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

Identifieur interne : 000280 ( Ncbi/Curation ); précédent : 000279; suivant : 000281

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

Auteurs : A-C. Baudoux [États-Unis] ; R. W. Hendrix [États-Unis] ; G. C. Lander [États-Unis] ; X. Bailly ; S. Podell [États-Unis] ; C. Paillard ; J. E. Johnson [États-Unis] ; C. S. Potter [États-Unis] ; B. Carragher [États-Unis] ; F. Azam [États-Unis]

Source :

Environmental microbiology [ 1462-2912 ] ; 2012.

RBID : PMC:3338904

Abstract

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.

Url:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338904

DOI: 10.1111/j.1462-2920.2011.02685.x
PubMed: 22225728
PubMed Central: 3338904

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X. Bailly

<affiliation><nlm:aff id="A5">CNRS/ UPMC Univ. Paris 06, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29682 Roscoff France</nlm:aff>
<wicri:noCountry code="subfield">29682 Roscoff France</wicri:noCountry>
</affiliation>

C. Paillard

<affiliation><nlm:aff id="A6">Institut Universitaire Européen de la Mer, Laboratoire des Sciences de l'Environnement Marin, 29280 Plouzané France</nlm:aff>
<wicri:noCountry code="subfield">29280 Plouzané France</wicri:noCountry>
</affiliation>

Le document en format XML

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<author><name sortKey="Baudoux, A C" sort="Baudoux, A C" uniqKey="Baudoux A" first="A-C." last="Baudoux">A-C. Baudoux</name>
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<author><name sortKey="Hendrix, R W" sort="Hendrix, R W" uniqKey="Hendrix R" first="R. W." last="Hendrix">R. W. Hendrix</name>
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<author><name sortKey="Lander, G C" sort="Lander, G C" uniqKey="Lander G" first="G. C." last="Lander">G. C. Lander</name>
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<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Californie</region>
</placeName>
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<author><name sortKey="Bailly, X" sort="Bailly, X" uniqKey="Bailly X" first="X." last="Bailly">X. Bailly</name>
<affiliation><nlm:aff id="A5">CNRS/ UPMC Univ. Paris 06, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29682 Roscoff France</nlm:aff>
<wicri:noCountry code="subfield">29682 Roscoff France</wicri:noCountry>
</affiliation>
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<author><name sortKey="Podell, S" sort="Podell, S" uniqKey="Podell S" first="S." last="Podell">S. Podell</name>
<affiliation wicri:level="2"><nlm:aff id="A1">Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA 92093 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Californie</region>
</placeName>
<wicri:cityArea>Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Paillard, C" sort="Paillard, C" uniqKey="Paillard C" first="C." last="Paillard">C. Paillard</name>
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<wicri:noCountry code="subfield">29280 Plouzané France</wicri:noCountry>
</affiliation>
</author>
<author><name sortKey="Johnson, J E" sort="Johnson, J E" uniqKey="Johnson J" first="J. E." last="Johnson">J. E. Johnson</name>
<affiliation wicri:level="2"><nlm:aff id="A4">Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Californie</region>
</placeName>
<wicri:cityArea>Department of Molecular Biology, The Scripps Research Institute, La Jolla</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Potter, C S" sort="Potter, C S" uniqKey="Potter C" first="C. S." last="Potter">C. S. Potter</name>
<affiliation wicri:level="2"><nlm:aff id="A3">National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA 92037 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Californie</region>
</placeName>
<wicri:cityArea>National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Carragher, B" sort="Carragher, B" uniqKey="Carragher B" first="B." last="Carragher">B. Carragher</name>
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<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Californie</region>
</placeName>
<wicri:cityArea>National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla</wicri:cityArea>
</affiliation>
</author>
<author><name sortKey="Azam, F" sort="Azam, F" uniqKey="Azam F" first="F." last="Azam">F. Azam</name>
<affiliation wicri:level="2"><nlm:aff id="A1">Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA 92093 USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName><region type="state">Californie</region>
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<series><title level="j">Environmental microbiology</title>
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<front><div type="abstract" xml:lang="en"><p id="P3">We report on a genomic and functional analysis of a novel marine siphovirus, the <italic>Vibrio</italic>
 phage SIO-2. This phage is lytic for related <italic>Vibrio</italic>
 species of great ecological interest including the broadly antagonistic bacterium <italic>Vibrio</italic>
 sp. SWAT3 as well as notable members of the Harveyi clade (<italic>V. harveyi</italic>
 ATTC BAA-1116 and <italic>V. campbellii</italic>
 ATCC 25920). <italic>Vibrio</italic>
 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.</p>
</div>
</front>
</TEI>
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Genomic and functional analysis of Vibrio phage SIO-2 reveals novel insights into ecology and evolution of marine siphoviruses

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

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Abstract

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