The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus
Identifieur interne : 000984 ( Pmc/Checkpoint ); précédent : 000983; suivant : 000985The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus
Auteurs : Rachel Brower-Sinning [États-Unis] ; Donald M. Carter [États-Unis] ; Corey J. Crevar [États-Unis] ; Elodie Ghedin [États-Unis] ; Ted M. Ross [États-Unis] ; Panayiotis V. Benos [États-Unis]Source :
- Genome Biology [ 1465-6906 ] ; 2009.
Abstract
RNA folding free energy is important for the evolution and host-adaptation of the influenza virus. Human virus polymerase genes are shown to have substantially higher folding free energy values than their avian counterparts.
Url:
DOI: 10.1186/gb-2009-10-2-r18
PubMed: 19216739
PubMed Central: 2688270
Affiliations:
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Carter</name><affiliation wicri:level="4"><nlm:aff id="I2">Center for Vaccine Research, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15260, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Vaccine Research, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15260</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université de Pittsburgh</orgName></affiliation></author><author><name sortKey="Crevar, Corey J" sort="Crevar, Corey J" uniqKey="Crevar C" first="Corey J" last="Crevar">Corey J. Crevar</name><affiliation wicri:level="4"><nlm:aff id="I2">Center for Vaccine Research, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15260, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Vaccine Research, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15260</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université de Pittsburgh</orgName></affiliation></author><author><name sortKey="Ghedin, Elodie" sort="Ghedin, Elodie" uniqKey="Ghedin E" first="Elodie" last="Ghedin">Elodie Ghedin</name><affiliation wicri:level="4"><nlm:aff id="I3">Department of Medicine, School of Medicine, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15261, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Medicine, School of Medicine, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15261</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université de Pittsburgh</orgName></affiliation></author><author><name sortKey="Ross, Ted M" sort="Ross, Ted M" uniqKey="Ross T" first="Ted M" last="Ross">Ted M. Ross</name><affiliation wicri:level="4"><nlm:aff id="I2">Center for Vaccine Research, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15260, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Vaccine Research, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15260</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université de Pittsburgh</orgName></affiliation><affiliation wicri:level="4"><nlm:aff id="I4">Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Lothrop Street, Pittsburgh, PA 15261, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Lothrop Street, Pittsburgh, PA 15261</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université de Pittsburgh</orgName></affiliation></author><author><name sortKey="Benos, Panayiotis V" sort="Benos, Panayiotis V" uniqKey="Benos P" first="Panayiotis V" last="Benos">Panayiotis V. Benos</name><affiliation wicri:level="4"><nlm:aff id="I1">Department of Computational Biology, School of Medicine, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15260, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computational Biology, School of Medicine, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15260</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université de Pittsburgh</orgName></affiliation><affiliation wicri:level="4"><nlm:aff id="I5">Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Meyran Avenue, Pittsburgh, PA 15260, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Meyran Avenue, Pittsburgh, PA 15260</wicri:regionArea><placeName><region type="state">Pennsylvanie</region><settlement type="city">Pittsburgh</settlement></placeName><orgName type="university">Université de Pittsburgh</orgName></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="2009">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>RNA folding free energy is important for the evolution and host-adaptation of the influenza virus. Human virus polymerase genes are shown to have substantially higher folding free energy values than their avian counterparts.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Biol</journal-id><journal-title>Genome Biology</journal-title><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">19216739</article-id><article-id pub-id-type="pmc">2688270</article-id><article-id pub-id-type="publisher-id">gb-2009-10-2-r18</article-id><article-id pub-id-type="doi">10.1186/gb-2009-10-2-r18</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research</subject></subj-group></article-categories><title-group><article-title>The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus</article-title></title-group><contrib-group><contrib id="A1" contrib-type="author"><name><surname>Brower-Sinning</surname><given-names>Rachel</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>rab71@pitt.edu</email></contrib><contrib id="A2" contrib-type="author"><name><surname>Carter</surname><given-names>Donald M</given-names></name><xref ref-type="aff" rid="I2">2</xref><email>dmc46@cvr.pitt.edu</email></contrib><contrib id="A3" contrib-type="author"><name><surname>Crevar</surname><given-names>Corey J</given-names></name><xref ref-type="aff" rid="I2">2</xref><email>cjc63@cvr.pitt.edu</email></contrib><contrib id="A4" contrib-type="author"><name><surname>Ghedin</surname><given-names>Elodie</given-names></name><xref ref-type="aff" rid="I3">3</xref><email>elg21@pitt.edu</email></contrib><contrib id="A5" contrib-type="author"><name><surname>Ross</surname><given-names>Ted M</given-names></name><xref ref-type="aff" rid="I2">2</xref><xref ref-type="aff" rid="I4">4</xref><email>tmr15@cvr.pitt.edu</email></contrib><contrib id="A6" corresp="yes" contrib-type="author"><name><surname>Benos</surname><given-names>Panayiotis V</given-names></name><xref ref-type="aff" rid="I1">1</xref><xref ref-type="aff" rid="I5">5</xref><email>benos@pitt.edu</email></contrib></contrib-group><aff id="I1"><label>1</label>Department of Computational Biology, School of Medicine, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15260, USA</aff><aff id="I2"><label>2</label>Center for Vaccine Research, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15260, USA</aff><aff id="I3"><label>3</label>Department of Medicine, School of Medicine, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15261, USA</aff><aff id="I4"><label>4</label>Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Lothrop Street, Pittsburgh, PA 15261, USA</aff><aff id="I5"><label>5</label>Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Meyran Avenue, Pittsburgh, PA 15260, USA</aff><pub-date pub-type="ppub"><year>2009</year></pub-date><pub-date pub-type="epub"><day>12</day><month>2</month><year>2009</year></pub-date><volume>10</volume><issue>2</issue><fpage>R18</fpage><lpage>R18</lpage><ext-link ext-link-type="uri" xlink:href="http://genomebiology.com/2009/10/2/R18"></ext-link><history><date date-type="received"><day>4</day><month>12</month><year>2008</year></date><date date-type="rev-recd"><day>29</day><month>1</month><year>2009</year></date><date date-type="accepted"><day>12</day><month>2</month><year>2009</year></date></history><permissions><copyright-statement>Copyright © 2009 Brower-Sinning et al.; licensee BioMed Central Ltd.</copyright-statement><copyright-year>2009</copyright-year><copyright-holder>Brower-Sinning et al.; licensee BioMed Central Ltd.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><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"></ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p><pmc-comment>
Brower-Sinning
Rachel
rab71@pitt.edu
The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus
2009 Genome Biology 10(2): R18-. (2009) 1465-6906(2009)10:2 urn:ISSN:1465-6906
</license></permissions><abstract abstract-type="short"><p>RNA folding free energy is important for the evolution and host-adaptation of the influenza virus. Human virus polymerase genes are shown to have substantially higher folding free energy values than their avian counterparts.</p></abstract><abstract><sec><title>Background</title><p>The influenza A virus genome is composed of eight single-stranded RNA segments of negative polarity. Although the hemagglutinin and neuraminidase genes are known to play a key role in host adaptation, the polymerase genes (which encode the polymerase segments PB2, PB1, PA) and the nucleoprotein gene are also important for the efficient propagation of the virus in the host and for its adaptation to new hosts. Current efforts to understand the host-specificity of the virus have largely focused on the amino acid differences between avian and human isolates.</p></sec><sec><title>Results</title><p>Here we show that the folding free energy of the RNA segments may play an equally important role in the evolution and host adaptation of the influenza virus. Folding free energy may affect the stability of the viral RNA and influence the rate of viral protein translation. We found that there is a clear distinction between the avian and human folding free energy distributions for the polymerase and the nucleoprotein genes, with human viruses having substantially higher folding free energy values. This difference is independent of the amino acid composition and the codon bias. Furthermore, the folding free energy values of the commonly circulating human viruses tend to shift towards higher values over the years, after they entered the human population. Finally, our results indicate that the temperature in which the cells grow affects infection efficiency.</p></sec><sec><title>Conclusions</title><p>Our data suggest for the first time that RNA structure stability may play an important role in the emergence and host shift of influenza A virus. The fact that cell temperature affects virus propagation in mammalian cells could help identify those avian strains that pose a higher threat to humans.</p></sec></abstract></article-meta></front></pmc><affiliations><list><country><li>États-Unis</li></country><region><li>Pennsylvanie</li></region><settlement><li>Pittsburgh</li></settlement><orgName><li>Université de Pittsburgh</li></orgName></list><tree><country name="États-Unis"><region name="Pennsylvanie"><name sortKey="Brower Sinning, Rachel" sort="Brower Sinning, Rachel" uniqKey="Brower Sinning R" first="Rachel" last="Brower-Sinning">Rachel Brower-Sinning</name></region><name sortKey="Benos, Panayiotis V" sort="Benos, Panayiotis V" uniqKey="Benos P" first="Panayiotis V" last="Benos">Panayiotis V. Benos</name><name sortKey="Benos, Panayiotis V" sort="Benos, Panayiotis V" uniqKey="Benos P" first="Panayiotis V" last="Benos">Panayiotis V. Benos</name><name sortKey="Carter, Donald M" sort="Carter, Donald M" uniqKey="Carter D" first="Donald M" last="Carter">Donald M. Carter</name><name sortKey="Crevar, Corey J" sort="Crevar, Corey J" uniqKey="Crevar C" first="Corey J" last="Crevar">Corey J. Crevar</name><name sortKey="Ghedin, Elodie" sort="Ghedin, Elodie" uniqKey="Ghedin E" first="Elodie" last="Ghedin">Elodie Ghedin</name><name sortKey="Ross, Ted M" sort="Ross, Ted M" uniqKey="Ross T" first="Ted M" last="Ross">Ted M. Ross</name><name sortKey="Ross, Ted M" sort="Ross, Ted M" uniqKey="Ross T" first="Ted M" last="Ross">Ted M. Ross</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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