Loss-of-function mutations in MGME1 impair mtDNA replication and cause multisystemic mitochondrial disease

Abstract

Known disease mechanisms in mitochondrial DNA (mtDNA) maintenance disorders alter either the mitochondrial replication machinery (POLG, POLG2 and C10orf2)1,2,3 or the biosynthesis pathways of deoxyribonucleoside 5′-triphosphates for mtDNA synthesis4,5,6,7,8,9,10,11. However, in many of these disorders, the underlying genetic defect has yet to be discovered. Here, we identify homozygous nonsense and missense mutations in the orphan gene C20orf72 in three families with a mitochondrial syndrome characterized by external ophthalmoplegia, emaciation and respiratory failure. Muscle biopsies showed mtDNA depletion and multiple mtDNA deletions. C20orf72, hereafter MGME1 (mitochondrial genome maintenance exonuclease 1), encodes a mitochondrial RecB-type exonuclease belonging to the PD–(D/E)XK nuclease superfamily. We show that MGME1 cleaves single-stranded DNA and processes DNA flap substrates. Fibroblasts from affected individuals do not repopulate after chemically induced mtDNA depletion. They also accumulate intermediates of stalled replication and show increased levels of 7S DNA, as do MGME1-depleted cells. Thus, we show that MGME1-mediated mtDNA processing is essential for mitochondrial genome maintenance.

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Figure 1: Protein sequence, domain architecture, disease-causing alterations and subcellular localization of MGME1.
Figure 2: Loss of MGME1 leads to mtDNA depletion and higher levels of 7S DNA.
Figure 3: Characterization of the enzymatic activity of MGME1.
Figure 4: Perturbed mitochondrial replication in mutant fibroblasts and MGME1-depleted cells.

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Acknowledgements

T.J.N. and M. Minczuk are grateful to S. Wood and I. Holt for stimulating discussions during the course of this work. We are grateful to S. Beyer, K. Kappes-Horn, M. Stepien-Mering, E. Botz and R. Hellinger for technical assistance. We thank R. Wiesner (University of Cologne) for providing the TFAM antibody. This work was supported by the Medical Research Council UK (T.J.N., J.R. and M. Minczuk) and the German Bundesministerium für Bildung und Forschung (BMBF) through funding of the Systems Biology of Metabotypes grant (SysMBo 0315494A), the E-Rare project GENOMIT (01GM1207) and the German Network for mitochondrial disorders (mitoNET), including C.K., T.K. (mitoNET 01GM0862 and 01GM1113A), T.M., H.P. (mitoNET 01GM0867 and 01GM1113C) and W.S.K. (mitoNET 01GM0868). W.S.K. was funded by the Deutsche Forschungsgemeinschaft (SFB TR3 A11 and D12). V.K.M. was supported by grants from the US National Institutes of Health (GM077465 and GM097136). The financial support of Associazione Amici del Centro Dino Ferrari, University of Milan, the Telethon project GTB07001ER, the Eurobiobank project QLTR-2001-02769 and R.F. 02.187 Criobanca Automatizzata di Materiale Biologico to M.M. and M.S. are gratefully acknowledged.

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C.K. identified, clinically characterized, collected samples and histochemically analyzed skeletal muscle biopsies from family I and the sporadic case and obtained fibroblasts from P1976. M.S., D.R., G.P.C., M. Moggio, C.M.Q. and S.D. identified, clinically characterized, collected samples and histochemically analyzed skeletal muscle biopsies from family II and obtained fibroblasts from P4050 and P4052. T.B.H., T.W., T.M.S., T.M. and H.P. performed exome sequencing and analysis of family I. S.E.C. and V.K.M. performed targeted mitochondrial exome sequencing and analysis of family II. T.J.N., G.Z. and M. Minczuk performed the computational analysis. T.J.N. analyzed protein amounts, performed subcellular localization studies, purified and characterized recombinant MGME1 and analyzed the cells with siRNA knockdown and P1976 fibroblasts. T.B.H., K.D., A.I. and H.P. performed subcellular localization and complementation experiments. S.S. performed the mtDNA repopulation experiments. V.P. performed copy-number and deletion quantification. K.H. screened PEO samples for MGME1 mutations and identified P931. J.R. contributed to the characterization of fibroblasts from P1976. T.K. and T.M. provided samples and coordinated the German network of mitochondrial disorders. C.K., G.Z., M. Minczuk, W.S.K. and H.P. planned the project and wrote the manuscript.

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Correspondence to Michal Minczuk or Wolfram S Kunz.

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The authors declare no competing financial interests.

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Supplementary Note, Supplementary Tables 1–5 and Supplementary Figures 1–8 (PDF 2064 kb)

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Kornblum, C., Nicholls, T., Haack, T. et al. Loss-of-function mutations in MGME1 impair mtDNA replication and cause multisystemic mitochondrial disease. Nat Genet 45, 214–219 (2013). https://doi.org/10.1038/ng.2501

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