Abstract
Mitochondrial transfer RNA (mt-tRNA) modification determines organelle translation and function. GTPBP3 and MTO1 catalyze 5-taurinomethyluridine (τm5U) modification at wobble uridine of five mt-tRNAs. τm5U hypomodification causes mitochondrial encephalomyopathy, but the underlying pathogenesis and intervention strategy due to GTPBP3 mutations are lacking. In this study, we identify two genetic variants (c.689 A > C (p.Q230P) and c.1120 A > G (p.N374D)) of GTPBP3 in a Chinese proband with metabolic disorders and multisystem dysfunction. Mechanistically, Q230P and N374D mutations induce protein multimerization/aggregation, protease degradation, decreased GTPase activity, and tRNA modification to varying degrees, affecting mitochondrial translation, respiration, dynamics, and function. Homozygous N374D mutations in mice cause embryonic lethality; homozygous E230P or compound heterozygous E230P/N374D knock-in mice develop cardiac and muscular dysfunction due to altered mitochondrial translation. Mitochondrial dysfunction and pathology are efficiently reversed by virus-mediated GTPBP3 expression in cells and animals. This study provides valuable insights into the etiology of and promising intervention strategies for GTPBP3-related diseases.
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Data availability
All data presented in this study are available within the Figures, Supplementary Information, and Supplementary Data 1. Request for resources and reagents should be sent to the lead contact Dr. Xiao-Long Zhou (xlzhou@sibcb.ac.cn). Source data are provided with this paper.
References
Zhang, J. H., Eriani, G. & Zhou, X. L. Pathophysiology of human mitochondrial tRNA metabolism. Trends Endocrinol. Metab. 35, 285–289 (2024).
Kummer, E. & Ban, N. E. Mechanisms and regulation of protein synthesis in mitochondria. Nat. Rev. Mol. Cell Biol. 22, 307–325 (2021).
Suzuki, T., Nagao, A. & Suzuki, T. Human mitochondrial tRNAs: biogenesis, function, structural aspects, and diseases. Annu Rev. Genet. 45, 299–329 (2011).
Zheng, W. Q. et al. Mammalian mitochondrial translation infidelity leads to oxidative stress-induced cell cycle arrest and cardiomyopathy. Proc. Natl. Acad. Sci. USA 120, e2309714120 (2023).
Suzuki, T. The expanding world of tRNA modifications and their disease relevance. Nat. Rev. Mol. Cell Biol. 22, 375–392 (2021).
Suzuki, T. et al. Complete chemical structures of human mitochondrial tRNAs. Nat Commun. 11, https://doi.org/10.1038/s41467-020-18068-6 (2020).
Lu, J. L. et al. Taurine hypomodification underlies mitochondrial tRNATrp-related genetic diseases. Nucleic Acids Res. 52, 13351–13367 (2024).
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. EMBO J. 21, 6581–6589 (2002).
Kirino, Y. et al. Codon-specific translational defect caused by a wobble modification deficiency in mutant tRNA from a human mitochondrial disease. Proc. Natl. Acad. Sci. USA 101, 15070–15075 (2004).
Yasukawa, T., Suzuki, T., Ishii, N., Ohta, S. & Watanabe, K. Wobble modification defect in tRNA disturbs codon-anticodon interaction in a mitochondrial disease. EMBO J. 20, 4794–4802 (2001).
Armengod, M. E. et al. Modification of the wobble uridine in bacterial and mitochondrial tRNAs reading NNA/NNG triplets of 2-codon boxes. RNA Biol. 11, 1495–1507 (2014).
Yim, L., Moukadiri, I., Bjork, G. R. & Armengod, M. E. Further insights into the tRNA modification process controlled by proteins MnmE and GidA of Escherichia coli. Nucleic Acids Res. 34, 5892–5905 (2006).
Meyer, S., Scrima, A., Versees, W. & Wittinghofer, A. Crystal structures of the conserved tRNA-modifying enzyme GidA: implications for its interaction with MnmE and substrate. J. Mol. Biol. 380, 532–547 (2008).
Li, X. & Guan, M. X. A human mitochondrial GTP binding protein related to tRNA modification may modulate phenotypic expression of the deafness-associated mitochondrial 12S rRNA mutation. Mol. Cell Biol. 22, 7701–7711 (2002).
Asano, K. et al. Metabolic and chemical regulation of tRNA modification associated with taurine deficiency and human disease. Nucleic Acids Res. 46, 1565–1583 (2018).
Moukadiri, I. et al. Evolutionarily conserved proteins MnmE and GidA catalyze the formation of two methyluridine derivatives at tRNA wobble positions. Nucleic Acids Res. 37, 7177–7193 (2009).
Meyer, S., Wittinghofer, A. & Versees, W. G-domain dimerization orchestrates the tRNA wobble modification reaction in the MnmE/GidA complex. J. Mol. Biol. 392, 910–922 (2009).
Scrima, A., Vetter, I. R., Armengod, M. E. & Wittinghofer, A. The structure of the TrmE GTP-binding protein and its implications for tRNA modification. EMBO J. 24, 23–33 (2005).
Peng, G. X. et al. The human tRNA taurine modification enzyme GTPBP3 is an active GTPase linked to mitochondrial diseases. Nucleic Acids Res. 49, 2816–2834 (2021).
Osawa, T. et al. Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon. Structure 17, 713–724 (2009).
Chujo, T. & Tomizawa, K. Human transfer RNA modopathies: diseases caused by aberrations in transfer RNA modifications. FEBS J. 288, 7096–7122 (2021).
Kazuhito, T. & Wei, F. Y. Posttranscriptional modifications in mitochondrial tRNA and its implication in mitochondrial translation and disease. J. Biochem. 168, 435–444 (2020).
Becker, L. et al. MTO1-deficient mouse model mirrors the human phenotype showing complex I defect and cardiomyopathy. PLoS ONE 9, e114918 (2014).
Tischner, C. et al. MTO1 mediates tissue specificity of OXPHOS defects via tRNA modification and translation optimization, which can be bypassed by dietary intervention. Hum. Mol. Genet. 24, 2247–2266 (2015).
Fakruddin, M. et al. Defective mitochondrial tRNA taurine modification activates global proteostress and leads to mitochondrial disease. Cell Rep. 22, 482–496 (2018).
Navarro-Gonzalez, C. et al. Mutations in the Caenorhabditis elegans orthologs of human genes required for mitochondrial tRNA modification cause similar electron transport chain defects but different nuclear responses. PloS Genet. 13, e1006921 (2017).
Zhang, Q. et al. Ablation of Mto1 in zebrafish exhibited hypertrophic cardiomyopathy manifested by mitochondrion RNA maturation deficiency. Nucleic Acids Res. 49, 4689–4704 (2021).
Ghezzi, D. et al. Mutations of the mitochondrial-tRNA modifier MTO1 cause hypertrophic cardiomyopathy and lactic acidosis. Am. J. Hum. Genet. 90, 1079–1087 (2012).
Charif, M. et al. Optic neuropathy, cardiomyopathy, cognitive disability in patients with a homozygous mutation in the nuclear MTO1 and a mitochondrial MT-TF variant. Am. J. Med. Genet A 167A, 2366–2374 (2015).
Chen, D. et al. Deletion of Gtpbp3 in zebrafish revealed the hypertrophic cardiomyopathy manifested by aberrant mitochondrial tRNA metabolism. Nucleic Acids Res. 47, 5341–5355 (2019).
Kopajtich, R. et al. Mutations in GTPBP3 cause a mitochondrial translation defect associated with hypertrophic cardiomyopathy, lactic acidosis, and encephalopathy. Am. J. Hum. Genet. 95, 708–720 (2014).
Li, Q. et al. Mutations in GTPBP3 cause aberrant mitochondrial respiration associated with combined oxidative phosphorylation deficiency 23. Genes Dis. https://doi.org/10.1016/j.gendis.2024.101232 (2024).
Wang, Y. et al. A novel mutation in GTPBP3 causes combined oxidative phosphorylation deficiency 23 by affecting pre-mRNA splicing. Heliyon 10, e27199 (2024).
Yan, H. M. et al. Novel mutations in the GTPBP3 gene for mitochondrial disease and characteristics of related phenotypic spectrum: the first three cases from China. Front. Genet. 12, 611226 (2021).
Zhang, Q. et al. Pathogenicity analysis of a novel variant in GTPBP3 causing mitochondrial disease and systematic literature review. Genes 14, https://doi.org/10.3390/genes14030552 (2023).
Elmas, M. et al. Comparison of clinical parameters with whole exome sequencing analysis results of autosomal recessive patients; a center experience. Mol. Biol. Rep. 46, 287–299 (2019).
Yang, Q. & Fu, Y. Mitochondrial diseases associated with mutations in GTPBP3: a case report and literature review. J. Clin. Pedia. 39, 818–821 (2021).
Nardecchia, F. et al. Biallelic variants in GTPBP3: new patients, phenotypic spectrum, and outcome. Ann. Clin. Transl. Neurol. 11, 819–825 (2024).
Yano, T., Takeda, A. & Murayama, K. A hidden cause of middle-aged onset heart failure with preserved ejection fraction: a GTPBP3 variant. Eur. Heart J. 45, 2794 (2024).
Tong, Q., Miao, Y. & Yin, H. Echocardiographic manifestations of mitochondrial disease with GTPBP3 gene mutations: a case report. Medicine 103, e37847 (2024).
Zhao, X. X. et al. Mitochondrial cardiomyopathy caused by nuclear gene mutation: a case report and literature review. Mol. Cardiol. China 21, 4387–4389 (2021).
Xie, Y. et al. Expanding the phenotypic and genetic spectrum of GTPBP3 deficiency: findings from nine Chinese pedigrees. Orphanet J. Rare Dis. 19, 488 (2024).
Richards, S. et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 17, 405–424 (2015).
Varadi, M. et al. AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences. Nucleic Acids Res. 52, D368–D375 (2024).
Meyer, S. et al. Kissing G domains of MnmE monitored by X-ray crystallography and pulse electron paramagnetic resonance spectroscopy. PLoS Biol. 7, e1000212 (2009).
Scrima, A. & Wittinghofer, A. Dimerisation-dependent GTPase reaction of MnmE: how potassium acts as GTPase-activating element. EMBO J. 25, 2940–2951 (2006).
Ahmad, R. N. R. et al. Pathological mutations promote proteolysis of mitochondrial tRNA-specific 2-thiouridylase 1 (MTU1) via mitochondrial caseinolytic peptidase (CLPP). Nucleic Acids Res. 52, 1341–1358 (2024).
Ghifari, A. S., Vazquez-Calvo, C., Carlstrom, A. & Ott, M. Interconnectivity of mitochondrial protein biogenesis and quality control. Trends Biochem. Sci. https://doi.org/10.1016/j.tibs.2025.09.004 (2025).
Umeda, N. et al. 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. J. Biol. Chem. 280, 1613–1624 (2005).
Sciarretta, S., Maejima, Y., Zablocki, D. & Sadoshima, J. The role of autophagy in the heart. Annu Rev. Physiol. 80, 1–26 (2018).
Fiorese, C. J. et al. The transcription factor ATF5 mediates a mammalian mitochondrial UPR. Curr. Biol. 26, 2037–2043 (2016).
Shpilka, T. & Haynes, C. M. The mitochondrial UPR: mechanisms, physiological functions and implications in ageing. Nat. Rev. Mol. Cell Biol. 19, 109–120 (2018).
Wang, D., Tai, P. W. L. & Gao, G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat. Rev. Drug Discov. 18, 358–378 (2019).
Wang, S. et al. AAV gene therapy prevents and reverses heart failure in a murine knockout model of Barth syndrome. Circ. Res. 126, 1024–1039 (2020).
Maes, L. et al. Cryo-EM structures of the MnmE-MnmG complex reveal large conformational changes and provide new insights into the mechanism of tRNA modification. Nucleic Acids Res. 53, https://doi.org/10.1093/nar/gkaf824 (2025).
Cunningham, J. T. et al. mTOR controls mitochondrial oxidative function through a YY1-PGC-1alpha transcriptional complex. Nature 450, 736–740 (2007).
Chung, C. Y. et al. Constitutive activation of the PI3K-Akt-mTORC1 pathway sustains the m.3243 A > G mtDNA mutation. Nat. Commun. 12, 6409 (2021).
Khan, N. A. et al. mTORC1 regulates mitochondrial integrated stress response and mitochondrial myopathy progression. Cell Metab. 26, 419–428 e415 (2017).
Ortells, M. C. et al. Transcriptional regulation of gene expression during osmotic stress responses by the mammalian target of rapamycin. Nucleic Acids Res. 40, 4368–4384 (2012).
Ito, T. et al. Expression of taurine transporter is regulated through the TonE (tonicity-responsive element)/TonEBP (TonE-binding protein) pathway and contributes to cytoprotection in HepG2 cells. Biochem. J. 382, 177–182 (2004).
Lambert, I. H., Jensen, J. V. & Pedersen, P. A. mTOR ensures increased release and reduced uptake of the organic osmolyte taurine under hypoosmotic conditions in mouse fibroblasts. Am. J. Physiol. Cell Physiol. 306, C1028–C1040 (2014).
Lightowlers, R. N., Taylor, R. W. & Turnbull, D. M. Mutations causing mitochondrial disease: what is new and what challenges remain? Science 349, 1494–1499 (2015).
Wallace, D. C. Mitochondrial genetic medicine. Nat. Genet. 50, 1642–1649 (2018).
Russell, O. M., Gorman, G. S., Lightowlers, R. N. & Turnbull, D. M. Mitochondrial diseases: hope for the future. Cell 181, 168–188 (2020).
Rikimaru, M. et al. Taurine ameliorates impaired the mitochondrial function and prevents stroke-like episodes in patients with MELAS. Intern. Med. 51, 3351–3357 (2012).
Ohsawa, Y. et al. Taurine supplementation for prevention of stroke-like episodes in MELAS: a multicentre, open-label, 52-week phase III trial. J. Neurol. Neurosurg. Psychiatry 90, 529–536 (2019).
Tomoda, E. et al. Restoration of mitochondrial function through activation of hypomodified tRNAs with pathogenic mutations associated with mitochondrial diseases. Nucleic Acids Res. 51, 7563–7579 (2023).
Zhang, Y., Zhou, J. B., Yin, Y., Wang, E. D. & Zhou, X. L. Multifaceted roles of t6A biogenesis in efficiency and fidelity of mitochondrial gene expression. Nucleic Acids Res. https://doi.org/10.1093/nar/gkae013 (2024).
Yu, T. et al. Selective degradation of tRNASer(AGY) is the primary driver for mitochondrial seryl-tRNA synthetase-related disease. Nucleic Acids Res. 50, 11755–11774 (2022).
Igloi, G. L. Interaction of tRNAs and of phosphorothioate-substituted nucleic acids with an organomercurial. Probing the chemical environment of thiolated residues by affinity electrophoresis. Biochemistry 27, 3842–3849 (1988).
Acknowledgements
We thank Dr. Gilbert Eriani (University of Strasbourg) for carefully reading the manuscript and valuable suggestions. We also thank the staff members of BL19U2 beamline at the National Facility for Protein Science in Shanghai, for providing technical support and assistance in SAXS data collection and analysis. This work was supported by the Natural Science Foundation of China (92581112 to X.L.Z.); the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB0570000 to X.L.Z.); the Natural Science Foundation of China (32271300 to X.L.Z.); Key project of Innovation and Development united Fund of Chongqing Natural Science Foundation (CSTB2022NSCQ-LZX0029 to C.S.); National Key Research and Development Program of China (2021YFA1300800 to X.L.Z.); the CAS Project for Young Scientists in Basic Research (YSBR-075 to X.L.Z.); Key Discipline Group for Discipline Construction of the Shanghai Pudong New Area Municipal Health Commission (PWZxq2022-07 to T.Y.); Shanghai Key Laboratory of Embryo Original Diseases (Shelab2025ZD04 to X.L.Z.); the Shanghai Academy of Natural Sciences (SANS to X.L.Z.); the Ruisi Center of Life Sciences, Minhang District, Shanghai.
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Y.Z.: Conceptualization, Methodology, Validation, Formal analysis, Investigation, Data curation, Visualization, Writing - original draft, Writing - review & editing. S.Y.Y.: Investigation, Formal analysis, Data curation. J.L., H.L., and C.S.: Clinical Data Collection. T.Y., Investigation. N.Z., G.X.P., and C.R.M.: Investigation. W.Q.Z. and E.D.W.: Methodology. X.L.Z.: Conceptualization, Supervision, Methodology, Project Administration, Writing - original draft, Writing - review & editing, Funding acquisition.
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Zhang, Y., Yao, SY., Li, J. et al. Molecular pathogenesis and gene therapy-based intervention of GTPBP3-related mitochondrial disease. Nat Commun (2026). https://doi.org/10.1038/s41467-026-71750-z
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DOI: https://doi.org/10.1038/s41467-026-71750-z
