title: Evolutionary Pressures on the Yeast Transcriptome.
abstract: Codon usage bias (CUB) is the well known phenomenon that the frequency of synonymous codons is unequal. This is presumably the result of adaptive pressures favouring some codons over others. The underlying reason for this pressure is unknown, although a large number of possible driver mechanisms have been proposed; one of them is the decoding time. The standard model to calculate decoding time is the Gromadski-Rodnina model. Yet, recently, there have been a number of studies arguing to the effect that this conventional speed-model is not relevant to understand the dynamics of translation. However, results remain inconclusive so far. This contribution takes a novel approach to address this issue based on comparing mRNA with random synonymous variants to estimate the evolutionary pressures that have acted on the transcriptome. It emerges that over 70 percent of ORFs have been subject to a strong selection pressure for translation speed and that there is also a strong selection pressure for the avoidance of traffic jams. Finally, it is also shown that both homogeneous and very heterogeneous transcripts are over-represented. These results corroborate the validity of the Gromadski-Rodnina model.
authors.forename: Dominique
authors.initials: D
authors.lastname: Chu
authors.forename: Anton
authors.initials: A
authors.lastname: Salykin
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D003062:Codon / Q000235:genetics*; D019143:Evolution, Molecular; D020869:Gene Expression Profiling / Q000379:methods*; D008969:Molecular Sequence Data; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D003062:Codon