Genome and proteome analysis of phage E3 infecting the soil-borne actinomycete Rhodococcus equi

Authors

  • Samson P. Salifu,

    1. School of Life, Sport and Social Sciences, Edinburgh Napier University, Edinburgh, UK
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    • Contributed equally to this work.
  • Ana Valero-Rello,

    1. Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection & Evolution, University of Edinburgh, Edinburgh, UK
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    • Contributed equally to this work.
  • Samantha A. Campbell,

    1. School of Life, Sport and Social Sciences, Edinburgh Napier University, Edinburgh, UK
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  • Neil F. Inglis,

    1. Moredun Proteomics Facility, Moredun Research Institute, Penicuik, UK
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  • Mariela Scortti,

    1. Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection & Evolution, University of Edinburgh, Edinburgh, UK
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  • Sophie Foley,

    Corresponding author
    • School of Life, Sport and Social Sciences, Edinburgh Napier University, Edinburgh, UK
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  • José A. Vázquez-Boland

    Corresponding author
    1. Grupo de Patogenómica Bacteriana, Facultad de Veterinaria, Universidad de León, León, Spain
    • Microbial Pathogenesis Unit, Centres for Infectious Diseases and Immunity, Infection & Evolution, University of Edinburgh, Edinburgh, UK
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For correspondence. E-mail s.foley@napier.ac.uk; Tel. (+44) 131 455 2626; Fax (+44) 131 455 2291; Email v.boland@ed.ac.uk; Tel. (+44) 131 651 3619; Fax (+44) 131 650 6564.

Summary

We report on the characterization and genomic analysis of bacteriophage E3 isolated from soil and propagating in Rhodococcus equi strains. Phage E3 has a circular genome of 142 563 bp and is the first Myoviridae reported for the genus Rhodococcus and for a non-mycobacterial actinomycete. Phylogenetic analyses placed E3 in a distinct Myoviridae clade together with Mycobacterium phages Bxz1 and Myrna. The highly syntenic genomes of this myoviridal group comprise vertically evolving core phage modules flanked by hyperplastic regions specific to each phage and rich in horizontally acquired DNA. The hyperplastic regions contain numerous tRNA genes in the mycobacteriophages which are absent in E3, possibly reflecting bacterial host-specific translation-related phage fitness constraints associated with rate-limiting tRNAs. A structural proteome analysis identified 28 E3 polypeptides, including 15 not previously known to be virion-associated proteins. The E3 genome and comparative analysis provide insight into short-term genome evolution and adaptive plasticity in tailed phages from the environmental microbiome.

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