The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus.
Identifieur interne : 000239 ( PubMed/Corpus ); précédent : 000238; suivant : 000240The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus.
Auteurs : Rachel Brower-Sinning ; Donald M. Carter ; Corey J. Crevar ; Elodie Ghedin ; Ted M. Ross ; Panayiotis V. BenosSource :
- Genome biology [ 1474-760X ] ; 2009.
English descriptors
- KwdEn :
- Animals, Birds, Evolution, Molecular, Humans, Influenza A Virus, H1N1 Subtype, Influenza A Virus, H2N2 Subtype, Influenza A Virus, H3N2 Subtype, Influenza A Virus, H5N1 Subtype, Influenza A virus (enzymology), Influenza A virus (genetics), Nucleic Acid Conformation, RNA Replicase (genetics), RNA Stability, RNA, Viral (chemistry), RNA, Viral (physiology), Temperature, Thermodynamics, Viral Proteins (genetics), Virus Replication.
- MESH :
- chemical , chemistry : RNA, Viral.
- chemical , genetics : RNA Replicase, Viral Proteins.
- enzymology : Influenza A virus.
- genetics : Influenza A virus.
- chemical , physiology : RNA, Viral.
- Animals, Birds, Evolution, Molecular, Humans, Influenza A Virus, H1N1 Subtype, Influenza A Virus, H2N2 Subtype, Influenza A Virus, H3N2 Subtype, Influenza A Virus, H5N1 Subtype, Nucleic Acid Conformation, RNA Stability, Temperature, Thermodynamics, Virus Replication.
Abstract
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.
DOI: 10.1186/gb-2009-10-2-r18
PubMed: 19216739
Links to Exploration step
pubmed:19216739Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus.</title><author><name sortKey="Brower Sinning, Rachel" sort="Brower Sinning, Rachel" uniqKey="Brower Sinning R" first="Rachel" last="Brower-Sinning">Rachel Brower-Sinning</name><affiliation><nlm:affiliation>Department of Computational Biology, School of Medicine, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15260, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Carter, Donald M" sort="Carter, Donald M" uniqKey="Carter D" first="Donald M" last="Carter">Donald M. Carter</name></author><author><name sortKey="Crevar, Corey J" sort="Crevar, Corey J" uniqKey="Crevar C" first="Corey J" last="Crevar">Corey J. Crevar</name></author><author><name sortKey="Ghedin, Elodie" sort="Ghedin, Elodie" uniqKey="Ghedin E" first="Elodie" last="Ghedin">Elodie Ghedin</name></author><author><name sortKey="Ross, Ted M" sort="Ross, Ted M" uniqKey="Ross T" first="Ted M" last="Ross">Ted M. Ross</name></author><author><name sortKey="Benos, Panayiotis V" sort="Benos, Panayiotis V" uniqKey="Benos P" first="Panayiotis V" last="Benos">Panayiotis V. Benos</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2009">2009</date><idno type="RBID">pubmed:19216739</idno><idno type="pmid">19216739</idno><idno type="doi">10.1186/gb-2009-10-2-r18</idno><idno type="wicri:Area/PubMed/Corpus">000239</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000239</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus.</title><author><name sortKey="Brower Sinning, Rachel" sort="Brower Sinning, Rachel" uniqKey="Brower Sinning R" first="Rachel" last="Brower-Sinning">Rachel Brower-Sinning</name><affiliation><nlm:affiliation>Department of Computational Biology, School of Medicine, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15260, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Carter, Donald M" sort="Carter, Donald M" uniqKey="Carter D" first="Donald M" last="Carter">Donald M. Carter</name></author><author><name sortKey="Crevar, Corey J" sort="Crevar, Corey J" uniqKey="Crevar C" first="Corey J" last="Crevar">Corey J. Crevar</name></author><author><name sortKey="Ghedin, Elodie" sort="Ghedin, Elodie" uniqKey="Ghedin E" first="Elodie" last="Ghedin">Elodie Ghedin</name></author><author><name sortKey="Ross, Ted M" sort="Ross, Ted M" uniqKey="Ross T" first="Ted M" last="Ross">Ted M. Ross</name></author><author><name sortKey="Benos, Panayiotis V" sort="Benos, Panayiotis V" uniqKey="Benos P" first="Panayiotis V" last="Benos">Panayiotis V. Benos</name></author></analytic><series><title level="j">Genome biology</title><idno type="eISSN">1474-760X</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Birds</term><term>Evolution, Molecular</term><term>Humans</term><term>Influenza A Virus, H1N1 Subtype</term><term>Influenza A Virus, H2N2 Subtype</term><term>Influenza A Virus, H3N2 Subtype</term><term>Influenza A Virus, H5N1 Subtype</term><term>Influenza A virus (enzymology)</term><term>Influenza A virus (genetics)</term><term>Nucleic Acid Conformation</term><term>RNA Replicase (genetics)</term><term>RNA Stability</term><term>RNA, Viral (chemistry)</term><term>RNA, Viral (physiology)</term><term>Temperature</term><term>Thermodynamics</term><term>Viral Proteins (genetics)</term><term>Virus Replication</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>RNA, Viral</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA Replicase</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Influenza A virus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Influenza A virus</term></keywords><keywords scheme="MESH" type="chemical" qualifier="physiology" xml:lang="en"><term>RNA, Viral</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Birds</term><term>Evolution, Molecular</term><term>Humans</term><term>Influenza A Virus, H1N1 Subtype</term><term>Influenza A Virus, H2N2 Subtype</term><term>Influenza A Virus, H3N2 Subtype</term><term>Influenza A Virus, H5N1 Subtype</term><term>Nucleic Acid Conformation</term><term>RNA Stability</term><term>Temperature</term><term>Thermodynamics</term><term>Virus Replication</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19216739</PMID><DateCompleted><Year>2010</Year><Month>04</Month><Day>15</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1474-760X</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><Issue>2</Issue><PubDate><Year>2009</Year><Month>Feb</Month><Day>12</Day></PubDate></JournalIssue><Title>Genome biology</Title><ISOAbbreviation>Genome Biol.</ISOAbbreviation></Journal><ArticleTitle>The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus.</ArticleTitle><Pagination><MedlinePgn>R18</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/gb-2009-10-2-r18</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">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.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">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.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Brower-Sinning</LastName><ForeName>Rachel</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Computational Biology, School of Medicine, University of Pittsburgh, Fifth Avenue, Pittsburgh, PA 15260, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Carter</LastName><ForeName>Donald M</ForeName><Initials>DM</Initials></Author><Author ValidYN="Y"><LastName>Crevar</LastName><ForeName>Corey J</ForeName><Initials>CJ</Initials></Author><Author ValidYN="Y"><LastName>Ghedin</LastName><ForeName>Elodie</ForeName><Initials>E</Initials></Author><Author ValidYN="Y"><LastName>Ross</LastName><ForeName>Ted M</ForeName><Initials>TM</Initials></Author><Author ValidYN="Y"><LastName>Benos</LastName><ForeName>Panayiotis V</ForeName><Initials>PV</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01GM083602</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>N01AI50018</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 GM083602</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>1R01LM009657-01</GrantID><Acronym>LM</Acronym><Agency>NLM NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>U01AI077771</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>U01 AI077771</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 LM009657</GrantID><Acronym>LM</Acronym><Agency>NLM NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2009</Year><Month>02</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Genome Biol</MedlineTA><NlmUniqueID>100960660</NlmUniqueID><ISSNLinking>1474-7596</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C061290">PA protein, influenza viruses</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C502893">PB2 protein, influenza virus</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012367">RNA, Viral</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014764">Viral Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C077346">influenza virus polymerase basic protein 1</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 2.7.7.48</RegistryNumber><NameOfSubstance UI="D012324">RNA Replicase</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001717" MajorTopicYN="N">Birds</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="Y">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D053118" MajorTopicYN="N">Influenza A Virus, H1N1 Subtype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D053121" MajorTopicYN="N">Influenza A Virus, H2N2 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