51
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Van Haute L, Hendrick AG, D'Souza AR, Powell CA, Rebelo-Guiomar P, Harbour ME, Ding S, Fearnley IM, Andrews B, Minczuk M. METTL15 introduces N4-methylcytidine into human mitochondrial 12S rRNA and is required for mitoribosome biogenesis. Nucleic Acids Res 2019; 47:10267-10281. [PMID: 31665743 PMCID: PMC6821322 DOI: 10.1093/nar/gkz735] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/03/2019] [Indexed: 01/08/2023] Open
Abstract
Post-transcriptional RNA modifications, the epitranscriptome, play important roles in modulating the functions of RNA species. Modifications of rRNA are key for ribosome production and function. Identification and characterization of enzymes involved in epitranscriptome shaping is instrumental for the elucidation of the functional roles of specific RNA modifications. Ten modified sites have been thus far identified in the mammalian mitochondrial rRNA. Enzymes responsible for two of these modifications have not been characterized. Here, we identify METTL15, show that it is the main N4-methylcytidine (m4C) methyltransferase in human cells and demonstrate that it is responsible for the methylation of position C839 in mitochondrial 12S rRNA. We show that the lack of METTL15 results in a reduction of the mitochondrial de novo protein synthesis and decreased steady-state levels of protein components of the oxidative phosphorylation system. Without functional METTL15, the assembly of the mitochondrial ribosome is decreased, with the late assembly components being unable to be incorporated efficiently into the small subunit. We speculate that m4C839 is involved in the stabilization of 12S rRNA folding, therefore facilitating the assembly of the mitochondrial small ribosomal subunits. Taken together our data show that METTL15 is a novel protein necessary for efficient translation in human mitochondria.
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Affiliation(s)
- Lindsey Van Haute
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Alan G Hendrick
- STORM Therapeutics Limited, Moneta Building, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Aaron R D'Souza
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Christopher A Powell
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Pedro Rebelo-Guiomar
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK.,Graduate Program in Areas of Basic and Applied Biology (GABBA), University of Porto, Rua Alfredo Allen 208, Porto 4200-135, Portugal
| | - Michael E Harbour
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK.,STORM Therapeutics Limited, Moneta Building, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Shujing Ding
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Ian M Fearnley
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Byron Andrews
- STORM Therapeutics Limited, Moneta Building, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
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52
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Zhao X, Cui L, Xiao Y, Mao Q, Aishanjiang M, Kong W, Liu Y, Chen H, Hong F, Jia Z, Wang M, Jiang P, Guan MX. Hypertension-associated mitochondrial DNA 4401A>G mutation caused the aberrant processing of tRNAMet, all 8 tRNAs and ND6 mRNA in the light-strand transcript. Nucleic Acids Res 2019; 47:10340-10356. [PMID: 31504769 PMCID: PMC6821173 DOI: 10.1093/nar/gkz742] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 08/12/2019] [Accepted: 08/22/2019] [Indexed: 12/31/2022] Open
Abstract
Mitochondrial tRNA processing defects were associated with human diseases but their pathophysiology remains elusively. The hypertension-associated m.4401A>G mutation resided at a spacer between mitochondrial tRNAMet and tRNAGln genes. An in vitro processing experiment revealed that the m.4401A>G mutation caused 59% and 69% decreases in the 5' end processing efficiency of tRNAGln and tRNAMet precursors, catalyzed by RNase P, respectively. Using human umbilical vein endothelial cells-derived cybrids, we demonstrated that the m.4401A>G mutation caused the decreases of all 8 tRNAs and ND6 and increases of longer and uncleaved precursors from the Light-strand transcript. Conversely, the m.4401A>G mutation yielded the reduced levels of tRNAMet level but did not change the levels of other 13 tRNAs, 12 mRNAs including ND1, 12S rRNA and 16S rRNA from the Heavy-strand transcript. These implicated the asymmetrical processing mechanisms of H-strand and L-strand polycistronic transcripts. The tRNA processing defects play the determined roles in the impairing mitochondrial translation, respiratory deficiency, diminishing membrane potential, increasing production of reactive oxygen species and altering autophagy. Furthermore, the m.4401A>G mutation altered the angiogenesis, evidenced by aberrant wound regeneration and weaken tube formation in mutant cybrids. Our findings provide new insights into the pathophysiology of hypertension arising from mitochondrial tRNA processing defects.
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Affiliation(s)
- Xiaoxu Zhao
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Limei Cui
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yun Xiao
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Qin Mao
- Institute of Genetics, and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Maerhaba Aishanjiang
- Institute of Genetics, and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Wanzhong Kong
- Department of Clinical Laboratory, Wenzhou Traditional Chinese Medicine Hospital, Wenzhou, Zhejiang 325000, China
| | - Yuqi Liu
- Cardiac Department, Chinese PLA General Hospital, Beijing 100853, China
| | - Hong Chen
- Emergy Medicine Department, Ningbo First Hospital, Zhejiang University School of Medicine, Ningbo, Zhejiang 315000, China
| | - Fang Hong
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Zidong Jia
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Meng Wang
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Pingping Jiang
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Min-Xin Guan
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Key lab of Reproductive Genetics, Ministry of Education of PRC, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Joint Institute of Genetics and Genome Medicine between Zhejiang University and University of Toronto, Hangzhou, Zhejiang 310058, China
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53
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Waltz F, Giegé P. Striking Diversity of Mitochondria-Specific Translation Processes across Eukaryotes. Trends Biochem Sci 2019; 45:149-162. [PMID: 31780199 DOI: 10.1016/j.tibs.2019.10.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/03/2019] [Accepted: 10/08/2019] [Indexed: 12/13/2022]
Abstract
Mitochondria are essential organelles that act as energy conversion powerhouses and metabolic hubs. Their gene expression machineries combine traits inherited from prokaryote ancestors and specific features acquired during eukaryote evolution. Mitochondrial research has wide implications ranging from human health to agronomy. We highlight recent advances in mitochondrial translation. Functional, biochemical, and structural data have revealed an unexpected diversity of mitochondrial translation systems, particularly of their key players, the mitochondrial ribosomes (mitoribosomes). Ribosome assembly and translation mechanisms, such as initiation, are discussed and put in perspective with the prevalence of eukaryote-specific families of mitochondrial translation factors such as pentatricopeptide repeat (PPR) proteins.
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Affiliation(s)
- Florent Waltz
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France; Institut Européen de Chimie et de Biologie, l'Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Bordeaux, 2 rue Robert Escarpit, 33607 Pessac, France.
| | - Philippe Giegé
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
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54
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Fan W, Zheng J, Kong W, Cui L, Aishanjiang M, Yi Q, Wang M, Cang X, Tang X, Chen Y, Mo JQ, Sondheimer N, Ge W, Guan MX. Contribution of a mitochondrial tyrosyl-tRNA synthetase mutation to the phenotypic expression of the deafness-associated tRNA Ser(UCN) 7511A>G mutation. J Biol Chem 2019; 294:19292-19305. [PMID: 31685661 DOI: 10.1074/jbc.ra119.010598] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/29/2019] [Indexed: 01/01/2023] Open
Abstract
Nuclear modifier genes have been proposed to modify the phenotypic expression of mitochondrial DNA mutations. Using a targeted exome-sequencing approach, here we found that the p.191Gly>Val mutation in mitochondrial tyrosyl-tRNA synthetase 2 (YARS2) interacts with the tRNASer(UCN) 7511A>G mutation in causing deafness. Strikingly, members of a Chinese family bearing both the YARS2 p.191Gly>Val and m.7511A>G mutations displayed much higher penetrance of deafness than those pedigrees carrying only the m.7511A>G mutation. The m.7511A>G mutation changed the A4:U69 base-pairing to G4:U69 pairing at the aminoacyl acceptor stem of tRNASer(UCN) and perturbed tRNASer(UCN) structure and function, including an increased melting temperature, altered conformation, instability, and aberrant aminoacylation of mutant tRNA. Using lymphoblastoid cell lines derived from symptomatic and asymptomatic members of these Chinese families and control subjects, we show that cell lines harboring only the m.7511A>G or p.191Gly>Val mutation revealed relatively mild defects in tRNASer(UCN) or tRNATyr metabolism, respectively. However, cell lines harboring both m.7511A>G and p.191Gly>Val mutations displayed more severe defective aminoacylations and lower tRNASer(UCN) and tRNATyr levels, aberrant aminoacylation, and lower levels of other tRNAs, including tRNAThr, tRNALys, tRNALeu(UUR), and tRNASer(AGY), than those in the cell lines carrying only the m.7511A>G or p.191Gly>Val mutation. Furthermore, mutant cell lines harboring both m.7511A>G and p.191Gly>Val mutations exhibited greater decreases in the levels of mitochondrial translation, respiration, and mitochondrial ATP and membrane potentials, along with increased production of reactive oxygen species. Our findings provide molecular-level insights into the pathophysiology of maternally transmitted deafness arising from the synergy between tRNASer(UCN) and mitochondrial YARS mutations.
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Affiliation(s)
- Wenlu Fan
- Division of Medical Genetics and Genomics, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Attardi Institute of Biomedicine, School of Life Sciences and Laboratory Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325600, China
| | - Jing Zheng
- Division of Medical Genetics and Genomics, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Wanzhong Kong
- Attardi Institute of Biomedicine, School of Life Sciences and Laboratory Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325600, China
| | - Limei Cui
- Division of Medical Genetics and Genomics, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Maerhaba Aishanjiang
- Division of Medical Genetics and Genomics, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Qiuzi Yi
- Division of Medical Genetics and Genomics, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Min Wang
- Attardi Institute of Biomedicine, School of Life Sciences and Laboratory Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325600, China
| | - Xiaohui Cang
- Division of Medical Genetics and Genomics, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xiaowen Tang
- Attardi Institute of Biomedicine, School of Life Sciences and Laboratory Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325600, China
| | - Ye Chen
- Division of Medical Genetics and Genomics, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jun Qin Mo
- Department of Pathology, Rady Children's Hospital, University of California School of Medicine, San Diego, California 92123
| | - Neal Sondheimer
- Department of Molecular Genetics, University of Toronto School of Medicine and the Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Wanzhong Ge
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Min-Xin Guan
- Division of Medical Genetics and Genomics, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China .,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Key Laboratory of Reproductive Genetics, Ministry of Education of PRC, Zhejiang University, Hangzhou, Zhejiang 310058, China.,Joint Institute of Genetics and Genome Medicine between Zhejiang University and the University of Toronto, Hangzhou, Zhejiang 310058, China
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55
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Genes and Variants Underlying Human Congenital Lactic Acidosis-From Genetics to Personalized Treatment. J Clin Med 2019; 8:jcm8111811. [PMID: 31683770 PMCID: PMC6912785 DOI: 10.3390/jcm8111811] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/22/2019] [Accepted: 10/24/2019] [Indexed: 02/07/2023] Open
Abstract
Congenital lactic acidosis (CLA) is a rare condition in most instances due to a range of inborn errors of metabolism that result in defective mitochondrial function. Even though the implementation of next generation sequencing has been rapid, the diagnosis rate for this highly heterogeneous allelic condition remains low. The present work reports our group’s experience of using a clinical/biochemical analysis system in conjunction with genetic findings that facilitates the taking of timely clinical decisions with minimum need for invasive procedures. The system’s workflow combines different metabolomics datasets and phenotypic information with the results of clinical exome sequencing and/or RNA analysis. The system’s use detected genetic variants in 64% of a cohort of 39 CLA-patients; these variants, 14 of which were novel, were found in 19 different nuclear and two mitochondrial genes. For patients with variants of unknown significance, the genetic analysis was combined with functional genetic and/or bioenergetics analyses in an attempt to detect pathogenicity. Our results warranted subsequent testing of antisense therapy to rescue the abnormal splicing in cultures of fibroblasts from a patient with a defective GFM1 gene. The discussed system facilitates the diagnosis of CLA by avoiding the need to use invasive techniques and increase our knowledge of the causes of this condition.
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56
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Saoura M, Powell CA, Kopajtich R, Alahmad A, AL‐Balool HH, Albash B, Alfadhel M, Alston CL, Bertini E, Bonnen PE, Bratkovic D, Carrozzo R, Donati MA, Di Nottia M, Ghezzi D, Goldstein A, Haan E, Horvath R, Hughes J, Invernizzi F, Lamantea E, Lucas B, Pinnock K, Pujantell M, Rahman S, Rebelo‐Guiomar P, Santra S, Verrigni D, McFarland R, Prokisch H, Taylor RW, Levinger L, Minczuk M. Mutations in ELAC2 associated with hypertrophic cardiomyopathy impair mitochondrial tRNA 3'-end processing. Hum Mutat 2019; 40:1731-1748. [PMID: 31045291 PMCID: PMC6764886 DOI: 10.1002/humu.23777] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 04/09/2019] [Accepted: 04/29/2019] [Indexed: 12/16/2022]
Abstract
Mutations in either the mitochondrial or nuclear genomes are associated with a diverse group of human disorders characterized by impaired mitochondrial respiration. Within this group, an increasing number of mutations have been identified in nuclear genes involved in mitochondrial RNA metabolism, including ELAC2. The ELAC2 gene codes for the mitochondrial RNase Z, responsible for endonucleolytic cleavage of the 3' ends of mitochondrial pre-tRNAs. Here, we report the identification of 16 novel ELAC2 variants in individuals presenting with mitochondrial respiratory chain deficiency, hypertrophic cardiomyopathy (HCM), and lactic acidosis. We provide evidence for the pathogenicity of the novel missense variants by studying the RNase Z activity in an in vitro system. We also modeled the residues affected by a missense mutation in solved RNase Z structures, providing insight into enzyme structure and function. Finally, we show that primary fibroblasts from the affected individuals have elevated levels of unprocessed mitochondrial RNA precursors. Our study thus broadly confirms the correlation of ELAC2 variants with severe infantile-onset forms of HCM and mitochondrial respiratory chain dysfunction. One rare missense variant associated with the occurrence of prostate cancer (p.Arg781His) impairs the mitochondrial RNase Z activity of ELAC2, suggesting a functional link between tumorigenesis and mitochondrial RNA metabolism.
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Affiliation(s)
| | | | - Robert Kopajtich
- Genetics of Mitochondrial Disorders, Institute of Human GeneticsTechnische Universität MünchenMunichGermany
- Genetics of Mitochondrial Disorders, Institute of Human GeneticsHelmholtz Zentrum MünchenNeuherbergGermany
| | - Ahmad Alahmad
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- Kuwait Medical Genetics CenterKuwait CityKuwait
| | | | | | - Majid Alfadhel
- Genetics Division, Department of Pediatrics, King Abdullah International Medical Research CentreKing Saud bin Abdulaziz University for Health SciencesRiyadhSaudi Arabia
| | - Charlotte L. Alston
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Enrico Bertini
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesu' Children's Research Hospital, IRCCSRomeItaly
| | - Penelope E. Bonnen
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Drago Bratkovic
- Metabolic ClinicWomen's and Children's HospitalNorth AdelaideSouth AustraliaAustralia
| | - Rosalba Carrozzo
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesu' Children's Research Hospital, IRCCSRomeItaly
| | | | - Michela Di Nottia
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesu' Children's Research Hospital, IRCCSRomeItaly
| | - Daniele Ghezzi
- Unit of Medical Genetics and NeurogeneticsFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
- Department of Pathophysiology and TransplantationUniversity of MilanMilanItaly
| | - Amy Goldstein
- Mitochondrial Medicine Frontier ProgramChildren's Hospital of PhiladelphiaPhiladelphiaUSA
| | - Eric Haan
- Metabolic ClinicWomen's and Children's HospitalNorth AdelaideSouth AustraliaAustralia
| | - Rita Horvath
- Wellcome Centre for Mitochondrial Research, Institute of Genetic MedicineNewcastle UniversityNewcastle upon TyneUK
| | - Joanne Hughes
- National Centre for Inherited Metabolic DisordersTemple Street Children's University HospitalDublinIreland
| | - Federica Invernizzi
- Unit of Medical Genetics and NeurogeneticsFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Eleonora Lamantea
- Unit of Medical Genetics and NeurogeneticsFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Benjamin Lucas
- York CollegeThe City University of New YorkJamaicaNew York
| | | | | | - Shamima Rahman
- Mitochondrial Research GroupUCL Great Ormond Street Institute of Child HealthLondonUK
| | - Pedro Rebelo‐Guiomar
- MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
- Graduate Program in Areas of Basic and Applied BiologyUniversity of PortoPortoPortugal
| | - Saikat Santra
- Department of Clinical Inherited Metabolic DisordersBirmingham Children's HospitalBirminghamUK
| | - Daniela Verrigni
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesu' Children's Research Hospital, IRCCSRomeItaly
| | - Robert McFarland
- Genetics of Mitochondrial Disorders, Institute of Human GeneticsHelmholtz Zentrum MünchenNeuherbergGermany
| | - Holger Prokisch
- Genetics of Mitochondrial Disorders, Institute of Human GeneticsTechnische Universität MünchenMunichGermany
- Genetics of Mitochondrial Disorders, Institute of Human GeneticsHelmholtz Zentrum MünchenNeuherbergGermany
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Louis Levinger
- York CollegeThe City University of New YorkJamaicaNew York
| | - Michal Minczuk
- MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
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57
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Van Haute L, Lee SY, McCann BJ, Powell CA, Bansal D, Vasiliauskaitė L, Garone C, Shin S, Kim JS, Frye M, Gleeson JG, Miska EA, Rhee HW, Minczuk M. NSUN2 introduces 5-methylcytosines in mammalian mitochondrial tRNAs. Nucleic Acids Res 2019; 47:8720-8733. [PMID: 31276587 PMCID: PMC6822013 DOI: 10.1093/nar/gkz559] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/16/2019] [Accepted: 07/02/2019] [Indexed: 02/02/2023] Open
Abstract
Expression of human mitochondrial DNA is indispensable for proper function of the oxidative phosphorylation machinery. The mitochondrial genome encodes 22 tRNAs, 2 rRNAs and 11 mRNAs and their post-transcriptional modification constitutes one of the key regulatory steps during mitochondrial gene expression. Cytosine-5 methylation (m5C) has been detected in mitochondrial transcriptome, however its biogenesis has not been investigated in details. Mammalian NOP2/Sun RNA Methyltransferase Family Member 2 (NSUN2) has been characterized as an RNA methyltransferase introducing m5C in nuclear-encoded tRNAs, mRNAs and microRNAs and associated with cell proliferation and differentiation, with pathogenic variants in NSUN2 being linked to neurodevelopmental disorders. Here we employ spatially restricted proximity labelling and immunodetection to demonstrate that NSUN2 is imported into the matrix of mammalian mitochondria. Using three genetic models for NSUN2 inactivation-knockout mice, patient-derived fibroblasts and CRISPR/Cas9 knockout in human cells-we show that NSUN2 is necessary for the generation of m5C at positions 48, 49 and 50 of several mammalian mitochondrial tRNAs. Finally, we show that inactivation of NSUN2 does not have a profound effect on mitochondrial tRNA stability and oxidative phosphorylation in differentiated cells. We discuss the importance of the newly discovered function of NSUN2 in the context of human disease.
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Affiliation(s)
- Lindsey Van Haute
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Song-Yi Lee
- Department of Chemistry, Seoul National University, Gwanak-ro 1, Seoul 08826, South Korea
| | - Beverly J McCann
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Christopher A Powell
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Dhiru Bansal
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Lina Vasiliauskaitė
- STORM Therapeutics Limited, Moneta Building, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Caterina Garone
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Sanghee Shin
- Center for RNA Research, Institute of Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute of Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Michaela Frye
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
- German Cancer Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Joseph G Gleeson
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA 92123, USA
| | - Eric A Miska
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Gwanak-ro 1, Seoul 08826, South Korea
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
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58
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Wang J, Xu J, Xia M, Yang Y, Shen Z, Chen G, Dong R, Zheng S. Correlation between hepatic oxidative damage and clinical severity and mitochondrial gene sequencing results in biliary atresia. Hepatol Res 2019; 49:695-704. [PMID: 30811072 DOI: 10.1111/hepr.13324] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 01/30/2019] [Accepted: 02/21/2019] [Indexed: 12/12/2022]
Abstract
AIM To assess the level of hepatic oxidative damage and its correlation with clinical severity in biliary atresia (BA), and to understand BA mitochondrial gene sequencing. METHODS Forty-eight BA patients and 28 control subjects (20 hepatoblastoma and 8 cholestasis patients) were enrolled. Hepatic oxidative damage was assessed by the expression of oxidation and antioxidant genes, and the correlation between oxidative damage and BA incidence, liver inflammation, and fibrosis was evaluated. Moreover, 8-hydroxyguanine (8-OHdG), mitochondrial DNA (mtDNA) copy number, and mitochondrial gene sequences were determined to evaluate oxidative mtDNA damage in BA. RESULTS The expression of oxidation gene cytochrome b-245 beta chain (CYBB) in BA was significantly increased and patients with a higher CYBB expression had the higher risk of BA incidence, liver inflammation, and cirrhosis. However, the expression of antioxidant genes was significantly decreased, and glutathione S-transferase alpha 1 (GSTA1) negatively correlated with BA incidence and cirrhosis. When GSTA1 mRNA expression was <0.5487, the sensitivity was 80.85% and the specificity was 80% for BA diagnosis. Moreover, 8-OHdG was increased, whereas mtDNA copy number was significantly decreased in BA. Using mitochondrial gene sequencing, 10 mutation sites were identified, and one family showed a maternal inheritance in genetic loci 15 326. CONCLUSIONS In BA, oxidative damage positively correlated with BA incidence, liver inflammation, and cirrhosis. GSTA1 could be a novel diagnostic indicator. Genetic loci 15 326 could be a maternal genetic mutation site. Taken together, antioxidation therapy after Kasai surgery might have great potential in relieving liver inflammation and fibrosis in BA patients.
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Affiliation(s)
- Junfeng Wang
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Jiayin Xu
- Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Mingyang Xia
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Yifan Yang
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Zhen Shen
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Gong Chen
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Rui Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Shan Zheng
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
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59
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Steiner RE, Ibba M. Regulation of tRNA-dependent translational quality control. IUBMB Life 2019; 71:1150-1157. [PMID: 31135095 DOI: 10.1002/iub.2080] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/01/2019] [Accepted: 05/14/2019] [Indexed: 02/06/2023]
Abstract
Translation is the most error-prone process in protein synthesis; however, it is important that accuracy is maintained because erroneous translation has been shown to affect all domains of life. Translational quality control is maintained by both proteins and RNA through intricate processes. The aminoacyl-tRNA synthetases help maintain high levels of translational accuracy through the esterification of tRNA and proofreading mechanisms. tRNA is often recognized by an aminoacyl-tRNA synthetase in a sequence and structurally dependent manner, sometimes involving modified nucleotides. Additionally, some proofreading mechanisms of aminoacyl-tRNA synthetases require tRNA elements for hydrolysis of a noncognate aminoacyl-tRNA. Finally, tRNA is also important for proper decoding of the mRNA message by codon and anticodon pairing. Here, recent developments regarding the importance of tRNA in maintenance of translational accuracy are reviewed. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1150-1157, 2019.
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Affiliation(s)
- Rebecca E Steiner
- The Ohio State University Biochemistry Program, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Michael Ibba
- The Ohio State University Biochemistry Program, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Microbiology, The Ohio State University, Columbus, OH, USA
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60
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Transcription, Processing, and Decay of Mitochondrial RNA in Health and Disease. Int J Mol Sci 2019; 20:ijms20092221. [PMID: 31064115 PMCID: PMC6540609 DOI: 10.3390/ijms20092221] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/01/2019] [Accepted: 05/03/2019] [Indexed: 12/16/2022] Open
Abstract
Although the large majority of mitochondrial proteins are nuclear encoded, for their correct functioning mitochondria require the expression of 13 proteins, two rRNA, and 22 tRNA codified by mitochondrial DNA (mtDNA). Once transcribed, mitochondrial RNA (mtRNA) is processed, mito-ribosomes are assembled, and mtDNA-encoded proteins belonging to the respiratory chain are synthesized. These processes require the coordinated spatio-temporal action of several enzymes, and many different factors are involved in the regulation and control of protein synthesis and in the stability and turnover of mitochondrial RNA. In this review, we describe the essential steps of mitochondrial RNA synthesis, maturation, and degradation, the factors controlling these processes, and how the alteration of these processes is associated with human pathologies.
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61
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Soler-Alfonso C, Pillai N, Cooney E, Mysore KR, Boyer S, Scaglia F. L-Cysteine supplementation prevents liver transplantation in a patient with TRMU deficiency. Mol Genet Metab Rep 2019; 19:100453. [PMID: 30740308 PMCID: PMC6355510 DOI: 10.1016/j.ymgmr.2019.100453] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 12/13/2022] Open
Abstract
Early recognition of rare mitochondrial respiratory chain defects has become readily available with the routine use of whole exome sequencing. Patients with oxidative phosphorylation defects present with a heterogenous phenotype, often rapidly progressive, and lethal. Clinicians aim for prompt identification of the specific molecular defect to provide timely management, decrease morbidity, and potentially improve survival rates. More recently, bi-allelic pathogenic variants in the TRMU gene responsible for encoding the mitochondrial tRNA-specific 2-thiouridylase were found in a syndrome characterized by infantile hepatopathy due to a mitochondrial translation defect (OMIM# 613070). This nuclear encoded enzyme catalyzes the addition of a sulfur-containing thiol group to the wobble position of mitochondrial specific tRNAs. TRMU deficiency is characterized by a combined respiratory chain deficiency without associated mitochondrial DNA depletion. This mitochondrial tRNA-modifying enzyme requires sulfur for its activity. Previous cellular models have suggested supplementation with cysteine, one of the sulfur containing amino acids, may play a role in increasing thiouridylation levels of mt-tRNAs by increasing sulfur availability for TRMU activity. Cysteine is considered a conditional essential amino acid due to limited availability in infants caused by immature cystathionine gamma-lyase (cystathionase) enzyme activity. The potential benefit of L-cysteine supplementation in TRMU deficiency has been previously proposed to ameliorate the severity and insidious course of the disease. Here we report the clinical, biochemical, and genetic findings of two siblings presenting with hepatopathy associated with hyperlactatemia due to bi-allelic pathogenic variants in TRMU. One patient died due to related complications. The other case was diagnosed prenatally allowing early implementation of L-cysteine supplementation, recovery of liver function, and avoidance of liver transplantation.
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Affiliation(s)
- Claudia Soler-Alfonso
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States.,Texas Children's Hospital, Houston, TX, United States
| | - Nishita Pillai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States.,Texas Children's Hospital, Houston, TX, United States
| | - Erin Cooney
- University of Texas Medical Branch, Galveston, TX, United States
| | - Krupa R Mysore
- Department of Pediatric Gastroenterology, Baylor College of Medicine, Houston, TX, United States
| | - Suzanne Boyer
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States.,Texas Children's Hospital, Houston, TX, United States
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States.,Texas Children's Hospital, Houston, TX, United States.,Joint BCM-CUHK Center of Medical Genetics, Prince of Wales Hospital, Hong Kong SAR
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62
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Rebelo-Guiomar P, Powell CA, Van Haute L, Minczuk M. The mammalian mitochondrial epitranscriptome. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:429-446. [PMID: 30529456 PMCID: PMC6414753 DOI: 10.1016/j.bbagrm.2018.11.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/16/2018] [Accepted: 11/23/2018] [Indexed: 01/08/2023]
Abstract
Correct expression of the mitochondrially-encoded genes is critical for the production of the components of the oxidative phosphorylation machinery. Post-transcriptional modifications of mitochondrial transcripts have been emerging as an important regulatory feature of mitochondrial gene expression. Here we review the current knowledge on how the mammalian mitochondrial epitranscriptome participates in regulating mitochondrial homeostasis. In particular, we focus on the latest breakthroughs made towards understanding the roles of the modified nucleotides in mitochondrially-encoded ribosomal and transfer RNAs, the enzymes responsible for introducing these modifications and on recent transcriptome-wide studies reporting modifications to mitochondrial messenger RNAs. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Matthias Soller and Dr. Rupert Fray. Human mtDNA encodes 13 proteins and all the RNAs necessary for their expression Post-transcriptional modifications of RNA, the epitranscriptome, play a regulatory role in mitochondrial gene expression Several enzymes involved in the shaping of the mitochondrial epitranscriptome have recently been characterised. Our understanding of the extent and nature of mtRNA modifications is rapidly expanding. Recent transcriptome-wide studies suggest modifications in mitochondrial mRNAs
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Affiliation(s)
- Pedro Rebelo-Guiomar
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK; Graduate Program in Areas of Basic and Applied Biology (GABBA), University of Porto, Porto, Portugal
| | | | - Lindsey Van Haute
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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63
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McCormick EM, Zolkipli-Cunningham Z, Falk MJ. Mitochondrial disease genetics update: recent insights into the molecular diagnosis and expanding phenotype of primary mitochondrial disease. Curr Opin Pediatr 2018; 30:714-724. [PMID: 30199403 PMCID: PMC6467265 DOI: 10.1097/mop.0000000000000686] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
PURPOSE OF REVIEW Primary mitochondrial disease (PMD) is a genetically and phenotypically diverse group of inherited energy deficiency disorders caused by impaired mitochondrial oxidative phosphorylation (OXPHOS) capacity. Mutations in more than 350 genes in both mitochondrial and nuclear genomes are now recognized to cause primary mitochondrial disease following every inheritance pattern. Next-generation sequencing technologies have dramatically accelerated mitochondrial disease gene discovery and diagnostic yield. Here, we provide an up-to-date review of recently identified, novel mitochondrial disease genes and/or pathogenic variants that directly impair mitochondrial structure, dynamics, and/or function. RECENT FINDINGS A review of PubMed publications was performed from the past 12 months that identified 16 new PMD genes and/or pathogenic variants, and recognition of expanded phenotypes for a wide variety of mitochondrial disease genes. SUMMARY Broad-based exome sequencing has become the standard first-line diagnostic approach for PMD. This has facilitated more rapid and accurate disease identification, and greatly expanded understanding of the wide spectrum of potential clinical phenotypes. A comprehensive dual-genome sequencing approach to PMD diagnosis continues to improve diagnostic yield, advance understanding of mitochondrial physiology, and provide strong potential to develop precision therapeutics targeted to diverse aspects of mitochondrial disease pathophysiology.
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Affiliation(s)
- Elizabeth M. McCormick
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, PA 19104
| | - Zarazuela Zolkipli-Cunningham
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, PA 19104
| | - Marni J. Falk
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, PA 19104
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104
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64
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Mitochondrial transcription and translation: overview. Essays Biochem 2018; 62:309-320. [PMID: 30030363 PMCID: PMC6056719 DOI: 10.1042/ebc20170102] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/14/2018] [Accepted: 05/14/2018] [Indexed: 12/13/2022]
Abstract
Mitochondria are the major source of ATP in the cell. Five multi-subunit complexes in the inner membrane of the organelle are involved in the oxidative phosphorylation required for ATP production. Thirteen subunits of these complexes are encoded by the mitochondrial genome often referred to as mtDNA. For this reason, the expression of mtDNA is vital for the assembly and functioning of the oxidative phosphorylation complexes. Defects of the mechanisms regulating mtDNA gene expression have been associated with deficiencies in assembly of these complexes, resulting in mitochondrial diseases. Recently, numerous factors involved in these processes have been identified and characterized leading to a deeper understanding of the mechanisms that underlie mitochondrial diseases.
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