title: Genome analysis of phage JS98 defines a fourth major subgroup of T4-like phages in Escherichia coli.
abstract: Numerous T4-like Escherichia coli phages were isolated from human stool and environmental wastewater samples in Bangladesh and Switzerland. The sequences of the major head gene (g23) revealed that these coliphages could be placed into four subgroups, represented by the phages T4, RB69, RB49, and JS98. Thus, JS98 defines a new major subgroup of E. coli T4-like phages. We conducted an analysis of the 169-kb JS98 genome sequence. Overall, 198 of the 266 JS98 open reading frames (ORFs) shared amino acid sequence identity with the reference T4 phage, 41 shared identity with other T4-like phages, and 27 ORFs lacked any database matches. Genes on the plus strand encoded virion proteins, which showed moderate to high sequence identity with T4 proteins. The right genome half of JS98 showed a higher degree of sequence conservation with T4 and RB69, even for the nonstructural genes, than did the left genome half, containing exclusively nonstructural genes. Most of the JS98-specific genes were found in the left genome half. Two came as a hypervariability cluster, but most represented isolated genes, suggesting that they were acquired separately in multiple acquisition events. No evidence for DNA exchange between JS98 phage and the E. coli host genome or coliphages other than T4 was observed. No undesired genes which could compromise its medical use were detected in the JS98 genome sequence.
authors: Nestlé Research Center, Nestec Ltd., P.O. Box 44, CH-1000 Lausanne 26, Switzerland.
authors: Sophie
authors: S
authors: Zuber
authors: Catherine
authors: C
authors: Ngom-Bru
authors: Caroline
authors: C
authors: Barretto
authors: Anne
authors: A
authors: Bruttin
authors: Harald
authors: H
authors: Brüssow
authors: Emmanuel
authors: E
authors: Denou
mesh_terms: D017122:Bacteriophage T4 / Q000145:classification* / Q000235:genetics*; D004279:DNA, Viral / Q000235:genetics; D004926:Escherichia coli / Q000821:virology*; D015967:Gene Expression Regulation, Viral; D016679:Genome, Viral; D008969:Molecular Sequence Data; D010802:Phylogeny; D014764:Viral Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D004279:DNA, Viral; D014764:Viral Proteins
references: Nucleic Acids Res. 1997 Mar 1;25(5):955-64
references: 9023104
references: Appl Environ Microbiol. 2007 Oct;73(19):5975-81
references: 17704275
references: Science. 1997 Oct 24;278(5338):631-7
references: 9381173
references: Genome Biol. 2004;5(2):R12
references: 14759262
references: Microbiol Mol Biol Rev. 2004 Sep;68(3):560-602, table of contents
references: 15353570
references: J Virol. 1972 Mar;9(3):399-407
references: 4335658
references: J Infect Dis. 1980 Jun;141(6):702-11
references: 6248600
references: J Infect Dis. 1980 Nov;142(5):660-4
references: 6257795
references: Bull World Health Organ. 1982;60(4):605-13
references: 6982783
references: Comput Appl Biosci. 1988 Mar;4(1):11-7
references: 3382986
references: Nucleic Acids Res. 1999 Dec 1;27(23):4636-41
references: 10556321
references: J Bacteriol. 2001 Jan;183(1):358-66
references: 11114936
references: Bioinformatics. 2000 Oct;16(10):944-5
references: 11120685
references: J Bacteriol. 2002 May;184(10):2789-804
references: 11976309
references: Pediatr Infect Dis J. 2002 Apr;21(4):322-30
references: 12075764
references: Microbiol Mol Biol Rev. 2003 Mar;67(1):86-156, table of contents
references: 12626685
references: Vaccine. 2003 Jun 2;21(19-20):2394-403
references: 12744870
references: Microbiol Mol Biol Rev. 2003 Jun;67(2):238-76, table of contents
references: 12794192
references: J Bacteriol. 2003 Sep;185(17):5220-33
references: 12923095
references: Bull World Health Organ. 1994;72(6):945-55
references: 7867142
references: J Bacteriol. 1998 Apr;180(8):2005-13
references: 9555879
references: J Mol Biol. 1998 Sep 25;282(3):543-56
references: 9737921
references: J Clin Microbiol. 1999 Nov;37(11):3458-64
references: 10523534
references: J Bacteriol. 2004 Dec;186(24):8276-86
references: 15576776
references: J Bacteriol. 2004 Dec;186(24):8287-94
references: 15576777
references: J Bacteriol. 2005 May;187(9):3188-200
references: 15838046
references: PLoS Biol. 2005 May;3(5):e144
references: 15828858
references: Proc Natl Acad Sci U S A. 2005 May 17;102(20):7163-8
references: 15878991
references: Antimicrob Agents Chemother. 2005 Jul;49(7):2874-8
references: 15980363
references: Microbiology. 2005 Jul;151(Pt 7):2133-40
references: 16000704
references: Proc Natl Acad Sci U S A. 2005 Aug 30;102(35):12471-6
references: 16116082
references: Nature. 2005 Sep 15;437(7057):376-80
references: 16056220
references: J Mol Biol. 2006 Aug 4;361(1):46-68
references: 16828113
references: Virol J. 2006;3:30
references: 16716236
references: FEMS Microbiol Lett. 2007 Apr;269(1):145-52
references: 17241245
references: Clin Gastroenterol Hepatol. 2007 Apr;5(4):451-6
references: 17382603
references: Virology. 2007 Jun 5;362(2):384-96
references: 17289101
references: FEBS Lett. 1997 Sep 22;415(1):75-80
references: 9326373