Selection on synonymous codons in mammalian rhodopsins: a possible role in optimizing translational processes.

ABSTRACT:

Background

Synonymous codon usage can affect many cellular processes, particularly those associated with translation such as polypeptide elongation and folding, mRNA degradation/stability, and splicing. Highly expressed genes are thought to experience stronger selection pressures on synonymous codons. This should result in codon usage bias even in species with relatively low effective population sizes, like mammals, where synonymous site selection is thought to be weak. Here we use phylogenetic codon-based likelihood models to explore patterns of codon usage bias in a dataset of 18 mammalian rhodopsin sequences, the protein mediating the first step in vision in the eye, and one of the most highly expressed genes in vertebrates. We use these patterns to infer selection pressures on

SUBMITTER: Du J 

PROVIDER: S-EPMC4021273 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature