Genomic and functional analysis of Vibrio phage SIO-2 reveals novel insights into ecology and evolution of marine siphoviruses
Identifieur interne : 000280 ( Ncbi/Merge ); précédent : 000279; suivant : 000281Genomic 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.
Abstract
We report on a genomic and functional analysis of a novel marine siphovirus, the
Url:
DOI: 10.1111/j.1462-2920.2011.02685.x
PubMed: 22225728
PubMed Central: 3338904
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PMC:3338904Le document en format XML
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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>
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<front><journal-meta><journal-id journal-id-type="nlm-journal-id">100883692</journal-id>
<journal-id journal-id-type="pubmed-jr-id">21501</journal-id>
<journal-id journal-id-type="nlm-ta">Environ Microbiol</journal-id>
<journal-id journal-id-type="iso-abbrev">Environ. Microbiol.</journal-id>
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<title-group><article-title>Genomic and functional analysis of <italic>Vibrio</italic>
phage SIO-2 reveals novel insights into ecology and evolution of marine siphoviruses</article-title>
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<contrib-group><contrib contrib-type="author"><name><surname>Baudoux</surname>
<given-names>A-C.</given-names>
</name>
<xref ref-type="aff" rid="A1">1</xref>
<xref ref-type="author-notes" rid="FN1">a</xref>
<xref ref-type="corresp" rid="CR1">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hendrix</surname>
<given-names>R.W.</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lander</surname>
<given-names>G.C.</given-names>
</name>
<xref ref-type="aff" rid="A3">3</xref>
<xref ref-type="aff" rid="A4">4</xref>
<xref ref-type="author-notes" rid="FN2">b</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Bailly</surname>
<given-names>X.</given-names>
</name>
<xref ref-type="aff" rid="A5">5</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Podell</surname>
<given-names>S.</given-names>
</name>
<xref ref-type="aff" rid="A1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Paillard</surname>
<given-names>C.</given-names>
</name>
<xref ref-type="aff" rid="A6">6</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Johnson</surname>
<given-names>J.E.</given-names>
</name>
<xref ref-type="aff" rid="A4">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Potter</surname>
<given-names>C.S.</given-names>
</name>
<xref ref-type="aff" rid="A3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Carragher</surname>
<given-names>B.</given-names>
</name>
<xref ref-type="aff" rid="A3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Azam</surname>
<given-names>F.</given-names>
</name>
<xref ref-type="aff" rid="A1">1</xref>
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</contrib-group>
<aff id="A1"><label>1</label>
Scripps Institution of Oceanography, Marine Biology Research Division, University of California San Diego, La Jolla, CA 92093 USA</aff>
<aff id="A2"><label>2</label>
Pittsburgh Bacteriophage Institute, Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA</aff>
<aff id="A3"><label>3</label>
National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA 92037 USA</aff>
<aff id="A4"><label>4</label>
Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037 USA</aff>
<aff id="A5"><label>5</label>
CNRS/ UPMC Univ. Paris 06, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29682 Roscoff France</aff>
<aff id="A6"><label>6</label>
Institut Universitaire Européen de la Mer, Laboratoire des Sciences de l'Environnement Marin, 29280 Plouzané France</aff>
<author-notes><fn id="FN1" fn-type="present-address"><label>a</label>
<p id="P1">present address : CNRS/ UPMC Univ. Paris 06, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, 29682 Roscoff France</p>
</fn>
<fn id="FN2" fn-type="present-address"><label>b</label>
<p id="P2">present address : Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA</p>
</fn>
<corresp id="CR1"><label>*</label>
Correspondence: <email>acbaudoux@sb-roscoff.fr</email>
</corresp>
</author-notes>
<pub-date pub-type="nihms-submitted"><day>21</day>
<month>12</month>
<year>2011</year>
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<pub-date pub-type="epub"><day>9</day>
<month>1</month>
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<pub-date pub-type="ppub"><month>8</month>
<year>2012</year>
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<pub-date pub-type="pmc-release"><day>01</day>
<month>8</month>
<year>2013</year>
</pub-date>
<volume>14</volume>
<issue>8</issue>
<fpage>2071</fpage>
<lpage>2086</lpage>
<abstract><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>
</abstract>
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