Mitochondrial tRNA modifications: functions, diseases caused by their loss, and treatment strategies

Abstract

Mitochondrial tRNA (mt-tRNA) modifications play pivotal roles in decoding and sustaining tRNA stability, thereby enabling the synthesis of essential respiratory complex proteins in mitochondria. Consequently, loss of human mt-tRNA modifications caused by mutations in the mitochondrial or nuclear genome can cause life-threatening mitochondrial diseases such as encephalopathy and cardiomyopathy. In this article, we first provide a comprehensive overview of the functions of mt-tRNA modifications, the responsible modification enzymes, and the diseases caused by the loss of mt-tRNA modifications. We then discuss progress and potential strategies to treat these diseases, including taurine supplementation for MELAS patients, targeted deletion of mtDNA variants, and overexpression of modification-related proteins. Finally, we discuss factors that need to be overcome to cure "mitochondrial tRNA modopathies."

Keywords: MELAS; mitoTALEN; mitochondrial disease; tRNA modification; tRNA modopathy.

FIGURE 1.

Human mt-tRNA modifications and the responsible modifying enzymes. (A) mt-tRNA modifications and the enzymes responsible for these modifications. The name of the modification enzyme (or its partner protein) and the type of reaction are presented alongside the species of tRNA modification. Proteins harboring pathogenic mutations are enclosed within rectangles. Proteins that harbor pathogenic mutations, but the disease caused is likely due to loss of cytoplasmic tRNA modifications, are enclosed within dotted rectangles. Abbreviations for RNA modifications: G–1, posttranscriptional G addition at 5′; m¹G, N¹-methylguanosine; m¹A, N¹-methyladenosine; m²G, N²-methylguanosine; m^2,2G, N²,N²-dimethylguanosine; Ψ, pseudouridine; m³C, 3-methylcytidine; τm⁵U, 5-taurinomethyluridine; τm⁵s²U, 5-taurinomethyl-2-thiouridine; cmnm⁵U, 5-carboxymethylaminomethyluridine; cmnm⁵s²U, 5-carboxymethylaminomethyl-2-thiouridine; f⁵C, 5-formylcytidine; Q, queuosine; m⁵U, 5-methyluridine; m⁵C, 5-methylcytidine; t⁶A, N⁶-threonylcarbamoyladenosine; i⁶A, N⁶-isopentenyladenosine; ms²i⁶A, 2-methylthio-N⁶-isopentenyladenosine. References: 1 (Nakamura et al. 2018), 2 (Vilardo et al. 2012), 3 (Dewe et al. 2017), 4 (Patton et al. 2005), 5 (Scholler et al. 2021), 6 (Fakruddin et al. 2018), 7 (Asano et al. 2018), 8 (Umeda et al. 2005), 9 (Nakano et al. 2016), 10 (Van Haute et al. 2016). 11 (Kawarada et al. 2017),12 (Haag et al. 2016),13 (Suzuki et al. 2020),14 (Chujo and Suzuki 2012), 15 (Powell and Minczuk 2020), 16 (Laptev et al. 2020), 17 (Shinoda et al. 2019), 18 (Van Haute et al. 2019), 19 (Zaganelli et al. 2017), 20 (Brule et al. 2004), 21 (Lin et al. 2018), 22 (Yarham et al. 2014), 23 (Wei et al. 2015). (B) Mammalian mt-tRNA modifications that are present only in mt-tRNAs and not in cytoplasmic tRNAs. (C) Other mt-tRNA modifications relevant to either the onset or potential treatment of the mitochondrial diseases referred to in this manuscript.

FIGURE 2.

Human mitochondrial codons are decoded using tRNA anticodon modifications. (A) Table of human mitochondrial codons. Codons, encoded amino acids, anticodon sequences (including the wobble modification), and the position 37 nt, are shown. Colored two-codon boxes: pink box decoded using τm⁵U-modified tRNAs; light blue box decoded using f⁵C-modified tRNA; green box decoded using Q-modified tRNAs; and blue framed box decoded using (τm⁵)s²U-modified tRNAs. Four codons that differ from the canonical genetic codes are underlined. (B) Decoding AUR codons as Met enabled by f⁵C modifications in the mt-tRNA^Met wobble position. (C) Decoding of UUR codons as Leu enabled by the τm⁵U modification in the mt-tRNA^Leu(UUR) wobble position. MELAS-causing mtDNA 3243 A > G mutation impedes MTO1–GTPBP3 complex from incorporating the τm⁵U modification. (D) Decoding of AAR codons as Lys enabled by the τm⁵s²U modification in the mt-tRNA^Lys wobble position. MERRF-causing mtDNA 8344 A > G mutation impedes MTO1–GTPBP3 complex and MTU1 from incorporating the τm⁵s²U modification and also impedes TRMT61B from incorporating the m¹A modification.

FIGURE 3.

MTU1 protein degradation caused by pathogenic mutations associated with RILF. MTU1 is responsible for 2-thiolation of the τm⁵s²U modification. The 16 pathogenic MTU1 mutants that cause RILF are degraded in mitochondria by the CLPX–CLPP protease. Among the 16 pathogenic MTU1 mutants, three are catalytically inactive, and 13 can restore 2-thiolation on mt-tRNAs upon overexpression (Ahmad et al. 2024).