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Complete genome sequence analysis and identification of putative metallo-beta-lactamase and SpoIIIE homologs in Bacillus cereus group phage BCP8-2, a new member of the proposed Bastille-like group

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Abstract

Bacillus cereus group-specific bacteriophage BCP8-2 exhibits a broad lysis spectrum among food and human isolates (330/364) of B. cereus while not infecting B. subtilis (50) or B. licheniformis (12) strains. Its genome is 159,071 bp long with 220 open reading frames, including genes for putative methyltransferases, metallo-beta-lactamase, and a sporulation-related SpoIIIE homolog, as wells as 18 tRNAs. Comparative genome analysis showed that BCP8-2 is related to the recently proposed Bastille-like phages, but not with either SPO1-like or Twort-like phages of the subfamily Spounavirinae.

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References

  1. Bandara N, Jo J, Ryu S, Kim K-P (2012) Bacteriophages BCP1-1 and BCP8-2 require divalent cations for efficient control of Bacillus cereus in fermented foods. Food Microbiol 31:9–16

    Article  CAS  PubMed  Google Scholar 

  2. Barylski J, Nowicki G, Goździcka-Józefiak A (2014) The discovery of phiAGATE, a novel phage infecting Bacillus pumilus, leads to new insights into the phylogeny of the subfamily Spounavirinae. PLoS ONE 9:e86632

    Article  PubMed Central  PubMed  Google Scholar 

  3. Bebrone C (2007) Metallo-beta-lactamases (classification, activity, genetic organization, structure, zinc coordination) and their superfamily. Biochem Pharmacol 74:1686–1701

    Article  CAS  PubMed  Google Scholar 

  4. Casjens SR, Gilcrease EB (2009) Determining DNA packaging strategy by analysis of the termini of the chromosomes in tailed-bacteriophage virions. Methods Mol Biol 502:91–111

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  5. Delcher AL, Bratke KA, Powers EC, Salzberg SL (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  6. El-Arabi TF, Griffiths MW, She Y-M, Villegas A, Lingohr EJ, Kropinski AM (2013) Genome sequence and analysis of a broad-host range lytic bacteriophage that infects the Bacillus cereus group. Virol J 10:48

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  7. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649

    Article  PubMed Central  PubMed  Google Scholar 

  8. Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11–16

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  9. Lee J-H, Shin H, Ryu S (2014) Characterization and comparative genomic analysis of bacteriophages infecting members of the Bacillus cereus group. Arch Virol 159:871–884

    Article  CAS  PubMed  Google Scholar 

  10. Mahadevan P, King JF, Seto D (2009) CGUG: in silico proteome and genome parsing tool for the determination of “core” and unique genes in the analysis of genomes up to ca. 1.9 Mb. BMC Res Notes 2:168

    Article  PubMed Central  PubMed  Google Scholar 

  11. Nakamura Y, Gojobori T, Ikemura T (2000) Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res 28:292

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  12. Omasits U, Ahrens CH, Müller S, Wollscheid B (2013) Protter: interactive protein feature visualization and integration with experimental proteomic data. Bioinformatics 30:884–886

    Article  PubMed  Google Scholar 

  13. Pope WH, Anders KR, Baird M et al (2014) Cluster M mycobacteriophages Bongo, PegLeg, and Rey with unusually large repertoires of tRNA isotypes. J Virol 88:2461–2480

    Article  PubMed Central  PubMed  Google Scholar 

  14. Ryazanova AY, Abrosimova L, Oretskaya T, Kubareva E (2012) Diverse domains of (cytosine-5)-DNA methyltransferases: structural and functional characterization. In: Dricu A (ed) Methylation—from DNA, RNA and histones to disease and treatment. InTech, Croatia, pp 29–69

    Google Scholar 

  15. Santos SB, Kropinski AM, Ceyssens P-J, Ackermann H-W, Villegas A, Lavigne R, Krylov VN, Carvalho CM, Ferreira EC, Azeredo J (2011) Genomic and proteomic characterization of the broad-host-range Salmonella phage PVP-SE1: creation of a new phage genus. J Virol 85:11265–11273

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  16. Schuch R, Pelzek AJ, Fazzini MM, Nelson DC, Fischetti VA (2014) Complete genome sequence of Bacillus cereus sensu lato bacteriophage Bcp1. Genome Announc 2:e00334-00314

    Article  Google Scholar 

  17. Sullivan MJ, Petty NK, Beatson SA (2011) Easyfig: a genome comparison visualizer. Bioinformatics 27:1009–1010

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  18. Yee LM, Matsumoto T, Yano K, Matsuoka S, Sadaie Y, Yoshikawa H, Asai K (2011) The genome of Bacillus subtilis phage SP10: a comparative analysis with phage. Biosci Biotechnol Biochem 75:944–995

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

This work was supported by the High Value-Added Food Technology Development Program (Project No. 112108-2 and 313037-3), Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries (IPET) of Republic of Korea.

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    Authors and Affiliations

    1. Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, Jeollabuk-do, 561-756, Korea

      Paul Tetteh Asare, Nadeeka Bandara, Tae-Yong Jeong & Kwang-Pyo Kim

    2. Department of Food and Animal Biotechnology, Center for Agricultural Biomaterials, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Korea

      Sangryeol Ryu

    3. Department of Agricultural Biotechnology, Center for Agricultural Biomaterials, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, Korea

      Sangryeol Ryu

    4. Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092, Zurich, Switzerland

      Jochen Klumpp

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    1. Paul Tetteh Asare
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    2. Nadeeka Bandara
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    3. Tae-Yong Jeong
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    4. Sangryeol Ryu
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    5. Jochen Klumpp
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    6. Kwang-Pyo Kim
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    Correspondence to Kwang-Pyo Kim.

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    P. T. Asare and N. Bandara contributed equally to this work.

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    Asare, P.T., Bandara, N., Jeong, TY. et al. Complete genome sequence analysis and identification of putative metallo-beta-lactamase and SpoIIIE homologs in Bacillus cereus group phage BCP8-2, a new member of the proposed Bastille-like group. Arch Virol 160, 2647–2650 (2015). https://doi.org/10.1007/s00705-015-2548-2

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    • DOI: https://doi.org/10.1007/s00705-015-2548-2

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