RNA structural constraints in the evolution of the influenza A virus genome NP segment
Identifieur interne : 000683 ( Main/Exploration ); précédent : 000682; suivant : 000684RNA structural constraints in the evolution of the influenza A virus genome NP segment
Auteurs : Alexander P. Gultyaev [Pays-Bas] ; Anton Tsyganov-Bodounov [Pays-Bas] ; Monique Ij Spronken [Pays-Bas] ; Sander Van Der Kooij [Pays-Bas] ; Ron Am Fouchier [Pays-Bas] ; René Cl Olsthoorn [Pays-Bas]Source :
- RNA Biology [ 1547-6286 ] ; 2014.
Abstract
Conserved RNA secondary structures were predicted in the nucleoprotein (NP) segment of the influenza A virus genome using comparative sequence and structure analysis. A number of structural elements exhibiting nucleotide covariations were identified over the whole segment length, including protein-coding regions. Calculations of mutual information values at the paired nucleotide positions demonstrate that these structures impose considerable constraints on the virus genome evolution. Functional importance of a pseudoknot structure, predicted in the NP packaging signal region, was confirmed by plaque assays of the mutant viruses with disrupted structure and those with restored folding using compensatory substitutions. Possible functions of the conserved RNA folding patterns in the influenza A virus genome are discussed.
Url:
DOI: 10.4161/rna.29730
PubMed: 25180940
PubMed Central: 4179967
Affiliations:
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Gultyaev</name><affiliation wicri:level="1"><nlm:aff id="A1">Department of Viroscience, Erasmus Medical Center, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Viroscience, Erasmus Medical Center</wicri:regionArea><wicri:noRegion>Erasmus Medical Center</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A2">Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Niels Bohrweg 1, The Netherlands;</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Niels Bohrweg 1</wicri:regionArea><wicri:noRegion>Niels Bohrweg 1</wicri:noRegion></affiliation></author><author><name sortKey="Tsyganov Bodounov, Anton" sort="Tsyganov Bodounov, Anton" uniqKey="Tsyganov Bodounov A" first="Anton" last="Tsyganov-Bodounov">Anton Tsyganov-Bodounov</name><affiliation wicri:level="1"><nlm:aff id="A3">Leiden Institute of Chemistry, Leiden University, P.O.Box 9502, 2300 RA Leiden, The Netherlands;</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Leiden Institute of Chemistry, Leiden University, P.O.Box 9502, 2300 RA Leiden</wicri:regionArea><wicri:noRegion>2300 RA Leiden</wicri:noRegion></affiliation></author><author><name sortKey="Spronken, Monique Ij" sort="Spronken, Monique Ij" uniqKey="Spronken M" first="Monique Ij" last="Spronken">Monique Ij Spronken</name><affiliation wicri:level="1"><nlm:aff id="A1">Department of Viroscience, Erasmus Medical Center, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Viroscience, Erasmus Medical Center</wicri:regionArea><wicri:noRegion>Erasmus Medical Center</wicri:noRegion></affiliation></author><author><name sortKey="Van Der Kooij, Sander" sort="Van Der Kooij, Sander" uniqKey="Van Der Kooij S" first="Sander" last="Van Der Kooij">Sander Van Der Kooij</name><affiliation wicri:level="1"><nlm:aff id="A1">Department of Viroscience, Erasmus Medical Center, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Viroscience, Erasmus Medical Center</wicri:regionArea><wicri:noRegion>Erasmus Medical Center</wicri:noRegion></affiliation></author><author><name sortKey="Fouchier, Ron Am" sort="Fouchier, Ron Am" uniqKey="Fouchier R" first="Ron Am" last="Fouchier">Ron Am Fouchier</name><affiliation wicri:level="1"><nlm:aff id="A1">Department of Viroscience, Erasmus Medical Center, The Netherlands</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Viroscience, Erasmus Medical Center</wicri:regionArea><wicri:noRegion>Erasmus Medical Center</wicri:noRegion></affiliation></author><author><name sortKey="Olsthoorn, Rene Cl" sort="Olsthoorn, Rene Cl" uniqKey="Olsthoorn R" first="René Cl" last="Olsthoorn">René Cl Olsthoorn</name><affiliation wicri:level="1"><nlm:aff id="A3">Leiden Institute of Chemistry, Leiden University, P.O.Box 9502, 2300 RA Leiden, The Netherlands;</nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Leiden Institute of Chemistry, Leiden University, P.O.Box 9502, 2300 RA Leiden</wicri:regionArea><wicri:noRegion>2300 RA Leiden</wicri:noRegion></affiliation></author></analytic><series><title level="j">RNA Biology</title><idno type="ISSN">1547-6286</idno><idno type="eISSN">1555-8584</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Conserved RNA secondary structures were predicted in the nucleoprotein (NP) segment of the influenza A virus genome using comparative sequence and structure analysis. A number of structural elements exhibiting nucleotide covariations were identified over the whole segment length, including protein-coding regions. Calculations of mutual information values at the paired nucleotide positions demonstrate that these structures impose considerable constraints on the virus genome evolution. Functional importance of a pseudoknot structure, predicted in the NP packaging signal region, was confirmed by plaque assays of the mutant viruses with disrupted structure and those with restored folding using compensatory substitutions. Possible functions of the conserved RNA folding patterns in the influenza A virus genome are discussed.</p></div></front></TEI><affiliations><list><country><li>Pays-Bas</li></country></list><tree><country name="Pays-Bas"><noRegion><name sortKey="Gultyaev, Alexander P" sort="Gultyaev, Alexander P" uniqKey="Gultyaev A" first="Alexander P" last="Gultyaev">Alexander P. Gultyaev</name></noRegion><name sortKey="Fouchier, Ron Am" sort="Fouchier, Ron Am" uniqKey="Fouchier R" first="Ron Am" last="Fouchier">Ron Am Fouchier</name><name sortKey="Gultyaev, Alexander P" sort="Gultyaev, Alexander P" uniqKey="Gultyaev A" first="Alexander P" last="Gultyaev">Alexander P. Gultyaev</name><name sortKey="Olsthoorn, Rene Cl" sort="Olsthoorn, Rene Cl" uniqKey="Olsthoorn R" first="René Cl" last="Olsthoorn">René Cl Olsthoorn</name><name sortKey="Spronken, Monique Ij" sort="Spronken, Monique Ij" uniqKey="Spronken M" first="Monique Ij" last="Spronken">Monique Ij Spronken</name><name sortKey="Tsyganov Bodounov, Anton" sort="Tsyganov Bodounov, Anton" uniqKey="Tsyganov Bodounov A" first="Anton" last="Tsyganov-Bodounov">Anton Tsyganov-Bodounov</name><name sortKey="Van Der Kooij, Sander" sort="Van Der Kooij, Sander" uniqKey="Van Der Kooij S" first="Sander" last="Van Der Kooij">Sander Van Der Kooij</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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