The dual methyltransferase METTL13 targets N terminus and Lys55 of eEF1A and modulates codon-specific translation rates

Abstract

Eukaryotic elongation factor 1 alpha (eEF1A) delivers aminoacyl-tRNA to the ribosome and thereby plays a key role in protein synthesis. Human eEF1A is subject to extensive post-translational methylation, but several of the responsible enzymes remain unknown. Using a wide range of experimental approaches, we here show that human methyltransferase (MTase)-like protein 13 (METTL13) contains two distinct MTase domains targeting the N terminus and Lys55 of eEF1A, respectively. Our biochemical and structural analyses provide detailed mechanistic insights into recognition of the eEF1A N terminus by METTL13. Moreover, through ribosome profiling, we demonstrate that loss of METTL13 function alters translation dynamics and results in changed translation rates of specific codons. In summary, we here unravel the function of a human MTase, showing that it methylates eEF1A and modulates mRNA translation in a codon-specific manner.

Chemical Biology of Protein N‐Terminal Methyltransferases

“…However, knowledge of the physiological consequences of protein α‐N‐terminal methylation is still very limited. Recent identifications of eukaryotic protein α‐NTMTs have prompted increasing discoveries of new protein substrates; thus supporting that α‐N‐terminal methylation is a widespread post‐translational modification.…”

“…In addition to α‐N‐terminal methylation on the classical X‐P‐K/R motif in eukaryotic cells, a novel N‐terminal methylation has been recently reported on eukaryotic elongation factor 1A (eEF1A) in both yeast and humans . YLR285W, also named elongation factor methyltransferase 7 (Efm7), is a dual MTase that installs methyl groups at both N‐terminal Gly1 and Lys2 residues of yeast eEF1A protein .…”

“…Recently, human MTase‐like protein 13 (METTL13) was identified as a dual MTase for both N‐terminal Gly1 and Lys55 of human eEF1A . Human eEF1A contains a very similar N‐terminal sequence, GKEKTHIN, with Thr substituted at the fifth position instead of Ser, as seen in yeast .…”

“…METTL13 has two distinct MTase domains: N‐ and C‐terminal domains that appear to have different recognition preferences. Specifically, the C‐terminal domain is able to methylate peptides derived from the first 15 amino acids of eEF1A, whereas the N‐terminal domain is sufficient for methylation of Lys55 . Structural alignment of the C‐terminal domain of METTL13 with NTMT1 displayed striking differences (Figure B).…”

“…Structural alignment of the C‐terminal domain of METTL13 with NTMT1 displayed striking differences (Figure B). So far, eEF1A is the only validated biological substrate for METTL13, although 49 potential substrates were suggested for METTL13 . This reflects the high specificity of METTL13 for eEF1A .…”