The mitochondrial epitranscriptome: the roles of RNA modifications in mitochondrial translation and human disease

Abstract

Mitochondrial protein synthesis is essential for the production of components of the oxidative phosphorylation system. RNA modifications in the mammalian mitochondrial translation apparatus play key roles in facilitating mitochondrial gene expression as they enable decoding of the non-conventional genetic code by a minimal set of tRNAs, and efficient and accurate protein synthesis by the mitoribosome. Intriguingly, recent transcriptome-wide analyses have also revealed modifications in mitochondrial mRNAs, suggesting that the concept of dynamic regulation of gene expression by the modified RNAs (the "epitranscriptome") extends to mitochondria. Furthermore, it has emerged that defects in RNA modification, arising from either mt-DNA mutations or mutations in nuclear-encoded mitochondrial modification enzymes, underlie multiple mitochondrial diseases. Concomitant advances in the identification of the mitochondrial RNA modification machinery and recent structural views of the mitochondrial translation apparatus now allow the molecular basis of such mitochondrial diseases to be understood on a mechanistic level.

Keywords: Epitranscriptome; Mitochondria; Mitochondrial disease; Protein synthesis; RNA modification; Ribosome; Translation; tRNA.

Fig. 1

Distribution of RNA modifications on the human mitochondrial ribosome (PDB 3J9M) [30]. The small ribosomal subunit (SSU) is coloured in teal, the large ribosomal subunit (LSU) in grey, and the structural tRNA^Val in black. The positions of mammalian mt-rRNA modifications are highlighted in various colours and the chemical structures of the corresponding modifications are indicated

Fig. 2

Defects in multiple mt-tRNA modification enzymes are associated with human diseases. Schematic view of the cloverleaf secondary structure of a typical tRNA on which the positions of nucleotides that are known to carry modifications in mitochondrial tRNAs are indicated with circles. Modifications that are associated with human diseases are indicated in red and the modifications present at these positions, the enzymes responsible for installing these modifications (putative modification enzymes based on homology are shown in italics) and the associated diseases are given. DEAF maternally inherited deafness; HCLA hypertrophic cardiomyopathy and lactic acidosis; ME myoclonic epilepsy; MELAS mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes; MERRF myoclonic epilepsy with ragged red fibres; MLASA myopathy, lactic acidosis and sideroblastic anemia; MM mitochondrial myopathy; RIRCD reversible infantile respiratory chain deficiency. Asterisks developmental disability, microcephaly, failure to thrive, recurrent increased lactate levels in plasma, muscular weakness, external ophthalmoplegia, and convergence nystagmus

Fig. 3

Modification pathways for selected mt-tRNA anticodon loop modifications. a NSUN3 methylates C5 of cytosine (C) at position 34 of mt-tRNA^Met to produce m⁵C, which can then be oxidised to 5-formylcytosine (f⁵C) by ALKBH1. b Uridine at position 34 of selected mt-tRNAs can be converted to τm⁵U by MTO1 and GTPBP3. τm⁵U can then undergo O/S exchange by MTU1 to produce τm⁵s²U. c TRIT1 isopentenylates N6 of adenosine at position 37 of several mt-tRNAs to produce N ⁶-isopentenyladenosine (i⁶A). CDK5RAP1 can then perform methylthiolation to generate 2-methylthio-N ⁶-isopentenyladenosine (ms²i⁶A)

Fig. 4

Pathogenic mutations resulting in sequence changes in mt-tRNAs can lead to decreased levels of anticodon loop modifications. Schematic view of the secondary structures of four mt-tRNAs, mt-tRNA^Met (a), mt-tRNA^Leu(URR) (b), mt-tRNA^Lys (c), and mt-tRNA^Ser(UCN) (d), with the positions of pathogenic mutations that lead to decreased levels of anticodon loop modifications (boxed), labelled, and highlighted in red. The diseases associated with each mutation are indicated. ASD autistic spectrum disorders; CPEO chronic progressive external ophthalmoplegia; DM diabetes mellitus; DMDF diabetes mellitus and deafness; FSGS focal segmental glomerulosclerosis; HiCM histiocytoid cardiomyopathy; LA lactic acidosis; LHON Leber hereditary optic neuropathy; LS Leigh syndrome; MELAS mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes; MERRF myoclonic epilepsy with ragged red fibres; MIDD maternally inherited diabetes and deafness; MLASA myopathy, lactic acidosis and sideroblastic anemia; MM mitochondrial myopathy; DEAF maternally inherited deafness; SNHL sensorineural hearing loss