Codon usage bias in prokaryotic genomes and environmental adaptation

In each genome, some codons are favored over others by selection likely because they are translated more efficiently and accurately. The selectively favored codons tend to correspond to the most highly expressed tRNAs. It has been recognized that this codon usage bias can influence the cellular fitness and that might be associated with the lifestyle of the organism. To test the impact of environments on genome evolution we studied the codon usage bias of 615 prokaryotes. We found that the extent of codon usage corresponds to the environment in witch the prokaryotes live. In particular, measuring the degree of codon usage bias by the tRNA adaptation index (tAI), we obtained that organisms living in a specialized habitat have high extents of codon usage bias, consistent with their need to adapt efficiently to specific environmental constraints. Differently, organisms able to live in multiple habitats exhibit low codon usage bias as they need to adapt to various physical and chemical conditions. Our results suggest the importance of co-evolution between tRNA availability and codon usage of an organism, in relation with the environmental adaptation.