Life with only 28 tRNAs: Reduced translation accuracy compensates for the lack of twelve tRNAs in Salmonella enterica

Abstract

Despite the link between codon usage bias and the composition of the tRNA pool, the evolutionary forces shaping codon usage and tRNA pools remain largely untested by experiment. This study investigates the relationship between tRNA pool composition and synonymous codon usage (SCU) by deleting twelve nonessential tRNAs in Salmonella enterica, generating an organism ({Delta}T12) with 28 essential tRNAs left, and a severe imbalance between its tRNA pool and SCU. Mutations selected during the construction of {Delta}T12 and in subsequent evolution experiments, suggest two key mechanisms for compensating the fitness effects of this imbalance: (i) Near-cognate tRNA adaptation: mutations or gene copy number variations allowed remaining tRNAs to better read codons originally assigned to missing tRNAs. (ii) Reduced translation accuracy: mutations in ribosomal proteins (S3, S4, S5, L7/L12) and EF-Tu likely increased the rate of near-cognate decoding, prioritizing translation speed over accuracy. These findings suggest that translation rate may be a stronger evolutionary pressure than maintaining perfect accuracy when there is a mismatch between the tRNA pool and SCU. The {Delta}T12 strain provides a valuable tool for further exploring the co-evolution of the tRNA pool and SCU.