New paper: Amino acid specific codon usage and translational selection

We have a new paper this month, in Genome Biology and Evolution. This paper follows from the lab’s long standing interest in codon usage bias, and describes Saurabh’s analysis to understand how codon use and tRNA gene numbers vary with bacterial growth rate. Typically, highly expressed genes use specific synonymous codons more often, compared to other genes in the genome. Across bacterial species, this “codon usage bias” (CUB) increases with growth rate. However, most previous studies focused on average CUB (of genes or genomes). We explored the possibility that selection could act differently on codons of different amino acids, depending on how often each amino acid is used to make proteins. The link between growth rate and CUB is thought to involve tRNA gene copies, which also increases with growth rate, and should co-evolve with codon use. Interestingly, there are detailed theoretical predictions about how CUB, tRNA gene copies, and amino acid usage should be related to each other. We tested these predictions, but found that the patterns don’t match the predictions. (What more can a theory ask for!) Specifically, we found that CUB of specific amino acids does not increase with usage of the amino acids as expected. This suggests that we are missing some pieces of the puzzle, and we have some new suggestions about the next steps to find them. For more, read the paper!