Abstract
A novel virulent phage named JL1 against Escherichia coli O157:H7 was isolated from raw sewage. It was found that JL1 has an icosahedral head and a long flexible non-contractile tail. The complete genome of JL1 is composed of a linear double-stranded DNA of 43,457 base pairs in length, with 54.77 % G+C content and 60 putative open reading frames. Morphology and bioinformatics analysis revealed that phage JL1 is a member of the family Siphoviridae of the order Caudovirales. It is different from previously reported phages of E. coli O157:H7 but is homologous to Sodalis phage SO-1, Shigella phage EP23, Escherichia phage HK578 and Escherichia phage SSL-2009a.
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References
Adams MH (1959) Bacteriophages. Interscience Publishers, New York
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Becker B, de la Fuente N, Gassel M, Günther D, Tavares P, Lurz R, Trautner TA, Alonso JC (1997) Head morphogenesis genes of the Bacillus subtilis Bacteriophage SPP1. J Mol Biol 268:822–839
Besemer J, Borodovsky M (1999) Heuristic approach to deriving models for gene finding. Nucleic Acids Res 27:3911–3920
Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J (2005) ACT: the Artemis comparison tool. Bioinformatics 21:3422–3423
Clokie M, Kropinski A (2009) Bacteriophages: methods and protocols, volume 1: isolation, characterization, and interactions. Humana, New York
Eisen JA, Sweder KS, Hanawalt PC (1995) Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res 23:2715–2723
Fauquet CM, Mayo M, Maniloff J, Desselberger U, Ball LA (2005) Virus taxonomy: VIIIth report of the International Committee on Taxonomy of Viruses. Academic Press, London
Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A (2005) Protein identification and analysis tools on the ExPASy server: the proteomics protocols handbook. Humana Press, Totowa, pp 571–607
Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 33:D121–D124
Kanamaru S, Leiman PG, Kostyuchenko VA, Chipman PR, Mesyanzhinov VV, Arisaka F, Rossmann MG (2002) Structure of the cell-puncturing device of bacteriophage T4. Nature 415:553–557
Kim J, Son J, Choi Y, Choresca Jr C, Shin S, Han J, Jun J, Park S (2012) Complete genome sequence and characterization of a broad-host range T4-like bacteriophage phiAS5 infecting Aeromonas salmonicida subsp. salmonicida. Vet Microbiol 157:164–171
Kutter E (2009) Phage host range and efficiency of plating: Bacteriophages. Springer, Berlin, pp 141–149
Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11–16
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:0955–0964
Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH (2011) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39:D225–D229
Panos GZ, Betsi GI, Falagas ME (2006) Systematic review: are antibiotics detrimental or beneficial for the treatment of patients with Escherichia coli O157: H7 infection? Aliment Pharm Ther 24:731–742
Patel PH, Suzuki M, Adman E, Shinkai A, Loeb LA (2001) Prokaryotic DNA polymerase I: evolution, structure, and “base flipping” mechanism for nucleotide selection. J Mol Biol 308:823–837
Pedersen M, Østergaard S, Bresciani J, Vogensen FK (2000) Mutational analysis of two structural genes of the temperate lactococcal bacteriophage TP901-1 involved in tail length determination and baseplate assembly. Virology 276:315–328
Reese MG (2001) Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput Chem 26:51–56
Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. CSHL press, New York
Young R, Wang IN, Roof WD (2000) Phages will out: strategies of host cell lysis. Trends Microbiol 8:120–128
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829
Acknowledgment
This work was supported by the Technical Center of Jilin Entry-Exit Inspection and Quarantine Bureau (JLCIQ) of People’s Republic China, and by grants from the General Administration of Quality Supervision, Inspection and Quarantine of the People’s Republic of China (Project Code: No. 2012IK163).
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Pan, F., Wu, H., Liu, J. et al. Complete genome sequence of Escherichia coli O157:H7 lytic phage JL1. Arch Virol 158, 2429–2432 (2013). https://doi.org/10.1007/s00705-013-1727-2
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DOI: https://doi.org/10.1007/s00705-013-1727-2