The human mitochondrial 12S rRNA m4C methyltransferase METTL15 is required for mitochondrial function

Hao Chen,Zhennan Shi,Jiaojiao Guo,Kao-Jung Chang,Qianqian Chen,Cong-Hui Yao,Marcia C Haigis,Yang Shi

doi:10.1074/jbc.ra119.012127

Abstract

Mitochondrial DNA gene expression is coordinately regulated both pre- and post-transcriptionally, and its perturbation can lead to human pathologies. Mitochondrial rRNAs (mt-rRNAs) undergo a series of nucleotide modifications after release from polycistronic mitochondrial RNA precursors, which is essential for mitochondrial ribosomal biogenesis. Cytosine N4-methylation (m4C) at position 839 (m4C839) of the 12S small subunit mt-rRNA was identified decades ago; however, its biogenesis and function have not been elucidated in detail. Here, using several approaches, including immunofluorescence, RNA immunoprecipitation and methylation assays, and bisulfite mapping, we demonstrate that human methyltransferase-like 15 (METTL15), encoded by a nuclear gene, is responsible for 12S mt-rRNA methylation at m4C839 both in vivo and in vitro We tracked the evolutionary history of RNA m4C methyltransferases and identified a difference in substrate preference between METTL15 and its bacterial ortholog rsmH. Additionally, unlike the very modest impact of a loss of m4C methylation in bacterial small subunit rRNA on the ribosome, we found that METTL15 depletion results in impaired translation of mitochondrial protein-coding mRNAs and decreases mitochondrial respiration capacity. Our findings reveal that human METTL15 is required for mitochondrial function, delineate the evolution of methyltransferase substrate specificities and modification patterns in rRNA, and highlight a differential impact of m4C methylation on prokaryotic ribosomes and eukaryotic mitochondrial ribosomes.

Highlights

Mitochondrial gene expression requires a series of interconnected processes encompassing mitochondrial DNA replication and repair, mitochondrial RNA transcription, maturation, and mitoribosome assembly [1, 2]
Our study reveals that methylation of 12S mitochondrial rRNA (mt-rRNA) m4C at position 839 (m4C839) by methyltransferaselike 15 (METTL15) is an important epitranscriptomic modification, critical for efficient mitochondrial protein synthesis and respiratory function
We found that METTL15 is highly conserved during evolution and is an ortholog of the bacterial methyltransferase, rsmH (Fig. 1A and Data File S1), which is responsible for the N4-methylation of m4Cm1402 in the 16S rRNA in almost all species of bacteria (Fig. S1A) [20]

Summary

Introduction

Mitochondrial gene expression requires a series of interconnected processes encompassing mitochondrial DNA (mtDNA) replication and repair, mitochondrial RNA transcription, maturation, and mitoribosome assembly [1, 2]. We demonstrate that human METTL15 protein, encoded by a nuclear gene, is localized in mitochondria and is responsible for methylation of the 12S mt-RNA at C839 Our study reveals that methylation of 12S mt-rRNA m4C839 by METTL15 is an important epitranscriptomic modification, critical for efficient mitochondrial protein synthesis and respiratory function.

Results

Conclusion