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WO2002059320A2 - Nouvelles sequences d'$i(e. coli) cft073 - Google Patents

Nouvelles sequences d'$i(e. coli) cft073 Download PDF

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Publication number
WO2002059320A2
WO2002059320A2 PCT/US2001/046833 US0146833W WO02059320A2 WO 2002059320 A2 WO2002059320 A2 WO 2002059320A2 US 0146833 W US0146833 W US 0146833W WO 02059320 A2 WO02059320 A2 WO 02059320A2
Authority
WO
WIPO (PCT)
Prior art keywords
nucleotide
sequence
seq
cft073
nucleic acid
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/US2001/046833
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English (en)
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WO2002059320A3 (fr
Inventor
Fredrick R. Blattner
Rodney A. Welch
Valerie D. Burland
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Wisconsin Alumni Research Foundation
Original Assignee
Wisconsin Alumni Research Foundation
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Wisconsin Alumni Research Foundation filed Critical Wisconsin Alumni Research Foundation
Priority to AU2002246592A priority Critical patent/AU2002246592A1/en
Publication of WO2002059320A2 publication Critical patent/WO2002059320A2/fr
Anticipated expiration legal-status Critical
Publication of WO2002059320A3 publication Critical patent/WO2002059320A3/fr
Ceased legal-status Critical Current

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/24—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Enterobacteriaceae (F), e.g. Citrobacter, Serratia, Proteus, Providencia, Morganella, Yersinia
    • C07K14/245—Escherichia (G)

Definitions

  • Escherichia coli is a common enteric bacterial strain that has both laboratory and human health importance.
  • One particular strain of E. coli, designated CFT073 is a human pathogen that causes urinary tract infections. Urinary tract infections are common in various populations throughout the human life span. Infant boys, women of childbearing years, and aged people of both sexes have relatively high incidences of this infection.
  • Acute pyelonephritis a bacterial infection of the kidneys, is a common complication of such infections. Acute pyelonephritis often requires hospitalization for treatment, and the disease can be severe including complications or life threatening conditions.
  • E. coli Various strains of E. coli are associated with urinary tract infections and are commonly found in the urine of patients with pyelonephritis. Certain phenotypes of E. coli are found more often in such association.
  • the strains associated with acute pyelonephritis often include a set of gene functions which, as a unit, have been thought to form a set of virulence factors that allow specific clones of E. coli to cause pyelonephritis.
  • Another object of the present invention is to provide a means of treating humans and livestock infected with CFT073.
  • the present invention includes many DNA sequences that are unique to E. coli CFT073.
  • One aspect of the present invention is two CFT073 DNA sequences that encode hemagglutinin-like proteins that are important for host cell adhesion.
  • Another aspect of the present invention is two CFT073 DNA sequences that encode for autotransporters.
  • Another aspect of the present invention is a CFT073 DNA sequence that encodes for a RTX-like protein.
  • Still another aspect of the present invention is a method for detecting E. coli CFT073 and distinguishing the strain from other strains of E. coli by genetic analysis and testing. [0017] It is a feature of the invention disclosed here that virtually the entire genome of E. coli CFT073 is set forth in the data contained here, combined with the information already published in the field.
  • E. coli CFT073 The investigators here have sequenced virtually the entire genome of E. coli CFT073. Presented in this specification is essentially all the DNA sequence which is contained in the genome of E. coli strain CFT073 and not found in the previously sequenced non-pathogenic laboratory E. coli strain K-12. The genome sequence is essentially complete, lacking only an occasional presumably small sequence linkage between established long sequences known. The availability of the sequence data presented here will enable intelligent design of diagnostic detection, prophylaxis and therapeutic tools for disease and infections caused by this organism.
  • E. coli CFT073 was, in brief, performed by shotgun cloning and duplicative random sequence analysis followed by computer assembly into contigs.
  • the contigs determined by shot gun clone sequencing were assembled using computer software designed for that purpose.
  • the first one is between nucleotide 12003 and nucleotide 20509 of SEQ ID NO.251.
  • ORF1 is a putative member of the ShlA/HecA/Fha exoprotein family that shows a 25% identity over 2,311 residues to a probable hemagglutinin (the nucleotide sequence GenBank accession number for the probable hemagglutinin is AE004443).
  • the second one (ORF2) is between nucleotide 31940 and nucleotide 34668 of SEQ ID NO:254.
  • ORF2 is a member of the Shl/Fha/Hpm family and amino acids 33-907 of ORF2 shows a 26% identity to amino acids 1,912-2,818 of hemagglutinin/hemolysin-related protein (the amino acid sequence and the nucleotide sequence GenBank accession numbers are AAG03431 and AE002405, respectively). Both ORF1 and ORF2 are believed to be important for host cell adhesion and thus infection.
  • the third one is the complementary sequence between nucleotide 1008 and nucleotide 1885 of SEQ ID NO: 85.
  • ORF3 is a member of the autotransporter family and is 57% identical over 292 residues to a putative beta-barrel outer membrane protein (the nucleotide sequence GenBank accession number is AE005210).
  • the fourth one is the complementary sequence between nucleotide 1996 and nucleotide 5607 of SEQ ID NO:85. ORF4 is also a member of the autotransporter family.
  • ORF4 has a 31% identity over 1103 residues to YapD protein (the nucleotide sequence GenBank accession number is AJ277627) and a 27% identity over 2952 residues to YapH protein (the nucleotide sequence GenBank accession number is AJ277631). Both ORF3 and ORF4 as autotransporters are believed to be important virulence factors of CFT073.
  • ORF5 The fifth one (ORF5) is between nucleotide 40329 and nucleotide 44950 of SEQ ID NO:251.
  • ORF5 is similar to RTX family members and is 23% identical over 1,461 residues to a putative RTX family exoprotein (the nucleotide sequence GenBank accession number is AE005229).
  • ORF5 is believed to be an exotoxin like RTX.
  • the DNA sequences of ORF 1-5 are also useful for treatment and prevention purposes.
  • antisense oligonucleotides can be designed given the knowledge of these sequences to block the expression of the corresponding proteins.
  • One of ordinary skill knows how to design and use antisense oligonucleotides.
  • the corresponding amino acid sequences of ORF 1-5 or an immunogenic fragment thereof are also valuable for diagnosis, treatment and prevention of uropathogenic E. coli strains.
  • the corresponding amino acid sequences or an immunogenic fragment thereof can be used to generate antibodies that can be used for diagnosis, treatment and prevention purposes.
  • One of ordinary skill in the art knows how to produce antibodies to the proteins encoded by ORF 1-5.
  • Vaccines may also be produced using the amino acid sequence information. It is well within the knowledge of a skilled artisan to generate vaccines.
  • the specific CFT073 strain from which the sequence data is derived is available from ATCC as ATCC 700928.
  • ATCC 700928 One wishing to practice the present invention using one of the disclosed DNA sequences can do so by isolating the sequence from ATCC 700928 using knowledge of the nucleotide sequence and standard methods known to one of ordinary skill in the art.
  • E. coli CFT073 -specific nucleotide sequences associated with nucleotide additions, deletions, and mutations, whether naturally occurring or introduced in vitro, would not interfere with the usefulness of these sequences in the detection of uropathogenic E. coli, in methods for preventing urinary tract infection, and in methods for treating pyelonephritis. Therefore, the scope of the present invention is intended to encompass minor variations in the claimed sequences, which include both DNA and RNA and can also contain non-standard bases such as inosine.
  • E. coli CFT073-specific nucleotide probe it is meant a sequence that is able to hybridize to E. coli CFT073 target DNA present in a sample containing E. coli CFT073 under suitable hybridization conditions and which does not hybridize with DNA from other E. coli strains or from other bacterial species.
  • a CFT073 specific probe will bind to CFT073 DNA but not to DNA from K-12.
  • the probe may be RNA or DNA. Depending on the detection means employed, the probe may be unlabeled, radiolabeled, or labeled with a dye.
  • the probe may be hybridized with a sample that has been immobilized on a solid support such as nitrocellulose or a nylon membrane, or the probe may be immobilized on a solid support, such as a silicon chip.
  • the sample to be tested may include blood, urine, feces, or other materials from a human or a livestock animal. Alternatively, the sample may include food intended for human consumption.
  • the sample may be tested directly, or may be treated in some manner prior to testing. For example, the sample may be subjected to PCR amplification using appropriate oligonucleotide primers.
  • sequence listing constituting essentially all of the DNA sequence in the CFT073 genome that do not appear in strain K-12, which is presented as SEQ ID NO:l to SEQ ID NO:251 and SEQ ID NO:254. Since all of these sequences are diagnostic of CFT073, as compared to K-12, sequence information from any of these sequences can be used to design diagnostic probes useful to distinguish strain CFT073 from strain K-12 using molecular techniques. To have reasonable assurance of success under conditions of variable stringency, it is preferred that such diagnostic probes use sequences which are at least 25 nucleotides or longer in length. Any 25-mer selected from amongst any of the sequences in any of SEQ ID NO:l through SEQ ID NO:251 and SEQ ID NO:254 may be used for such a probe.

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  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • General Health & Medical Sciences (AREA)
  • Biochemistry (AREA)
  • Biophysics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Medicinal Chemistry (AREA)
  • Molecular Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Gastroenterology & Hepatology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Saccharide Compounds (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)

Abstract

Le génome entier de la souche d'E.coli pathogène CFT073 a été séquencé. Presque toutes les séquences d'ADN génomique présentes dans CFT073 et absentes dans la souche de laboratoire séquencée précédemment K-12 sont présentées.
PCT/US2001/046833 2000-10-19 2001-10-19 Nouvelles sequences d'$i(e. coli) cft073 Ceased WO2002059320A2 (fr)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2002246592A AU2002246592A1 (en) 2000-10-19 2001-10-19 Dna sequences of escherichia coli cft073

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US24241200P 2000-10-19 2000-10-19
US60/242,412 2000-10-19

Publications (2)

Publication Number Publication Date
WO2002059320A2 true WO2002059320A2 (fr) 2002-08-01
WO2002059320A3 WO2002059320A3 (fr) 2003-09-04

Family

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PCT/US2001/046833 Ceased WO2002059320A2 (fr) 2000-10-19 2001-10-19 Nouvelles sequences d'$i(e. coli) cft073

Country Status (2)

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AU (1) AU2002246592A1 (fr)
WO (1) WO2002059320A2 (fr)

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP2298795A1 (fr) * 2005-02-18 2011-03-23 Novartis Vaccines and Diagnostics, Inc. Immunogènes d'E. coli uropathogène
EP2351772A1 (fr) * 2005-02-18 2011-08-03 Novartis Vaccines and Diagnostics, Inc. Protéines et acides nucléiques d'Escherichia coli associé à la méningite/sepsie

Family Cites Families (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP0942964A2 (fr) * 1996-11-22 1999-09-22 Human Genome Sciences, Inc. Polymerases thermostables a fidelite modifiee

Cited By (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP2298795A1 (fr) * 2005-02-18 2011-03-23 Novartis Vaccines and Diagnostics, Inc. Immunogènes d'E. coli uropathogène
EP2351772A1 (fr) * 2005-02-18 2011-08-03 Novartis Vaccines and Diagnostics, Inc. Protéines et acides nucléiques d'Escherichia coli associé à la méningite/sepsie
US8758764B2 (en) 2005-02-18 2014-06-24 Novartis Vaccines And Diagnostics Srl Proteins and nucleic acids from meningitis/sepsis-associated Escherichia coli
US9334313B2 (en) 2005-02-18 2016-05-10 Glaxosmithkline Biologicals Sa Proteins and nucleic acids from meningitis/sepsis-associated Escherichia coli
US10035826B2 (en) 2005-02-18 2018-07-31 Glaxosmithkline Biologicals Sa Proteins and nucleic acids from meningitis/sepsis-associated Escherichia coli

Also Published As

Publication number Publication date
AU2002246592A1 (en) 2002-08-06
WO2002059320A3 (fr) 2003-09-04

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