Variation in the strength of selected codon usage bias among bacteria

Abstract

Among bacteria, many species have synonymous codon usage patterns that have been influenced by natural selection for those codons that are translated more accurately and/or efficiently. However, in other species selection appears to have been ineffective. Here, we introduce a population genetics-based model for quantifying the extent to which selection has been effective. The approach is applied to 80 phylogenetically diverse bacterial species for which whole genome sequences are available. The strength of selected codon usage bias, S, is found to vary substantially among species; in 30% of the genomes examined, there was no significant evidence that selection had been effective. Values of S are highly positively correlated with both the number of rRNA operons and the number of tRNA genes. These results are consistent with the hypothesis that species exposed to selection for rapid growth have more rRNA operons, more tRNA genes and more strongly selected codon usage bias. For example, Clostridium perfringens, the species with the highest value of S, can have a generation time as short as 7 min.

Genomic Insights into Xylella fastidiosa Interactions with Plant and Insect Hosts

“…This reduction in genome size is consistent with the stereotypical genome degradation process that has been described for assorted host-dependent bacteria (Moran and Plague 2004). The genome erosion syndrome is also revealed in the absence of detectable selection on codon usage and the slow growth rate of X. fastidiosa (Sharp et al 2005;Rocha 2004), relative to Xanthomonas species. Two explanations are available for this evolutionary pattern.…”

Analysis of Core Housekeeping and Virulence Genes Reveals Cryptic Lineages ofClostridium perfringensThat Are Associated With Distinct Disease Presentations

“…In studies of eukaryotic taxa, a negative correlation has been found between the degree of codon usage bias and the strength of recombination (Kliman and Hey 1993;Comeron et al 1999;McVean and Charlesworth 2000). In the case of bacteria, similar results have been found (Sharp et al 2005), although there are certain notable exceptions (Feil et al 2001). Because a high amount of codon usage bias in bacteria is believed to be the result of selection for translational efficiency (Sharp and Li 1987;Bulmer 1991), the negative correlation between recombination and codon usage bias may be attributed to the Hill-Robertson effect in which the efficacy of natural selection is reduced in regions of low recombination (Hill and Robertson 1966;Felsenstein 1974).…”

Adaptive synonymous mutations in an experimentally evolved Pseudomonas fluorescens population

“…Pervasive variation in the frequencies of synonymous codons across genes and genomes (codon usage bias) 1 suggests that selection may favour some synonymous codons over others. Moreover, direct measures of the impact of synonymous mutations from nucleotide replacement studies demonstrate that they can impact gene expression 2,3 , presumably through changes to the rate or accuracy of transcription and/or translation 4 , mRNA stability and folding 5 , protein secondary structure 6,7 and even fitness 3,[8][9][10][11] .…”