Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast

Translation elongation efficiency is largely thought of as the sum of decoding efficiencies for individual codons. Here, we find that adjacent codon pairs modulate translation efficiency. Deploying an approach in Saccharomyces cerevisiae that scored the expression of over 35,000 GFP variants in which three adjacent codons were randomized, we have identified 17 pairs of adjacent codons associated with reduced expression. For many pairs, codon order is obligatory for inhibition, implying a more complex interaction than a simple additive effect. Inhibition mediated by adjacent codons occurs during translation itself as GFP expression is restored by increased tRNA levels or by non-native tRNAs with exact-matching anticodons. Inhibition operates in endogenous genes, based on analysis of ribosome profiling data. Our findings suggest translation efficiency is modulated by an interplay between tRNAs at adjacent sites in the ribosome and that this concerted effect needs to be considered in predicting the functional consequences of codon choice. [Display omitted] •17 codon pairs in yeast mediate strong inhibition of translation•Inhibition by codon pairs is distinct from dipeptide and individual codon effects•Inhibitory pairs slow the ribosome on native mRNAs and involve wobble decoding•Codon order is key to inhibition, implying distinct roles for each position Rather than protein synthesis relying solely on readout of individual codons, pairs of codons dictate translational efficiency, suggesting unexpected coupling between tRNA binding sites within the ribosome.