WO1998018323A1 - Nucleic acid and amino acid sequences relating to helicobacter pylori and vaccine compositions thereof - Google Patents

Nucleic acid and amino acid sequences relating to helicobacter pylori and vaccine compositions thereof Download PDF

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Publication number
WO1998018323A1
WO1998018323A1 PCT/US1997/019575 US9719575W WO9818323A1 WO 1998018323 A1 WO1998018323 A1 WO 1998018323A1 US 9719575 W US9719575 W US 9719575W WO 9818323 A1 WO9818323 A1 WO 9818323A1
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Prior art keywords
seq
pylori
polypeptide
nucleic acid
fragment
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PCT/US1997/019575
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English (en)
French (fr)
Inventor
Douglas Smith
Richard A. Alm
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Astra Aktiebolag
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Publication date
Priority to NZ334568A priority Critical patent/NZ334568A/xx
Application filed by Astra Aktiebolag filed Critical Astra Aktiebolag
Priority to EP97913847A priority patent/EP0973394A4/en
Priority to AU50933/98A priority patent/AU734052B2/en
Priority to SK346-99A priority patent/SK34699A3/sk
Priority to JP52071098A priority patent/JP2001504329A/ja
Priority to BR9712587-3A priority patent/BR9712587A/pt
Priority to CA002265523A priority patent/CA2265523A1/en
Priority to EEP199900176A priority patent/EE9900176A/xx
Priority to IL12939797A priority patent/IL129397A0/xx
Publication of WO1998018323A1 publication Critical patent/WO1998018323A1/en
Priority to IS5005A priority patent/IS5005A/is
Priority to NO991995A priority patent/NO991995L/no
Priority to US10/335,977 priority patent/US20040052799A1/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
    • C12N15/86—Viral vectors
    • 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
    • C07K14/205—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Campylobacter (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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide

Definitions

  • H. pylori is a gram-negative, S-shaped, microaerophilic bacterium that was discovered and cultured from a human gastric biopsy specimen. (Warren, J.R. and B. Marshall, (1983) Lancet ⁇ : 1273-1275; and Marshall et al., (1984) Microbios Lett. 25: 83-88). H. pylori has been strongly linked to chronic gastritis and duodenal ulcer disease. (Rathbone et. al.. (1986) Gut 27_: 635-641).
  • H. pylori colonizes the human gastric mucosa, establishing an infection that usually persists for decades. Infection by H. pylori is prevalent worldwide. Developed countries have infection rates over 50% of the adult population, while developing countries have infection rates reaching 90% of the adults over the age of 20. (Hopkins R. J. and J. G. Morris (1994) Am. J. Med. 97: 265-277).
  • urease an enzyme that may play a role in neutralizing gastric acid pH
  • Ferrero, R.L. and A. Lee 1991 ) Microb. Ecol Hlth. Dis. 4: 121-134; Labigne et al., (1991 ) J. Bacterial. 173: 1920-1931
  • the bacterial flagellar proteins responsible for motility across the mucous layer (Hazell et al., (1986) J. Inf. Dis.
  • This invention relates to novel genes, e.g., genes encoding polypeptides such as bacterial surface proteins, from the organism Helicobacter pylori (H. pylori), and other related genes, their products, and uses thereof.
  • the nucleic acids and peptides of the present invention have utility for diagnostic and therapeutics for H. pylori and other Helicobacter species. They can also be used to detect the presence of//, pylori and other Helicobacter species in a sample; and for use in screening compounds for the ability to interfere with the H. pylori life cycle or to inhibit H. pylori infection. More specifically, this invention features compositions of nucleic acids corresponding to entire coding sequences of H.
  • pylori proteins including surface or secreted proteins or parts thereof, nucleic acids capable of binding mRNA from H. pylori proteins to block protein translation, and methods for producing H. pylori proteins or parts thereof using peptide synthesis and recombinant DNA techniques.
  • This invention also features antibodies and nucleic acids useful as probes to detect H. pylori infection.
  • vaccine compositions and methods for the protection or treatment of infection by //. pylori are within the scope of this invention.
  • Figure 1 is a bar graph that depicts the antibody titer in serum of mice following immunization with specific H. pylori antigens.
  • Figure 2 is a bar graph that depicts the antibody titer in mucous of mice following immunization with specific H. pylori antigens.
  • Figure 3 is a bar graph that depicts therapeutic immunization of H. pylori infected mice with specific antigens dissolved in HEPES buffer.
  • Figure 4 is a bar graph that depicts therapeutic immunization of H. pylori infected mice with specific antigens dissolved in buffer containing DOC. - :> -
  • Figure 5 depicts the amino acid sequence alignment in a portion of the sequence of five H. pylori proteins (depicted in the single letter amino acid code; shown N- terminal to C-terminal, left to right).
  • Figure 6 depicts the amino acid sequence alignment in a portion of the sequence of four H. pylori proteins (depicted in the single letter amino acid code; shown N- terminal to C-terminal, left to right).
  • Figure 7 depicts the amino acid sequence alignment in a portion of the sequence of two H. pylori proteins (depicted in the single letter amino acid code; shown N- terminal to C-terminal, left to right).
  • Figure 8 depicts the amino acid sequence alignment in a portion of the sequence of two H. pylori proteins (depicted in the single letter amino acid code; shown N- terminal to C-terminal, left to right).
  • the invention features a recombinant or substantially pure preparation of //, pylori polypeptide of SEQ ID NO: 74.
  • the invention also includes substantially pure nucleic acid encoding an H. pylori polypeptide of SEQ ID NO: 74, such nucleic acid is contained in SEQ ID NO: 1.
  • the H. pylori polypeptide sequences of the invention described herein are contained in the Sequence Listing, and the nucleic acids encoding H. pylori polypeptides of the invention are contained in the Sequence Listing.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 75, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 2.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 76, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 3.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 77, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 4.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 78, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 5.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 79, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 6.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 80, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 7.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 81, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 8.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 82, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 9.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 83, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 10.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 84, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 11.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 85, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 12.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 86, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 13.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 87, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 14.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 88, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 15.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 89, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 16.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 90, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 17.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 91 , such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 18.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 92, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 19.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 93, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 20.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 94, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 21.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 95, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 22.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 96, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 23.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 97, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 24.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 98, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 25.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 99, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 26.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 100, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 27.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 101, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 28.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 102, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 29.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 103, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 30.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 104, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 31.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 105, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 32.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 106, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 33.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 107, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 34.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 108, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 35.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 109, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 36.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 110, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 37.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 1 11, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 38.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 1 12, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 39.
  • the invention features a substantially pure nucleic acid encoding an H pylori polypeptide having an amino acid sequence of SEQ ID NO: 1 13, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 40.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 1 14, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 41.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 115, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 42.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 1 16, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO:43.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 117, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 44.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 1 18, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 45.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 1 19, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 46.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 120, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 47.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 121, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 48.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 122, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 49.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 123, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 50.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 124, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 51.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 125, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 52.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 126, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 53.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 127, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 54.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 128, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 55.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 129, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 56.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 130, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 57.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 131, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 58.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 132, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 59.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 133, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 60.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 134, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 61.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 135, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 62.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 136, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 63.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 137, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 64.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 138, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 65.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 139, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 66.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 140, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 67.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 141 , such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 68.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 142, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 69.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 143, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 70.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 144, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 71.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 145, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 72.
  • the invention features a substantially pure nucleic acid encoding an H. pylori polypeptide having an amino acid sequence of SEQ ID NO: 146, such as a nucleic acid comprising a nucleotide sequence of SEQ ID NO: 73.
  • nucleic acid comprising a nucleotide sequence encoding an H. pylori cell envelope polypeptide or a fragment thereof.
  • nucleic acid is selected from the group consisting of SEQ ID NO: 3, SEQ ID NO: 25, SEQ ID NO: 48, SEQ ID NO: 16, SEQ ID NO: 10, SEQ ID NO: 45, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 7, SEQ ID NO: 39, SEQ ID NO: 55, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 1, SEQ ID NO: 42, SEQ ID NO: 14, SEQ ID NO: 43, SEQ ID NO: 1 1 , SEQ ID NO: 71, SEQ ID NO: 17, SEQ ID NO: 57, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO:
  • the H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori inner membrane polypeptide or a fragment thereof encoded by the nucleic acid selected from the group consisting of SEQ ID NO: 3, SEQ ID NO: 25, and SEQ ID NO: 48.
  • the H. pylori cell envelope polypeptide or a fragment thereof is an H.
  • the H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue and a C- terminal tyrosine cluster or a fragment thereof encoded by the nucleic acid selected from the group consisting of SEQ ID NO: 1 , SEQ ID NO: 42, SEQ ID NO: 14, SEQ ID NO: 43, SEQ ID NO: 1 1, and SEQ ID NO:71.
  • the H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue or a fragment thereof encoded by the nucleic acid selected from the group consisting of SEQ ID NO: 16, SEQ ID NO: 45, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 7, SEQ ID NO: 39, SEQ ID NO: 55, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 56, and SEQ ID NO: 58.
  • nucleic acid comprising a nucleotide sequence encoding an H. pylori secreted polypeptide or a fragment thereof.
  • nucleic acid is selected from the group consisting of SEQ ID NO: 72, SEQ ID NO: 32, SEQ ID NO: 51, SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 9, SEQ ID NO: 13, SEQ ID NO: 22, SEQ ID NO: 29, SEQ ID NO: 31 , SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 38, SEQ ID NO: 40.
  • SEQ ID NO: 41 SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 49, SEQ ID NO: 53, SEQ ID NO: 59, SEQ ID NO: 61 , SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 67, and SEQ ID NO: 68.
  • nucleic acid comprising a nucleotide sequence encoding an H. pylori cellular polypeptide or a fragment thereof.
  • nucleic acid is selected from the group consisting of SEQ ID NO: 12, SEQ ID NO: 15, SEQ ID NO: 20, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 47, SEQ ID NO: 50, SEQ ID NO: 60, SEQ ID NO: 64, SEQ ID NO: 69, SEQ ID NO: 70, and SEQ ID NO: 73.
  • H. pylori cell envelope polypeptide or a fragment thereof wherein the polypeptide is selected from the group consisting of SEQ ID NO: 76, SEQ ID NO: 98, SEQ ID NO: 121, SEQ ID NO: 89, SEQ ID NO: 83, SEQ ID NO: 1 18, SEQ ID NO: 108, SEQ ID NO: 1 10, SEQ ID NO: 80, SEQ ID NO: 1 12, SEQ ID NO: 128, SEQ ID NO: 91, SEQ ID NO: 92, SEQ ID NO: 101, SEQ ID NO: 103, SEQ ID NO: 125, SEQ ID NO: 127, SEQ ID NO: 129, SEQ ID NO: 131, SEQ ID NO: 74, SEQ ID NO: 1 15, SEQ ID NO: 87, SEQ ID NO: 1 16, SEQ ID NO: 84, SEQ ID NO: 144, SEQ ID NO: 90, SEQ ID NO: 130, SEQ ID NO: 78
  • the H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori inner membrane polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 76, SEQ ID NO: 98, and SEQ ID NO: 121.
  • the H. pylori cell envelope polypeptide or a fragment thereof is an H. pylori outer membrane polypeptide or a fragment thereof selected from the group consisting of SEQ ID NO: 89, SEQ ID NO: 83, SEQ ID NO: 1 18, SEQ ID NO: 108, SEQ ID NO: 1 10, SEQ ID NO: 80, SEQ ID NO: 1 12, SEQ ID NO: 128, SEQ ID NO: 91, SEQ ID NO: 92, SEQ ID NO: 101 , SEQ ID NO: 103, SEQ ID NO: 125, SEQ ID NO: 127, SEQ ID NO: 129, SEQ ID NO: 131 , SEQ ID NO: 74.
  • the H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue and a C- terminal tyrosine cluster or a fragment thereof selected from the group consisting of SEQ ID NO: 74, SEQ ID NO: 1 15, SEQ ID NO: 87, SEQ ID NO: 1 16. SEQ ID NO: 84, and SEQ ID NO: 144.
  • the H. pylori outer membrane polypeptide or a fragment thereof is an H. pylori polypeptide having a terminal phenylalanine residue or a fragment thereof selected from the group consisting of SEQ ID NO: 89.
  • H. pylori secreted polypeptide or a fragment thereof wherein the polypeptide is selected from the group consisting of SEQ ID NO: 145, SEQ ID NO: 105, SEQ ID NO: 124, SEQ ID NO: 75, SEQ ID NO: 77, SEQ ID NO: 82, SEQ ID NO: 86, SEQ ID NO: 95, SEQ ID NO: 102, SEQ ID NO: 104, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 109, SEQ ID NO: 1 1 1, SEQ ID NO: 113, SEQ ID NO: 1 14, SEQ ID NO: 1 17, SEQ ID NO: 1 19, SEQ ID NO: 122, SEQ ID NO: 126, SEQ ID NO: 132, SEQ ID NO: 134, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140, and SEQ ID NO: 145, SEQ ID NO
  • H. pylori cellular polypeptide or a fragment thereof wherein the polypeptide is selected from the group consisting of SEQ ID NO: 85, SEQ ID NO: 88, SEQ ID NO: 93, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 99, SEQ ID NO: 100.
  • the invention pertains to any individual H. pylori polypeptide member or nucleic acid encoding such a member from the above-identified groups of//. pylori polypeptides.
  • the invention features nucleic acids capable of binding mRNA of //, pylori. Such nucleic acid is capable of acting as antisense nucleic acid to control the translation of mRNA of H. pylori.
  • a further aspect features a nucleic acid which is capable of binding specifically to an H pylori nucleic acid. These nucleic acids are also referred to herein as complements and have utility as probes and as capture reagents.
  • the invention features an expression system comprising an open reading frame corresponding to H. pylori nucleic acid.
  • the nucleic acid further comprises a control sequence compatible with an intended host.
  • the expression system is useful for making polypeptides corresponding to H pylori nucleic acid.
  • the invention features a cell transformed with the expression system to produce H. pylori polypeptides.
  • the invention features a method of generating antibodies against H. pylori polypeptides which are capable of binding specifically to H pylori polypeptides.
  • Such antibodies have utility as reagents for immunoassays to evaluate the abundance and distribution of , antigens.
  • the invention features a method of generating vaccines for immunizing an individual against H pylori.
  • the vaccination method includes: immunizing a subject with at least one H pylori polypeptide according to the present invention, e.g., a surface or secreted polypeptide, or active portion thereof, and a pharmaceutically acceptable carrier.
  • H pylori polypeptide e.g., a surface or secreted polypeptide, or active portion thereof, and a pharmaceutically acceptable carrier.
  • Such vaccines have therapeutic and/or prophylactic utilities.
  • the invention provides a method for generating a vaccine comprising a modified immunogenic H. pylori polypeptide, e.g., a surface or secreted polypeptide, or active portion thereof, and a pharmacologically acceptable carrier.
  • the invention features a method of evaluating a compound, e.g. a polypeptide, e.g., a fragment of a host cell polypeptide, for the ability to bind an H. pylori polypeptide. The method includes: contacting the candidate compound with an H pylori polypeptide and determining if the compound binds or otherwise interacts with an H. pylori polypeptide. Compounds which bind H.
  • the invention features a method of evaluating a compound, e.g. a polypeptide, e.g., a fragment of a host cell polypeptide, for the ability to bind an H. pylori nucleic acid, e.g., DNA or RNA.
  • the method includes: contacting the candidate compound with an H pylori nucleic acid and determining if the compound binds or otherwise interacts with an H. pylori polypeptide.
  • Compounds which bind H pylori are candidates as activators or inhibitors of the bacterial life cycle. These assays can be performed in vitro or in vivo.
  • the invention features H. pylori polypeptides, preferably a substantially pure preparation of an H. pylori polypeptide, or a recombinant H. pylori polypeptide.
  • the polypeptide has biological activity; the polypeptide has an amino acid sequence at least 60%, 70%, 80%, 90%, 95%, 98%, or 99% identical or homologous to an amino acid sequence of the invention contained in the Sequence Listing, preferably it has about 65% sequence identity with an amino acid sequence of the invention contained in the Sequence Listing, and most preferably it has about 92% to about 99% sequence identity with an amino acid sequence of the invention contained in the Sequence Listing; the polypeptide has an amino acid sequence essentially the same as an amino acid sequence of the invention contained in the Sequence Listing; the polypeptide is at least 5, 10, 20, 50, 100, or 150 amino acid residues in length; the polypeptide includes at least 5, preferably at least 10, more preferably at least 20, more preferably at least 50, 100, or 150 contiguous amino
  • the amino acid sequence which differs in sequence identity by about 7% to about 8% from the H. pylori amino acid sequences of the invention contained in the Sequence Listing is also encompassed by the invention.
  • the H pylori polypeptide is encoded by a nucleic acid of the invention contained in the Sequence Listing, or by a nucleic acid having at least 60%, 70%, 80%, 90%, 95%, 98%, or 99% homology with a nucleic acid of the invention contained in the Sequence Listing.
  • the subject H. pylori polypeptide differs in amino acid sequence at 1 , 2, 3, 5, 10 or more residues from a sequence of the invention contained in the Sequence Listing. The differences, however, are such that the H. pylori polypeptide exhibits an H. pylori biological activity, e.g., the H. pylori polypeptide retains a biological activity of a naturally occurring H. pylori polypeptide.
  • the polypeptide includes all or a fragment of an amino acid sequence of the invention contained in the Sequence Listing; fused, in reading frame, to additional amino acid residues, preferably to residues encoded by genomic DNA 5' or 3' to the genomic DNA which encodes a sequence of the invention contained in the Sequence Listing.
  • the H. pylori polypeptide is a recombinant fusion protein having a first H. pylori polypeptide portion and a second polypeptide portion, e.g., a second polypeptide portion having an amino acid sequence unrelated to
  • the second polypeptide portion can be, e.g., any of glutathione-S-transferase, a DNA binding domain, or a polymerase activating domain.
  • the fusion protein can be used in a two-hybrid assay.
  • Polypeptides of the invention include those which arise as a result of alternative transcription events, alternative RNA splicing events, and alternative translational and postranslational events.
  • the invention also encompasses an immunogenic component which includes at least one H. pylori polypeptide in an immunogenic preparation; the immunogenic component being capable of eliciting an immune response specific for the H. pylori polypeptide, e.g., a humoral response, an antibody response, or a cellular response.
  • the immunogenic component comprises at least one antigenic determinant from a polypeptide of the invention contained in the Sequence Listing.
  • the invention provides a substantially pure nucleic acid having a nucleotide sequence which encodes an H. pylori polypeptide.
  • the encoded polypeptide has biological activity; the encoded polypeptide has an amino acid sequence at least 60%), 70%, 80%, 90%, 95%, 98%, or 99% homologous to an amino acid sequence of the invention contained in the Sequence
  • the encoded polypeptide has an amino acid sequence essentially the same as an amino acid sequence of the invention contained in the Sequence Listing; the encoded polypeptide is at least 5, 10, 20, 50, 100, or 150 amino acids in length; the encoded polypeptide comprises at least 5, preferably at least 10, more preferably at least 20, more preferably at least 50, 100, or 150 contiguous amino acids of the invention contained in the Sequence Listing.
  • the nucleic acid of the invention is that contained in the Sequence Listing; the nucleic acid is at least 60%, 70%, 80%, 90%, 95%, 98%, or
  • the encoded H. pylori polypeptide differs (e.g., by amino acid substitution, addition or deletion of at least one amino acid residue) in amino acid sequence at 1, 2, 3, 5, 10 or more residues, from a sequence of the invention contained in the Sequence Listing.
  • the differences are such that: the H. pylori encoded polypeptide exhibits a H. pylori biological activity, e.g., the encoded H. pylori enzyme retains a biological activity of a naturally occurring H. pylori.
  • the encoded polypeptide includes all or a fragment of an amino acid sequence of the invention contained in the Sequence Listing; fused, in reading frame, to additional amino acid residues, preferably to residues encoded by genomic DNA 5' or 3' to the genomic DNA which encodes a sequence of the invention contained in the Sequence Listing.
  • the subject H. pylori nucleic acid will include a transcriptional regulatory sequence, e.g. at least one of a transcriptional promoter or transcriptional enhancer sequence, operably linked to the H. pylori gene sequence, e.g., to render the H. pylori gene sequence suitable for expression in a recombinant host cell.
  • a transcriptional regulatory sequence e.g. at least one of a transcriptional promoter or transcriptional enhancer sequence
  • operably linked to the H. pylori gene sequence e.g., to render the H. pylori gene sequence suitable for expression in a recombinant host cell.
  • the nucleic acid which encodes an H. pylori polypeptide of the invention hybridizes under stringent conditions to a nucleic acid probe corresponding to at least 8 consecutive nucleotides of the invention contained in the Sequence Listing; more preferably to at least 12 consecutive nucleotides of the invention contained in the Sequence Listing; more preferably to at least 20 consecutive nucleotides of the invention contained in the Sequence Listing; more preferably to at least 40 consecutive nucleotides of the invention contained in the Sequence Listing.
  • the nucleic acid encodes a peptide which differs by at least one amino acid residue from the sequences of the invention contained in the Sequence Listing.
  • the nucleic acid differs by at least one nucleotide from a nucleotide sequence of the invention contained in the Sequence Listing which encodes amino acids of the invention contained in the Sequence Listing.
  • the invention encompasses: a vector including a nucleic acid which encodes an H. pylori polypeptide or an H pylori polypeptide variant as described herein; a host cell transfected with the vector; and a method of producing a recombinant H. pylori polypeptide or H. pylori polypeptide variant; including culturing the cell, e.g., in a cell culture medium, and isolating the H. pylori or H. pylori polypeptide variant, e.g., from the cell or from the cell culture medium.
  • the invention features, a purified recombinant nucleic acid having at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, or 99% homology with a sequence of the invention contained in the Sequence Listing.
  • the invention also provides a probe or primer which includes a substantially purified oligonucleotide.
  • the oligonucleotide includes a region of nucleotide sequence which hybridizes under stringent conditions to at least 8 consecutive nucleotides of sense or antisense sequence of the invention contained in the Sequence Listing, or naturally occurring mutants thereof.
  • the probe or primer further includes a label group attached thereto.
  • the label group can be, e.g., a radioisotope, a fluorescent compound, an enzyme, and/or an enzyme co-factor.
  • the oligonucleotide is at least 8 and less than 10, 20, 30, 50, 100, or 150 nucleotides in length.
  • the invention also provides an isolated H. pylori polypeptide which is encoded by a nucleic acid which hybridizes under stringent hybridization conditions to a nucleic acid contained in the Sequence Listing.
  • the invention further provides nucleic acids, e.g., RNA or DNA, encoding a polypeptide of the invention.
  • nucleic acids e.g., RNA or DNA
  • the H. pylori strain from which genomic sequences have been sequenced, has been deposited in the American Type Culture Collection (ATCC # 55679; deposited by Genome Therapeutics Corporation, 100 Beaver Street, Waltham, MA 02154) as strain HP-J99.
  • allelic variations include allelic variations; natural mutants; induced mutants; proteins encoded by DNA that hybridizes under high or low stringency conditions to a nucleic acid which encodes a polypeptide of the invention contained in the Sequence Listing (for definitions of high and low stringency see Current Protocols in Molecular Biology, John Wiley & Sons, New York, 1989, 6.3.1 - 6.3.6 and 6.4.1-6.4.10, hereby incorporated by reference); and, polypeptides specifically bound by antisera to H. pylori polypeptides, especially by antisera to an active site or binding domain of//. pylori polypeptide.
  • the invention also includes fragments, preferably biologically active fragments. These and other polypeptides are also referred to herein as H. pylori polypeptide analogs or variants.
  • H. pylori polypeptides characterized as shown in Table 1 below, including: H. pylori cell envelope proteins, H. pylori secreted proteins, and H. pylori cellular proteins. Members of these groups were identified by BLAST homology searches and by searches for secretion signal or transmembrane protein motifs. Polypeptides related by significant homology to the polypeptides of Table 1 are also considered to be classified in the manner of the homologs shown in Table 1. TABLE 1
  • nt represents nucleotide Seq. ID number and “aa” represents amino acid Seq. ID number]
  • purified polypeptide and “isolated polypeptide” and “a substantially pure preparation of a polypeptide” are used interchangeably herein and. as used herein, from other proteins, lipids, and nucleic acids with which it naturally occurs.
  • the polypeptide is also separated from substances, e.g., antibodies or gel matrix, e.g., polyacrylamide, which are used to purify it.
  • the polypeptide constitutes at least 10, 20, 50 70, 80 or 95%> dry weight of the purified preparation.
  • the preparation contains: sufficient polypeptide to allow protein sequencing; at least 1, 10, or 100 ⁇ g of the polypeptide; at least 1, 10, or 100 mg of the polypeptide.
  • purified polypeptide and isolated polypeptide and “a substantially pure preparation of a polypeptide,” as used herein, refer to both a polypeptide obtained from nature or produced by recombinant DNA techniques as described herein.
  • an “isolated” or “purified” protein or biologically active portion thereof is substantially free of cellular material or other contaminating proteins from the cell or tissue source from which the H pylori protein is derived, or substantially free from chemical precursors or other chemicals when chemically synthesized.
  • substantially free of cellular material includes preparations of//, pylori protein in which the protein is separated from cellular components of the cells from which it is isolated or recombinantly produced.
  • the language "substantially free of cellular material” includes preparations of H. pylori protein having less than about 30%) (by dry weight) of non-H. pylori protein (also referred to herein as a "contaminating protein"), more preferably less than about 20%) of non-H. pylori protein, still more preferably less than about 10% of non-H. pylori protein, and most preferably less than about 5%> non-H. pylori protein.
  • H pylori protein or biologically active portion thereof is recombinantly produced, it is also preferably substantially free of culture medium, i.e., culture medium represents less than about 20%, more preferably less than about 10%>, and most preferably less than about 5%> of the volume of the protein preparation.
  • the language “substantially free of chemical precursors or other chemicals” includes preparations of H pylori protein in which the protein is separated from chemical precusors or other chemicals which are involved in the synthesis of the protein.
  • the language “substantially free of chemical precursors or other chemicals” includes preparations of H pylori protein having less than about 30%> (by dry weight) of chemical precursors or non-H. pylori chemicals, more preferably less than about 20%) chemical precursors or non-H. pylori chemicals, still more preferably less than about 10%> chemical precursors or non-H. pylori chemicals, and most preferably less than about 5% chemical precursors or non-H pylori chemicals.
  • a purified preparation of cells refers to, in the case of plant or animal cells, an in vitro preparation of cells and not an entire intact plant or animal. In the case of cultured cells or microbial cells, it consists of a preparation of at least 10%> and more preferably 50%) of the subject cells.
  • a purified or isolated or a substantially pure nucleic acid is a nucleic acid which is one or both of the following: not immediately contiguous with both of the coding sequences with which it is immediately contiguous (i.e., one at the 5' end and one at the 3' end) in the naturally-occurring genome of the organism from which the nucleic acid is derived; or which is substantially free of a nucleic acid with which it occurs in the organism from which the nucleic acid is derived.
  • the term includes, for example, a recombinant DNA which is incorporated into a vector, e.g., into an autonomously replicating plasmid or virus, or into the genomic DNA of a prokaryote or eukaryote, or which exists as a separate molecule (e.g., a cDNA or a genomic DNA fragment produced by PCR or restriction endonuclease treatment) independent of other DNA sequences.
  • Substantially pure DNA also includes a recombinant DNA which is part of a hybrid gene encoding additional H. pylori DNA sequence.
  • a "contig” as used herein is a nucleic acid representing a continuous stretch of genomic sequence of an organism.
  • ORF an "open reading frame”, also referred to herein as ORF, is a region of nucleic acid which encodes a polypeptide. This region may represent a portion of a coding sequence or a total sequence and can be determined from a stop to stop codon or from a start to stop codon.
  • a "coding sequence” is a nucleic acid which is transcribed into messenger RNA and/or translated into a polypeptide when placed under the control of appropriate regulatory sequences. The boundaries of the coding sequence are determined by a translation start codon at the five prime terminus and a translation stop code at the three prime terminus.
  • a coding sequence can include but is not limited to messenger RNA, synthetic DNA, and recombinant nucleic acid sequences.
  • a "complement" of a nucleic acid as used herein referes to an anti-parallel or antisense sequence that participates in Watson-Crick base-pairing with the original sequence.
  • a “gene product” is a protein or structural RNA which is specifically encoded by a gene.
  • probe refers to a nucleic acid, peptide or other chemical entity which specifically binds to a molecule of interest. Probes are often associated with or capable of associating with a label.
  • a label is a chemical moiety capable of detection. Typical labels comprise dyes, radioisotopes, luminescent and chemiluminescent moieties, fluorophores, enzymes, precipitating agents, amplification sequences, and the like.
  • a nucleic acid, peptide or other chemical entity which specifically binds to a molecule of interest and immobilizes such molecule is referred herein as a "capture ligand".
  • Capture ligands are typically associated with or capable of associating with a support such as nitro-cellulose, glass, nylon membranes, beads, particles and the like.
  • the specificity of hybridization is dependent on conditions such as the base pair composition of the nucleotides, and the temperature and salt concentration of the reaction. These conditions are readily discernable to one of ordinary skill in the art using routine experimentation.
  • Homologous refers to the sequence similarity or sequence identity between two polypeptides or between two nucleic acid molecules. When a position in both of the two compared sequences is occupied by the same base or amino acid monomer subunit, e.g., if a position in each of two DNA molecules is occupied by adenine, then the molecules are homologous at that position.
  • the percent of homology between two sequences is a function of the number of matching or homologous positions shared by the two sequences divided by the number of positions compared x 100. For example, if 6 of 10 of the positions in two sequences are matched or homologous then the two sequences are 60%) homologous.
  • the DNA sequences ATTGCC and TATGGC share 50%> homology.
  • a comparison is made when two sequences are aligned to give maximum homology.
  • Nucleic acids are hybridizable to each other when at least one strand of a nucleic acid can anneal to the other nucleic acid under defined stringency conditions. Stringency of hybridization is determined by: (a) the temperature at which hybridization and/or washing is performed; and (b) the ionic strength and polarity of the hybridization and washing solutions. Hybridization requires that the two nucleic acids contain complementary sequences; depending on the stringency of hybridization, however, mismatches may be tolerated.
  • hybridization of two sequences at high stingency requires that the sequences be essentially completely homologous.
  • Conditions of intermediate stringency such as, for example, 2X SSC at 65 ° C
  • low stringency such as, for example 2X SSC at 55° C
  • IX SSC is 0.15 M NaCl, 0.015 M Na citrate.
  • a preferred, non-limiting example of stringent hybridization conditions are hybridization in 6X sodium chloride/sodium citrate (SSC) at about 45°C, followed by one or more washes in 0.2 X SSC, 0.1% SDS at 50-65°C.
  • SSC sodium chloride/sodium citrate
  • peptides, proteins, and polypeptides are used interchangeably herein.
  • surface protein refers to all surface accessible proteins, e.g. inner and outer membrane proteins, proteins adhering to the cell wall, and secreted proteins.
  • a polypeptide has H pylori biological activity if it has one, two and preferably more of the following properties: (1) if when expressed in the course of an H pylori infection, it can promote, or mediate the attachment of H pylori to a cell; (2) it has an enzymatic activity, structural or regulatory function characteristic of an H pylori protein; (3) the gene which encodes it can rescue a lethal mutation in an H. pylori gene; (4) or it is immunogenic in a subject.
  • a polypeptide has biological activity if it is an antagonist, agonist, or super-agonist of a polypeptide having one of the above-listed properties.
  • a biologically active fragment or analog is one having an in vivo or in vitro activity which is characteristic of the H pylori polypeptides of the invention contained in the Sequence Listing, or of other naturally occurring H. pylori polypeptides, e.g., one or more of the biological activities described herein.
  • fragments which exist in vivo e.g., fragments which arise from post transcriptional processing or which arise from translation of alternatively spliced RNA's. Fragments include those expressed in native or endogenous cells as well as those made in expression systems, e.g., in C ⁇ O cells. Because peptides such as H.
  • H pylori polypeptides often exhibit a range of physiological properties and because such properties may be attributable to different portions of the molecule, a useful H pylori fragment or H pylori analog is one which exhibits a biological activity in any biological assay for H pylori activity. Most preferably the fragment or analog possesses 10%>, preferably 40%>, more preferably 60%>, 70%), 80%) or 90%) or greater of the activity of H. pylori, in any in vivo or in vitro assay. Analogs can differ from naturally occurring H. pylori polypeptides in amino acid sequence or in ways that do not involve sequence, or both.
  • Non-sequence modifications include changes in acetylation, methylation, phosphorylation, carboxylation, or glycosylation.
  • Preferred analogs include H. pylori polypeptides (or biologically active fragments thereof) whose sequences differ from the wild-type sequence by one or more conservative amino acid substitutions or by one or more non-conservative amino acid substitutions, deletions, or insertions which do not substantially diminish the biological activity of the H pylori polypeptide.
  • Conservative substitutions typically include the substitution of one amino acid for another with similar characteristics, e.g., substitutions within the following groups: valine, glycine; glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid; asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine.
  • Other conservative substitutions can be made in view of the table below.
  • analogs within the invention are those with modifications which increase peptide stability; such analogs may contain, for example, one or more non-peptide bonds (which replace the peptide bonds) in the peptide sequence. Also included are: analogs that include residues other than naturally occurring L-amino acids, e.g., D-amino acids or non-naturally occurring or synthetic amino acids, e.g., ⁇ or ⁇ amino acids; and cyclic analogs.
  • fragment as applied to an H pylori analog, will ordinarily be at least about 20 residues, more typically at least about 40 residues, preferably at least about 60 residues in length. Fragments of H pylori polypeptides can be generated by methods known to those skilled in the art. The ability of a candidate fragment to exhibit a biological activity of H pylori polypeptide can be assessed by methods known to those skilled in the art as described herein. Also included are H. pylori polypeptides containing residues that are not required for biological activity of the peptide or that result from alternative mRNA splicing or alternative protein processing events.
  • an "immunogenic component” as used herein is a moiety, such as an H pylori polypeptide, analog or fragment thereof, that is capable of eliciting a humoral and/or cellular immune response in a host animal alone or in combination with an adjuvant.
  • an "antigenic component” as used herein is a moiety, such as an H. pylori polypeptide, analog or fragment thereof, that is capable of binding to a specific antibody with sufficiently high affinity to form a detectable antigen-antibody complex.
  • transgene means a nucleic acid (encoding, e.g., one or more polypeptides), which is partly or entirely heterologous, i.e., foreign, to the transgenic animal or cell into which it is introduced, or, is homologous to an endogenous gene of the transgenic animal or cell into which it is introduced, but which is designed to be inserted, or is inserted, into the cell's genome in such a way as to alter the genome of the cell into which it is inserted (e.g., it is inserted at a location which differs from that of the natural gene or its insertion results in a knockout).
  • a transgene can include one or more transcriptional regulatory sequences and any other nucleic acid, such as introns, that may be necessary for optimal expression of the selected nucleic acid, all operably linked to the selected nucleic acid, and may include an enhancer sequence.
  • transgenic cell refers to a cell containing a transgene.
  • a "transgenic animal” is any animal in which one or more, and preferably essentially all, of the cells of the animal includes a transgene.
  • the transgene can be introduced into the cell, directly or indirectly by introduction into a precursor of the cell, by way of deliberate genetic manipulation, such as by a process of transformation of competent cells or by microinjection or by infection with a recombinant virus.
  • This molecule may be integrated within a chromosome, or it may be extrachromosomally replicating DNA.
  • the term "antibody” as used herein is intended to include fragments thereof which are specifically reactive with H pylori polypeptides.
  • the term "cell-specific promoter” means a DNA sequence that serves as a promoter, i.e., regulates expression of a selected DNA sequence operably linked to the promoter, and which effects expression of the selected DNA sequence in specific cells of a tissue.
  • the term also covers so-called “leaky” promoters, which regulate expression of a selected DNA primarily in one tissue, but cause expression in other tissues as well.
  • Misexpression refers to a non-wild type pattern of gene expression. It includes: expression at non-wild type levels, i.e., over or under expression; a pattern of expression that differs from wild type in terms of the time or stage at which the gene is expressed, e.g., increased or decreased expression (as compared with wild type) at a predetermined developmental period or stage; a pattern of expression that differs from wild type in terms of decreased expression (as compared with wild type) in a predetermined cell type or tissue type; a pattern of expression that differs from wild type in terms of the splicing size, amino acid sequence, post- transitional modification, or biological activity of the expressed polypeptide; a pattern of expression that differs from wild type in terms of the effect of an environmental stimulus or extracellular stimulus on expression of the gene, e.g., a pattern of increased or decreased expression (as compared with wild type) in the presence of an increase or decrease in the strength of the stimulus.
  • host cells and other such terms denoting microorganisms or higher eukaryotic cell lines cultured as unicellular entities refers to cells which can become or have been used as recipients for a recombinant vector or other transfer DNA, and include the progeny of the original cell which has been transfected. It is understood by individuals skilled in the art that the progeny of a single parental cell may not necessarily be completely identical in genomic or total DNA compliment to the original parent, due to accident or deliberate mutation.
  • control sequence refers to a nucleic acid having a base sequence which is recognized by the host organism to effect the expression of encoded sequences to which they are ligated.
  • the nature of such control sequences differs depending upon the host organism; in prokaryotes, such control sequences generally include a promoter, ribosomal binding site, terminators, and in some cases operators; in eukaryotes, generally such control sequences include promoters, terminators and in some instances, enhancers.
  • the term control sequence is intended to include at a minimum, all components whose presence is necessary for expression, and may also include additional components whose presence is advantageous, for example, leader sequences.
  • operably linked refers to sequences joined or ligated to function in their intended manner.
  • a control sequence is operably linked to coding sequence by ligation in such a way that expression of the coding sequence is achieved under conditions compatible with the control sequence and host cell.
  • the metabolism of a substance means any aspect of the, expression, function, action, or regulation of the substance.
  • the metabolism of a substance includes modifications, e.g., covalent or non-covalent modifications of the substance.
  • the metabolism of a substance includes modifications, e.g., covalent or non- covalent modification, the substance induces in other substances.
  • the metabolism of a substance also includes changes in the distribution of the substance.
  • the metabolism of a substance includes changes the substance induces in the distribution of other substances.
  • sample refers to a biological sample, such as, for example, tissue or fluid isloated from an individual (including without limitation plasma, serum, cerebrospinal fluid, lymph, tears, saliva and tissue sections) or from in vitro cell culture constituents, as well as samples from the environment.
  • tissue or fluid isloated from an individual (including without limitation plasma, serum, cerebrospinal fluid, lymph, tears, saliva and tissue sections) or from in vitro cell culture constituents, as well as samples from the environment.
  • tissue or fluid isloated from an individual (including without limitation plasma, serum, cerebrospinal fluid, lymph, tears, saliva and tissue sections) or from in vitro cell culture constituents, as well as samples from the environment.
  • the practice of the invention will employ, unless otherwise indicated, conventional techniques of chemistry, molecular biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature. See e.g., Sambrook, Fritsch, and Maniatis,
  • This invention provides nucleotide sequences of the genome of H. pylori which thus comprises a DNA sequence library of H. pylori genomic DNA.
  • the detailed description that follows provides nucleotide sequences of H. pylori, and also describes how the sequences were obtained and how ORFs and protein-coding sequences were identified. Also described are methods of using the disclosed H. pylori sequences in methods including diagnostic and therapeutic applications.
  • the library can be used as a database for identification and comparison of medically important sequences in this and other strains of H. pylori. To determine the genomic sequence of H. pylori.
  • DNA was isolated from a strain of H pylori (ATCC # 55679; deposited by Genome Therapeutics Corporation, 100 Beaver Street, Waltham, MA 02154) and mechanically sheared by nebulization to a median size of 2 kb. Following size fractionation by gel electrophoresis, the fragments were blunt-ended, ligated to adapter oligonucleotides, and cloned into each of 20 different pMPX vectors (Rice et al., abstracts of Meeting of Genome Mapping and
  • DNA sequencing was achieved using multiplex sequencing procedures essentially as disclosed in Church et al., 1988, Science 240:185; U.S. Patents No. 4,942,124 and 5,149,625).
  • DNA was extracted from pooled cultures and subjected to chemical or enzymatic sequencing. Sequencing reactions were resolved by electrophoresis, and the products were transferred and covalently bound to nylon membranes. Finally, the membranes were sequentially hybridized with a series of labelled oligonucleotides complimentary to "tag" sequences present in the different shotgun cloning vectors. In this manner, a large number of sequences could be obtained from a single set of sequencing reactions. The cloning and sequencing procedures are described in more detail in the Exemplification.
  • Synthetic oligonucleotides are designed that are complementary to sequences at the end of each contig. These oligonucleotides may be hybridized to libaries of H. pylori genomic DNA in, for example, lambda phage vectors or plasmid vectors to identify clones that contain sequences corresponding to the junctional regions between individual contigs. Such clones are then used to isolate template DNA and the same oligonucleotides are used as primers in polymerase chain reaction (PCR) to amplify junctional fragments, the nucleotide sequence of which is then determined.
  • PCR polymerase chain reaction
  • ORFs open reading frames
  • ORFs open reading frames
  • These ORFs may not correspond to the ORF of a naturally-occurring H. pylori polypeptide.
  • These ORFs may contain start codons which indicate the initiation of protein synthesis of a naturally- occurring H. pylori polypeptide.
  • Such start codons within the ORFs provided herein can be identified by those of ordinary skill in the relevant art, and the resulting ORF and the encoded H. pylori polypeptide is within the scope of this invention.
  • a codon such as AUG or GUG encoding methionine or valine
  • the ORF modified to correspond to a naturally-occurring H pylori polypeptide.
  • the predicted coding regions were defined by evaluating the coding potential of such sequences with the program GENEMARKTM (Borodovsky and Mclninch, 1993, Comp. Chem. J :123).
  • the nucleic acids of this invention may be obtained directly from the DNA of the above referenced H. pylori strain by using the polymerase chain reaction (PCR). See “PCR, A Practical Approach” (McPherson, Quirke, and Taylor, eds., IRL Press, Oxford, UK, 1991) for details about the PCR. High fidelity PCR can be used to ensure a faithful DNA copy prior to expression. In addition, the authenticity of amplified products can be checked by conventional sequencing methods.
  • PCR polymerase chain reaction
  • Clones carrying the desired sequences described in this invention may also be obtained by screening the libraries by means of the PCR or by hybridization of synthetic oligonucleotide probes to filter lifts of the library colonies or plaques as known in the art (see, e.g., Sambrook et al., Molecular Cloning, A Laboratory Manual 2nd edition, 1989, Cold Spring Harbor Press, NY).
  • nucleic acids encoding H. pylori polypeptides from a cDNA library in accordance with protocols herein described.
  • a cDNA encoding an H. pylori polypeptide can be obtained by isolating total mRNA from an appropriate strain. Double stranded cDNAs can then be prepared from the total mRNA. Subsequently, the cDNAs can be inserted into a suitable plasmid or viral (e.g., bacteriophage) vector using any one of a number of known techniques.
  • nucleic acids of the invention can be DNA or RNA.
  • Preferred nucleic acids of the invention are contained in the Sequence Listing.
  • the nucleic acids of the invention can also be chemically synthesized using standard techniques.
  • Various methods of chemically synthesizing polydeoxynucleotides are known, including solid-phase synthesis which, like peptide synthesis, has been fully automated in commercially available DNA synthesizers (See e.g., Itakura et al. U.S. Patent No. 4,598,049; Caruthers et al U.S. Patent No. 4,458,066; and Itakura U.S. Patent Nos. 4,401,796 and 4,373,071, incorporated by reference herein).
  • nucleic acids isolated or synthesized in accordance with features of the present invention are useful, by way of example, without limitation, as probes, primers, capture ligands. antisense genes and for developing expression systems for the synthesis of proteins and peptides corresponding to such sequences.
  • the nucleic acid normally consists of all or part (approximately twenty or more nucleotides for specificity as well as the ability to form stable hybridization products) of the nucleic acids of the invention contained in the Sequence Listing. These uses are described in further detail below.
  • Probes A nucleic acid isolated or synthesized in accordance with the sequence of the invention contained in the Sequence Listing can be used as a probe to specifically detect H pylori. With the sequence information set forth in the present application, sequences of twenty or more nucleotides are identified which provide the desired inclusivity and exclusivity with respect to H pylori, and extraneous nucleic acids likely to be encountered during hybridization conditions. More preferably, the sequence will comprise at least twenty to thirty nucleotides to convey stability to the hybridization product formed between the probe and the intended target molecules.
  • nucleic acids for use as probes, can be provided with a label to facilitate detection of a hybridization product.
  • nucleic acid selected in the manner described above with respect to probes can be readily associated with a support.
  • the manner in which nucleic acid is associated with supports is well known.
  • Nucleic acid having twenty or more nucleotides in a sequence of the invention contained in the Sequence Listing have utility to separate H. pylori nucleic acid from the nucleic acid of each other and other organisms.
  • Nucleic acid having twenty or more nucleotides in a sequence of the invention contained in the Sequence Listing can also have utility to separate other Helicobacter species from each other and from other organisms.
  • the sequence will comprise at least twenty nucleotides to convey stability to the hybridization product formed between the probe and the intended target molecules. Sequences larger than 1000 nucleotides in length are difficult to synthesize but can be generated by recombinant DNA techniques.
  • Nucleic acid isolated or synthesized in accordance with the sequences described herein have utility as primers for the amplification of H pylori nucleic acid. These nucleic acids may also have utility as primers for the amplification of nucleic acids in other Helicobacter species.
  • PCR polymerase chain reaction
  • nucleic acid sequences of > 10-15 nucleotides of the invention contained in the Sequence Listing have utility in conjunction with suitable enzymes and reagents to create copies of H. pylori nucleic acid. More preferably, the sequence will comprise twenty or more nucleotides to convey stability to the hybridization product formed between the primer and the intended target molecules. Binding conditions of primers greater than 100 nucleotides are more difficult to control to obtain specificity. High fidelity PCR can be used to ensure a faithful DNA copy prior to expression. In addition, amplified products can be checked by conventional sequencing methods.
  • the copies can be used in diagnostic assays to detect specific sequences, including genes from H. pylori and/or other Helicobacter species.
  • the copies can also be incorporated into cloning and expression vectors to generate polypeptides corresponding to the nucleic acid synthesized by PCR, as is described in greater detail herein.
  • Antisense Nucleic acid or nucleic acid-hybridizing derivatives isolated or synthesized in accordance with the sequences described herein have utility as antisense agents to prevent the expression of H. pylori genes. These sequences also have utility as antisense agents to prevent expression of genes of other Helicobacter species.
  • nucleic acid or derivatives corresponding to H. pylori nucleic acids is loaded into a suitable carrier such as a liposome or bacteriophage for introduction into bacterial cells.
  • a nucleic acid having twenty or more nucleotides is capable of binding to bacteria nucleic acid or bacteria messenger RNA.
  • the antisense nucleic acid is comprised of 20 or more nucleotides to provide necessary stability of a hybridization product of non-naturally occurring nucleic acid and bacterial nucleic acid and/or bacterial messenger RNA.
  • Nucleic acid having a sequence greater than 1000 nucleotides in length is difficult to synthesize but can be generated by recombinant DNA techniques.
  • H pylori Nucleic Acids Nucleic acid isolated or synthesized in accordance with the sequences described herein have utility to generate polypeptides.
  • the nucleic acid of the invention exemplified in the Sequence Listing or fragments of said nucleic acid encoding active portions of H pylori polypeptides can be cloned into suitable vectors or used to isolate nucleic acid.
  • the isolated nucleic acid is combined with suitable DNA linkers and cloned into a suitable vector.
  • a gene product may be produced in large quantities in an expressing strain for use as an antigen, an industrial reagent, for structural studies, etc. This expression can be accomplished in a mutant strain which lacks the activity of the gene to be tested, or in a strain that does not produce the same gene product(s). This includes, but is not limited to other Helicobacter strains, or other bacterial strains such as E. coli, Norcardia, Corynebacterium, Campylobacter, and Streptomyces species.
  • the expression host will utilize the natural Helicobacter promoter whereas in others, it will be necessary to drive the gene with a promoter sequence derived from the expressing organism (e.g., an E. coli beta-galactosidase promoter for expression in E. coli).
  • a promoter sequence derived from the expressing organism e.g., an E. coli beta-galactosidase promoter for expression in E. coli.
  • telomere sequence data is cloned into an appropriate recombinant plasmid containing an origin of replication that functions in the host organism and an appropriate selectable marker. This can be accomplished by a number of procedures known to those skilled in the art. It is most preferably done by cutting the plasmid and the fragment to be cloned with the same restriction enzyme to produce compatible ends that can be ligated to join the two pieces together.
  • the recombinant plasmid is introduced into the host organism by, for example, electroporation and cells containing the recombinant plasmid are identified by selection for the marker on the plasmid. Expression of the desired gene product is detected using an assay specific for that gene product.
  • a suitable host cell for expression of a gene can be any procaryotic or eucaryotic cell.
  • an H pylori polypeptide can be expressed in bacterial cells such as E. coli, insect cells (baculovirus), yeast, or mammalian cells such as Chinese hamster ovary cell (C ⁇ O).
  • Other suitable host cells are known to those skilled in the art.
  • yeast S. cerivisae examples include pYepSecl (Baldari. et al., (1987) Embo J. 6:229-234), pMFa (Kurjan and ⁇ erskowitz, (1982) Cell 30:933-943), pJRY88 (Schultz et al., (1987) Gene 54:1 13-123), and pYES2 (Invitrogen Corporation, San Diego, CA).
  • Baculovirus vectors available for expression of proteins in cultured insect cells include the pAc series (Smith et al., (1983) Mol Cell Biol 3:2156-2165) and the pVL series (Lucklow, V.A., and Summers, M.D., (1989) Virology 170:31-39).
  • COS cells Gluzman, Y., (1981) Cell 23: 175-182
  • pCDM 8 Aruffo, A. and Seed, B., (1987) Proc. Natl Acad. Sci. USA 84:8573-8577
  • C ⁇ O dhfr Chinese
  • Hamster Ovary cells are used with vectors such as pMT2PC (Kaufman et al. (1987), EMBO J. 6: 187- 195) for stable amplification/expression in mammalian cells.
  • Vector DNA can be introduced into mammalian cells via conventional techniques such as calcium phosphate or calcium chloride co-precipitation. DEAE-dextran-mediated transfection, or electroporation. Suitable methods for transforming host cells can be found in Sambrook et al. (Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory press (1989)), and other laboratory textbooks.
  • Fusion vectors usually add a number of NH2 terminal amino acids to the expressed target gene. These NH2 terminal amino acids often are referred to as a reporter group. Such reporter groups usually serve two purposes: 1) to increase the solubility of the target recombinant protein; and 2) to aid in the purification of the target recombinant protein by acting as a ligand in affinity purification. Often, in fusion expression vectors, a proteolytic cleavage site is introduced at the junction of the reporter group and the target recombinant protein to enable separation of the target recombinant protein from the reporter group subsequent to purification of the fusion protein.
  • Such enzymes, and their cognate recognition sequences include Factor Xa, thrombin and enterokinase.
  • Typical fusion expression vectors include pGEX (Amrad Corp., Melbourne, Australia), pMAL (New England Biolabs, Beverly. MA) and pRIT5 (Pharmacia, Piscataway, NJ) which fuse glutathione S-transferase, maltose E binding protein, or protein A, respectively, to the target recombinant protein.
  • a preferred reporter group is poly(His), which may be fused to the amino or carboxy terminus of the protein and which renders the recombinant fusion protein easily purifiable by metal chelate chromatography.
  • Inducible non-fusion expression vectors include pTrc (Amann et al., (1988) Gene 69:301-315) and pETl Id (Studier et al.. Gene Expression Technology: Methods in Enzvmology 185. Academic Press, San Diego, California ( 1990) 60-89). While target gene expression relies on host RNA polymerase transcription from the hybrid trp-lac fusion promoter in pTrc, expression of target genes inserted into pETl Id relies on transcription from the T7 gnlO-lac 0 fusion promoter mediated by coexpressed viral RNA polymerase (T7 gnl). This viral polymerase is supplied by host strains BL21(DE3) or HMS174(DE3) from a resident ⁇ prophage harboring a T7 gnl under the transcriptional control of the lacUV 5 promoter.
  • T7 gnl coexpressed viral RNA polymerase
  • a host cell transfected with a nucleic acid vector directing expression of a nucleotide sequence encoding an H. pylori polypeptide can be cultured under appropriate conditions to allow expression of the polypeptide to occur.
  • the polypeptide may be secreted and isolated from a mixture of cells and medium containing the peptide.
  • the polypeptide may be retained cytoplasmically and the cells harvested, lysed and the protein isolated.
  • a cell culture includes host cells, media and other byproducts. Suitable media for cell culture are well known in the art.
  • Polypeptides of the invention can be isolated from cell culture medium, host cells, or both using techniques known in the art for purifying proteins including ion-exchange chromatography, gel filtration chromatography, ultrafiltration, electrophoresis, and immunoaffinity purification with antibodies specific for such polypeptides. Additionally, in many situations, polypeptides can be produced by chemical cleavage of a native protein (e.g., tryptic digestion) and the cleavage products can then be purified by standard techniques.
  • membrane bound proteins these can be isolated from a host cell by contacting a membrane-associated protein fraction with a detergent forming a solubilized complex, where the membrane-associated protein is no longer entirely embedded in the membrane fraction and is solubilized at least to an extent which allows it to be chromatographically isolated from the membrane fraction.
  • a detergent suitable for solubilizing these complexes For example, one property considered is the ability of the detergent to solubilize the H. pylori protein within the membrane fraction at minimal denaturation of the membrane- associated protein allowing for the activity or functionality of the membrane-associated protein to return upon reconstitution of the protein.
  • CMC critical micelle concentration
  • a third property considered when selecting a detergent is the hydrophobicity of the detergent.
  • membrane-associated proteins are very hydrophobic and therefore detergents which are also hydrophobic, e.g., the triton series, would be useful for solubilizing the hydrophobic proteins.
  • Another property important to a detergent can be the capability of the detergent to remove the H pylori protein with minimal protein-protein interaction facilitating further purification.
  • a fifth property of the detergent which should be considered is the charge of the detergent.
  • detergent should be an uncharged detergent.
  • Chromatographic techniques which can be used in the final purification step are known in the art and include hydrophobic interaction, lectin affinity, ion exchange, dye affinity and immunoaffinity.
  • One strategy to maximize recombinant H pylori peptide expression in E. coli is to express the protein in a host bacteria with an impaired capacity to proteolytically cleave the recombinant protein (Gottesman, S., Gene Expression Technology: Methods in Enzvmology 185, Academic Press, San Diego, California (1990) 119-128).
  • Another strategy would be to alter the nucleic acid encoding an H pylori peptide to be inserted into an expression vector so that the individual codons for each amino acid would be those preferentially utilized in highly expressed E. coli proteins (Wada et al., (1992) Nuc. Acids Res. 20:21 1 1-2118).
  • Such alteration of nucleic acids of the invention can be carried out by standard DNA synthesis techniques.
  • the nucleic acids of the invention can also be chemically synthesized using standard techniques.
  • Various methods of chemically synthesizing polydeoxynucleotides are known, including solid-phase synthesis which, like peptide synthesis, has been fully automated in commercially available DNA synthesizers (See, e.g., Itakura et al. U.S. Patent No. 4,598,049; Caruthers et al. U.S. Patent No. 4,458,066; and Itakura U.S. Patent Nos. 4,401,796 and 4,373,071, incorporated by reference herein).
  • This invention encompasses isolated H pylori polypeptides encoded by the disclosed H. pylori genomic sequences, including the polypeptides of the invention contained in the Sequence Listing. Polypeptides of the invention are preferably at least 5 amino acid residues in length. Using the DNA sequence information provided herein, the amino acid sequences of the polypeptides encompassed by the invention can be deduced using methods well-known in the art. It will be understood that the sequence of an entire nucleic acid encoding an H pylori polypeptide can be isolated and identified based on an ORF that encodes only a fragment of the cognate protein-coding region.
  • polypeptides of the invention can be isolated from wild-type or mutant H pylori cells or from heterologous organisms or cells (including, but not limited to, bacteria, yeast, insect, plant and mammalian cells) into which an H. pylori nucleic acid has been introduced and expressed.
  • the polypeptides can be part of recombinant fusion proteins.
  • H pylori polypeptides of the invention can be chemically synthesized using commercially automated procedures such as those referenced herein.
  • the disclosed H. pylori genome sequence includes segments that direct the synthesis of ribonucleic acids and polypeptides, as well as origins of replication, promoters, other types of regulatory sequences, and intergenic nucleic acids.
  • the invention encompasses nucleic acids encoding immunogenic components of vaccines and targets for agents effective against H pylori. Identification of said immunogenic components involved in the determination of the function of the disclosed sequences can be achieved using a variety of approaches. Non-limiting examples of these approaches are described briefly below.
  • H. pylori nucleic acid and polypeptide sequences Computer-assisted comparison of the disclosed H. pylori sequences with previously reported sequences present in publicly available databases is useful for identifying functional H. pylori nucleic acid and polypeptide sequences.
  • protein-coding sequences may be compared as a whole, and that a high degree of sequence homology between two proteins (such as, for example, >80-90%>) at the amino acid level indicates that the two proteins also possess some degree of functional homology, such as, for example, among enzymes involved in metabolism, DNA synthesis, or cell wall synthesis, and proteins involved in transport, cell division, etc.
  • H pylori proteins identified as containing putative signal sequences and/or transmembrane domains are useful as immunogenic components of vaccines.
  • H pylori genes Nucleic acids that encode proteins essential for growth or viability of H pylori are preferred drug targets. H pylori genes can be tested for their biological relevance to the organism by examining the effect of deleting and/or disrupting the genes, i.e., by so-called gene "knockout", using techniques known to those skilled in the relevant art. In this manner, essential genes may be identified. Strain-specific sequences: Because of the evolutionary relationship between different H pylori strains, it is believed that the presently disclosed H pylori sequences are useful for identifying, and/or discriminating between, previously known and new H pylori strains. It is believed that other H.
  • pylori strains will exhibit at least 70% sequence homology with the presently disclosed sequence.
  • Systematic and routine analyses of DNA sequences derived from samples containing H pylori strains, and comparison with the present sequence allows for the identification of sequences that can be used to discriminate between strains, as well as those that are common to all H pylori strains.
  • the invention provides nucleic acids, including probes, and peptide and polypeptide sequences that discriminate between different strains of H pylori.
  • Strain-specific components can also be identified functionally by their ability to elicit or react with antibodies that selectively recognize one or more H pylori strains.
  • the invention provides nucleic acids, including probes, and peptide and polypeptide sequences that are common to all H. pylori strains but are not found in other bacterial species.
  • the selection of candidate protein antigens for vaccine development can be derived from the nucleic acids encoding H. pylori polypeptides.
  • the ORF's can be analyzed for homology to other known exported or membrane proteins and analyzed using the discriminant analysis described by Klein, et al. (Klein, P., Kanehsia, M., and DeLisi, C. (1985) Biochimica et Biophysica Acta 815, 468-476) for predicting exported and membrane proteins.
  • Homology searches can be performed using the BLAST algorithm contained in the Wisconsin Sequence Analysis Package (Genetics Computer Group, University Research Park, 575 Science Drive, Madison, WI 5371 1 ) to compare each predicted ORF amino acid sequence with all sequences found in the current GenBank, SWISS-PROT and PIR databases.
  • BLAST searches for local alignments between the ORF and the databank sequences and reports a probability score which indicates the probability of finding this sequence by chance in the database.
  • ORF's with significant homology e.g. probabilities lower than lxlO" 6 that the homology is only due to random chance
  • membrane or exported proteins represent protein antigens for vaccine development. Possible functions can be provided to H. pylori genes based on sequence homology to genes cloned in other organisms.
  • ORF amino acid sequence and compares it to information derived from the properties of known membrane and exported proteins. This comparison predicts which proteins will be exported, membrane associated or cytoplasmic. ORF amino acid sequences identified as exported or membrane associated by this algorithm are likely protein antigens for vaccine development.
  • outer membrane proteins are likely to represent the best antigens to provide a protective immune response against H. pylori.
  • algorithms that can be used to aid in prediction of these outer membrane proteins include the presence of an amphipathic beta-sheet region at their C-terminus. This region which has been detected in a large number of outer membrane proteins in Gram negative bacteria is often characterized by hydrophobic residues (Phe or Tyr) clustered at alternating positions from the C-terminus (e.g., see Figure 5, block F; Figure 7, block E). Importantly, these sequences have not been detected at the C-termini of periplasmic proteins, thus allowing preliminary distinction between these classes of proteins based on primary sequence data. This phenomenon has been reported previously by Struyve et al. (J. Mol Biol. 218: 141-148. 1991).
  • FIG. 5 Also illustrated in Figure 5 are additional amino acid sequence motifs found in many outer membrane proteins of H. pylori.
  • the amino acid sequence alignment in Figure 5 depicts portions of the sequence of five H. pylori proteins (depicted in the single letter amino acid code) labeled with their amino acid Sequence ID Numbers and shown N-terminal to C-terminal, left to right.
  • Five or six distinct blocks (labeled A through E or F) of similar amino acid residues are found including the distinctive hydrophobic residues (Phe or Tyr; F or Y according to the single letter code for amino acid residues) frequently found at positions near the C-terminus of outer membrane proteins.
  • the presence of several shared motifs clearly establishes the similarity between members of this group of proteins.
  • V Not-T (not-U) ⁇ A or C or G)
  • amino acid translations of this invention account for the ambiguity in the nucleic acid sequence by translating the ambiguous codon as the letter "X". In all cases, the permissible amino acid residues at a position are clear from an examination of the nucleic acid sequence based on the standard genetic code.
  • H pylori Nucleic Acids and Polypeptides
  • one skilled in the art can alter the disclosed structure (of H pylori genes), e.g., by producing fragments or analogs, and test the newly produced structures for activity. Examples of techniques known to those skilled in the relevant art which allow the production and testing of fragments and analogs are discussed below.
  • These, or analogous methods can be used to make and screen libraries of polypeptides, e.g., libraries of random peptides or libraries of fragments or analogs of cellular proteins for the ability to bind H pylori polypeptides. Such screens are useful for the identification of inhibitors of H. pylori.
  • Fragments of a protein can be produced in several ways, e.g., recombinantly, by proteolytic digestion, or by chemical synthesis.
  • Internal or terminal fragments of a polypeptide can be generated by removing one or more nucleotides from one end (for a terminal fragment) or both ends (for an internal fragment) of a nucleic acid which encodes the polypeptide.
  • Expression of the mutagenized DNA produces polypeptide fragments. Digestion with "end-nibbling" endonucleases can thus generate DNA's which encode an array of fragments.
  • DNA's which encode fragments of a protein can also be generated by random shearing, restriction digestion or a combination of the above-discussed methods.
  • Fragments can also be chemically synthesized using techniques known in the art such as conventional Merrifield solid phase f-Moc or t-Boc chemistry.
  • peptides of the present invention may be arbitrarily divided into fragments of desired length with no overlap of the fragments, or divided into overlapping fragments of a desired length.
  • Amino acid sequence variants of a protein can be prepared by random mutagenesis of DNA which encodes a protein or a particular domain or region of a protein. Useful methods include PCR mutagenesis and saturation mutagenesis. A library of random amino acid sequence variants can also be generated by the synthesis of a set of degenerate oligonucleotide sequences. (Methods for screening proteins in a library of variants are elsewhere herein). (A) PCR Mutagenesis
  • PCR mutagenesis reduced Taq polymerase fidelity is used to introduce random mutations into a cloned fragment of DNA (Leung et al., 1989, Technique 1:11- 15).
  • the DNA region to be mutagenized is amplified using the polymerase chain reaction (PCR) under conditions that reduce the fidelity of DNA synthesis by Taq DNA polymerase. e.g., by using a dGTP/dATP ratio of five and adding Mn2+ to the PCR reaction.
  • the pool of amplified DNA fragments are inserted into appropriate cloning vectors to provide random mutant libraries.
  • Saturation mutagenesis allows for the rapid introduction of a large number of single base substitutions into cloned DNA fragments (Mayers et al., 1985, Science 229:242).
  • This technique includes generation of mutations, e.g., by chemical treatment or irradiation of single-stranded DNA in vitro, and synthesis of a complimentary DNA strand.
  • the mutation frequency can be modulated by modulating the severity of the treatment, and essentially all possible base substitutions can be obtained. Because this procedure does not involve a genetic selection for mutant fragments both neutral substitutions, as well as those that alter function, are obtained. The distribution of point mutations is not biased toward conserved sequence elements.
  • a library of homologs can also be generated from a set of degenerate oligonucleotide sequences. Chemical synthesis of a degenerate sequences can be carried out in an automatic DNA synthesizer, and the synthetic genes then ligated into an appropriate expression vector. The synthesis of degenerate oligonucleotides is known in the art (see for example, Narang, SA (1983) Tetrahedron 39:3; Itakura et al. (1981) Recombinant DNA, Proc 3rd Cleveland Sympos. Macromolecules, ed. AG Walton, Amsterdam: Elsevier pp273-289; Itakura et al. (1984) Annu. Rev. Biochem.
  • Non-random or directed, mutagenesis techniques can be used to provide specific sequences or mutations in specific regions. These techniques can be used to create variants which include, e.g., deletions, insertions, or substitutions, of residues of the known amino acid sequence of a protein.
  • the sites for mutation can be modified individually or in series, e.g., by (1) substituting first with conserved amino acids and then with more radical choices depending upon results achieved, (2) deleting the target residue, or (3) inserting residues of the same or a different class adjacent to the located site, or combinations of options 1-3.
  • Alanine scanning mutagenesis is a useful method for identification of certain residues or regions of the desired protein that are preferred locations or domains for mutagenesis, Cunningham and Wells (Science 244: 1081-1085, 1989).
  • a residue or group of target residues are identified (e.g., charged residues such as Arg, Asp, His, Lys, and Glu) and replaced by a neutral or negatively charged amino acid (most preferably alanine or polyalanine).
  • Replacement of an amino acid can affect the interaction of the amino acids with the surrounding aqueous environment in or outside the cell.
  • Those domains demonstrating functional sensitivity to the substitutions are then refined by introducing further or other variants at or for the sites of substitution.
  • the site for introducing an amino acid sequence variation is predetermined, the nature of the mutation per se need not be predetermined.
  • alanine scanning or random mutagenesis may be conducted at the target codon or region and the expressed desired protein subunit variants are screened for the optimal combination of desired activity.
  • Oligonucleotide-mediated mutagenesis is a useful method for preparing substitution, deletion, and insertion variants of DNA, see, e.g., Adelman et al., (DNA 2: 183, 1983). Briefly, the desired DNA is altered by hybridizing an oligonucleotide encoding a mutation to a DNA template, where the template is the single-stranded form of a plasmid or bacteriophage containing the unaltered or native DNA sequence of the desired protein.
  • a DNA polymerase is used to synthesize an entire second complementary strand of the template that will thus incorporate the oligonucleotide primer, and will code for the selected alteration in the desired protein DNA.
  • oligonucleotides of at least 25 nucleotides in length are used.
  • An optimal oligonucleotide will have 12 to 15 nucleotides that are completely complementary to the template on either side of the nucleotide(s) coding for the mutation. This ensures that the oligonucleotide will hybridize properly to the single- stranded DNA template molecule.
  • the oligonucleotides are readily synthesized using techniques known in the art such as that described by Crea et al. (Proc. Natl. Acad. Sci. USA, 75: 5765[1978]).
  • the starting material is a plasmid (or other vector) which includes the protein subunit DNA to be mutated.
  • the codon(s) in the protein subunit DNA to be mutated are identified.
  • a double-stranded oligonucleotide encoding the sequence of the DNA between the restriction sites but containing the desired mutation(s) is synthesized using standard procedures. The two strands are synthesized separately and then hybridized together using standard techniques.
  • This double-stranded oligonucleotide is referred to as the cassette.
  • This cassette is designed to have 3' and 5' ends that are comparable with the ends of the linearized plasmid, such that it can be directly ligated to the plasmid.
  • This plasmid now contains the mutated desired protein subunit DNA sequence.
  • Combinatorial mutagenesis can also be used to generate mutants (Ladner et al., WO 88/06630).
  • the amino acid sequences for a group of homologs or other related proteins are aligned, preferably to promote the highest homology possible. All of the amino acids which appear at a given position of the aligned sequences can be selected to create a degenerate set of combinatorial sequences.
  • the variegated library of variants is generated by combinatorial mutagenesis at the nucleic acid level, and is encoded by a variegated gene library.
  • a mixture of synthetic oligonucleotides can be enzymatically ligated into gene sequences such that the degenerate set of potential sequences are expressible as individual peptides, or alternatively, as a set of larger fusion proteins containing the set of degenerate sequences.
  • Other Modifications of H pylori Nucleic Acids and Polypeptides can be enzymatically ligated into gene sequences such that the degenerate set of potential sequences are expressible as individual peptides, or alternatively, as a set of larger fusion proteins containing the set of degenerate sequences.
  • H. pylori polypeptide it is possible to modify the structure of an H. pylori polypeptide for such purposes as increasing solubility, enhancing stability (e.g., shelf life ex vivo and resistance to proteolytic degradation in vivo).
  • a modified H. pylori protein or peptide can be produced in which the amino acid sequence has been altered, such as by amino acid substitution, deletion, or addition as described herein.
  • H pylori peptide can also be modified by substitution of cysteine residues preferably with alanine, serine, threonine, leucine or glutamic acid residues to minimize dimerization via disulfide linkages.
  • amino acid side chains of fragments of the protein of the invention can be chemically modified. Another modification is cyclization of the peptide.
  • an H. pylori polypeptide can be modified to incorporate one or more polymorphisms in the amino acid sequence of the protein resulting from any natural allelic variation. Additionally, D-amino acids, non- natural amino acids, or non-amino acid analogs can be substituted or added to produce a modified protein within the scope of this invention. Furthermore, an H pylori polypeptide can be modified using polyethylene glycol (PEG) according to the method of A. Sehon and co-workers (Wie et al., supra) to produce a protein conjugated with PEG. In addition, PEG can be added during chemical synthesis of the protein.
  • PEG polyethylene glycol
  • H pylori proteins include reduction/alky lation (Tarr, Methods of Protein Microcharacterization, J. E. Silver ed., Humana Press, Clifton NJ 155-194 (1986)); acylation (Tarr, supra); chemical coupling to an appropriate carrier (Mishell and Shiigi, eds, Selected Methods in Cellular Immunology, WH Freeman, San Francisco, CA (1980), U.S. Patent 4,939,239; or mild formalin treatment (Marsh, (1971) Int. Arch, of Allergy andAppl Immunol. , 4J_: 199 - 215).
  • an amino acid fusion moiety to the peptide backbone.
  • hexa-histidine can be added to the protein for purification by immobilized metal ion affinity chromatography (Hochuli, E. et al., (1988) Bio/Technology, 6: 1321 - 1325).
  • specific endoprotease cleavage sites can be introduced between the sequences of the fusion moiety and the peptide.
  • canonical protease sensitive sites can be engineered between regions, each comprising at least one epitope via recombinant or synthetic methods.
  • charged amino acid pairs such as KK or RR
  • the resulting peptide can be rendered sensitive to cleavage by cathepsin and/or other trypsin-like enzymes which would generate portions of the protein containing one or more epitopes.
  • such charged amino acid residues can result in an increase in the solubility of the peptide.
  • Techniques for screening large gene libraries often include cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the genes under conditions in which detection of a desired activity, e.g., in this case, binding to H pylori polypeptide or an interacting protein, facilitates relatively easy isolation of the vector encoding the gene whose product was detected.
  • detection of a desired activity e.g., in this case, binding to H pylori polypeptide or an interacting protein.
  • Two hybrid assays such as the system described above (as with the other screening methods described herein), can be used to identify polypeptides, e.g., fragments or analogs of a naturally-occurring H. pylori polypeptide, e.g., of cellular proteins, or of randomly generated polypeptides which bind to an H. pylori protein.
  • the H. pylori domain is used as the bait protein and the library of variants are expressed as fish fusion proteins.
  • a two hybrid assay (as with the other screening methods described herein), can be used to find polypeptides which bind a H. pylori polypeptide.
  • the candidate peptides are displayed on the surface of a cell or viral particle, and the ability of particular cells or viral particles to bind an appropriate receptor protein via the displayed product is detected in a "panning assay".
  • the gene library can be cloned into the gene for a surface membrane protein of a bacterial cell, and the resulting fusion protein detected by panning (Ladner et al., WO 88/06630; Fuchs et al. (1991) Bio/Technology 9:1370-1371 ; and Goward et al. (1992) TIBS 18:136-140).
  • a detectably labeled ligand can be used to score for potentially functional peptide homologs.
  • Fluorescently labeled ligands e.g., receptors, can be used to detect homologs which retain ligand- binding activity.
  • the use of fluorescently labeled ligands allows cells to be visually inspected and separated under a fluorescence microscope, or, where the morphology of the cell permits, to be separated by a fluorescence-activated cell sorter.
  • a gene library can be expressed as a fusion protein on the surface of a viral particle.
  • foreign peptide sequences can be expressed on the surface of infectious phage, thereby conferring two significant benefits.
  • coli filamentous phages M13, fd., and fl are most often used in phage display libraries. Either of the phage gill or gVIII coat proteins can be used to generate fusion proteins without disrupting the ultimate packaging of the viral particle.
  • Foreign epitopes can be expressed at the NH2- terminal end of pill and phage bearing such epitopes recovered from a large excess of phage lacking this epitope (Ladner et al. PCT publication WO 90/02909; Garrard et al., PCT publication WO 92/09690; Marks et al. (1992) J. Biol. Chem. 267: 16007-16010; Griffiths et al. (1993) EMBO J 12:725-734; Clackson et al. ( ⁇ 99 ⁇ ) Nature 352:624-628; and Barbas et al. (1992) PNAS 89:4457-4461).
  • E. coli the outer membrane protein, LamB
  • LamB the outer membrane protein
  • Oligonucleotides have been inserted into plasmids encoding the LamB gene to produce peptides fused into one of the extracellular loops of the protein. These peptides are available for binding to ligands. e.g., to antibodies, and can elicit an immune response when the cells are administered to animals.
  • Other cell surface proteins e.g., OmpA (Schorr et al. (1991) Vaccines 91, pp. 387-392), PhoE (Agterberg, et al.
  • Peptides can be fused to pilin, a protein which polymerizes to form the pilus-a conduit for interbacterial exchange of genetic information (Thiry et al. (1989) Appl Environ. Microbiol. 55, 984-993). Because of its role in interacting with other cells, the pilus provides a useful support for the presentation of peptides to the extracellular environment.
  • Another large surface structure used for peptide display is the bacterial motive organ, the flagellum.
  • Fusion of peptides to the subunit protein flagellin offers a dense array of many peptide copies on the host cells (Kuwajima et al. (1988) Bio/Tech. 6, 1080-1083).
  • Surface proteins of other bacterial species have also served as peptide fusion partners. Examples include the Staphylococcus protein A and the outer membrane IgA protease of Neisseria (Hansson et al. (1992) J. Bacteriol 174, 4239-4245 and Klauser et al. (1990) EMBO J. 9, 1991 - 1999).
  • the physical link between the peptide and its encoding DNA occurs by the containment of the DNA within a particle (cell or phage) that carries the peptide on its surface.
  • An alternative scheme uses the DNA-binding protein Lad to form a link between peptide and DNA (Cull et al. (1992) PNAS USA 89: 1865-1869).
  • This system uses a plasmid containing the Lad gene with an oligonucleotide cloning site at its 3 '-end. Under the controlled induction by arabinose, a Lacl-peptide fusion protein is produced. This fusion retains the natural ability of Lad to bind to a short DNA sequence known as LacO operator (LacO). By installing two copies of LacO on the expression plasmid, the Lacl-peptide fusion binds tightly to the plasmid that encoded it.
  • LacO LacO operator
  • the plasmids in each cell contain only a single oligonucleotide sequence and each cell expresses only a single peptide sequence, the peptides become specifically and stably associated with the DNA sequence that directed its synthesis.
  • the cells of the library are gently lysed and the peptide-DNA complexes are exposed to a matrix of immobilized receptor to recover the complexes containing active peptides.
  • the associated plasmid DNA is then reintroduced into cells for amplification and DNA sequencing to determine the identity of the peptide ligands.
  • the peptides are attached to the C-terminus of the fusion protein, resulting in the display of the library members as peptides having free carboxy termini.
  • Both of the filamentous phage coat proteins, pill and pVIII are anchored to the phage through their C-termini, and the guest peptides are placed into the outward-extending N-terminal domains.
  • the phage- displayed peptides are presented right at the amino terminus of the fusion protein. (Cwirla, et al. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 6378-6382)
  • a second difference is the set of biological biases affecting the population of peptides actually present in the libraries.
  • the Lad fusion molecules are confined to the cytoplasm of the host cells.
  • the phage coat fusions are exposed briefly to the cytoplasm during translation but are rapidly secreted through the inner membrane into the periplasmic compartment, remaining anchored in the membrane by their C-terminal hydrophobic domains, with the N-termini, containing the peptides, protruding into the periplasm while awaiting assembly into phage particles.
  • the peptides in the Lad and phage libraries may differ significantly as a result of their exposure to different proteolytic activities.
  • the phage coat proteins require transport across the inner membrane and signal peptidase processing as a prelude to inco ⁇ oration into phage.
  • RNA from the bound complexes is recovered, converted to cDNA, and amplified by PCR to produce a template for the next round of synthesis and screening.
  • the polysome display method can be coupled to the phage display system. Following several rounds of screening, cDNA from the enriched pool of polysomes was cloned into a phagemid vector. This vector serves as both a peptide expression vector, displaying peptides fused to the coat proteins, and as a DNA sequencing vector for peptide identification.
  • polysome-derived peptides on phage By expressing the polysome-derived peptides on phage, one can either continue the affinity selection procedure in this format or assay the peptides on individual clones for binding activity in a phage ⁇ LISA, or for binding specificity in a completion phage ⁇ LISA (Barret, et al. (1992) Anal. Biochem 204,357-364). To identify the sequences of the active peptides one sequences the DNA produced by the phagemid host.
  • the high through-put assays described above can be followed by secondary screens in order to identify further biological activities which will, e.g., allow one skilled in the art to differentiate agonists from antagonists.
  • the type of a secondary screen used will depend on the desired activity that needs to be tested.
  • an assay can be developed in which the ability to inhibit an interaction between a protein of interest and its respective ligand can be used to identify antagonists from a group of peptide fragments isolated though one of the primary screens described above.
  • the invention also provides for reduction of the protein binding domains of the subject H pylori polypeptides to generate mimetics, e.g. peptide or non-peptide agents.
  • mimetics e.g. peptide or non-peptide agents.
  • the peptide mimetics are able to disrupt binding of a polypeptide to its counter ligand, e.g., in the case of an H. pylori polypeptide binding to a naturally occurring ligand.
  • the critical residues of a subject H pylori polypeptide which are involved in molecular recognition of a polypeptide can be determined and used to generate H /r ⁇ / ⁇ r/-derived peptidomimetics which competitively or noncompetitively inhibit binding of the H pylori polypeptide with an interacting polypeptide (see, for example, European patent applications EP-412,762A and EP-B31,080A).
  • scanning mutagenesis can be used to map the amino acid residues of a particular H pylori polypeptide involved in binding an interacting polypeptide
  • peptidomimetic compounds e.g. diazepine or isoquinoline derivatives
  • non- hydrolyzable peptide analogs of such residues can be generated using benzodiazepine (e.g., see Freidinger et al. in Peptides: Chemistry and Biology, G.R.
  • This invention also features vaccine compositions or formulations (used interchangeably herein) for protection against infection by H pylori or for treatment of H. pylori infection.
  • treatment of H pylori infection refers to therapeutic treatment of an existing or established H. pylori infection.
  • protection against H. pylori infection or “prophylactic treatment” refer to the use of H pylori vaccine formulation for reducing the risk of or preventing an infection in a subject at risk for H pylori infection.
  • the vaccine compositions contain one or more immunogenic components, such as a surface protein, from H pylori, or portion thereof, and a pharmaceutically acceptable carrier.
  • the vaccine formulations of the invention contain at least one or combination of H pylori polypeptides or fragments thereof, from same or different H pylori antigens.
  • Nucleic acids and H. pylori polypeptides for use in the vaccine formulations of the invention include the nucleic acids and polypeptides set forth in the Sequence Listing, preferably those H pylori nucleic acids that encode surface proteins and surface proteins or fragments thereof.
  • a preferred nucleic acid and H. pylori polypeptide for use in a vaccine composition of the invention is selected from the group of nucleic acids which encode cell envelope proteins and H pylori cell envelope proteins as set forth in Table 1.
  • any nucleic acid encoding an immunogenic H. pylori protein and H. pylori polypetide, or portion thereof can be used in the present invention. These vaccines have therapeutic and/or prophylactic utilities.
  • One aspect of the invention provides a vaccine composition for protection against infection by H. pylori which contains at least one immunogenic fragment of an H. pylori protein and a pharmaceutically acceptable carrier.
  • Preferred fragments include peptides of at least about 10 amino acid residues in length, preferably about 10-20 amino acid residues in length, and more preferably about 12-16 amino acid residues in length.
  • Immunogenic components of the invention can be obtained, for example, by screening polypeptides recombinantly produced from the corresponding fragment of the nucleic acid encoding the full-length H pylori protein.
  • fragments can be chemically synthesized using techniques known in the art such as conventional Merrifield solid phase f-Moc or t-Boc chemistry.
  • immunogenic components are identified by the ability of the peptide to stimulate T cells.
  • Peptides which stimulate T cells as determined by, for example, T cell proliferation or cytokine secretion are defined herein as comprising at least one T cell epitope.
  • T cell epitopes are believed to be involved in initiation and perpetuation of the immune response to the protein allergen which is responsible for the clinical symptoms of allergy. These T cell epitopes are thought to trigger early events at the level of the T helper cell by binding to an appropriate HLA molecule on the surface of an antigen presenting cell, thereby stimulating the T cell subpopulation with the relevant T cell receptor for the epitope.
  • a T cell epitope is the basic element, or smallest unit of recognition by a T cell receptor, where the epitope comprises amino acids essential to receptor recognition (e.g., approximately 6 or 7 amino acid residues). Amino acid sequences which mimic those of the T cell epitopes are within the scope of this invention.
  • immunogenic components of the invention are identified through genomic vaccination.
  • the basic protocol is based on the idea that expression libraries consisting of all or parts of a pathogen genome, e.g., an H. pylori genome, can confer protection when used to genetically immunize a host.
  • This expression library immunization (ELI) is analogous to expression cloning and involves reducing a genomic expression library of a pathogen, e.g., H. pylori, into plasmids that can act as genetic vaccines.
  • the plasmids can also be designed to encode genetic adjuvants which can dramatically stimulate the humoral response. These genetic adjuvants can be introduced at remote sites and act as well extracelluraly as intracellularly.
  • An expression library of pathogen DNA is used to immunize a host thereby producing the effects of antigen presentation of a live vaccine without the risk.
  • random fragments from the H. pylori genome or from cosmid or plasmid clones, as well as PCR products from genes identified by genomic sequencing can be used to immunize a host.
  • ELI is a technique that allows for production of a non-infectious multipartite vaccine, even when little is known about pathogen's biology, because ELI uses the immune system to screen candidate genes. Once isolated, these genes can be used as genetic vaccines or for development of recombinant protein vaccines. Thus, ELI allows for production of vaccines in a systematic, largely mechanized fashion.
  • Screening immunogenic components can be accomplished using one or more of several different assays.
  • peptide T cell stimulatory activity is assayed by contacting a peptide known or suspected of being immunogenic with an antigen presenting cell which presents appropriate MHC molecules in a T cell culture.
  • Presentation of an immunogenic H. pylori peptide in association with appropriate MHC molecules to T cells in conjunction with the necessary costimulation has the effect of transmitting a signal to the T cell that induces the production of increased levels of cytokines, particularly of interleukin-2 and interleukin-4.
  • the culture supernatant can be obtained and assayed for interleukin-2 or other known cytokines.
  • any one of several conventional assays for interleukin-2 can be employed, such as the assay described in Proc. Natl. Acad. Sci USA, 86: 1333 (1989) the pertinent portions of which are inco ⁇ orated herein by reference.
  • a kit for an assay for the production of interferon is also available from Genzyme Co ⁇ oration (Cambridge, MA).
  • a common assay for T cell proliferation entails measuring tritiated thymidine inco ⁇ oration.
  • the proliferation of T cells can be measured in vitro by determining the amount of ⁇ H-labeled thymidine inco ⁇ orated into the replicating DNA of cultured cells. Therefore, the rate of DNA synthesis and, in turn, the rate of cell division can be quantified.
  • Vaccine compositions or formulations of the invention containing one or more immunogenic components preferably include a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable carrier is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and abso ⁇ tion delaying agents, and the like, compatible with pharmaceutical administration.
  • Suitable pharmaceutically acceptable carriers include, for example, one or more of water, saline, phosphate buffered saline, dextrose, glycerol, ethanol and the like, as well as combinations thereof.
  • Pharmaceutically acceptable carriers may further comprise minor amounts of auxiliary substances such as wetting or emulsifying agents, preservatives or buffers, which enhance the shelf life or effectiveness of the H. pylori nucleic acid or polypeptide.
  • auxiliary substances such as wetting or emulsifying agents, preservatives or buffers, which enhance the shelf life or effectiveness of the H. pylori nucleic acid or polypeptide.
  • the polypeptide is preferably coadministered with a suitable adjuvant and/or a delivery system described herein.
  • the therapeutically effective amount of DNA or protein of this invention will depend, inter alia, upon the administration schedule, the unit dose of an H pylori nucleic acid or polypeptide administered, whether the protein or nucleic acid is administered in combination with other therapeutic agents, the immune status and health of the patient, and the therapeutic activity of the particular protein or nucleic acid.
  • Vaccine formulations are conventionally administered parenterally, e.g., by injection, either subcutaneously or intramuscularly. Methods for intramuscular immunization are described by Wolff et al. (1990) Science 247: 1465-1468 and by Sedegah et al. (1994) Immunology 9j 9866-9870. Other modes of administration include oral and pulmonary formulations, suppositories, and transdermal applications. Oral immunization is preferred over parenteral methods for inducing protection against infection by H pylori. Czinn et. al. (1993) Vaccine V ⁇ _: 637-642. Oral formulations include such normally employed excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, and the like.
  • the vaccine formulation includes, as a pharmaceutically acceptable carrier, an adjuvant.
  • suitable adjuvants for use in the vaccine formulations of the invention include, but are not limited, to aluminum hydroxide; N-acetyl-muramyl—L-threonyl-D-isoglutamine (thr-MDP); N-acetyl-nor- muramyl-L-alanyl-D-isoglutamine (CGP 1 1637, referred to as nor-MDP); N- acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(r-2'-dipalmitoyl-sn-glycero-3- hydroxyphos-phoryloxy)-ethylamine (CGP 19835 A, referred to a MTP-PE); RIBI, which contains three components from bacteria; monophosphoryl lipid A; trehalose dimycoloate; cell wall skeleton (MPL +
  • Non-toxic derivatives of cholera toxin including its B subunit, and/or conjugates or genetically engineered fusions of the H pylori polypeptide with cholera toxin or its B subunit, procholeragenoid, fungal polysaccharides, including schizophyllan, muramyl dipeptide, muramyl dipeptide derivatives, phorbol esters, labile toxin of E. coli. non-H. pylori bacterial lysates, block polymers or saponins.
  • the vaccine formulation includes, as a pharmaceutically acceptable carrier, a delivery system.
  • Suitable delivery systems for use in the vaccine formulations of the invention include biodegradable microcapsules or immuno- stimulating complexes (ISCOMs), cochleates, or liposomes, genetically engineered attenuated live vectors such as viruses or bacteria, and recombinant (chimeric) virus-like particles, e.g., bluetongue.
  • the vaccine formulation includes both a delivery system and an adjuvant.
  • Delivery systems in humans may include enteric release capsules protecting the antigen from the acidic environment of the stomach, and including H pylori polypeptide in an insoluble form as fusion proteins.
  • Suitable carriers for the vaccines of the invention are enteric coated capsules and polylactide-glycolide microspheres.
  • Suitable diluents are 0.2 N Na ⁇ CO3 and/or saline.
  • Vaccines of the invention can be administered as a primary prophylactic agent in adults or in children, as a secondary prevention, after successful eradication of H. pylori in an infected host, or as a therapeutic agent in the aim to induce an immune response in a susceptible host to prevent infection by H. pylon.
  • the vaccines of the invention are administered in amounts readily determined by persons of ordinary skill in the art.
  • a suitable dosage will be in the range of 10 ⁇ g to 10 g, preferably 10 ⁇ g to 100 mg, for example 50 ⁇ g to 50 mg.
  • a suitable dosage for adults will also be in the range of 5 ⁇ g to 500 mg. Similar dosage ranges will be applicable for children.
  • the amount of adjuvant employed will depend on the type of adjuvant used.
  • the mucosal adjuvant is cholera toxin
  • it is suitably used in an amount of 5 ⁇ g to 50 ⁇ g, for example 10 ⁇ g to 35 ⁇ g.
  • the amount used will depend on the amount employed in the matrix of the microcapsule to achieve the desired dosage. The determination of this amount is within the skill of a person of ordinary skill in the art.
  • the optimal dose may be more or less depending upon the patient's body weight, disease, the route of administration, and other factors.
  • appropriate dosage levels can be obtained based on results with known oral vaccines such as, for example, a vaccine based on an E. coli lysate (6 mg dose daily up to total of 540 mg) and with an enterotoxigenic E. coli purified antigen (4 doses of 1 mg) (Schulman et al., J. Urol 150:917-921 (1993)); Boedecker et al., American Gastroenterological Assoc. 999:A-222 (1993)).
  • the number of doses will depend upon the disease, the formulation, and efficacy data from clinical trials. Without intending any limitation as to the course of treatment, the treatment can be administered over 3 to 8 doses for a primary immunization schedule over 1 month (Boedeker, American Gastroenterological Assoc. 888 :A-222 (1993)).
  • a vaccine composition of the invention can be based on a killed whole E. coli preparation with an immunogenic fragment of an H. pylori protein of the invention expressed on its surface or it can be based on an E. coli lysate, wherein the killed E. coli acts as a carrier or an adjuvant. It will be apparent to those skilled in the art that some of the vaccine compositions of the invention are useful only for preventing H pylori infection, some are useful only for treating H. pylori infection, and some are useful for both preventing and treating H pylori infection. In a preferred embodiment, the vaccine composition of the invention provides protection against H.
  • H. pylori infection by stimulating humoral and/or cell-mediated immunity against H pylori. It should be understood that amelioration of any of the symptoms of H. pylori infection is a desirable clinical goal, including a lessening of the dosage of medication used to treat H. ⁇ y/or ' -caused disease, or an increase in the production of antibodies in the serum or mucous of patients.
  • the invention also includes antibodies specifically reactive with the subject H pylori polypeptide.
  • Anti-protein/anti-peptide antisera or monoclonal antibodies can be made by standard protocols (See, for example, Antibodies: A Laboratory Manual ed. by Harlow and Lane (Cold Spring Harbor Press: 1988)).
  • a mammal such as a mouse, a hamster or rabbit can be immunized with an immunogenic form of the peptide.
  • Techniques for conferring immunogenicity on a protein or peptide include conjugation to carriers or other techniques well known in the art.
  • An immunogenic portion of the subject H. pylori polypeptide can be administered in the presence of adjuvant. The progress of immunization can be monitored by detection of antibody titers in plasma or serum. Standard ELISA or other immunoassays can be used with the immunogen as antigen to assess the levels of antibodies.
  • the subject antibodies are immunospecific for antigenic determinants of the H. pylori polypeptides of the invention, e.g. antigenic determinants of a polypeptide of the invention contained in the Sequence Listing, or a closely related human or non-human mammalian homolog (e.g., 90% homologous, more preferably at least 95%> homologous).
  • the anti-H. pylori antibodies do not substantially cross react (i.e., react specifically) with a protein which is for example, less than 80%> percent homologous to a sequence of the invention contained in the Sequence Listing.
  • the antibody has a binding affinity for a non-homologous protein which is less than 10 percent, more preferably less than 5 percent, and even more preferably less than 1 percent, of the binding affinity for a protein of the invention contained in the Sequence Listing. In a most preferred embodiment, there is no crossreactivity between bacterial and mammalian antigens.
  • antibody as used herein is intended to include fragments thereof which are also specifically reactive with H pylori polypeptides.
  • Antibodies can be fragmented using conventional techniques and the fragments screened for utility in the same manner as described above for whole antibodies. For example, F(ab')2 fragments can be generated by treating antibody with pepsin. The resulting F(ab')2 fragment can be treated to reduce disulfide bridges to produce Fab' fragments.
  • the antibody of the invention is further intended to include bispecific and chimeric molecules having an anti-H. pylori portion.
  • Both monoclonal and polyclonal antibodies (Ab) directed against H pylori polypeptides or H pylori polypeptide variants, and antibody fragments such as Fab' and F(ab')2, can be used to block the action of H. pylori polypeptide and allow the study of the role of a particular H. pylori polypeptide of the invention in aberrant or unwanted intracellular signaling, as well as the normal cellular function of the H. pylori and by microinjection of anti-H. pylori polypeptide antibodies of the present invention.
  • Antibodies which specifically bind H pylori epitopes can also be used in immunohistochemical staining of tissue samples in order to evaluate the abundance and pattern of expression of H pylori antigens.
  • Anti H pylori polypeptide antibodies can be used diagnostically in immuno-precipitation and immuno-blotting to detect and evaluate H. pylori levels in tissue or bodily fluid as part of a clinical testing procedure.
  • the ability to monitor H. pylori polypeptide levels in an individual can allow determination of the efficacy of a given treatment regimen for an individual afflicted with such a disorder.
  • pylori polypeptide can be measured in cells found in bodily fluid, such as in urine samples or can be measured in tissue, such as produced by gastric biopsy. Diagnostic assays using anti-H. pylori antibodies can include, for example, immunoassays designed to aid in early diagnosis of H. pylori infections. The present invention can also be used as a method of detecting antibodies contained in samples from individuals infected by this bacterium using specific H. pylori antigens.
  • anti-H. pylori polypeptide antibodies of the invention is in the immunological screening of cDNA libraries constructed in expression vectors such as ⁇ gtl 1, ⁇ gtl 8-23, ⁇ ZAP, and ⁇ ORF8.
  • Messenger libraries of this type having coding sequences inserted in the correct reading frame and orientation, can produce fusion proteins.
  • ⁇ gtl 1 will produce fusion proteins whose amino termini consist of ⁇ -galactosidase amino acid sequences and whose carboxy termini consist of a foreign polypeptide.
  • Antigenic epitopes of a subject H. pylori polypeptide can then be detected with antibodies, as, for example, reacting nitrocellulose filters lifted from infected plates with anti-H.
  • H pylori polypeptide antibodies Phage, scored by this assay, can then be isolated from the infected plate. Thus, the presence of H pylori gene homologs can be detected and cloned from other species, and alternate isoforms (including splicing variants) can be detected and cloned.
  • Kits Containing Nucleic Acids, Polypeptides or Antibodies of the Invention can be combined with other reagents and articles to form kits.
  • Kits for diagnostic pu ⁇ oses typically comprise the nucleic acid, polypeptides or antibodies in vials or other suitable vessels.
  • Kits typically comprise other reagents for performing hybridization reactions, polymerase chain reactions (PCR), or for reconstitution of lyophilized components, such as aqueous media, salts, buffers, and the like.
  • Kits may also comprise reagents for sample processing such as detergents, chaotropic salts and the like.
  • Kits may also comprise immobilization means such as particles, supports, wells, dipsticks and the like.
  • Kits may also comprise labeling means such as dyes, developing reagents, radioisotopes, fluorescent agents, luminescent or chemiluminescent agents, enzymes, intercalating agents and the like. With the nucleic acid and amino acid sequence information provided herein, individuals skilled in art can readily assemble kits to serve their particular pu ⁇ ose. Kits further can include instructions for use.
  • labeling means such as dyes, developing reagents, radioisotopes, fluorescent agents, luminescent or chemiluminescent agents, enzymes, intercalating agents and the like.
  • H. pylori Polypeptides By making available purified and recombinant H. pylori polypeptides, the present invention provides assays which can be used to screen for drugs which are either agonists or antagonists of the normal cellular function, in this case, of the subject H pylori polypeptides, or of their role in intracellular signaling. Such inhibitors or potentiators may be useful as new therapeutic agents to combat H pylori infections in humans. A variety of assay formats will suffice and, in light of the present inventions, will be comprehended by the skilled artisan.
  • the effects of cellular toxicity and/or bioavailability of the test compound can be generally ignored in the in vitro system, the assay instead being focused primarily on the effect of the drug on the molecular target as may be manifest in an alteration of binding affinity with other proteins or change in enzymatic properties of the molecular target. Accordingly, in an exemplary screening assay of the present invention, the compound of interest is contacted with an isolated and purified H pylori polypeptide.
  • Screening assays can be constructed in vitro with a purified H pylori polypeptide or fragment thereof, such as an H. pylori polypeptide having enzymatic activity, such that the activity of the polypeptide produces a detectable reaction product.
  • the efficacy of the compound can be assessed by generating dose response curves from data obtained using various concentrations of the test compound.
  • a control assay can also be performed to provide a baseline for comparison. Suitable products include those with distinctive abso ⁇ tion, fluorescence, or chemi-luminescence properties, for example, because detection may be easily automated.
  • a variety of synthetic or naturally occurring compounds can be tested in the assay to identify those which inhibit or potentiate the activity of the H pylori polypeptide. Some of these active compounds may directly, or with chemical alterations to promote membrane permeability or solubility, also inhibit or potentiate the same activity (e.g., enzymatic activity) in whole, live H pylori cells.
  • H pylori chromosomal DNA was isolated according to a basic DNA protocol outlined in Schleif R.F. and Wensink P.C, Practical Methods in Molecular Biology, p.98, Springer- Verlag, NY., 1981, with minor modifications. Briefly, cells were pelleted, resuspended in TE (10 mM Tris, 1 mM EDTA, p ⁇ 7.6) and GES lysis buffer (5.1 M guanidium thiocyanate, 0.1 M EDTA, p ⁇ 8.0, 0.5%) N-laurylsarcosine) was added. Suspension was chilled and ammonium acetate (N ⁇ 4 AC) was added to final concentration of 2.0 M. DNA was extracted, first with chloroform, then with phenol- chloroform, and reextracted with chloroform. DNA was precipitated with isopropanol, washed twice with 70% EtOH, dried and resuspended in TE.
  • the purified DNA fragments were then blunt-ended using T4 DNA polymerase.
  • the healed DNA was then ligated to unique BstXI-linker adapters in 100-1000 fold molar excess.
  • These linkers are complimentary to the BstXI-cut pMPX vectors, while the overhang is not self-complimentary. Therefore, the linkers will not concatemerize nor will the cut- vector religate itself easily.
  • the linker-adopted inserts were separated from the uninco ⁇ orated linkers on a 1%> agarose gel and purified using GeneClean. The linker-adopted inserts were then ligated to each of the 20 pMPX vectors to construct a series of "shotgun" subclone libraries.
  • the vectors contain an out-of- frame lacZ gene at the cloning site which becomes in-frame in the event that an adapter-dimer is cloned, allowing these to be avoided by their blue-color.
  • each of the 20 vectors was then transformed into DH5 competent cells (Gibco/BRL, DH5 ⁇ transformation protocol).
  • the libraries were assessed by plating onto antibiotic plates containing ampicillin, methicillin and IPTG/Xgal. The plates were incubated overnight at 37°C. Successful transformants were then used for plating of clones and pooling into the multiplex pools. The clones were picked and pooled into 40 ml growth medium cultures. The cultures were grown overnight at 37°C.
  • DNA was purified using the Qiagen Midi-prep kits and Tip- 100 columns (Qiagen, Inc.). In this manner, 100 ⁇ g of DNA was obtained per pool. Fifteen 96-well plates of DNA were generated to obtain a 5-10 fold sequence redundancy assuming 250-300 base average read-lengths. These purified DNA samples were then sequenced using the multiplex DNA sequencing based on chemical degradation methods (Church G.M. and Kieffer-Higgins S., Science 240:185-188, 1988) or by Sequithrem (Epicenter Technologies) dideoxy sequencing protocols. The sequencing reactions were electrophoresed and transferred onto nylon membranes by direct transfer electrophoresis from 40 cm gels (Richterich P. and Church G.M., Methods in Enzymology 218:187-222, 1993) or by electroblotting
  • each gel produced a large number of films, each containing new sequencing information. Whenever a new blot was processed, it was initially probed for an internal standard sequence added to each of the pools.
  • Digital images of the films were generated using a laser-scanning densitometer (Molecular Dynamics, Sunnyvale, CA).
  • the digitized images were processed on computer workstations (VaxStation 4000's) using the program REPLICATM (Church et al., Automated DNA Sequencing and Analysis (J.C. Venter, ed.), Academic Press, 1994).
  • Image processing included lane straightening, contrast adjustment to smooth out intensity differences, and resolution enhancement by iterative gaussian deconvolution.
  • the sequences were then automatically picked in REPLICATM and displayed for interactive proofreading before being stored in a project database. The proofreading was accomplished by a quick visual scan of the film image followed by mouse clicks on the bands of the displayed image to modify the base calls.
  • sequence errors could be detected and corrected because multiple sequence reads covering the same portion of the genomic DNA provide adequate sequence redundancy for editing.
  • Each sequence automatically received an identification number (corresponding to microtiter plate, probe information, and lane set number). This number serves as a permanent identifier of the sequence so it is always possible to identify the original of any particular sequence without recourse to a specialized database.
  • GelAssemble developed by the Genetics Computer Group (GCG) (Devereux et al., Nucleic Acid Res. 12:387-95, 1984) that interacts with REPLICATM. This provided for an integrated editor that allows multiple sequence gel images to be instantaneously called up from the REPLICATM database and displayed to allow rapid scanning of contigs and proofreading of gel traces where discrepancies occurred between different sequence reads in the assembly.
  • GCG Genetics Computer Group
  • the pET System Novagen
  • a DNA sequence encoding a peptide tag, the ⁇ is-Tag was fused to the 3 ' end of DNA sequences of interest in order to facilitate purification of the recombinant protein products.
  • the 3' end was selected for fusion in order to avoid alteration of any 5' terminal signal sequence.
  • ppiB a gene cloned for use as a control in the expression studies.
  • the sequence for H pylori ppiB contains a DNA sequence encoding a ⁇ is-Tag fused to the 5' end of the full length gene, because the protein product of this gene does not contain a signal sequence and is expressed as a cytosolic protein.
  • Sequences chosen (from the list of the DNA sequences of the invention) for cloning from the J99 strain of H. pylori were prepared for amplification cloning by polymerase chain reaction (PCR).
  • Synthetic oligonucleotide primers (Table 3) specific for the 5' and 3' ends of open reading frames (ORFs) were designed and purchased (GibcoBRL Life Technologies, Gaithersburg, MD, USA). All forward primers (specific for the 5' end of the sequence) were designed to include an Ncol cloning site at the extreme 5' terminus, except for ⁇ pSeq. 4821082 where Ndel was used.
  • H pylori sequence 4821082 where the initiator methionine is immediately followed by the remainder of the native H pylori DNA sequence.
  • All reverse primers included a EcoRI site at the extreme 5' terminus to permit cloning of each H pylori sequence into the reading frame of the pET-28b.
  • the pET-28b vector provides sequence encoding an additional 20 carboxy-terminal amino acids (only 19 amino acids in ⁇ pSeq.
  • Oligonucleotide primers used for PCR amplification of H pylori DNA sequences Oligonucleotide primers used for PCR amplification of H pylori DNA sequences
  • Genomic DNA prepared from the J99 strain of H. pylori (ATCC #55679; deposited by Genome Therapeutics Co ⁇ oration, 100 Beaver Street, Waltham, MA 02154) was used as the source of template DNA for PCR amplification reactions (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
  • genomic DNA 50 nanograms was introduced into a reaction vial containing 2 mM MgCl2, 1 micromolar synthetic oligonucleotide primers (forward and reverse primers) complementary to and flanking a defined H pylori ORF, 0.2 mM of each deoxynucleotide triphosphate; dATP, dGTP. dCTP, dTTP and 2.5 units of heat stable DNA polymerase (Amplitaq, Roche Molecular Systems. Inc., Branchburg, NJ, USA) in a final volume of 100 microliters.
  • the following thermal cycling conditions were used to obtain amplified DNA products for each ORF using a Perkin Elmer Cetus/ GeneAmp PCR System 9600 thermal cycler:
  • each sample of amplified DNA was washed and purified using the Qiaquick Spin PCR purification kit (Qiagen, Gaithersburg, MD, USA). All amplified DNA samples were subjected to digestion with the restriction endonucleases, Ncol and EcoRI (New England BioLabs, Beverly, MA, USA), or in the case of HpSeq. 4821082 (SEQ ID NO: 1309), with Ndd and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
  • DNA samples were then subjected to electrophoresis on 1.0 %> NuSeive (FMC BioProducts, Rockland, ME USA) agarose gels. DNA was visualized by exposure to ethidium bromide and long wave uv irradiation. DNA contained in slices isolated from the agarose gel was purified using the Bio 101 GeneClean Kit protocol (Bio 101 Vista, C A, USA).
  • the pET-28b vector was prepared for cloning by digestion with Ncol and EcoRI, or in the case of H pylori protein 4821082 with Ndel and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
  • cloning ppiB the pET-28a vector, which encodes a ⁇ is-Tag that can be fused to the 5' end of an inserted gene, was used and the cloning site prepared for cloning with the ppiB gene by digestion with Bam ⁇ I and Xhol restriction endonucleases.
  • DNA inserts were cloned (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994) into the previously digested pET-28b expression vector, except for the amplified insert for ppiB, which was cloned into the pET-28a expression vector. Products of the ligation reaction were then used to transform the BL21 strain of E. coli (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994) as described below.
  • Competent bacteria E coli strain BL21 or E. coli strain BL21(DE3), were transformed with recombinant pET expression plasmids carrying the cloned H. pylori sequences according to standard methods (Current Protocols in Molecular, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).
  • the pET vector can be propagated in any E. coli K-12 strain e.g. ⁇ MS174, HB101, JM109, DH5, etc. for the pu ⁇ ose of cloning or plasmid preparation.
  • Hosts for expression include E. coli strains containing a chromosomal copy of the gene for T7 RNA polymerase. These hosts are lysogens of bacteriophage DE3, a lambda derivative that carries the lad gene, the lacUV5 promoter and the gene for T7 RNA polymerase.
  • T7 RNA polymerase is induced by addition of isopropyl-B-D-thiogalactoside (IPTG), and the T7 RNA polymerase transcribes any target plasmid, such as pET-28b, carrying a T7 promoter and a gene of interest.
  • Strains used include: BL21(DE3) (Studier, F.W., Rosenberg, A.H., Dunn, J.J., and Dubendorff, J.W. (1990) Meth. Enzymol. 185, 60-89).
  • H. pylori sequences 50 nanograms of plasmid DNA isolated as described above was used to transform competent BL21(DE3) bacteria as described above (provided by Novagen as part of the pET expression system kit).
  • the lacZ gene (beta-galactosidase) was expressed in the pET- System as described for the H. pylori recombinant constructions.
  • Transformed cells were cultured in SOC medium for 1 hour, and the culture was then plated on LB plates containing 25 micrograms/ml kanamycin sulfate.
  • bacterial colonies were pooled and grown in LB medium containing kanamycin sulfate (25 micrograms/ml) to an optical density at 600 nM of 0.5 to 1.0 O.D. units, at which point, 1 millimolar IPTG was added to the culture for 3 hours to induce gene expression of the H. pylori recombinant DNA constructions.
  • the concentrations of purified protein preparations were quantified spectrophotometrically using absorbance coefficients calculated from amino acid content (Perkins, S.J. 1986 Eur. J. Biochem. 157, 169-180). Protein concentrations were also measured by the method of Bradford, M.M. (1976) Anal. Biochem. 72, 248-254, and Lowry, O.H., Rosebrough, N., Farr, A.L. & Randall, R.J. (1951) J. Biol. Chem. 193, pages 265-275, using bovine serum albumin as a standard.
  • SDS-polyacrylamide gels (12%> or 4.0 to 25 %> acrylamide gradient gels) were purchased from BioRad (Hercules, CA, USA), and stained with Coomassie blue.
  • Molecular weight markers included rabbit skeletal muscle myosin (200 kDa), E. coli (- galactosidase (1 16 kDa), rabbit muscle phosphorylase B (97.4 kDa), bovine serum albumin (66.2 kDa), ovalbumin (45 kDa), bovine carbonic anhydrase (31 kDa), soybean trypsin inhibitor (21.5 kDa), egg white lysozyme (14.4 kDa) and bovine aprotinin (6.5 kDa).
  • NTA Ni ⁇ " - nitrilotriacetate-agarose
  • the column was washed with 250 ml (50 bed volumes) of lysis buffer containing 10 %> glycerol, 0.1 %> Brij 35, and was eluted with sequential steps of lysis buffer containing 10 %> glycerol, 0.05 %> Brij 35, 1 mM PMSF, and 20, 100, 200, and 500 mM imidazole in succession. Fractions were monitored by absorbance at OD28O nm ' anc peak fractions were analyzed by SDS-PAGE. Fractions containing the recombinant protein eluted at 100 mM imidazole.
  • Fractions containing the recombinant proteins from the Ni2 + -NTA-agarose columns were pooled and then concentrated to approximately 5 ml by centrifugal filtration (Centriprep-10, Amicon, MA), and loaded directly onto a 180-ml column (1.6 X 91 cm) of Sephacryl S-100 HR gel filtration medium equilibrated in Buffer A (10 mM Hepes, pH 7.5. 150 mM NaCl, 0.1 mM EGTA) and run in Buffer A at 18 ml/h. Fractions containing the recombinant protein were identified by absorbance at 280 nm and analyzed by SDS-PAGE. Fractions were pooled and concentrated by centrifugal filtration.
  • buffer B (10 mM MOPS, pH 6.5, 0.1 mM EGTA) containing 50 mM NaCl.
  • the column was washed with 10 bed volumes of buffer B containing 50 mM NaCl, and developed with a 50-ml linear gradient of increasing NaCl (50 to 500 mM).
  • Recombinant protein 71 16626 eluted as a sha ⁇ peak at 300 mM NaCl.
  • the pellets were washed with lysis buffer containing 10 %> glycerol, 10 mM EDTA, 1% Triton X-100, 1 mM PMSF and 0.1% -mercaptoethanol, followed by several washes with lysis buffer containing 1 M urea, 1 mM PMSF and 0.1 % 2- mercaptoethanol.
  • the resulting white pellet was composed primarily of inclusion bodies, free of unbroken cells and membranous materials..
  • the column was washed with 250 ml (50 bed volumes) of lysis buffer containing 8 M urea, 1.0 mM PMSF and 0.1 % 2-mercaptoethanol, and developed with sequential steps of lysis buffer containing 8M urea, 1 mM PMSF, 0.1 %> 2- mercaptoethanol and 20, 100, 200, and 500 mM imidazole in succession.
  • Fractions were monitored by absorbance at OD28O nrn - an ⁇ ⁇ P ea ⁇ fractions were analyzed by SDS- PAGE. Fractions containing the recombinant protein eluted at 100 mM imidazole.
  • the pellet containing the inclusion bodies was solubilized in buffer B containing
  • H. pylori To investigate the immunomodulatory effect of H. pylori proteins, a mouse/H pylori model was used. This model mimics the human H. pylori infection in many respects. The focus is on the effect of oral immunization in H. pylori infected animals in order to test the concept of therapeutic oral immuno therapy.
  • mice Female SPF BALB/c mice were purchased from Bomholt Breeding center
  • H pylori H pylori
  • strain 244 originally isolated from an ulcer patient
  • This strain has earlier proven to be a good colonizer of the mouse stomach.
  • the bacteria were grown overnight in Brucella broth supplemented with 10 %> fetal calf serum, at 37°C in a microaerophilic atmosphere (10% CO 2 , 5%>O ).
  • the animals were given an oral dose of omeprazole (400 ⁇ mol/kg) and 3-5 h after this an oral inoculation of H. pylori in broth (approximately 10 cfu/animal). Positive take of the infection was checked in some animals 2-3 weeks after the inoculation.
  • Recombinant H pylori antigens were chosen based on their association with externally exposed H. pylori cell membrane. These antigens were selected from the following groups: (1.) Outer Membrane Proteins; (2.) Periplastic/Secreted proteins; (3.) Outer Surface proteins; and (4.) Inner Membrane proteins. All recombinant proteins were constructed with a hexa- ⁇ IS tag for purification reasons and the non-Helicobacter pylori control protein (b-galactosidase from E. coli; LacZ), was constructed in the same way.
  • the antigens are listed in Table 5 below.
  • mice in each group were immunized 4 times over a 34 day period (day 1, 15, 25 and 35).
  • Purified antigens in solution or suspension were given at a dose of 100 mg/mouse.
  • CT Cholera toxin
  • Omeprazole (400 mmol/kg) was given orally to the animals 3-5 h prior to immunization as a way of protecting the antigens from acid degradation.
  • Infected control animals received HEPES buffer + CT or DOC buffer + CT. Animals were sacrificed 2-4 weeks after final immunization. A general outline of the study is shown in Table 6 below.
  • mice were all infected with H. pylori strain Ah244 at day 30
  • Protein 26054702 100 ⁇ g + CT 10 ⁇ gg BBaallbb//cc 0.3 ml 0, 14, 24, 34 5. Protein 26380318, 100 ⁇ g + CT 10 ⁇ g Balb/c 0.3 ml 0, 14, 24, 34
  • Mucosal infection The mice were sacrificed by CO 2 and cervical dislocation. The abdomen was opened and the stomach removed. After cutting the stomach along the greater curvature, it was rinsed in saline. The mucosa from the antrum and co ⁇ us of an area of 25mm was scraped separately with a surgical scalpel. The mucosa scraping was suspended in Brucella broth and plated onto Blood Skirrow selective plates. The plates were incubated under microaerophilic conditions for 3-5 days and the number of colonies was counted. The identity of H pylori was ascertained by urease and catalase test and by direct microscopy or Gram staining.
  • the urease test was performed essentially as follows.
  • the reagent, Urea Agar Base Concentrate, was purchased from DIFCO Laboratories, Detroit, MI (Catalog # 0284-61-3).
  • Urea agar base concentrate was diluted 1 : 10 with water. 1 ml of if the diluted concentrate was mixed with 100-200 ml of actively growing H. pylori cells. Color change to magenta indicated that cells were urease positive.
  • the catalase test was performed essentially as follows.
  • a solution of the regent (1% w/v in water) was prepared.
  • H. pylori cells were swabbed onto Whatman filter paper and overlaid with the 1%> solution. Color change to dark blue indicated that the cells were catalase positive.
  • Serum antibodies From all mice serum was prepared from blood drawn by heart puncture. Serum antibodies were identified by regular ELISA techniques, where the specific antigens of Helicobacter pylori were plated.
  • Mucosal antibodies Gentle scrapings of a defined part of the co ⁇ us and of 4 cm of duodenum were performed in 50%> of the mice in order to detect the presence of antibodies in the mucous.
  • the antibody titers were determined by regular ELISA technique as for serum antibodies.
  • Antibodies in mucus In the mucus scrapings, specific antibodies against all antigens tested were seen. By far the strongest response was seen with Protein 30100332, followed by Protein 14640637, and Protein 26380318 (see Figure 2).
  • H pylori associated proteins included in this study, when used as oral immunogens in conjunction with the oral adjuvant CT, resulted in stimulation of an immune response as measured by specific serum and mucosal antibodies.
  • a majority of the proteins led to a reduction, and in some cases complete clearance of the colonization of H pylori in this animal model.
  • the reduction or clearance was due to heterologous protection rather than homologous protection (the polypeptides were based on the H. pylori J99 strain sequence and used in the therapeutic immunization studies against a different (AH244) challenge strain, indicating the vaccine potential against a wide variety of H. pylori strains.
  • H. pylori Four genes were cloned and sequenced from several strains of H. pylori to compare the DNA and deduced amino acid sequences. This information was used to determine the sequence variation between the H. pylori strain, J99, and other H. pylori strains isolated from human patients.
  • H. pylori strains (as listed in Table 9) were grown in BLBB (1% Tryptone, 1% Peptamin 0.1% Glucose, 0.2% Yeast Extract 0.5% Sodium Chloride, 5% Fetal Bovine Serum) to an OD 600 of 0.2. Cells were centrifuged in a Sorvall RC-3B at 3500 x g at 4°C for 15 minutes and the pellet resuspended in 0.95 mis of 10 mM Tris- HCl, 0.1 mM EDTA (TE).
  • BLBB 1% Tryptone, 1% Peptamin 0.1% Glucose, 0.2% Yeast Extract 0.5% Sodium Chloride, 5% Fetal Bovine Serum
  • Lysozyme was added to a final concentration of 1 mg/ml along with, SDS to 1% and RNAse A + TI to 0.5mg/ml and 5 units/ml respectively, and incubated at 37°C for one hour. Proteinase K was then added to a final concentration of 0.4mg/ml and the sample was incubated at 55 C for more than one hour. NaCl was added to the sample to a concentration of 0.65 M, mixed carefully, and 0.15 ml of 10% CTAB in 0.7M NaCL (final is 1% CTAB/70mM NaCL) was added followed by incubation at 65°C for 20 minutes.
  • Genomic DNA prepared from twelve strains of Helicobacter pylori was used as the source of template DNA for PCR amplification reactions (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., editors, 1994).
  • genomic DNA (10 nanograms) was introduced into a reaction vial containing 2 mM MgCl 2 , 1 micromolar synthetic oligonucleotide primers (forward and reverse primers, see Table 7) complementary to and flanking a defined H.
  • pylori ORF 0.2 mM of each deoxynucleotide triphosphate; dATP, dGTP, dCTP, dTTP and 0.5 units of heat stable DNA polymerase (Amplitaq, Roche Molecular Systems, Inc., Branchburg, NJ, USA) in a final volume of 20 microliters in duplicate reactions.
  • each pair of samples were combined and used directly for cloning into the pCR cloning vector as described below.
  • Competent bacteria E coli strain TOPI OF' or E. coli strain INVaF' were transformed with recombinant pCR expression plasmids carrying the cloned H. pylori sequences according to standard methods (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., editors, 1994). Briefly, 2 microliters of 0.5 micromolar BM ⁇ was added to each vial of 50 microliters of competent cells.
  • Oligonucleotide primers used for sequencing of H. pylori DNA sequences Oligonucleotide primers used for sequencing of H. pylori DNA sequences.
  • the data demonstrate that there is variation in the DNA sequence ranging from as little as 0.12 % difference (Protein 346, J99 strain) to approximately 7% change (Protein 26054702, strain A ⁇ 5).
  • the deduced protein sequences show either no variation ( Protein 346, strains AH 18 and AH24) or up to as much as 7.66% amino acid changes (Protein 26054702, Strain AH5).
  • Therapeutic targets are chosen from genes whose protein products appear to play key roles in essential cell pathways such as cell envelope synthesis, DNA synthesis, transcription, translation, regulation and colonization/virulence.
  • H. pylori Gene Sequences The sequences of the genes or ORFs (open reading frames) selected as knock-out targets are identified from the H. pylori genomic sequence and used to design primers to specifically amplify the genes/ORFs. All synthetic oligonucleotide primers are designed with the aid of the OLIGO program (National Biosciences, Inc., Madison, MN 55447, USA), and can be purchased from Gibco/BRL Life Technologies (Gaithersburg, MD, USA). If the ORF is smaller than 800 to 1000 base pairs, flanking primers are chosen outside of the open reading frame.
  • Genomic DNA prepared from the Helicobacter pylori ⁇ pJ99 strain (ATCC 55679; deposited by Genome Therapeutics Co ⁇ oration, 100 Beaver Street, Waltham, MA 02154) is used as the source of template DNA for amplification of the ORFs by PCR (polymerase chain reaction) (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al.. editors, 1994).
  • PCR polymerase chain reaction
  • PCR products are cloned into the pT7Blue T-Vector (catalog#69820-l, Novagen, Inc., Madison, WI, USA) using the TA cloning strategy (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., editors, 1994).
  • the ligation of the PCR product into the vector is accomplished by mixing a 6 fold molar excess of the PCR product, 10 ng of pT7Blue-T vector (Novagen), 1 microliter of T4 DNA Ligase Buffer (New England Biolabs, Beverly, MA, USA), and 200 units of T4 DNA Ligase (New England Biolabs) into a final reaction volume of 10 microliters. Ligation is allowed to proceed for 16 hours at 16°C.
  • Ligation products are electroporated (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al.. editors, 1994) into electroporation- competent XL-1 Blue or DH5-a E.coli cells (Clontech Lab., Inc. Palo Alto, CA, USA).
  • 1 microliter of ligation reaction is mixed with 40 microliters of electrocompetent cells and subjected to a high voltage pulse (25 microFarads, 2.5 kV, 200 ohms) after which the samples are incubated in 0.45 ml SOC medium (0.5%) yeast extract, 2% tryptone, 10 mM NaCl, 2.5 mM KCl, 10 mM MgCl 2 , 10 mM MgSO 4 and 20 mM glucose) at 37°C with shaking for 1 hour.
  • a high voltage pulse 25 microFarads, 2.5 kV, 200 ohms
  • these pT7Blue plasmid DNAs are used as templates for PCR amplification of the cloned inserts, using the same forward and reverse primers used for the initial amplification of the J99 Hpylori sequence. Recognition of the primers and a PCR product of the correct size as visualized on a 2% TAE, ethidium bromide stained agarose gel are confirmation that the correct inserts had been cloned. Two to six such verified clones are obtained for each knock-out target, and frozen at -70°C for storage.
  • plasmid DNA from these verified clones are pooled, and used in subsequent cloning steps.
  • the sequences of the genes/ORFs are again used to design a second pair of primers which flank the region of H. pylori DNA to be either interrupted or deleted (up to 250 basepairs) within the ORFs but are oriented away from each other.
  • the pool of circular plasmid DNAs of the previously isolated clones are used as templates for this round of PCR. Since the orientation of amplification of this pair of deletion primers is away from each other, the portion of the ORF between the primers is not included in the resultant PCR product.
  • the PCR product is a linear piece of DNA with H.
  • a Kanamycin-resistance cassette (Labigne-Roussel et al, 1988 J. Bacteriology 170, 1704- 1708) is ligated to this PCR product by the TA cloning method used previously (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., editors, 1994).
  • the Kanamycin cassette containing a Campylobacter kanamycin resistance gene is obtained by carrying out an EcoRI digestion of the recombinant plasmid pCTB8:te? (Cover et al.,1994, J. Biological Chemistry 269, pp. 10566-10573).
  • the proper fragment (1.4 kb) is isolated on a 1% TAE gel, and isolated using the QIAquick gel extraction kit (Qiagen, Gaithersburg, MD, USA).
  • the fragment is end repaired using the Klenow fill-in protocol, which involved mixing 4ug of the DNA fragment, 1 microliter of dATP,dGTP, dCTP, dTTP at 0.5 mM, 2 microliter of Klenow Buffer (New England Biolabs) and 5 units of Klenow DNA Polymerase I Large (Klenow) Fragment (New England Biolabs) into a 20 microliter reaction, incubating at 30°C for 15 min, and inactivating the enzyme by heating to 75°C for 10 minutes.
  • This blunt-ended Kanamycin cassette is then purified through a Qiaquick column (Qiagen, Gaithersburg, MD, USA) to eliminate nucleotides.
  • the "T" overhang is then generated by mixing 5 micrograms of the blunt-ended kanamycin cassette, 10 mM Tris pH 8.3, 50 mM KCl, 2 mM MgCl 2 , 5 units of DNA Polymerase (Amplitaq, Roche Molecular
  • the "Kan-T" cassette is purified using a QIAquick column (Qiagen, Gaithersburg, MD, USA).
  • the PCR product of the deletion primers (F2 and R2) is ligated to the Kan-T cassette by mixing 10 to 25 ng of deletion primer PCR product, 50 - 75 ng Kan-T cassette DNA, 1 microliter lOx T4 DNA Ligase reaction mixture, 0.5 microliter T4 DNA Ligase (New England Biolabs, Beverly, MA, USA) in a 10 microliter reaction and incubating for 16 hours at 16°C.
  • the ligation products are transformed into XL-1 Blue or DH5-a E.coli cells by electroporation as described previously. After recovery in SOC, cells are plated onto LB plates containing 100 microgram/ml Ampicillin and grown overnight at 37°C. These plates are then replica plated onto plates containing 25 microgram ml Kanamycin and allowed to grow overnight. Resultant colonies have both the Ampicillin resistance gene present in the pT7Blue vector, and the newly introduced Kanamycin resistance gene. Colonies are picked into LB containing 25 microgram/ml Kanamycin and plasmid DNA is isolated from the cultured cells using the Qiagen miniprep protocol (Qiagen, Gaithersburg, MD. USA).
  • Several tests by PCR amplification are conducted on these plasmids to verify that the Kanamycin is inserted in the H. pylori gene/ORF, and to determine the orientation of the insertion of the Kanamycin-resistance gene relative to the H. pylori gene/ORF.
  • the plasmid DNAs are used as templates for PCR amplification with the set of primers originally used to clone the H pylori gene/ORFs.
  • the correct PCR product is the size of the deleted gene/ORF but increased in size by the addition of a 1.4 kilobase Kanamycin cassette.
  • the orientation of the Kanamycin resistance gene with respect to the knock-out gene/ORF is determined and both orientations are eventually used in H pylori transformations (see below).
  • primers are designed from the ends of the kanamycin resistance gene ("Kan-1 " 5'-ATCTTACCTATCACCTCAAAT-3' (SEQ ID NO:207)), and "Kan-2" 5'-AGACAGCAACATCTTTGTGAA-3' (SEQ ID NO:208)).
  • the orientation of the Kanamycin cassette relative to the H. pylori sequence is determined. Positive clones are classified as either in the "A" orientation (the same direction of transcription is present for both the H. pylori gene and the Kanamycin resistance gene), or in the "B" orientation (the direction of transcription for the H. pylori gene is opposite to that of the Kanamycin resistance gene). Clones which share the same orientation (A or B) are pooled for subsequent experiments and independently transformed into H pylori.
  • H. pylori cells Two strains of H pylori are used for transformation: ATCC 55679, the clinical isolate which provided the DNA from which the H. pylori sequence database is obtained, and A ⁇ 244, an isolate which had been passaged in, and has the ability to colonize the mouse stomach.
  • Cells for transformation are grown at 37°C, 10%> CO 2 , 100%) humidity, either on Sheep-Blood agar plates or in Brucella Broth liquid. Cells are grown to exponential phase, and examined microscopically to determine that the cells are "healthy" (actively moving cells) and not contaminated.
  • cells are harvested by scraping cells from the plate with a sterile loop, suspended in 1 ml of Brucella Broth, spun down (1 minute, top speed in eppendorf microfuge) and resuspended in 200 microliters Brucella Broth. If grown in Brucella Broth liquid, cells are centrifuged (15 minutes at 3000 rpm in a Beckman TJ6 centrifuge) and the cell pellet resuspended in 200 microliters of Brucella broth. An aliquot of cells is taken to determine the optical density at 600 nm, in order to calculate the concentration of cells.
  • Cells are then spread onto that plate using a swab wetted in Brucella broth, and grown for 20 hours at 37°C, 6%o CO 2 .
  • Cells are then transferred to a Sheep-Blood agar plate containing 25 micrograms/ml Kanamycin, and allowed to grow for 3 to 5 days at 37°C, 6% CO 2 , 100%) humidity. If colonies appear, they are picked and regrown as patches on a fresh Sheep-Blood agar plate containing 25 micrograms/ml Kanamycin.
  • the template for PCR (DNA from the colony) is obtained by a rapid boiling DNA preparation method as follows. An aliquot of the colony (stab of the colony with a toothpick) is introduced into 100 microliters of 1% Triton X-100, 20 mM Tris, pH 8.5, and boiled for 6 minutes. An equal volume of phenol : chloroform (1 : 1) is added and vortexed. The mixture is microfuged for 5 minutes and the supernatant is used as DNA template for PCR with combinations of the following primers to verify homologous recombination at the proper chromosomal location.
  • TEST 1 PCR with cloning primers originally used to amplify the gene/ORF.
  • a positive result of homologous recombination at the correct chromosomal location should show a single PCR product whose size is expected to be the size of the deleted gene/ORF but increased in size by the addition of a 1.4 kilobase Kanamycin cassette.
  • a PCR product of just the size of the gene/ORF is proof that the gene had not been knocked out and that the transformant is not the result of homologous recombination at the correct chromosome location.
  • TEST 2 PCR with F3 (primer designed from sequences upstream of the gene/ORF and not present on the plasmid), and either primer Kan-1 or Kan-2 (primers designed from the ends of the kanamycin resistance gene), depending on whether the plasmid DNA used was of "A" or "B” orientation. Homologous recombination at the correct chromosomal location will result in a single PCR product of the expected size (i.e., from the location of F3 to the insertion site of kanamycin resistance gene). No PCR product or PCR product(s) of incorrect size(s) will prove that the plasmid had not integrated at the correct site and that the gene had not been knocked out. TEST 3.
  • PCR with R3 primer designed from sequences downstream of the gene/ORF and not present on the plasmid
  • primer Kan-1 or Kan-2 depending on whether the plasmid DNA used was of "A" or "B” orientation.
  • Homologous recombination at the correct chromosomal location will result in a single PCR product of the expected size (i.e., from the insertion site of kanamycin resistance gene to the downstream location of R3).
  • no PCR product or PCR product(s) of incorrect size(s) will prove that the plasmid had not integrated at the correct site and that the gene had not been knocked out.
  • Transformants showing positive results for all three tests above indicate that the gene is not essential for survival in vitro.
  • a negative result in any of the three above tests for each transformant indicates that the gene had not been disrupted, and that the gene is essential for survival in vitro.
  • the plasmid DNA is further analyzed by PCR on DNA from transformant populations prior to plating for colony formation. This will verify that the plasmid can enter the cells and undergo homologous recombination at the correct site. Briefly, plasmid DNA is incubated according to the transformation protocol described above. DNA is extracted from the H.
  • TEST 2 and TEST 3 Positive results in TEST 2 and TEST 3 would verify that the plasmid DNA could enter the cells and undergo homologous recombination at the correct chromosomal location. If TEST
  • H. pylori target gene and its protein product e.g., an H. pylori enzyme
  • the assay is essentially as described by Fisher (Fischer, G., et.al. (1984) Biomed. Biochim. Ada 43:1101-1111).
  • the assay measures the cis-trans isomerization of the Ala-Pro bond in the test peptide N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide (Sigma # S- 7388, lot # 84H5805).
  • the assay is coupled with ⁇ -chymotrypsin, where the ability of the protease to cleave the test peptide occurs only when the Ala-Pro bond is in trans.
  • test peptide The conversion of the test peptide to the trans isomer in the assay is followed at 390 nm on a Beckman Model DU-650 spectophotometer. The data are collected every second with an average scanning of time of 0.5 second. Assays are carried out in 35 mM Hepes, pH 8.0, in a final volume of 400 ul, with 10 ⁇ M ⁇ -chymotrypsin (type 1-5 from bovine Pancreas, Sigma # C-7762, lot 23H7020) and 10 nM PPIase. To initiate the reaction. 10 ⁇ l of the substrate ( 2 mM N-Succinyl-Ala-Ala-Pro-Phe-p-nitroanilide in DMSO) is added to 390 ⁇ l of reaction mixture at room temperature.
  • substrate 2 mM N-Succinyl-Ala-Ala-Pro-Phe-p-nitroanilide in DMSO
  • a 50 ml culture of Helicobacter pylori (strain J99) in Brucella broth is harvested at mid-log phase (OD oo nm ⁇ 1 ) an d resuspended in lysis buffer with the following protease inhibitors: 1 mM PMSF, and 10 ⁇ g/ml of each of aprotinin, leupeptin, pepstatine, TLCK, TPCK, and soybean trypsin inhibitor.
  • the suspension is subjected to 3 cycles of freeze-thaw (15 minutes at -70 C, then 30 minutes at room temperature), followed by sonication (three 20 second bursts).
  • the lysate is centrifuged (12,000 g x 30 minutes) and the supernatant is assayed for enzymatic activity as described above.
  • H. pylori enzymes can be expressed at high levels and in an active form in E. coli. Such high yields of purified proteins provide for the design of various high throughput drug screening assays.
  • MOLECULE TYPE DNA (genomic)
  • HYPOTHETICAL NO
  • MOLECULE TYPE DNA (genomic)
  • HYPOTHETICAL NO
  • ANTI -SENSE NO
  • ORGANISM Helicobacter pylori
  • FEATURE FEATURE
  • MOLECULE TYPE DNA (genomic)
  • HYPOTHETICAL NO
  • ANTI -SENSE NO
  • ORGANISM Helicobacter pylori
  • MOLECULE TYPE DNA (genomic)
  • ORGANISM Helicobacter pylori
  • MOLECULE TYPE DNA (genomic)
  • HYPOTHETICAL NO
  • ANTI-SENSE NO
  • ORGANISM Helicobacter pylori
  • FEATURE FEATURE
  • CTAGGTGCTA CTGCTCCCTT AATGGCAAAG CCTTTATTAA GCGATGAAGA CTTATTGAAA 120
  • MOLECULE TYPE DNA (genomic)
  • HYPOTHETICAL NO
  • MOLECULE TYPE DNA (genomic)
  • ORGANISM Helicobacter pylori
  • MOLECULE TYPE DNA (genomic)
  • ORGANISM Helicobacter pylori
  • MOLECULE TYPE DNA (genomic)
  • ORGANISM Helicobacter pylori
  • TTCTTGCCTT ATAATTTAAA TAATGTTAAG CTTAGTTTTA CAGACGCTCA AGGCAATGTG 360 ATCGATCTAG GCGTGATAGA GACTATCCCC AAACACTCTA AGATTGTTTT GCCCGGAGAG 420 GCATTTGATA GTCTAAAAAT TGACCCCTAT ACTTTATTTC TTCCAAAAAT TGAAGCCACT 480
  • MOLECULE TYPE DNA (genomic)
  • HYPOTHETICAL NO
  • GATTTAGGTA AACAAGTTTA TGCACCTAAT AAAATCCAGT TGGATATGGT CTCTTGGGGT 420 GTGGGGAGCG ATTTGTTAGC TGATATTATT GATAAAGACA ACGCTTCTTT TGGTATTTTT 480
  • MOLECULE TYPE DNA (genomic)
  • MOLECULE TYPE DNA (genomic)
  • HYPOTHETICAL NO
  • ORGANISM Helicobacter pylori
  • GACTACGCTC ATGCCAATTC TATTAAGCTT AAAAACCCTA ACTATAATAG CGAAGCGGCG 300 CAAGTGGCTA GTCAAATTCT TGGGAAACAA GAAATCAATC GTTTAACAAA CATTGCCGAT 360
  • ORGANISM Helicobacter pylori
  • GAAAGCGCTA CAACGCAAAT AAACGCCAAT AAGCAAGAAG CAATAAATAA CATCACGCAA 720
  • ORGANISM Helicobacter pylori
  • CTCATCAATC AAAACGCCTT GCCGATCAAC TACGCTAACT TGGGGAGTCA AACAAACTAC 1020
  • MOLECULE TYPE DNA (genomic)
  • HYPOTHETICAL NO
  • ANTI -SENSE NO
  • ORGANISM Helicobacter pylori

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PCT/US1997/019575 1996-10-28 1997-10-28 Nucleic acid and amino acid sequences relating to helicobacter pylori and vaccine compositions thereof WO1998018323A1 (en)

Priority Applications (12)

Application Number Priority Date Filing Date Title
BR9712587-3A BR9712587A (pt) 1996-10-28 1997-10-28 ‡cido nucléico, molécula de ácido nucléico, sonda, vetor de expressão recombinante, célula, processos para produzir um polipeptìdeo de h. pylori e para detectar a presença de um ácido nucléico de helicobacter pylori em uma amostra, polipeptìdeo de h. pylori isolado, polipeptìdeos de envelope de célula, celular e secretado de h. pylori ou seus fragmentos, proteìna de fusão, formulação de vacina para a profilaxia ou tratamento de uma infecção por h. pylori, e, processos para tratar ou reduzir um risco de infecção por h. pylori em um sujeito e para produzir uma formulação de vacina.
EP97913847A EP0973394A4 (en) 1996-10-28 1997-10-28 NUCLEIC ACID AND AMINO ACID SEQUENCES RELATING TO HELICOBACTER PYLORI, AND VACCINE COMPOSITIONS CONTAINING SAME
AU50933/98A AU734052B2 (en) 1996-10-28 1997-10-28 Nucleic acid and amino acid sequences relating to helicobacter pylori and vaccine compositions thereof
SK346-99A SK34699A3 (en) 1996-10-28 1997-10-28 Nucleic acid and amino acid sequences relating to helicobacter pylori and vaccine compositions thereof
JP52071098A JP2001504329A (ja) 1996-10-28 1997-10-28 ヘリコバクター・ピロリに関連する核酸およびアミノ酸配列ならびにそのワクチン組成物
NZ334568A NZ334568A (en) 1996-10-28 1997-10-28 Nucleic acid and amino acid sequences relating to helicobacter pylori and vaccine compositions thereof
CA002265523A CA2265523A1 (en) 1996-10-28 1997-10-28 Nucleic acid and amino acid sequences relating to helicobacter pylori and vaccine compositions thereof
EEP199900176A EE9900176A (et) 1996-10-28 1997-10-28 Helicobacter pylori'ga seotud nukleiinhapete ja aminohapete järjestused ning nende vaktsiinikompositsioonid
IL12939797A IL129397A0 (en) 1996-10-28 1997-10-28 Nucleic acid and amino acid sequences relating to helicobacter pylori and vaccine compositions thereof
IS5005A IS5005A (is) 1996-10-28 1999-03-18 Kjarnsýrur og amínósýruraðir er tengjast Helicobacter pylori og bóluefni úr þeim
NO991995A NO991995L (no) 1996-10-28 1999-04-27 Nukleinsyre- og aminosyresekvenser relatert til Heliobacter pylori og vaksinesammensetninger derav
US10/335,977 US20040052799A1 (en) 1996-11-15 2002-12-30 Nucleic acid and amino acid sequences relating to Helicobacter pylori for diagnostics and therapeutics

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US73915096A 1996-10-28 1996-10-28
US08/739,150 1996-10-28
US75973996A 1996-12-06 1996-12-06
US08/759,739 1996-12-06
US89192897A 1997-07-14 1997-07-14
US08/891,928 1997-07-14

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EP (1) EP0973394A4 (es)
JP (1) JP2001504329A (es)
KR (1) KR20000052831A (es)
CN (1) CN1235513A (es)
AR (1) AR009600A1 (es)
AU (1) AU734052B2 (es)
BR (1) BR9712587A (es)
CA (1) CA2265523A1 (es)
EE (1) EE9900176A (es)
ID (1) ID22065A (es)
IL (1) IL129397A0 (es)
IS (1) IS5005A (es)
NO (1) NO991995L (es)
NZ (1) NZ334568A (es)
PL (1) PL333169A1 (es)
SA (1) SA98180918A (es)
SK (1) SK34699A3 (es)
TR (1) TR199900940T2 (es)
WO (1) WO1998018323A1 (es)

Cited By (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2000006743A2 (en) * 1998-07-27 2000-02-10 Connaught Laboratories Limited Chlamydia antigens and corresponding dna fragments and uses thereof
US6129923A (en) * 1993-07-27 2000-10-10 Csl Limited Treatment of H. pylori associated gastroduodenal disease
WO2000066624A1 (en) * 1999-04-29 2000-11-09 Astrazeneca Ab Helicobacter pylori antigens
WO2001000837A1 (en) * 1999-06-25 2001-01-04 Smithkline Beecham Biologicals S.A. Basb111 polypeptide and polynucleotide from moraxella catharrhalis
WO2001083533A1 (en) * 2000-04-29 2001-11-08 Astrazeneca Ab Helicobacter pylori antigens: fusion of hpaa and hpa44
WO2001083532A1 (en) * 2000-04-29 2001-11-08 Astrazeneca Ab Helicobacter pylori antigens: fusion of fay 31 and hpa 44
US6406703B1 (en) 1993-07-27 2002-06-18 Csl Limited Treatment of H. pylori associated gastroduodenal disease
JP2004505606A (ja) * 2000-03-08 2004-02-26 ノボザイムス　アクティーゼルスカブ 改変された特性を有する変異体
US7786260B1 (en) * 1999-10-15 2010-08-31 Csl Limited Polypeptide fragments comprising c terminal portion of helicobacter catalase
US9359627B2 (en) 2011-03-17 2016-06-07 National University Corporation Mie University Antibody production method

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
DE19730425A1 (de) 1997-07-16 1999-01-21 Henkel Teroson Gmbh Heißhärtende wäschefeste Rohbau-Versiegelung
WO2017102779A1 (en) * 2015-12-14 2017-06-22 Technische Universität München Helicobacter pylori vaccines
CN115724922B (zh) * 2022-07-19 2023-08-22 四川大学华西医院 一种幽门螺杆菌疫苗重组蛋白抗原TonB及其制备方法与应用
CN115581201A (zh) * 2022-08-26 2023-01-10 云南省农业科学院花卉研究所 以茎段为外植体诱导的二倍体月季f1-61的植株再生方法

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* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
SE9300139L (sv) * 1993-01-19 1994-07-20 Medicarb Ab Framställning av ett nytt läkemedel

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
JOURNAL OF BACTERIOLOGY, November 1992, Vol. 174, No. 21, TAYLOR et al., "Construction of a Helicobacter Pylori Genome Map and Demonstration of Diversity at the Genome Level", pages 6800-6806. *
NUCLEIC ACIDS RESEARCH, 1992, Vol. 20, No. 19, AKOPYANZ et al., "DNA Diversity Among Clinical Isolates of Helicobacter Pylori Detected by PCR-Based RAPD Fingerprinting", pages 5137-5142. *
See also references of EP0973394A4 *

Cited By (15)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6129923A (en) * 1993-07-27 2000-10-10 Csl Limited Treatment of H. pylori associated gastroduodenal disease
US6406703B1 (en) 1993-07-27 2002-06-18 Csl Limited Treatment of H. pylori associated gastroduodenal disease
WO2000006743A3 (en) * 1998-07-27 2000-05-04 Connaught Lab Chlamydia antigens and corresponding dna fragments and uses thereof
WO2000006743A2 (en) * 1998-07-27 2000-02-10 Connaught Laboratories Limited Chlamydia antigens and corresponding dna fragments and uses thereof
WO2000066624A1 (en) * 1999-04-29 2000-11-09 Astrazeneca Ab Helicobacter pylori antigens
JP2003503058A (ja) * 1999-06-25 2003-01-28 スミスクライン ビーチャム バイオロジカルズ ソシエテ アノニム モラクセラ・カタラーリス（Ｍｏｒａｘｅｌｌａｃａｔａｒｒｈａｌｉｓ）由来のＢＡＳＢ１１１ポリペプチドおよびポリヌクレオチド
WO2001000837A1 (en) * 1999-06-25 2001-01-04 Smithkline Beecham Biologicals S.A. Basb111 polypeptide and polynucleotide from moraxella catharrhalis
US7786260B1 (en) * 1999-10-15 2010-08-31 Csl Limited Polypeptide fragments comprising c terminal portion of helicobacter catalase
JP2004505606A (ja) * 2000-03-08 2004-02-26 ノボザイムス　アクティーゼルスカブ 改変された特性を有する変異体
US8609811B2 (en) 2000-03-08 2013-12-17 Novozymes A/S Amylase variants
US8883970B2 (en) 2000-03-08 2014-11-11 Novozymes A/S Alpha-amylase variants
US9856437B2 (en) 2000-03-08 2018-01-02 Novozymes A/S Amylase variants
WO2001083532A1 (en) * 2000-04-29 2001-11-08 Astrazeneca Ab Helicobacter pylori antigens: fusion of fay 31 and hpa 44
WO2001083533A1 (en) * 2000-04-29 2001-11-08 Astrazeneca Ab Helicobacter pylori antigens: fusion of hpaa and hpa44
US9359627B2 (en) 2011-03-17 2016-06-07 National University Corporation Mie University Antibody production method

Also Published As

Publication number Publication date
NO991995D0 (no) 1999-04-27
JP2001504329A (ja) 2001-04-03
NO991995L (no) 1999-06-28
AU5093398A (en) 1998-05-22
BR9712587A (pt) 1999-10-26
NZ334568A (en) 2000-04-28
EP0973394A4 (en) 2005-03-30
AU734052B2 (en) 2001-05-31
SA98180918A (ar) 2005-12-03
EE9900176A (et) 1999-12-15
EP0973394A1 (en) 2000-01-26
PL333169A1 (en) 1999-11-22
CA2265523A1 (en) 1998-05-07
ID22065A (id) 1999-08-26
IS5005A (is) 1999-03-18
IL129397A0 (en) 2000-02-17
CN1235513A (zh) 1999-11-17
SK34699A3 (en) 2000-04-10
KR20000052831A (ko) 2000-08-25
TR199900940T2 (xx) 1999-09-21
AR009600A1 (es) 2000-04-26

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