tRNA modification in the mitochondrion (Homo sapiens)

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Bibliography

1. Fernandez-Vizarra E, Berardinelli A, Valente L, Tiranti V, Zeviani M.; ''Nonsense mutation in pseudouridylate synthase 1 (PUS1) in two brothers affected by myopathy, lactic acidosis and sideroblastic anaemia (MLASA).''; PubMed Europe PMC Scholia
2. Vilardo E, Rossmanith W.; ''Molecular insights into HSD10 disease: impact of SDR5C1 mutations on the human mitochondrial RNase P complex.''; PubMed Europe PMC Scholia
3. Holzmann J, Frank P, Löffler E, Bennett KL, Gerner C, Rossmanith W.; ''RNase P without RNA: identification and functional reconstitution of the human mitochondrial tRNA processing enzyme.''; PubMed Europe PMC Scholia
4. Salinas-Giegé T, Giegé R, Giegé P.; ''tRNA biology in mitochondria.''; PubMed Europe PMC Scholia
5. Chujo T, Suzuki T.; ''Trmt61B is a methyltransferase responsible for 1-methyladenosine at position 58 of human mitochondrial tRNAs.''; PubMed Europe PMC Scholia
6. Zeharia A, Shaag A, Pappo O, Mager-Heckel AM, Saada A, Beinat M, Karicheva O, Mandel H, Ofek N, Segel R, Marom D, Rötig A, Tarassov I, Elpeleg O.; ''Acute infantile liver failure due to mutations in the TRMU gene.''; PubMed Europe PMC Scholia
7. Sasarman F, Antonicka H, Horvath R, Shoubridge EA.; ''The 2-thiouridylase function of the human MTU1 (TRMU) enzyme is dispensable for mitochondrial translation.''; PubMed Europe PMC Scholia
8. Ghezzi D, Baruffini E, Haack TB, Invernizzi F, Melchionda L, Dallabona C, Strom TM, Parini R, Burlina AB, Meitinger T, Prokisch H, Ferrero I, Zeviani M.; ''Mutations of the mitochondrial-tRNA modifier MTO1 cause hypertrophic cardiomyopathy and lactic acidosis.''; PubMed Europe PMC Scholia
9. Baruffini E, Dallabona C, Invernizzi F, Yarham JW, Melchionda L, Blakely EL, Lamantea E, Donnini C, Santra S, Vijayaraghavan S, Roper HP, Burlina A, Kopajtich R, Walther A, Strom TM, Haack TB, Prokisch H, Taylor RW, Ferrero I, Zeviani M, Ghezzi D.; ''MTO1 mutations are associated with hypertrophic cardiomyopathy and lactic acidosis and cause respiratory chain deficiency in humans and yeast.''; PubMed Europe PMC Scholia
10. Patton JR, Bykhovskaya Y, Mengesha E, Bertolotto C, Fischel-Ghodsian N.; ''Mitochondrial myopathy and sideroblastic anemia (MLASA): missense mutation in the pseudouridine synthase 1 (PUS1) gene is associated with the loss of tRNA pseudouridylation.''; PubMed Europe PMC Scholia
11. Sibert BS, Patton JR.; ''Pseudouridine synthase 1: a site-specific synthase without strict sequence recognition requirements.''; PubMed Europe PMC Scholia
12. Vilardo E, Nachbagauer C, Buzet A, Taschner A, Holzmann J, Rossmanith W.; ''A subcomplex of human mitochondrial RNase P is a bifunctional methyltransferase--extensive moonlighting in mitochondrial tRNA biogenesis.''; PubMed Europe PMC Scholia
13. Guan MX, Yan Q, Li X, Bykhovskaya Y, Gallo-Teran J, Hajek P, Umeda N, Zhao H, Garrido G, Mengesha E, Suzuki T, del Castillo I, Peters JL, Li R, Qian Y, Wang X, Ballana E, Shohat M, Lu J, Estivill X, Watanabe K, Fischel-Ghodsian N.; ''Mutation in TRMU related to transfer RNA modification modulates the phenotypic expression of the deafness-associated mitochondrial 12S ribosomal RNA mutations.''; PubMed Europe PMC Scholia
14. Gaignard P, Gonzales E, Ackermann O, Labrune P, Correia I, Therond P, Jacquemin E, Slama A.; ''Mitochondrial Infantile Liver Disease due to TRMU Gene Mutations: Three New Cases.''; PubMed Europe PMC Scholia
15. Boczonadi V, Smith PM, Pyle A, Gomez-Duran A, Schara U, Tulinius M, Chinnery PF, Horvath R.; ''Altered 2-thiouridylation impairs mitochondrial translation in reversible infantile respiratory chain deficiency.''; PubMed Europe PMC Scholia
16. Suzuki T, Nagao A, Suzuki T.; ''Human mitochondrial tRNAs: biogenesis, function, structural aspects, and diseases.''; PubMed Europe PMC Scholia
17. Bykhovskaya Y, Casas K, Mengesha E, Inbal A, Fischel-Ghodsian N.; ''Missense mutation in pseudouridine synthase 1 (PUS1) causes mitochondrial myopathy and sideroblastic anemia (MLASA).''; PubMed Europe PMC Scholia
18. Lamichhane TN, Mattijssen S, Maraia RJ.; ''Human cells have a limited set of tRNA anticodon loop substrates of the tRNA isopentenyltransferase TRIT1 tumor suppressor.''; PubMed Europe PMC Scholia
19. Charette M, Gray MW.; ''Pseudouridine in RNA: what, where, how, and why.''; PubMed Europe PMC Scholia
20. Yarham JW, Lamichhane TN, Pyle A, Mattijssen S, Baruffini E, Bruni F, Donnini C, Vassilev A, He L, Blakely EL, Griffin H, Santibanez-Koref M, Bindoff LA, Ferrero I, Chinnery PF, McFarland R, Maraia RJ, Taylor RW.; ''Defective i6A37 modification of mitochondrial and cytosolic tRNAs results from pathogenic mutations in TRIT1 and its substrate tRNA.''; PubMed Europe PMC Scholia
21. Tischner C, Hofer A, Wulff V, Stepek J, Dumitru I, Becker L, Haack T, Kremer L, Datta AN, Sperl W, Floss T, Wurst W, Chrzanowska-Lightowlers Z, De Angelis MH, Klopstock T, Prokisch H, Wenz T.; ''MTO1 mediates tissue specificity of OXPHOS defects via tRNA modification and translation optimization, which can be bypassed by dietary intervention.''; PubMed Europe PMC Scholia
22. Umeda N, Suzuki T, Yukawa M, Ohya Y, Shindo H, Watanabe K, Suzuki T.; ''Mitochondria-specific RNA-modifying enzymes responsible for the biosynthesis of the wobble base in mitochondrial tRNAs. Implications for the molecular pathogenesis of human mitochondrial diseases.''; PubMed Europe PMC Scholia
23. Ofman R, Ruiter JP, Feenstra M, Duran M, Poll-The BT, Zschocke J, Ensenauer R, Lehnert W, Sass JO, Sperl W, Wanders RJ.; ''2-Methyl-3-hydroxybutyryl-CoA dehydrogenase deficiency is caused by mutations in the HADH2 gene.''; PubMed Europe PMC Scholia
24. Asano K, Suzuki T, Saito A, Wei FY, Ikeuchi Y, Numata T, Tanaka R, Yamane Y, Yamamoto T, Goto T, Kishita Y, Murayama K, Ohtake A, Okazaki Y, Tomizawa K, Sakaguchi Y, Suzuki T.; ''Metabolic and chemical regulation of tRNA modification associated with taurine deficiency and human disease.''; PubMed Europe PMC Scholia
25. Torres AG, Batlle E, Ribas de Pouplana L.; ''Role of tRNA modifications in human diseases.''; PubMed Europe PMC Scholia
26. Sibert BS, Fischel-Ghodsian N, Patton JR.; ''Partial activity is seen with many substitutions of highly conserved active site residues in human Pseudouridine synthase 1.''; PubMed Europe PMC Scholia
27. Suzuki T, Suzuki T, Wada T, Saigo K, Watanabe K.; ''Taurine as a constituent of mitochondrial tRNAs: new insights into the functions of taurine and human mitochondrial diseases.''; PubMed Europe PMC Scholia
28. Helm M, Brulé H, Degoul F, Cepanec C, Leroux JP, Giegé R, Florentz C.; ''The presence of modified nucleotides is required for cloverleaf folding of a human mitochondrial tRNA.''; PubMed Europe PMC Scholia
29. Hou YM, Gamper H, Yang W.; ''Post-transcriptional modifications to tRNA--a response to the genetic code degeneracy.''; PubMed Europe PMC Scholia

History

External references

DataNodes

Name	Type	Database reference	Comment
AdoHcy	Metabolite	CHEBI:16680 (ChEBI)
AdoMet	Metabolite	CHEBI:15414 (ChEBI)
GTPBP3	Protein	Q969Y2 (Uniprot-TrEMBL)
HSD17B10	Protein	Q99714 (Uniprot-TrEMBL)
KIAA0391	Protein	O15091 (Uniprot-TrEMBL)
L-Cys	Metabolite	CHEBI:35235 (ChEBI)
MTO1	Protein	Q9Y2Z2 (Uniprot-TrEMBL)
PPi	Metabolite	CHEBI:29888 (ChEBI)
PUS1-1	Protein	Q9Y606-1 (Uniprot-TrEMBL)
TRIT1	Protein	Q9H3H1 (Uniprot-TrEMBL)
TRMT10C	Protein	Q7L0Y3 (Uniprot-TrEMBL)
TRMT61B	Protein	Q9BVS5 (Uniprot-TrEMBL)
TRMT61B tetramer	Complex	R-HSA-6787508 (Reactome)
TRMU	Protein	O75648 (Uniprot-TrEMBL)
dimethylallyl-PP	Metabolite	CHEBI:16057 (ChEBI)
mtRNase P	Complex	R-HSA-6785726 (Reactome)
tRNA containing 1-methylA-9		R-HSA-6787584 (Reactome)
tRNA containing 1-methylG-9		R-HSA-6787587 (Reactome)
tRNA containing A-9		R-HSA-6787556 (Reactome)
tRNA containing G-9		R-HSA-6787559 (Reactome)
tRNA(Leu) containing 5-taurinomethyl-2-thiouridine-34		R-HSA-6787459 (Reactome)
tRNA(Leu) containing 5-taurinomethyluridine-34		R-HSA-6787375 (Reactome)
tRNA(Leu) containing U-34		R-HSA-6787474 (Reactome)
tRNA(Leu)(UUR) containing 1-methylA-58		R-HSA-6787522 (Reactome)
tRNA(Leu)(UUR) containing A-58		R-HSA-6787514 (Reactome)
tRNA(Leu,Lys) containing U-34	Complex	R-HSA-6787446 (Reactome)
tRNA(Leu,Lys,Ser) containing 1-methylA-58	Complex	R-HSA-6787517 (Reactome)
tRNA(Leu,Lys,Ser) containing A-58	Complex	R-HSA-6787519 (Reactome)
tRNA(Lys) containing 1-methylA-58		R-HSA-6787509 (Reactome)
tRNA(Lys) containing 5-taurinomethyl-2-thiouridine-34		R-HSA-6787463 (Reactome)
tRNA(Lys) containing 5-taurinomethyluridine-34		R-HSA-6787395 (Reactome)
tRNA(Lys) containing A-58		R-HSA-6787520 (Reactome)
tRNA(Lys) containing U-34		R-HSA-6787392 (Reactome)
tRNA(Lys)(UUU) containing U-27,28		R-HSA-6787590 (Reactome)
tRNA(Lys)(UUU) containing pseudoU-27,28		R-HSA-6787593 (Reactome)
tRNA(Lys,Leu) containing 5-taurinomethyl-2-thioU-34	Complex	R-HSA-6787387 (Reactome)
tRNA(Lys,Leu) containing 5-taurinomethylU-34	Complex	R-HSA-6787473 (Reactome)
tRNA(Lys,Ser) containing pseudoU-27,28	Complex	R-HSA-6787558 (Reactome)
tRNA(Lys,Ser) containing U-27,U28	Complex	R-HSA-6787562 (Reactome)
tRNA(Ser)(UCN) containing isopentenylA-37		R-HSA-6787597 (Reactome)
tRNA(Ser)(UCN) containing A-37		R-HSA-6787583 (Reactome)
tRNA(Ser)(UCN) containing 1-methylA-58		R-HSA-6787518 (Reactome)
tRNA(Ser)(UCN) containing A-58		R-HSA-6787511 (Reactome)
tRNA(Ser)(UGA) containing U-27,U28		R-HSA-6787586 (Reactome)
tRNA(Ser)(UGA) containing pseudoU-27,28		R-HSA-6787557 (Reactome)

Annotated Interactions

Source	Target	Type	Database reference	Comment
	AdoHcy	Arrow	R-HSA-6787525 (Reactome)
	AdoHcy	Arrow	R-HSA-6787591 (Reactome)
	AdoHcy	Arrow	R-HSA-6787594 (Reactome)
AdoMet			R-HSA-6787525 (Reactome)
AdoMet			R-HSA-6787591 (Reactome)
AdoMet			R-HSA-6787594 (Reactome)
GTPBP3		Arrow	R-HSA-6787403 (Reactome)
L-Cys			R-HSA-6787447 (Reactome)
MTO1		Arrow	R-HSA-6787403 (Reactome)
	PPi	Arrow	R-HSA-6787567 (Reactome)
PUS1-1		mim-catalysis	R-HSA-6787566 (Reactome)
			R-HSA-6787403 (Reactome)	A conserved pathway consisting of at least GTPBP3 (MSS1 in Saccharomyces cerevisiae, MnmE in Escherichia coli) and MTO1 (MTO1 in S. cerevisiae, MnmG in E. coli) modifies the wobble nucleotide uridine-34 in mitochondrial tRNA (Asano et al. 2018). In humans a methyl group and a taurine group (2-aminoethylsulfonic acid) are conjugated to the 5 position of the uracil ring (Suzuki et al. 2002). In yeast and E. coli a methyl group and a glycine group are conjugated, yielding 5-carboxymethylaminomethyluridine. The details of the reaction mechanism are unknown. Modification of the wobble nucleotide is required for efficient and accurate translation. Mutations in constituents of the pathway cause disease symptoms characteristic of mitochondrial dysfunction: lactic acidosis, hypertrophic cardiomyopathy, respiratory chain defect, and, in association with the A1555G mutation in 12S rRNA, deafness (Ghezzi et al. 2012, Baruffini et al. 2013, Tischner et al. 2015).
			R-HSA-6787447 (Reactome)	TRMU (MTU1) transfers a sulfur atom from L-cysteine to the 2 position of 5-taurinomethyluridine-34 in tRNAs (Umeda et al. 2005, Sasarman et al. 2011). In Escherichia coli the sulfur is transferred along a relay system of proteins from L-cysteine to uridine. It is unknown if such a relay system also exists in humans. In yeast, mutations in MTU1, the homolog of TRMU act synergistically with mutations in the homologs of GTPBP3 and MTO1 to impair mitochondrial function (Umeda et al. 2005). In humans mutations in TRMU cause mitochondrial infantile liver disease (Zeharia et al. 2009, Gaignard et al. 2013), infantile respiratory chain disease (Boczonadi et al. 2013), and modify the severity of deafness associated with mutations in mitochondrial 12S rRNA (Guan et al. 2006), however abrogation of the thiouridylase function of TRMU may not be responsible for the phenotypes (Sasarman et al. 2011).
			R-HSA-6787525 (Reactome)	A TRMT61B oligomer, probably a tetramer, transfers a methyl group from S-adenosylmethionine to the (N)1 position of adenosine-58 in 3 mitochondrial tRNAs (tRNA(Leu)(UUR), tRNA(Lys), tRNA(Ser(UCN)) (Chujo and Suzuki 2012).
			R-HSA-6787566 (Reactome)	PUS1-1, the longer isoform of PUS1 located in the mitochondrion (Fernandez-Vizarra et al. 2007), converts uridine-27 and uridine-28 to pseudouridine residues in the anticodon stems of mitochondrial tRNA(Lys)(UUU) and tRNA(Ser)(UGA) (Patton et al. 2005, Fernandez-Vizarra et al. 2007, Sibert et al. 2008, Sibert and Patton 2012). Isomerization of uracil to pseudouridine creates an extra hydrogen bond donor and increases base stacking, acting to rigidify the RNA structure (reviewed in Charette and Gray 2000). As inferred from yeast Pus1p, PUS1 may also convert uridine to pseudouridine in other tRNAs and pre-tRNAs. Mutations in PUS1 cause mitochondrial myopathy and sideroblastic anemia (MLSA) (Bykhovskaya et al. 2004, Patton et al. 2005, Fernandez-Vizarra et al. 2007)
			R-HSA-6787567 (Reactome)	TRIT1 transfers a dimethylallyl group (isopentenyl group) from dimethylallyl diphosphate to the N6 position of adenosine-37 in mitochondrial tRNA(Ser,UCN), yielding N6-dimethylallyladenosine-37 (N6-isopentenyladenosine-37) (Lamichhane et al. 2013, Yarham et al. 2014). TRIT1 modifies both cytosolic and mitochondrial tRNAs and a mutation in TRIT1 causes defects in mitochondrial protein synthesis and respiration (Yarham et al. 2014).
			R-HSA-6787591 (Reactome)	TRMT10C in TRMT10C:HSD17B10 (TRMT10C:SDR5C1), a subcomplex of the mitochondrial RNase P complex, methylates the 1 position of guanosine-9 in mitochondrial tRNAs (Vilardo et al. 2012). 5 of 22 mitochondrial tRNAs have a G9 residue. Methylation of G9 appears to be important for correct folding of tRNA. Mutations in the SDR5C1 dehydrogenase subunit of RNase P impair dehydrogenation, tRNA methylation, and tRNA processing, causing HSD10 disease, which is characterized by progressive neurodegeneration and cardiomyopathy (Vilardo and Rossmanith 2015).
			R-HSA-6787594 (Reactome)	TRMT10C of TRMT10C:HSD17B10 (TRMT10C:SDR5C1), a subcomplex of the mitochondrial RNase P complex, methylates the 1 position of adenosine-9 in mitochondrial tRNAs (Vilardo et al. 2012). 14 of 22 mitochondrial tRNAs have an A9 residue. Methylation of A9 appears to be important for correct folding of tRNA (Helm et al. 1998). Mutations in the HSD17B10 (SDR5C1) dehydrogenase subunit of RNase P impair dehydrogenation, tRNA methylation, and tRNA processing, causing HSD10 disease, which is characterized by progressive neurodegeneration and cardiomyopathy (Vilardo and Rossmanith 2015).
TRIT1		mim-catalysis	R-HSA-6787567 (Reactome)
TRMT61B tetramer		mim-catalysis	R-HSA-6787525 (Reactome)
TRMU		mim-catalysis	R-HSA-6787447 (Reactome)
dimethylallyl-PP			R-HSA-6787567 (Reactome)
mtRNase P		mim-catalysis	R-HSA-6787591 (Reactome)
mtRNase P		mim-catalysis	R-HSA-6787594 (Reactome)
	tRNA containing 1-methylA-9	Arrow	R-HSA-6787594 (Reactome)
	tRNA containing 1-methylG-9	Arrow	R-HSA-6787591 (Reactome)
tRNA containing A-9			R-HSA-6787594 (Reactome)
tRNA containing G-9			R-HSA-6787591 (Reactome)
tRNA(Leu,Lys) containing U-34			R-HSA-6787403 (Reactome)
	tRNA(Leu,Lys,Ser) containing 1-methylA-58	Arrow	R-HSA-6787525 (Reactome)
tRNA(Leu,Lys,Ser) containing A-58			R-HSA-6787525 (Reactome)
	tRNA(Lys,Leu) containing 5-taurinomethyl-2-thioU-34	Arrow	R-HSA-6787447 (Reactome)
	tRNA(Lys,Leu) containing 5-taurinomethylU-34	Arrow	R-HSA-6787403 (Reactome)
tRNA(Lys,Leu) containing 5-taurinomethylU-34			R-HSA-6787447 (Reactome)
	tRNA(Lys,Ser) containing pseudoU-27,28	Arrow	R-HSA-6787566 (Reactome)
tRNA(Lys,Ser) containing U-27,U28			R-HSA-6787566 (Reactome)
	tRNA(Ser)(UCN) containing isopentenylA-37	Arrow	R-HSA-6787567 (Reactome)
tRNA(Ser)(UCN) containing A-37			R-HSA-6787567 (Reactome)