Please use this identifier to cite or link to this item: http://hdl.handle.net/10773/27671
Title: Codon-triplet context unveils unique features of the Candida albicans protein coding genome
Author: Moura, Gabriela R.
Lousado, José P.
Pinheiro, Miguel
Carreto, Laura
Silva, Raquel M.
Oliveira, José L.
Santos, Manuel A. S.
Issue Date: 29-Nov-2007
Publisher: BMC
Abstract: 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.
Peer review: yes
URI: http://hdl.handle.net/10773/27671
DOI: 10.1186/1471-2164-8-444
Appears in Collections:CESAM - Artigos
DBio - Artigos
IEETA - Artigos

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