TRMT10A maintains lipid homeostasis independently of its tRNA m1G9 methyltransferase activity.

TRMT10A is an evolutionarily conserved tRNA m1G9 methyltransferase in vertebrates. However, the physiological functions and in vivo substrates of TRMT10A are still unclear. Here, we generated Trmt10anull/null mice and observed phenotypic effects, including smaller body size and unexpected dysregulated lipid homeostasis, relative to wild-type mice. We also observed that TRMT10A mediates conserved catalytic activity-dependent m1G9 methylation in tRNAiMet(CAT), tRNAArg(CCT), tRNAGln(CTG), tRNAGln(TTG), tRNAGlu(CTC), tRNAGlu(TTC), and tRNAIle(TAT) across liver tissue, BAT, WAT, and hepatocyte AML12 cells. Through lipidomic analysis, we revealed that a broad range of lipids were dysregulated in Trmt10anull/null mouse livers, and glycerophospholipids and glycerolipids accounted for the majority of lipids with decreased abundance. Furthermore, we demonstrated that PPARα is a mediator of TRMT10A-regulated lipid homeostasis. By utilizing both murine and human TRMT10A catalytic-deficient mutants, we found that TRMT10A regulates lipid homeostasis through mechanisms beyond its canonical tRNA methylation function. Collectively, our findings reveal the organ-conserved tRNA substrates of TRMT10A and its previously unrecognized role in maintaining lipid homeostasis in a noncanonical regulatory manner.