METTL15 interacts with the assembly intermediate of murine mitochondrial small ribosomal subunit to form m4C840 12S rRNA residue

Abstract

Mammalian mitochondrial ribosomes contain a set of modified nucleotides, which is distinct from that of the cytosolic ribosomes. Nucleotide m4C840 of the murine mitochondrial 12S rRNA is equivalent to the dimethylated m4Cm1402 residue of Escherichia coli 16S rRNA. Here we demonstrate that mouse METTL15 protein is responsible for the formation of m4C residue of the 12S rRNA. Inactivation of Mettl15 gene in murine cell line perturbs the composition of mitochondrial protein biosynthesis machinery. Identification of METTL15 interaction partners revealed that the likely substrate for this RNA methyltransferase is an assembly intermediate of the mitochondrial small ribosomal subunit containing an assembly factor RBFA.

Epitranscriptomics of Mammalian Mitochondrial Ribosomal RNA

“…NSUN4 ability to modify the 12S mitochondrial rRNA do not require its association with MTERF4 [ 98 ], since Mterf4 gene inactivation has not abolished m 5 C841 formation. It is also likely that NSUN4 methylates 12S rRNA after the formation of m 4 C839 by METTL15, since inactivation of the latter inhibits NSUN4 ability to modify 12S rRNA [ 10 , 12 , 13 ]. Inactivation of a mitochondrial methyltransferase METTL17, whose target is yet unknown, also leads to a decrease in the efficiency of C841 methylation [ 103 ].…”

“…In mammalian mitochondria, this nucleotide is methylated by a homologue of bacterial RsmH, METTL15 [ 10 , 12 , 13 ]. The phenotype of METTL15 gene inactivation is a matter of some discrepancies.…”

“…Studies performed on HAP1, human haploid adherent cell line, demonstrated that METTL15 inactivation resulted in impaired mitochondrial translation, decreased activity of ETC complexes and decreased level of SSU and LSU association [ 10 , 12 ]. In the case of Mettl15 gene inactivation in murine suspension cell line NS0, no decrease in mitochondrial translation or ETC complexes activity were observed [ 13 ]. However, the amount of free LSU and SSU was shown to slightly increase in the case of overexpression of the catalytically dead METTL15 protein.…”

“…METTL15 is involved in the assembly of the mitochondrial small ribosomal subunit. Immunoprecipitation of METTL15 allowed our group to identify a composition of its substrate complex [ 13 ]. While it contains the 12S rRNA and almost entire set of the small subunit mitochondrial r-proteins, it lacks mS37, mS38 and mS39 proteins.…”

“…Still, up to 2012 [ 8 ], only a single gene coding for the mammalian mitochondrial rRNA modification enzyme was known. Only recently, in 2019–2020 the list of mammalian mt-rRNA modification enzymes has been completed [ 9 , 10 , 11 , 12 , 13 ], allowing us to summarize the entire inventory of mammalian mt-RNA modification machinery ( Table 1 ), which is the subject of current review and several other excellent reviews on this topic [ 14 , 15 , 16 ].…”