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Evolutionary pressures on the yeast transcriptome

Chu, Dominique, Salykin, Anton (2015) Evolutionary pressures on the yeast transcriptome. IEEE/ACM Transactions on Computational Biology and Bioinformatics, (99). p. 1. ISSN 1545-5963. (doi:10.1109/TCBB.2015.2420554) (KAR id:48293)


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%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.

Item Type: Article
DOI/Identification number: 10.1109/TCBB.2015.2420554
Subjects: Q Science > Q Science (General) > Q335 Artificial intelligence
Divisions: Divisions > Division of Computing, Engineering and Mathematical Sciences > School of Computing
Depositing User: Dominique Chu
Date Deposited: 07 May 2015 20:47 UTC
Last Modified: 08 Dec 2022 23:05 UTC
Resource URI: (The current URI for this page, for reference purposes)

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