Cdk5rap1-Mediated 2-Methylthio Modification of Mitochondrial tRNAs Governs Protein Translation and Contributes to Myopathy in Mice and Humans

Abstract

Transfer RNAs (tRNAs) contain a wide variety of posttranscriptional modifications that are important for accurate decoding. Mammalian mitochondrial tRNAs (mt-tRNAs) are modified by nuclear-encoded tRNA-modifying enzymes; however, the physiological roles of these modifications remain largely unknown. In this study, we report that Cdk5 regulatory subunit-associated protein 1 (Cdk5rap1) is responsible for 2-methylthio (ms(2)) modifications of mammalian mt-tRNAs for Ser(UCN), Phe, Tyr, and Trp codons. Deficiency in ms(2) modification markedly impaired mitochondrial protein synthesis, which resulted in respiratory defects in Cdk5rap1 knockout (KO) mice. The KO mice were highly susceptive to stress-induced mitochondrial remodeling and exhibited accelerated myopathy and cardiac dysfunction under stressed conditions. Furthermore, we demonstrate that the ms(2) modifications of mt-tRNAs were sensitive to oxidative stress and were reduced in patients with mitochondrial disease. These findings highlight the fundamental role of ms(2) modifications of mt-tRNAs in mitochondrial protein synthesis and their pathological consequences in mitochondrial disease.

Lack of tRNA-i6A modification causes mitochondrial-like metabolic deficiency in S. pombe by limiting activity of cytosolic tRNATyr, not mito-tRNA

“…The ectopic tRNA devoid of i6A37 when overexpressed by approximately threefold nicely fits with and significantly extends previous results that indicate that i6A37 increases the activity of tRNA by about threefold (Lamichhane et al 2013a). It is important to note here that S. cerevisiae, S. pombe and humans modify different subsets of tRNAs with i6A37, both the cy-and mt-tRNAs (Lamichhane et al 2011(Lamichhane et al , 2013bHorvath and Chinnery 2015;Wei et al 2015). Differences in tRNA-i6A37 subsets is part of a wider variability in the overall tRNA gene content of different eukaryotic genomes and in the tRNA anticodon modification systems, which together with corresponding codon-content may contribute to plasticity of genetic information (Iben and Maraia 2012;Maraia and Iben 2014).…”

“…Recent work has shown that Cdk5rap1, a homolog of bacterial MiaB, is a mitochondrial enzyme that hypermodifies the i6A37 found on several human mt-tRNAs to ms2i6A (Wei et al 2015), in agreement with the finding of ms2i6A on bovine mt-tRNAs (Suzuki and Suzuki 2014). However, cy-tRNAs from eukaryotes contain i6A37 that is not further modified.…”

“…Second, i6A37 hypomodification was associated with a significant decrease in the levels of the human mt-tRNA Ser but not the S. pombe mt-tRNA Trp (Lamichhane et al 2013a,b;Yarham et al 2014). Third, an additional activity, catalyzed by Cdk5rap1, a mitochondrial enzyme, hypermodifies i6A37 to ms2i6A37 on human mt-tRNAs (Wei et al 2015) while as shown in this study, ms2i6A37 is absent from yeast (Fig. 6).…”

“…In bacteria, i6A37 is hypermodified to 2-methylthio-N 6 -isopentenyl-A37 (ms2i6A37). Whereas eukaryotic cy-tRNAs contain i6A37 that is not hypermodified, the i6A37 on mammalian mt-tRNAs are hypermodified to ms2i6A37 (Wei et al 2015), consistent with the bacterial origin of mitochondria (Andersson and Kurland 1999). Genetic knockout of the nuclear-encoded, mitochondrial enzyme, Cdk5rap1, which converts i6A37 on mt-tRNA to ms2i6A37, causes mitochondrial translation associated respiratory deficiency, oxidative stress, and myopathy in mice (Wei et al 2015).…”

“…While multiple mttRNAs carry i6A37 in human cells, only one mt-tRNA in S. pombe, mt-tRNA Trp , has the sequence motif, A37-A37-A38, required for i6A37 modification (Lamichhane et al 2013a,b;Wei et al 2015). Moreover, Trp is infrequent in mitochondria-encoded proteins relative to all other amino acids.…”