Metabolic reprogramming by viruses in the sunlit and dark ocean
Identifieur interne : 000337 ( Pmc/Curation ); précédent : 000336; suivant : 000338Metabolic reprogramming by viruses in the sunlit and dark ocean
Auteurs : Bonnie L. Hurwitz [États-Unis] ; Steven J. Hallam [Canada] ; Matthew B. Sullivan [États-Unis]Source :
- Genome Biology [ 1465-6906 ] ; 2013.
Abstract
Marine ecosystem function is largely determined by matter and energy transformations mediated by microbial community interaction networks. Viral infection modulates network properties through mortality, gene transfer and metabolic reprogramming.
Here we explore the nature and extent of viral metabolic reprogramming throughout the Pacific Ocean depth continuum. We describe 35 marine viral gene families with potential to reprogram metabolic flux through central metabolic pathways recovered from Pacific Ocean waters. Four of these families have been previously reported but 31 are novel. These known and new carbon pathway auxiliary metabolic genes were recovered from a total of 22 viral metagenomes in which viral auxiliary metabolic genes were differentiated from low-level cellular DNA inputs based on small subunit ribosomal RNA gene content, taxonomy, fragment recruitment and genomic context information. Auxiliary metabolic gene distribution patterns reveal that marine viruses target overlapping, but relatively distinct pathways in sunlit and dark ocean waters to redirect host carbon flux towards energy production and viral genome replication under low nutrient, niche-differentiated conditions throughout the depth continuum.
Given half of ocean microbes are infected by viruses at any given time, these findings of broad viral metabolic reprogramming suggest the need for renewed consideration of viruses in global ocean carbon models.
Url:
DOI: 10.1186/gb-2013-14-11-r123
PubMed: 24200126
PubMed Central: 4053976
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Hurwitz</name><affiliation wicri:level="1"><nlm:aff id="I1">Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="I4">Current address: Office of the Senior Vice President of Health Sciences, University of Arizona, Tucson, AZ 85724, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Current address: Office of the Senior Vice President of Health Sciences, University of Arizona, Tucson, AZ 85724</wicri:regionArea></affiliation></author><author><name sortKey="Hallam, Steven J" sort="Hallam, Steven J" uniqKey="Hallam S" first="Steven J" last="Hallam">Steven J. Hallam</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="I3">Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC V6T 1Z4</wicri:regionArea></affiliation></author><author><name sortKey="Sullivan, Matthew B" sort="Sullivan, Matthew B" uniqKey="Sullivan M" first="Matthew B" last="Sullivan">Matthew B. Sullivan</name><affiliation wicri:level="1"><nlm:aff id="I1">Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24200126</idno><idno type="pmc">4053976</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053976</idno><idno type="RBID">PMC:4053976</idno><idno type="doi">10.1186/gb-2013-14-11-r123</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000337</idno><idno type="wicri:Area/Pmc/Curation">000337</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Metabolic reprogramming by viruses in the sunlit and dark ocean</title><author><name sortKey="Hurwitz, Bonnie L" sort="Hurwitz, Bonnie L" uniqKey="Hurwitz B" first="Bonnie L" last="Hurwitz">Bonnie L. Hurwitz</name><affiliation wicri:level="1"><nlm:aff id="I1">Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="I4">Current address: Office of the Senior Vice President of Health Sciences, University of Arizona, Tucson, AZ 85724, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Current address: Office of the Senior Vice President of Health Sciences, University of Arizona, Tucson, AZ 85724</wicri:regionArea></affiliation></author><author><name sortKey="Hallam, Steven J" sort="Hallam, Steven J" uniqKey="Hallam S" first="Steven J" last="Hallam">Steven J. Hallam</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="I3">Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC V6T 1Z4</wicri:regionArea></affiliation></author><author><name sortKey="Sullivan, Matthew B" sort="Sullivan, Matthew B" uniqKey="Sullivan M" first="Matthew B" last="Sullivan">Matthew B. Sullivan</name><affiliation wicri:level="1"><nlm:aff id="I1">Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721</wicri:regionArea></affiliation></author></analytic><series><title level="j">Genome Biology</title><idno type="ISSN">1465-6906</idno><idno type="eISSN">1465-6914</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Marine ecosystem function is largely determined by matter and energy transformations mediated by microbial community interaction networks. Viral infection modulates network properties through mortality, gene transfer and metabolic reprogramming.</p></sec><sec><title>Results</title><p>Here we explore the nature and extent of viral metabolic reprogramming throughout the Pacific Ocean depth continuum. We describe 35 marine viral gene families with potential to reprogram metabolic flux through central metabolic pathways recovered from Pacific Ocean waters. Four of these families have been previously reported but 31 are novel. These known and new carbon pathway auxiliary metabolic genes were recovered from a total of 22 viral metagenomes in which viral auxiliary metabolic genes were differentiated from low-level cellular DNA inputs based on small subunit ribosomal RNA gene content, taxonomy, fragment recruitment and genomic context information. Auxiliary metabolic gene distribution patterns reveal that marine viruses target overlapping, but relatively distinct pathways in sunlit and dark ocean waters to redirect host carbon flux towards energy production and viral genome replication under low nutrient, niche-differentiated conditions throughout the depth continuum.</p></sec><sec><title>Conclusions</title><p>Given half of ocean microbes are infected by viruses at any given time, these findings of broad viral metabolic reprogramming suggest the need for renewed consideration of viruses in global ocean carbon models.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Falkowski, Pg" uniqKey="Falkowski P">PG Falkowski</name></author><author><name sortKey="Barber, Rt" uniqKey="Barber R">RT Barber</name></author><author><name sortKey="Smetacek, V" uniqKey="Smetacek V">V Smetacek</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kasting, Jf" 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Biol</journal-id><journal-id journal-id-type="iso-abbrev">Genome Biol</journal-id><journal-title-group><journal-title>Genome Biology</journal-title></journal-title-group><issn pub-type="ppub">1465-6906</issn><issn pub-type="epub">1465-6914</issn><publisher><publisher-name>BioMed Central</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24200126</article-id><article-id pub-id-type="pmc">4053976</article-id><article-id pub-id-type="publisher-id">gb-2013-14-11-r123</article-id><article-id pub-id-type="doi">10.1186/gb-2013-14-11-r123</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research</subject></subj-group></article-categories><title-group><article-title>Metabolic reprogramming by viruses in the sunlit and dark ocean</article-title></title-group><contrib-group><contrib contrib-type="author" id="A1"><name><surname>Hurwitz</surname><given-names>Bonnie L</given-names></name><xref ref-type="aff" rid="I1">1</xref><xref ref-type="aff" rid="I4">4</xref><email>bhurwitz@email.arizona.edu</email></contrib><contrib contrib-type="author" corresp="yes" id="A2"><name><surname>Hallam</surname><given-names>Steven J</given-names></name><xref ref-type="aff" rid="I2">2</xref><xref ref-type="aff" rid="I3">3</xref><email>shallam@mail.ubc.ca</email></contrib><contrib contrib-type="author" corresp="yes" id="A3"><name><surname>Sullivan</surname><given-names>Matthew B</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>mbsulli@email.arizona.edu</email></contrib></contrib-group><aff id="I1"><label>1</label>Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA</aff><aff id="I2"><label>2</label>Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada</aff><aff id="I3"><label>3</label>Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada</aff><aff id="I4"><label>4</label>Current address: Office of the Senior Vice President of Health Sciences, University of Arizona, Tucson, AZ 85724, USA</aff><pub-date pub-type="ppub"><year>2013</year></pub-date><pub-date pub-type="epub"><day>7</day><month>11</month><year>2013</year></pub-date><volume>14</volume><issue>11</issue><fpage>R123</fpage><lpage>R123</lpage><history><date date-type="received"><day>14</day><month>8</month><year>2013</year></date><date date-type="accepted"><day>7</day><month>11</month><year>2013</year></date></history><permissions><copyright-statement>Copyright © 2013 Hurwitz et al.; licensee BioMed Central Ltd.</copyright-statement><copyright-year>2013</copyright-year><copyright-holder>Hurwitz et al.; 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://genomebiology.com/2013/14/11/R123"></self-uri><abstract><sec><title>Background</title><p>Marine ecosystem function is largely determined by matter and energy transformations mediated by microbial community interaction networks. Viral infection modulates network properties through mortality, gene transfer and metabolic reprogramming.</p></sec><sec><title>Results</title><p>Here we explore the nature and extent of viral metabolic reprogramming throughout the Pacific Ocean depth continuum. We describe 35 marine viral gene families with potential to reprogram metabolic flux through central metabolic pathways recovered from Pacific Ocean waters. Four of these families have been previously reported but 31 are novel. These known and new carbon pathway auxiliary metabolic genes were recovered from a total of 22 viral metagenomes in which viral auxiliary metabolic genes were differentiated from low-level cellular DNA inputs based on small subunit ribosomal RNA gene content, taxonomy, fragment recruitment and genomic context information. Auxiliary metabolic gene distribution patterns reveal that marine viruses target overlapping, but relatively distinct pathways in sunlit and dark ocean waters to redirect host carbon flux towards energy production and viral genome replication under low nutrient, niche-differentiated conditions throughout the depth continuum.</p></sec><sec><title>Conclusions</title><p>Given half of ocean microbes are infected by viruses at any given time, these findings of broad viral metabolic reprogramming suggest the need for renewed consideration of viruses in global ocean carbon models.</p></sec></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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