Codon-triplet context unveils unique features of the Candida albicans protein coding genome.
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.


CONCLUSIONS
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.
Moura
Gabriela R
GR
Department of Biology and CESAM, University of Aveiro, 3810-193 Aveiro, Portugal. gmoura@bio.ua.pt
Lousado
José P
JP
Pinheiro
Miguel
M
Carreto
Laura
L
Silva
Raquel M
RM
Oliveira
José L
JL
Santos
Manuel A S
MA
D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D002176:Candida albicans / Q000235:genetics*; D003062:Codon; D018387:Codon, Initiator; D018388:Codon, Terminator; D019295:Computational Biology / Q000379:methods; D005656:Fungal Proteins / Q000235:genetics*; D018628:Gene Dosage; D016681:Genome, Fungal; D016366:Open Reading Frames; D010802:Phylogeny; D012333:RNA, Messenger / Q000378:metabolism; D012343:RNA, Transfer / Q000235:genetics
D003062:Codon; D018387:Codon, Initiator; D018388:Codon, Terminator; D005656:Fungal Proteins; D012333:RNA, Messenger; D012343:RNA, Transfer