (in) an isolated polypeptide which is the ammo acid sequence of SEQ ID NO 2, and (iv) a polypeptide which is encoded by a recombinant polynucleotide comprising the polynucleotide sequence of SEQ ID NO 1, said process comprising the step of transforming or transfecting a cell with an expression system compnsmg a polynucleotide capable of producing said polypeptide of (I), (u), (m) or (iv) when said expression system is present in a compatible host cell such the host cell, under appropriate culture conditions, produces said polypeptide of (l). (n). (m) or (iv)
12 A host cell produced by the process of claim 11 or a membrane thereof expressing a polypeptide selected from the group consisting of
(1) an isolated polypeptide composing an amino acid sequence selected from the group having at least
(a) 70% identity,
(b) 80% identity,
(c) 90% identity, or
(d) 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 comprising the amino acid sequence of SEQ ID NO 2, (in) an isolated polypeptide which is the amino acid sequence of SEQ ID NO 2, and (iv) a polypeptide which is encoded by a recombinant polynucleotide comprising the polynucleotide sequence of SEQ ID NO 1
13 A computer readable medium having stored thereon a member selected from the group consisting of a polynucleotide composing the sequence of SEQ ID NO 1. a polypeptide comprising the sequence of SEQ ID NO 2. a set of polynucleotide sequences wherein at least one of said sequences comprises the sequence of SEQ ID NO 1, a set of polypeptide sequences wherein at least one of said sequences comprises the sequence ofSEQ ID NO 2. a data set representing a polynucleotide sequence composing the sequence of SEQ ID NO 1. a data set representing a polynucleotide sequence encoding a polypeptide sequence composing the sequence of SEQ ID NO 2, a polynucleotide comprising the sequence of SEQ ID NO 1, a polypeptide comprising the sequence of SEQ ID NO 2. a set of polynucleotide sequences wherein at least one of said sequences comprises the sequence of SEQ ID NO 1. a set of polypeptide sequences wherein at least one of said sequences comprises the sequence of SEQ ID NO 2. a data set representing a polynucleotide sequence composing the sequence of SEQ ID NO 1. a data set representing a polynucleotide sequence encoding a polypeptide sequence composing the sequence of SEQ ID NO 2
14 A computer based method for performing homology identification, said method composing the steps of providing a polynucleotide sequence comprising the sequence of SEQ ID NO 1 in a computer readable medium, and comparing said polynucleotide sequence to at least one polynucleotide or polypeptide sequence to identify homology
15 A further embodiment of the invention provides a computer based method for polynucleotide assembly, said method comprising the steps of providing a first polynucleotide sequence composing the sequence of SEQ ID NO 1 in a computer readable medium, and screening for at least one overlapping region between said first polynucleotide sequence and a second polynucleotide sequence
PCT/US1999/017545 1998-08-10 1999-08-02 nrdE WO2000009541A1 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
JP2000564991A JP2002522059A (en) 1998-08-10 1999-08-02 nrdE
EP99939673A EP1105411A1 (en) 1998-08-10 1999-08-02 nrdE

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US09/132,028 1998-08-10
US09/132,028 US6222014B1 (en) 1998-08-10 1998-08-10 NrdE of staphylococcus aureus

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WO2000009541A1 true WO2000009541A1 (en) 2000-02-24

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US7718737B2 (en) * 2004-03-02 2010-05-18 Bridgestone Corporation Rubber composition containing functionalized polymer nanoparticles

Citations (1)

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Publication number Priority date Publication date Assignee Title
EP0786519A2 (en) * 1996-01-05 1997-07-30 Human Genome Sciences, Inc. Staphylococcus aureus polynucleotides and sequences

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP0786519A2 (en) * 1996-01-05 1997-07-30 Human Genome Sciences, Inc. Staphylococcus aureus polynucleotides and sequences

Non-Patent Citations (1)

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Title
DATABASE GENBANK *

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