Format

Send to

Choose Destination
See comment in PubMed Commons below
Philos Trans R Soc Lond B Biol Sci. 2010 Apr 27;365(1544):1203-12. doi: 10.1098/rstb.2009.0305.

Forces that influence the evolution of codon bias.

Author information

1
Institute of Evolutionary Biology, University of Edinburgh, , Kings Buildings, Edinburgh EH9 3JT, UK. paul.sharp@ed.ac.uk

Abstract

The frequencies of alternative synonymous codons vary both among species and among genes from the same genome. These patterns have been inferred to reflect the action of natural selection. Here we evaluate this in bacteria. While intragenomic variation in many species is consistent with selection favouring translationally optimal codons, much of the variation among species appears to be due to biased patterns of mutation. The strength of selection on codon usage can be estimated by two different approaches. First, the extent of bias in favour of translationally optimal codons in highly expressed genes, compared to that in genes where selection is weak, reveals the long-term effectiveness of selection. Here we show that the strength of selected codon usage bias is highly correlated with bacterial growth rate, suggesting that selection has favoured translational efficiency. Second, the pattern of bias towards optimal codons at polymorphic sites reveals the ongoing action of selection. Using this approach we obtained results that were completely consistent with the first method; importantly, the frequency spectra of optimal codons at polymorphic sites were similar to those predicted under an equilibrium model. Highly expressed genes in Escherichia coli appear to be under continuing strong selection, whereas selection is very weak in genes expressed at low levels.

PMID:
20308095
PMCID:
PMC2871821
DOI:
10.1098/rstb.2009.0305
[Indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for HighWire Icon for PubMed Central
    Loading ...
    Support Center