tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast

Protein synthesis rate and accuracy are tightly controlled by the cell and are essential for proteome homoeostasis (proteostasis); however, the full picture of how mRNA translational factors maintain protein synthesis accuracy and co-translational protein folding are far from being fully understood. To address this question, we evaluated the role of 70 yeast tRNA-modifying enzyme genes on protein aggregation and used mass spectrometry to identify the aggregated proteins. We show that modification of uridine at anticodon position 34 (U34) by the tRNA-modifying enzymes Elp1, Elp3, Sml3 and Trm9 is critical for proteostasis, the mitochondrial tRNA-modifying enzyme Slm3 plays a fundamental role in general proteostasis and that stress response proteins whose genes are enriched in codons decoded by tRNAs lacking mcm(5)U(34), mcm(5)s(2)U(34), ncm(5)U(34), ncm(5)Um(34), modifications are overrepresented in protein aggregates of theELP1, SLM3andTRM9KO strains. Increased rates of amino acid misincorporation were also detected in these strains at protein sites that specifically mapped to the codons sites that are decoded by the hypomodified tRNAs, demonstrating that U(34)tRNA modifications safeguard the proteome from translational errors, protein misfolding and proteotoxic stress.

Automated summary

The study reveals the critical role of yeast tRNA-modifying enzymes in proteostasis, with U34 modification safeguarding the proteome from translational errors, protein misfolding, and proteotoxic stress.