Opposing regulation of METTL11A by its family members METTL11B and METTL13

N-terminal protein methylation (N-methylation) is a post-translational modification (PTM) that influences a variety of biological processes by regulating protein stability, protein-DNA interactions, and protein-protein interactions. Although significant progress has been made in understanding the biological roles of this PTM, we still do not completely understand how the methyltransferases that place it are regulated. A common mode of methyltransferase regulation is through complex formation with close family members, and we have previously shown that the N-trimethylase METTL11A (NRMT1/NTMT1) is activated through binding of its close homolog METTL11B (NRMT2/NTMT2). It has also recently been reported that METTL11A co-fractionates with a third METTL family member METTL13, which methylates both the N-terminus and lysine 55 (K55) of eukaryotic elongation factor 1 alpha (eEF1A). Here we confirm a regulatory interaction between METTL11A and METTL13 and show that, while METTL11B is an activator of METTL11A, METTL13 inhibits METTL11A activity. This is the first example of a methyltransferase being opposingly regulated by different family members. Similarly, we find that METTL11A promotes the K55 methylation activity of METTL13 but inhibits its N-methylation activity. We also find that catalytic activity is not needed for these regulatory effects, demonstrating new, non-catalytic functions for METTL11A and METTL13. Finally, we show METTL11A, METTL11B, and METTL13 can complex together, and when all three are present, the regulatory effects of METTL13 take precedence over those of METTL11B. These findings provide a better understanding of the regulation of N-methylation, and suggest a model where these methyltransferases can serve in both catalytic and non-catalytic roles.