Species-specific codon context rules unveil non-neutrality effects of synonymous mutations
Autor(a) principal: | |
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Data de Publicação: | 2011 |
Outros Autores: | , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10773/27639 |
Resumo: | Background: 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. Methodologies/Principal findings: 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. Conclusions: Since in vivo studies provide evidence for a role of codon context on decoding fidelity in E. coli 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. |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Species-specific codon context rules unveil non-neutrality effects of synonymous mutationsBackground: 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. Methodologies/Principal findings: 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. Conclusions: Since in vivo studies provide evidence for a role of codon context on decoding fidelity in E. coli 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.Public Library of Science2020-02-26T10:22:39Z2011-01-01T00:00:00Z2011info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10773/27639eng10.1371/journal.pone.0026817Moura, Gabriela R.Pinheiro, MiguelFreitas, AdelaideOliveira, José L.Frommlet, Jörg C.Carreto, LauraSoares, Ana R.Bezerra, Ana R.Santos, Manuel A. S.info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-02-22T11:53:34Zoai:ria.ua.pt:10773/27639Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:00:22.734182Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Species-specific codon context rules unveil non-neutrality effects of synonymous mutations |
title |
Species-specific codon context rules unveil non-neutrality effects of synonymous mutations |
spellingShingle |
Species-specific codon context rules unveil non-neutrality effects of synonymous mutations Moura, Gabriela R. |
title_short |
Species-specific codon context rules unveil non-neutrality effects of synonymous mutations |
title_full |
Species-specific codon context rules unveil non-neutrality effects of synonymous mutations |
title_fullStr |
Species-specific codon context rules unveil non-neutrality effects of synonymous mutations |
title_full_unstemmed |
Species-specific codon context rules unveil non-neutrality effects of synonymous mutations |
title_sort |
Species-specific codon context rules unveil non-neutrality effects of synonymous mutations |
author |
Moura, Gabriela R. |
author_facet |
Moura, Gabriela R. Pinheiro, Miguel Freitas, Adelaide Oliveira, José L. Frommlet, Jörg C. Carreto, Laura Soares, Ana R. Bezerra, Ana R. Santos, Manuel A. S. |
author_role |
author |
author2 |
Pinheiro, Miguel Freitas, Adelaide Oliveira, José L. Frommlet, Jörg C. Carreto, Laura Soares, Ana R. Bezerra, Ana R. Santos, Manuel A. S. |
author2_role |
author author author author author author author author |
dc.contributor.author.fl_str_mv |
Moura, Gabriela R. Pinheiro, Miguel Freitas, Adelaide Oliveira, José L. Frommlet, Jörg C. Carreto, Laura Soares, Ana R. Bezerra, Ana R. Santos, Manuel A. S. |
description |
Background: 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. Methodologies/Principal findings: 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. Conclusions: Since in vivo studies provide evidence for a role of codon context on decoding fidelity in E. coli 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. |
publishDate |
2011 |
dc.date.none.fl_str_mv |
2011-01-01T00:00:00Z 2011 2020-02-26T10:22:39Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10773/27639 |
url |
http://hdl.handle.net/10773/27639 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
10.1371/journal.pone.0026817 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Public Library of Science |
publisher.none.fl_str_mv |
Public Library of Science |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799137659461828608 |