Differences in mRNA decoding efficiency influence protein synthesis. However, whether the translation elongation machinery harbors an intrinsic mechanism that selectively decodes codons, and how it shapes proteomes in homeostasis and disease, remains unknown. The eukaryotic translation elongation factor 1 alpha (eEF1A) delivers aminoacyl-tRNAs (aa-tRNA) to translating ribosomes as a ternary complex with GTP. Through engagement of the eEF1A G-domain with the ribosome GTPase-activating center and subsequent conformational changes that result in GTP hydrolysis, eEF1A influences the speed and fidelity of mRNA decoding. Notably, eEF1A is one of the most methylated proteins in the human proteome, where each lysine is targeted by a dedicated methyltransferase. The activities of these methyltransferases are implicated in cancer progression and severity. Here, we find that METTL13-catalyzed dimethylation of the elongation factor eEF1A at lysine 55 (eEF1AK55me2) enhances decoding of select codons, thereby preferentially increasing synthesis of pro-oncogenic proteins, to promote tumorigenesis and drug resistance in vivo. We used proteomic profiling, cell-based assays, and camera-based single-molecule FRET to reveal that eEF1AK55me2 increases decoding efficiency, particularly for underrepresented codons with weak wobble-position base-pairing. In cancer cells, METTL13 knockdown reduces synthesis of oncogenic proteins encoded by genes enriched in eEF1AK55me2-dependent codons, an effect reversed by synonymous recoding with eEF1AK55me2-independent codons. Mechanistically, we find that eEF1AK55me2 decreases the stability of the eEF1A:GTP:aa-tRNA ternary complex and increases the rate and efficiency of cognate aa-tRNA accommodation into the ribosome A-site in a codon-dependent manner. These findings identify an eEF1AK55me2-mediated mRNA decoding mechanism that promotes selective oncogenic protein synthesis and suggest that METTL13 targeting may counteract tumor resistance to KRAS inhibitors.
Navarrete et al. (Sun,) studied this question.