Bruno, B. S.; Platten, E. M.; Houston, L.; Brule, C. E.; Grayhack, E. J.

Translation elongation and efficiency are modulated by the genetic code. In the yeast Saccharomyces cerevisiae, 17 inhibitory codon pairs, distinguished by requirements for wobble decoding and distinct codon order, result in reduced translation efficiency and slow translation. Nine of these inhibitory pairs are functionally important as they are disproportionately strongly conserved within the orthologous genes in Saccharomyces sensu stricto. For three pairs, including CGA-CGA, inhibition is triggered by ribosome collisions and known quality control responses, but the mechanisms by which other pairs cause inhibition is unknown. Here, we examined of the molecular basis of inhibition by the slowly translated, highly conserved Leu Pro CUC-CCG codon pair yielding four findings. First, inhibition is mediated by tRNALeu(UAG), which decodes CUC by a U[bullet]C wobble interaction and effectively competes with the nonessential W[bullet]C base pairing tRNALeu(GAG). Second, despite nearly universal conservation of U33 in tRNAs, the C33 alteration in tRNALeu(GAG) does not significantly impair its function. Third, inhibition is likely due to ribosome collisions as many suppressors have mutations predicted to reduce ribosome concentration, including mutations in large ribosomal subunit proteins, RNA polymerase I, and ribosome assembly factors. Furthermore, local reduction in ribosome concentration suppresses inhibition. Fourth, we find a link between the metabolic state and CUC-CCG inhibition, as we find six suppressor mutations in SCH9, a downstream effector of TORC1 that mediates ribosome production. As Sch9 is inactive during starvation, causing reduced ribosome concentration, one biological function of inhibitory pairs may be to mediate a change in relative expression during starvation conditions.