Translation elongation as a rate-limiting step of protein production

Synonymous codons are decoded at different speeds, but simple models predict that this should not drive protein output: translation initiation, not elongation, should limit the rate of protein production. We showed previously that the output of a series of synonymous fluorescent reporters in yeast spanned a 7-fold range corresponding to translation elongation speed. Here, we show that this effect is not due primarily to the established impact of slow elongation on mRNA stability. Rather, slow elongation further decreases the number of proteins made per mRNA. Our simulations, experiments on fluorescent reporters, and analysis of endogenous protein synthesis in yeast show that translation is limited on non-optimally encoded transcripts. Using a genome-wide CRISPRi screen, we find that impairing initiation attenuates the impact of slow elongation, showing a dynamic balance between rate-limiting steps of protein production. Our results show that codon choice can directly limit protein production across the full range of endogenous codon usage.