Species-Specific Codon Context Rules Unveil Non-Neutrality Effects of Synonymous Mutations
Identifieur interne : 000749 ( Ncbi/Checkpoint ); précédent : 000748; suivant : 000750Species-Specific Codon Context Rules Unveil Non-Neutrality Effects of Synonymous Mutations
Auteurs : Gabriela R. Moura [Portugal] ; Miguel Pinheiro [Portugal] ; Adelaide Freitas [Portugal] ; José L. Oliveira [Portugal] ; Jörg C. Frommlet [Portugal] ; Laura Carreto [Portugal] ; Ana R. Soares [Portugal] ; Ana R. Bezerra [Portugal] ; Manuel A. S. Santos [Portugal]Source :
- PLoS ONE [ 1932-6203 ] ; 2011.
Abstract
Codon pair usage (codon context) is a species specific gene primary structure feature whose evolutionary and functional roles are poorly understood. The data available show that codon-context has direct impact on both translation accuracy and efficiency, but one does not yet understand how it affects these two translation variables or whether context biases shape gene evolution.
Here we study codon-context biases using a set of 72 orthologous highly conserved genes from bacteria, archaea, fungi and high eukaryotes to identify 7 distinct groups of codon context rules. We show that synonymous mutations, i.e., neutral mutations that occur in synonymous codons of codon-pairs, are selected to maintain context biases and that non-synonymous mutations, i.e., non-neutral mutations that alter protein amino acid sequences, are also under selective pressure to preserve codon-context biases.
Since
Url:
DOI: 10.1371/journal.pone.0026817
PubMed: 22046369
PubMed Central: 3202573
Affiliations:
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Frommlet</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal</addr-line></nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro</wicri:regionArea><wicri:noRegion>Aveiro</wicri:noRegion></affiliation></author><author><name sortKey="Carreto, Laura" sort="Carreto, Laura" uniqKey="Carreto L" first="Laura" last="Carreto">Laura Carreto</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal</addr-line></nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro</wicri:regionArea><wicri:noRegion>Aveiro</wicri:noRegion></affiliation></author><author><name sortKey="Soares, Ana R" sort="Soares, Ana R" uniqKey="Soares A" first="Ana R." last="Soares">Ana R. Soares</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal</addr-line></nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro</wicri:regionArea><wicri:noRegion>Aveiro</wicri:noRegion></affiliation></author><author><name sortKey="Bezerra, Ana R" sort="Bezerra, Ana R" uniqKey="Bezerra A" first="Ana R." last="Bezerra">Ana R. Bezerra</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal</addr-line></nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro</wicri:regionArea><wicri:noRegion>Aveiro</wicri:noRegion></affiliation></author><author><name sortKey="Santos, Manuel A S" sort="Santos, Manuel A S" uniqKey="Santos M" first="Manuel A. S." last="Santos">Manuel A. S. Santos</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro, Portugal</addr-line></nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>RNA Biology Laboratory, Department of Biology and CESAM, University of Aveiro, Aveiro</wicri:regionArea><wicri:noRegion>Aveiro</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Codon pair usage (codon context) is a species specific gene primary structure feature whose evolutionary and functional roles are poorly understood. The data available show that codon-context has direct impact on both translation accuracy and efficiency, but one does not yet understand how it affects these two translation variables or whether context biases shape gene evolution.</p></sec><sec><title>Methodologies/Principal Findings</title><p>Here we study codon-context biases using a set of 72 orthologous highly conserved genes from bacteria, archaea, fungi and high eukaryotes to identify 7 distinct groups of codon context rules. We show that synonymous mutations, i.e., neutral mutations that occur in synonymous codons of codon-pairs, are selected to maintain context biases and that non-synonymous mutations, i.e., non-neutral mutations that alter protein amino acid sequences, are also under selective pressure to preserve codon-context biases.</p></sec><sec><title>Conclusions</title><p>Since <italic>in vivo</italic> studies provide evidence for a role of codon context on decoding fidelity in <italic>E. coli</italic> and for decoding efficiency in mammalian cells, our data support the hypothesis that, like codon usage, codon context modulates the evolution of gene primary structure and fine tunes the structure of open reading frames for high genome translational fidelity and efficiency in the 3 domains of life.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Hershberg, R" uniqKey="Hershberg R">R Hershberg</name></author><author><name sortKey="Petrov, 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Petrov</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rocha, Ep" uniqKey="Rocha E">EP Rocha</name></author><author><name sortKey="Feil, Ej" uniqKey="Feil E">EJ Feil</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Marck, C" uniqKey="Marck C">C Marck</name></author><author><name sortKey="Grosjean, H" uniqKey="Grosjean H">H Grosjean</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kramer, Eb" uniqKey="Kramer E">EB Kramer</name></author><author><name sortKey="Farabaugh, Pj" uniqKey="Farabaugh P">PJ Farabaugh</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Curran, Jf" uniqKey="Curran J">JF Curran</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pinheiro, M" uniqKey="Pinheiro M">M Pinheiro</name></author><author><name sortKey="Afreixo, V" uniqKey="Afreixo V">V Afreixo</name></author><author><name sortKey="Moura, G" uniqKey="Moura G">G Moura</name></author><author><name sortKey="Freitas, A" uniqKey="Freitas A">A Freitas</name></author><author><name sortKey="Santos, Ma" uniqKey="Santos M">MA Santos</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fitzpatrick, Da" uniqKey="Fitzpatrick D">DA Fitzpatrick</name></author><author><name sortKey="Logue, Me" uniqKey="Logue M">ME Logue</name></author><author><name sortKey="Stajich, Je" uniqKey="Stajich J">JE Stajich</name></author><author><name sortKey="Butler, G" uniqKey="Butler G">G Butler</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Portugal</li></country></list><tree><country name="Portugal"><noRegion><name sortKey="Moura, Gabriela R" sort="Moura, Gabriela R" uniqKey="Moura G" first="Gabriela R." last="Moura">Gabriela R. Moura</name></noRegion><name sortKey="Bezerra, Ana R" sort="Bezerra, Ana R" uniqKey="Bezerra A" first="Ana R." last="Bezerra">Ana R. Bezerra</name><name sortKey="Carreto, Laura" sort="Carreto, Laura" uniqKey="Carreto L" first="Laura" last="Carreto">Laura Carreto</name><name sortKey="Freitas, Adelaide" sort="Freitas, Adelaide" uniqKey="Freitas A" first="Adelaide" last="Freitas">Adelaide Freitas</name><name sortKey="Frommlet, Jorg C" sort="Frommlet, Jorg C" uniqKey="Frommlet J" first="Jörg C." last="Frommlet">Jörg C. Frommlet</name><name sortKey="Oliveira, Jose L" sort="Oliveira, Jose L" uniqKey="Oliveira J" first="José L." last="Oliveira">José L. Oliveira</name><name sortKey="Pinheiro, Miguel" sort="Pinheiro, Miguel" uniqKey="Pinheiro M" first="Miguel" last="Pinheiro">Miguel Pinheiro</name><name sortKey="Santos, Manuel A S" sort="Santos, Manuel A S" uniqKey="Santos M" first="Manuel A. S." last="Santos">Manuel A. S. Santos</name><name sortKey="Soares, Ana R" sort="Soares, Ana R" uniqKey="Soares A" first="Ana R." last="Soares">Ana R. Soares</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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