Dynamic changes in translational efficiency are deduced from codon usage of the transcriptome

Abstract

Translation of a gene is assumed to be efficient if the supply of the tRNAs that translate it is high. Yet high-abundance tRNAs are often also at high demand since they correspond to preferred codons in genomes. Thus to fully model translational efficiency one must gauge the supply-to-demand ratio of the tRNAs that are required by the transcriptome at a given time. The tRNAs’ supply is often approximated by their gene copy number in the genome. Yet neither the demand for each tRNA nor the extent to which its concentration changes across environmental conditions has been extensively examined. Here we compute changes in the codon usage of the transcriptome across different conditions in several organisms by inspecting conventional mRNA expression data. We find recurring dynamics of codon usage in the transcriptome in multiple stressful conditions. In particular, codons that are translated by rare tRNAs become over-represented in the transcriptome in response to stresses. These results raise the possibility that the tRNA pool might dynamically change upon stress to support efficient translation of stress-transcribed genes. Alternatively, stress genes may be typically translated with low efficiency, presumably due to lack of sufficient evolutionary optimization pressure on their codon usage.