Codon-triplet context unveils unique features of the <it>Candida albicans </it>protein coding genome
<p>Abstract</p> <p>Background</p> <p>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 sca...
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doaj-2e21f885dc0545dc8ccf9200e7afeb1e2020-11-24T22:19:47ZengBMCBMC Genomics1471-21642007-11-018144410.1186/1471-2164-8-444Codon-triplet context unveils unique features of the <it>Candida albicans </it>protein coding genomeOliveira José LSilva Raquel MCarreto LauraPinheiro MiguelLousado José PMoura Gabriela RSantos Manuel AS<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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. <it>Candida albicans </it>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.</p> <p>Conclusion</p> <p>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.</p> http://www.biomedcentral.com/1471-2164/8/444 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Oliveira José L Silva Raquel M Carreto Laura Pinheiro Miguel Lousado José P Moura Gabriela R Santos Manuel AS |
spellingShingle |
Oliveira José L Silva Raquel M Carreto Laura Pinheiro Miguel Lousado José P Moura Gabriela R Santos Manuel AS Codon-triplet context unveils unique features of the <it>Candida albicans </it>protein coding genome BMC Genomics |
author_facet |
Oliveira José L Silva Raquel M Carreto Laura Pinheiro Miguel Lousado José P Moura Gabriela R Santos Manuel AS |
author_sort |
Oliveira José L |
title |
Codon-triplet context unveils unique features of the <it>Candida albicans </it>protein coding genome |
title_short |
Codon-triplet context unveils unique features of the <it>Candida albicans </it>protein coding genome |
title_full |
Codon-triplet context unveils unique features of the <it>Candida albicans </it>protein coding genome |
title_fullStr |
Codon-triplet context unveils unique features of the <it>Candida albicans </it>protein coding genome |
title_full_unstemmed |
Codon-triplet context unveils unique features of the <it>Candida albicans </it>protein coding genome |
title_sort |
codon-triplet context unveils unique features of the <it>candida albicans </it>protein coding genome |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2007-11-01 |
description |
<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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. <it>Candida albicans </it>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.</p> <p>Conclusion</p> <p>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.</p> |
url |
http://www.biomedcentral.com/1471-2164/8/444 |
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