Structural insights into the specific recognition of mitochondrial ribosome-binding factor hsRBFA and 12 S rRNA by methyltransferase METTL15

Abstract

Mitochondrial rRNA modifications are essential for mitoribosome assembly and its proper function. The m4C methyltransferase METTL15 maintains mitochondrial homeostasis by catalyzing m4C839 located in 12 S rRNA helix 44 (h44). This modification is essential to fine-tuning the ribosomal decoding center and increasing decoding fidelity according to studies of a conserved site in Escherichia coli. Here, we reported a series of crystal structures of human METTL15–hsRBFA–h44–SAM analog, METTL15–hsRBFA–SAM, METTL15–SAM and apo METTL15. The structures presented specific interactions of METTL15 with different substrates and revealed that hsRBFA recruits METTL15 to mitochondrial small subunit for further modification instead of 12 S rRNA. Finally, we found that METTL15 deficiency caused increased reactive oxygen species, decreased membrane potential and altered cellular metabolic state. Knocking down METTL15 caused an elevated lactate secretion and increased levels of histone H4K12-lactylation and H3K9-lactylation. METTL15 might be a suitable model to study the regulation between mitochondrial metabolism and histone lactylation.

The catalytic activity of methyltransferase METTL15 is dispensable for its role in mitochondrial ribosome biogenesis

“…This also enabled visualization of mito-specific RBFA hindering mRNA binding. Concurrently, METTL15 binding and rRNA maturation prompt a significant conformational alteration in RBFA during pre-mtSSU-3 (transitioning from an ‘RBFA-in’ to an ‘RBFA-out’ state), confirming our hypothesis that METTL15 acts as an assembly factor and in line with previous findings that METTL15 co-precipitates with RBFA and a recent structural study confirming their interaction and recognition interface [ 19 , 25 ]. Importantly, the conformational shift is a distinctive trait of human RBFA, unlike its bacterial counterpart.…”

“…Thus, our goal was to discern whether the indispensability of METTL15 for mitochondrial function stems from its catalytic activity or its function as an assembly factor. In order to investigate this, METTL15 KO cells were complemented with cDNA encoding for METTL15 that contained amino acid substitutions (D119A and R120A) impairing its ability to bind S-adenosyl methionine and catalysis [ 17 , 25 ]. Cells complemented with an empty plasmid and with WT METTL15 cDNA were used as controls.…”