Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure
Autor(a) principal: | |
---|---|
Data de Publicação: | 2007 |
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/10773/27684 |
Resumo: | Background. Codon usage and codon-pair context are important gene primary structure features that influence mRNA decoding fidelity. In order to identify general rules that shape codon-pair context and minimize mRNA decoding error, we have carried out a large scale comparative codon-pair context analysis of 119 fully sequenced genomes. Methodologies/Principal Findings. We have developed mathematical and software tools for large scale comparative codon-pair context analysis. These methodologies unveiled general and species specific codon-pair context rules that govern evolution of mRNAs in the 3 domains of life. We show that evolution of bacterial and archeal mRNA primary structure is mainly dependent on constraints imposed by the translational machinery, while in eukaryotes DNA methylation and tri-nucleotide repeats impose strong biases on codon-pair context. Conclusions. The data highlight fundamental differences between prokaryotic and eukaryotic mRNA decoding rules, which are partially independent of codon usage. |
id |
RCAP_3da39090e802134039023b0a8c966108 |
---|---|
oai_identifier_str |
oai:ria.ua.pt:10773/27684 |
network_acronym_str |
RCAP |
network_name_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository_id_str |
7160 |
spelling |
Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structureBackground. Codon usage and codon-pair context are important gene primary structure features that influence mRNA decoding fidelity. In order to identify general rules that shape codon-pair context and minimize mRNA decoding error, we have carried out a large scale comparative codon-pair context analysis of 119 fully sequenced genomes. Methodologies/Principal Findings. We have developed mathematical and software tools for large scale comparative codon-pair context analysis. These methodologies unveiled general and species specific codon-pair context rules that govern evolution of mRNAs in the 3 domains of life. We show that evolution of bacterial and archeal mRNA primary structure is mainly dependent on constraints imposed by the translational machinery, while in eukaryotes DNA methylation and tri-nucleotide repeats impose strong biases on codon-pair context. Conclusions. The data highlight fundamental differences between prokaryotic and eukaryotic mRNA decoding rules, which are partially independent of codon usage.Public Library of Science2020-02-27T10:22:38Z2007-09-05T00:00:00Z2007-09-05info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10773/27684eng10.1371/journal.pone.0000847Moura, GabrielaPinheiro, MiguelArrais, JoelGomes, Ana CristinaCarreto, LauraFreitas, AdelaideOliveira, José L.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:RCAAP2024-02-22T11:53:36Zoai:ria.ua.pt:10773/27684Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:00:23.246224Repositório 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 |
Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure |
title |
Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure |
spellingShingle |
Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure Moura, Gabriela |
title_short |
Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure |
title_full |
Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure |
title_fullStr |
Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure |
title_full_unstemmed |
Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure |
title_sort |
Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure |
author |
Moura, Gabriela |
author_facet |
Moura, Gabriela Pinheiro, Miguel Arrais, Joel Gomes, Ana Cristina Carreto, Laura Freitas, Adelaide Oliveira, José L. Santos, Manuel A. S. |
author_role |
author |
author2 |
Pinheiro, Miguel Arrais, Joel Gomes, Ana Cristina Carreto, Laura Freitas, Adelaide Oliveira, José L. Santos, Manuel A. S. |
author2_role |
author author author author author author author |
dc.contributor.author.fl_str_mv |
Moura, Gabriela Pinheiro, Miguel Arrais, Joel Gomes, Ana Cristina Carreto, Laura Freitas, Adelaide Oliveira, José L. Santos, Manuel A. S. |
description |
Background. Codon usage and codon-pair context are important gene primary structure features that influence mRNA decoding fidelity. In order to identify general rules that shape codon-pair context and minimize mRNA decoding error, we have carried out a large scale comparative codon-pair context analysis of 119 fully sequenced genomes. Methodologies/Principal Findings. We have developed mathematical and software tools for large scale comparative codon-pair context analysis. These methodologies unveiled general and species specific codon-pair context rules that govern evolution of mRNAs in the 3 domains of life. We show that evolution of bacterial and archeal mRNA primary structure is mainly dependent on constraints imposed by the translational machinery, while in eukaryotes DNA methylation and tri-nucleotide repeats impose strong biases on codon-pair context. Conclusions. The data highlight fundamental differences between prokaryotic and eukaryotic mRNA decoding rules, which are partially independent of codon usage. |
publishDate |
2007 |
dc.date.none.fl_str_mv |
2007-09-05T00:00:00Z 2007-09-05 2020-02-27T10:22:38Z |
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/10773/27684 |
url |
http://hdl.handle.net/10773/27684 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
10.1371/journal.pone.0000847 |
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 |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
|
_version_ |
1799137659472314368 |