TRMT2B is responsible for both tRNA and rRNA m⁵U-methylation in human mitochondria

Abstract

RNA species play host to a plethora of post-transcriptional modifications which together make up the epitranscriptome. 5-methyluridine (m 5 U) is one of the most common modifications made to cellular RNA, where it is found almost ubiquitously in bacterial and eukaryotic cytosolic tRNAs at position 54. Here, we demonstrate that m 5 U54 in human mitochondrial tRNAs is catalysed by the nuclear-encoded enzyme TRMT2B, and that its repertoire of substrates is expanded to ribosomal RNAs, catalysing m 5 U429 in 12S rRNA. We show that TRMT2B is not essential for viability in human cells and that knocking-out the gene shows no obvious phenotype with regards to RNA stability, mitochondrial translation, or cellular growth.

Methylation of Ribosomal RNA: A Mitochondrial Perspective

“…Sequence homology analysis identified two mammalian proteins, TRMT2A and TRMT2B, as m 5 U methyltransferase candidates (Carter et al, 2019). TRMT2A was identified as the enzyme responsible for m 5 U54 in the cytosol (Carter et al, 2019;Powell and Minczuk, 2020), while TRMT2B was suggested to methylate tRNAs in mitochondria (de Crécy-Lagard et al, 2019). 2 A937 (Cotney and Shadel, 2006;Liu et al, 2019) KsgA/RsmA m 6 2 A1518 m 6 2 A1519 16S rRNA (Helser et al, 1972;Poldermans et al, 1979;Formenoy et al, 1994) (Droogmans et al, 2003) A recent study by Laptev et al showed that Trmt2b knock-out in mouse cells leads to a lack of m 5 U425 methylation (mouse numbering, equivalent to human m 5 U429, mtDNA position: m.1076T) in mt-12S rRNA as well as of U54 in certain mitochondrial tRNAs, indicating that TRMT2B might act as a dual tRNA/rRNA methyltransferase (Laptev et al, 2019).…”

“…2 A937 (Cotney and Shadel, 2006;Liu et al, 2019) KsgA/RsmA m 6 2 A1518 m 6 2 A1519 16S rRNA (Helser et al, 1972;Poldermans et al, 1979;Formenoy et al, 1994) (Droogmans et al, 2003) A recent study by Laptev et al showed that Trmt2b knock-out in mouse cells leads to a lack of m 5 U425 methylation (mouse numbering, equivalent to human m 5 U429, mtDNA position: m.1076T) in mt-12S rRNA as well as of U54 in certain mitochondrial tRNAs, indicating that TRMT2B might act as a dual tRNA/rRNA methyltransferase (Laptev et al, 2019). At the same time, Powell and Minczuk showed that TRMT2B is located in human mitochondria and plays an essential role in methylation of both tRNAs and 12S rRNA (Powell and Minczuk, 2020). Similar to yeast Trm2 (Nordlund et al, 2000), no apparent impairment of mitochondrial tRNA stability, mitoribosome integrity, or mitochondrial protein synthesis was detected upon TRMT2B loss in human cells (Powell and Minczuk, 2020).…”

Epitranscriptomics of Mammalian Mitochondrial Ribosomal RNA

“…Modified 12S rRNA nucleotide m 5 U429 is unique for vertebrate mitochondria; equivalent nucleotides in other types of ribosomes are not modified. It was recently demonstrated that U429 is methylated by protein TRMT2B [ 9 , 11 ], a dual specificity enzyme which is also capable to form m 5 U54 residue in the T-loop of a number of mitochondrial tRNAs. Although equivalent nucleotides in other ribosomes are not modified, bacteria and yeast have homologues tRNA-specific methyltransferases TrmA [ 130 ] and Trm2 [ 131 ].…”

“…This evolutionary history is reminiscent to the emergence of the dual specificity methyltransferase TRMT61B. However, unlike TRMT61B gene inactivation, which is phenotypically silent, TRMT2B gene inactivation resulted in a moderate decrease in the activity of ETC complexes containing mitochondrially encoded subunits, while the efficiency of mitochondrial translation was apparently unaffected [ 9 , 11 ].…”

“…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 ].…”