A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses
Identifieur interne : 000504 ( Pmc/Curation ); précédent : 000503; suivant : 000505A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses
Auteurs : Geoffrey S. Diemer [États-Unis] ; Kenneth M. Stedman [États-Unis]Source :
- Biology Direct [ 1745-6150 ] ; 2012.
Abstract
Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to resolve deep evolutionary histories of the known major virus groups. Metagenomics offers a potential means of establishing a more comprehensive view of viral evolution as vast amounts of new sequence data becomes available for comparative analysis.
Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar to those found only in single-stranded RNA viruses. The presence and circular configuration of the complete virus genome was confirmed by inverse PCR amplification from native DNA extracted from lake sediment. The virus genome appears to be the result of a RNA-DNA recombination event between two ostensibly unrelated virus groups. Environmental sequence databases were examined for homologous genes arranged in similar configurations and three similar putative virus genomes from marine environments were identified. This result indicates the existence of a widespread but previously undetected group of viruses.
This unique viral genome carries implications for theories of virus emergence and evolution, as no mechanism for interviral RNA-DNA recombination has yet been identified, and only scant evidence exists that genetic exchange occurs between such distinct virus lineages.
This article was reviewed by EK, MK (nominated by PF) and AM. For the full reviews, please go to the Reviewers' comments section.
Url:
DOI: 10.1186/1745-6150-7-13
PubMed: 22515485
PubMed Central: 3372434
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses</title><author><name sortKey="Diemer, Geoffrey S" sort="Diemer, Geoffrey S" uniqKey="Diemer G" first="Geoffrey S" last="Diemer">Geoffrey S. Diemer</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biology, and the Center for Life in Extreme Environments, Portland State University, 1719 SW 10th Avenue, SRTC room 246, Portland, OR, 97201, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, and the Center for Life in Extreme Environments, Portland State University, 1719 SW 10th Avenue, SRTC room 246, Portland, OR, 97201</wicri:regionArea></affiliation></author><author><name sortKey="Stedman, Kenneth M" sort="Stedman, Kenneth M" uniqKey="Stedman K" first="Kenneth M" last="Stedman">Kenneth M. Stedman</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biology, and the Center for Life in Extreme Environments, Portland State University, 1719 SW 10th Avenue, SRTC room 246, Portland, OR, 97201, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, and the Center for Life in Extreme Environments, Portland State University, 1719 SW 10th Avenue, SRTC room 246, Portland, OR, 97201</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22515485</idno><idno type="pmc">3372434</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372434</idno><idno type="RBID">PMC:3372434</idno><idno type="doi">10.1186/1745-6150-7-13</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000504</idno><idno type="wicri:Area/Pmc/Curation">000504</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses</title><author><name sortKey="Diemer, Geoffrey S" sort="Diemer, Geoffrey S" uniqKey="Diemer G" first="Geoffrey S" last="Diemer">Geoffrey S. Diemer</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biology, and the Center for Life in Extreme Environments, Portland State University, 1719 SW 10th Avenue, SRTC room 246, Portland, OR, 97201, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, and the Center for Life in Extreme Environments, Portland State University, 1719 SW 10th Avenue, SRTC room 246, Portland, OR, 97201</wicri:regionArea></affiliation></author><author><name sortKey="Stedman, Kenneth M" sort="Stedman, Kenneth M" uniqKey="Stedman K" first="Kenneth M" last="Stedman">Kenneth M. Stedman</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Biology, and the Center for Life in Extreme Environments, Portland State University, 1719 SW 10th Avenue, SRTC room 246, Portland, OR, 97201, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, and the Center for Life in Extreme Environments, Portland State University, 1719 SW 10th Avenue, SRTC room 246, Portland, OR, 97201</wicri:regionArea></affiliation></author></analytic><series><title level="j">Biology Direct</title><idno type="eISSN">1745-6150</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to resolve deep evolutionary histories of the known major virus groups. Metagenomics offers a potential means of establishing a more comprehensive view of viral evolution as vast amounts of new sequence data becomes available for comparative analysis.</p></sec><sec><title>Results</title><p>Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar to those found only in single-stranded RNA viruses. The presence and circular configuration of the complete virus genome was confirmed by inverse PCR amplification from native DNA extracted from lake sediment. The virus genome appears to be the result of a RNA-DNA recombination event between two ostensibly unrelated virus groups. Environmental sequence databases were examined for homologous genes arranged in similar configurations and three similar putative virus genomes from marine environments were identified. This result indicates the existence of a widespread but previously undetected group of viruses.</p></sec><sec><title>Conclusions</title><p>This unique viral genome carries implications for theories of virus emergence and evolution, as no mechanism for interviral RNA-DNA recombination has yet been identified, and only scant evidence exists that genetic exchange occurs between such distinct virus lineages.</p></sec><sec><title>Reviewers</title><p>This article was reviewed by EK, MK (nominated by PF) and AM. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Biol Direct</journal-id><journal-id journal-id-type="iso-abbrev">Biol. Direct</journal-id><journal-title-group><journal-title>Biology Direct</journal-title></journal-title-group><issn pub-type="epub">1745-6150</issn><publisher><publisher-name>BioMed Central</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">22515485</article-id><article-id pub-id-type="pmc">3372434</article-id><article-id pub-id-type="publisher-id">1745-6150-7-13</article-id><article-id pub-id-type="doi">10.1186/1745-6150-7-13</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research</subject></subj-group></article-categories><title-group><article-title>A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses</article-title></title-group><contrib-group><contrib contrib-type="author" id="A1"><name><surname>Diemer</surname><given-names>Geoffrey S</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>geod@pdx.edu</email></contrib><contrib contrib-type="author" corresp="yes" id="A2"><name><surname>Stedman</surname><given-names>Kenneth M</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>kstedman@pdx.edu</email></contrib></contrib-group><aff id="I1"><label>1</label>Department of Biology, and the Center for Life in Extreme Environments, Portland State University, 1719 SW 10th Avenue, SRTC room 246, Portland, OR, 97201, USA</aff><pub-date pub-type="collection"><year>2012</year></pub-date><pub-date pub-type="epub"><day>11</day><month>6</month><year>2012</year></pub-date><volume>7</volume><fpage>13</fpage><lpage>13</lpage><history><date date-type="received"><day>9</day><month>1</month><year>2012</year></date><date date-type="accepted"><day>19</day><month>4</month><year>2012</year></date></history><permissions><copyright-statement>Copyright ©2012 Diemer and Stedman; licensee BioMed Central Ltd.</copyright-statement><copyright-year>2012</copyright-year><copyright-holder>Diemer and Stedman; licensee BioMed Central Ltd.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><self-uri xlink:href="http://www.biology-direct.com/content/7/1/13"></self-uri><abstract><sec><title>Background</title><p>Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to resolve deep evolutionary histories of the known major virus groups. Metagenomics offers a potential means of establishing a more comprehensive view of viral evolution as vast amounts of new sequence data becomes available for comparative analysis.</p></sec><sec><title>Results</title><p>Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar to those found only in single-stranded RNA viruses. The presence and circular configuration of the complete virus genome was confirmed by inverse PCR amplification from native DNA extracted from lake sediment. The virus genome appears to be the result of a RNA-DNA recombination event between two ostensibly unrelated virus groups. Environmental sequence databases were examined for homologous genes arranged in similar configurations and three similar putative virus genomes from marine environments were identified. This result indicates the existence of a widespread but previously undetected group of viruses.</p></sec><sec><title>Conclusions</title><p>This unique viral genome carries implications for theories of virus emergence and evolution, as no mechanism for interviral RNA-DNA recombination has yet been identified, and only scant evidence exists that genetic exchange occurs between such distinct virus lineages.</p></sec><sec><title>Reviewers</title><p>This article was reviewed by EK, MK (nominated by PF) and AM. For the full reviews, please go to the Reviewers' comments section.</p></sec></abstract><kwd-group><kwd>Non-retroviral RNA virus integration</kwd><kwd>RNA-DNA recombination</kwd><kwd>Viral metagenomics</kwd><kwd>Metaviromics</kwd><kwd>Virus ecology</kwd><kwd>Viral diversity</kwd><kwd>Modular theory of virus evolution</kwd><kwd>Interviral lateral gene transfer</kwd><kwd>RNA World</kwd><kwd>DNA World</kwd><kwd>Virus World</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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