Codon-triplet context unveils unique features of the Candida albicans protein coding genome
Autor(a) principal: | |
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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/10400.19/967 |
Resumo: | BACKGROUND: The evolutionary forces that determine the arrangement of synonymous codons within open reading frames and fine tune mRNA translation efficiency are not yet understood. In order to tackle this question we have carried out a large scale study of codon-triplet contexts in 11 fungal species to unravel associations or relationships between codons present at the ribosome A-, P- and E-sites during each decoding cycle. RESULTS: Our analysis unveiled high bias within the context of codon-triplets, in particular strong preference for triplets of identical codons. We have also identified a surprisingly large number of codon-triplet combinations that vanished from fungal ORFeomes. Candida albicans exacerbated these features, showed an unbalanced tRNA population for decoding its pool of codons and used near-cognate decoding for a large set of codons, suggesting that unique evolutionary forces shaped the evolution of its ORFeome. CONCLUSION: We have developed bioinformatics tools for large-scale analysis of codon-triplet contexts. These algorithms identified codon-triplets context biases, allowed for large scale comparative codon-triplet analysis, and identified rules governing codon-triplet context. They could also detect alterations to the standard genetic code. |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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7160 |
spelling |
Codon-triplet context unveils unique features of the Candida albicans protein coding genomeAlgorithmsAmino Acid SequenceBase SequenceComputational Biology/methodsBACKGROUND: The evolutionary forces that determine the arrangement of synonymous codons within open reading frames and fine tune mRNA translation efficiency are not yet understood. In order to tackle this question we have carried out a large scale study of codon-triplet contexts in 11 fungal species to unravel associations or relationships between codons present at the ribosome A-, P- and E-sites during each decoding cycle. RESULTS: Our analysis unveiled high bias within the context of codon-triplets, in particular strong preference for triplets of identical codons. We have also identified a surprisingly large number of codon-triplet combinations that vanished from fungal ORFeomes. Candida albicans exacerbated these features, showed an unbalanced tRNA population for decoding its pool of codons and used near-cognate decoding for a large set of codons, suggesting that unique evolutionary forces shaped the evolution of its ORFeome. CONCLUSION: We have developed bioinformatics tools for large-scale analysis of codon-triplet contexts. These algorithms identified codon-triplets context biases, allowed for large scale comparative codon-triplet analysis, and identified rules governing codon-triplet context. They could also detect alterations to the standard genetic code.Biomed CentralRepositório Científico do Instituto Politécnico de ViseuMoura, GabrielaLousado, JoséPinheiro, MiguelCarreto, LauraSilva, RaquelOliveira, JoséSantos, Manuel2011-03-03T00:30:40Z2007-11-292007-11-29T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.19/967eng1471-2164info: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:RCAAP2023-01-16T15:24:33Zoai:repositorio.ipv.pt:10400.19/967Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T16:40:22.822613Repositório 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 |
Codon-triplet context unveils unique features of the Candida albicans protein coding genome |
title |
Codon-triplet context unveils unique features of the Candida albicans protein coding genome |
spellingShingle |
Codon-triplet context unveils unique features of the Candida albicans protein coding genome Moura, Gabriela Algorithms Amino Acid Sequence Base Sequence Computational Biology/methods |
title_short |
Codon-triplet context unveils unique features of the Candida albicans protein coding genome |
title_full |
Codon-triplet context unveils unique features of the Candida albicans protein coding genome |
title_fullStr |
Codon-triplet context unveils unique features of the Candida albicans protein coding genome |
title_full_unstemmed |
Codon-triplet context unveils unique features of the Candida albicans protein coding genome |
title_sort |
Codon-triplet context unveils unique features of the Candida albicans protein coding genome |
author |
Moura, Gabriela |
author_facet |
Moura, Gabriela Lousado, José Pinheiro, Miguel Carreto, Laura Silva, Raquel Oliveira, José Santos, Manuel |
author_role |
author |
author2 |
Lousado, José Pinheiro, Miguel Carreto, Laura Silva, Raquel Oliveira, José Santos, Manuel |
author2_role |
author author author author author author |
dc.contributor.none.fl_str_mv |
Repositório Científico do Instituto Politécnico de Viseu |
dc.contributor.author.fl_str_mv |
Moura, Gabriela Lousado, José Pinheiro, Miguel Carreto, Laura Silva, Raquel Oliveira, José Santos, Manuel |
dc.subject.por.fl_str_mv |
Algorithms Amino Acid Sequence Base Sequence Computational Biology/methods |
topic |
Algorithms Amino Acid Sequence Base Sequence Computational Biology/methods |
description |
BACKGROUND: The evolutionary forces that determine the arrangement of synonymous codons within open reading frames and fine tune mRNA translation efficiency are not yet understood. In order to tackle this question we have carried out a large scale study of codon-triplet contexts in 11 fungal species to unravel associations or relationships between codons present at the ribosome A-, P- and E-sites during each decoding cycle. RESULTS: Our analysis unveiled high bias within the context of codon-triplets, in particular strong preference for triplets of identical codons. We have also identified a surprisingly large number of codon-triplet combinations that vanished from fungal ORFeomes. Candida albicans exacerbated these features, showed an unbalanced tRNA population for decoding its pool of codons and used near-cognate decoding for a large set of codons, suggesting that unique evolutionary forces shaped the evolution of its ORFeome. CONCLUSION: We have developed bioinformatics tools for large-scale analysis of codon-triplet contexts. These algorithms identified codon-triplets context biases, allowed for large scale comparative codon-triplet analysis, and identified rules governing codon-triplet context. They could also detect alterations to the standard genetic code. |
publishDate |
2007 |
dc.date.none.fl_str_mv |
2007-11-29 2007-11-29T00:00:00Z 2011-03-03T00:30:40Z |
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/10400.19/967 |
url |
http://hdl.handle.net/10400.19/967 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
1471-2164 |
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 |
Biomed Central |
publisher.none.fl_str_mv |
Biomed Central |
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 |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
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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