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Genomic and functional analysis of Vibrio phage SIO-2 reveals novel insights into ecology and evolution of marine siphoviruses

Authors

  • A.-C. Baudoux,

    Corresponding author
    1. Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA 92093, USA
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    • Present addresses: CNRS/UPMC Univ. Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29682 Roscoff, France;

  • R. W. Hendrix,

    1. Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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  • G. C. Lander,

    1. National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA 92037, USA
    2. Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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    • Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

  • X. Bailly,

    1. CNRS/UPMC Univ. Paris 06, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29682 Roscoff, France
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  • S. Podell,

    1. Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA 92093, USA
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  • C. Paillard,

    1. Institut Universitaire Européen de la Mer, Laboratoire des Sciences de l’Environnement Marin, 29280 Plouzané, France
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  • J. E. Johnson,

    1. Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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  • C. S. Potter,

    1. National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA 92037, USA
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  • B. Carragher,

    1. National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA 92037, USA
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  • F. Azam

    1. Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA 92093, USA
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E-mail acbaudoux@sb-roscoff.fr; Tel. (+33) 298 292 323; Fax (+33) 298 292 324.

Summary

We report on a genomic and functional analysis of a novel marine siphovirus, the Vibrio phage SIO-2. This phage is lytic for related Vibrio species of great ecological interest including the broadly antagonistic bacterium Vibrio sp. SWAT3 as well as notable members of the Harveyi clade (V. harveyi ATTC BAA-1116 and V. campbellii ATCC 25920). Vibrio phage SIO-2 has a circularly permuted genome of 80 598 bp, which displays unusual features. This genome is larger than that of most known siphoviruses and only 38 of the 116 predicted proteins had homologues in databases. Another divergence is manifest by the origin of core genes, most of which share robust similarities with unrelated viruses and bacteria spanning a wide range of phyla. These core genes are arranged in the same order as in most bacteriophages but they are unusually interspaced at two places with insertions of DNA comprising a high density of uncharacterized genes. The acquisition of these DNA inserts is associated with morphological variation of SIO-2 capsid, which assembles as a large (80 nm) shell with a novel T = 12 symmetry. These atypical structural features confer on SIO-2 a remarkable stability to a variety of physical, chemical and environmental factors. Given this high level of functional and genomic novelty, SIO-2 emerges as a model of considerable interest in ecological and evolutionary studies.

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