1
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An J, Nam CH, Kim R, Lee Y, Won H, Park S, Lee WH, Park H, Yoon CJ, An Y, Kim JH, Jun JK, Bae JM, Shin EC, Kim B, Cha YJ, Kwon HW, Oh JW, Park JY, Kim MJ, Ju YS. Mitochondrial DNA mosaicism in normal human somatic cells. Nat Genet 2024; 56:1665-1677. [PMID: 39039280 PMCID: PMC11319206 DOI: 10.1038/s41588-024-01838-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 06/21/2024] [Indexed: 07/24/2024]
Abstract
Somatic cells accumulate genomic alterations with age; however, our understanding of mitochondrial DNA (mtDNA) mosaicism remains limited. Here we investigated the genomes of 2,096 clones derived from three cell types across 31 donors, identifying 6,451 mtDNA variants with heteroplasmy levels of ≳0.3%. While the majority of these variants were unique to individual clones, suggesting stochastic acquisition with age, 409 variants (6%) were shared across multiple embryonic lineages, indicating their origin from heteroplasmy in fertilized eggs. The mutational spectrum exhibited replication-strand bias, implicating mtDNA replication as a major mutational process. We evaluated the mtDNA mutation rate (5.0 × 10-8 per base pair) and a turnover frequency of 10-20 per year, which are fundamental components shaping the landscape of mtDNA mosaicism over a lifetime. The expansion of mtDNA-truncating mutations toward homoplasmy was substantially suppressed. Our findings provide comprehensive insights into the origins, dynamics and functional consequences of mtDNA mosaicism in human somatic cells.
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Affiliation(s)
- Jisong An
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Chang Hyun Nam
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Ryul Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Inocras Inc, Daejeon, Republic of Korea
| | - Yunah Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Hyein Won
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Seongyeol Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Inocras Inc, Daejeon, Republic of Korea
| | - Won Hee Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Hansol Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Inocras Inc, Daejeon, Republic of Korea
| | - Christopher J Yoon
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Yohan An
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jie-Hyun Kim
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Kwan Jun
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jeong Mo Bae
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Eui-Cheol Shin
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Bun Kim
- Center for Colorectal Cancer, Research Institute and Hospital, National Cancer Center, Goyang, Republic of Korea
| | - Yong Jun Cha
- Center for Colorectal Cancer, Research Institute and Hospital, National Cancer Center, Goyang, Republic of Korea
| | - Hyun Woo Kwon
- Department of Nuclear Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Ji Won Oh
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jee Yoon Park
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Min Jung Kim
- Department of Surgery, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
- Inocras Inc, Daejeon, Republic of Korea.
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2
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Wang Y, Yang JS, Zhao M, Chen JQ, Xie HX, Yu HY, Liu NH, Yi ZJ, Liang HL, Xing L, Jiang HL. Mitochondrial endogenous substance transport-inspired nanomaterials for mitochondria-targeted gene delivery. Adv Drug Deliv Rev 2024; 211:115355. [PMID: 38849004 DOI: 10.1016/j.addr.2024.115355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/16/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
Mitochondrial genome (mtDNA) independent of nuclear gene is a set of double-stranded circular DNA that encodes 13 proteins, 2 ribosomal RNAs and 22 mitochondrial transfer RNAs, all of which play vital roles in functions as well as behaviors of mitochondria. Mutations in mtDNA result in various mitochondrial disorders without available cures. However, the manipulation of mtDNA via the mitochondria-targeted gene delivery faces formidable barriers, particularly owing to the mitochondrial double membrane. Given the fact that there are various transport channels on the mitochondrial membrane used to transfer a variety of endogenous substances to maintain the normal functions of mitochondria, mitochondrial endogenous substance transport-inspired nanomaterials have been proposed for mitochondria-targeted gene delivery. In this review, we summarize mitochondria-targeted gene delivery systems based on different mitochondrial endogenous substance transport pathways. These are categorized into mitochondrial steroid hormones import pathways-inspired nanomaterials, protein import pathways-inspired nanomaterials and other mitochondria-targeted gene delivery nanomaterials. We also review the applications and challenges involved in current mitochondrial gene editing systems. This review delves into the approaches of mitochondria-targeted gene delivery, providing details on the design of mitochondria-targeted delivery systems and the limitations regarding the various technologies. Despite the progress in this field is currently slow, the ongoing exploration of mitochondrial endogenous substance transport and mitochondrial biological phenomena may act as a crucial breakthrough in the targeted delivery of gene into mitochondria and even the manipulation of mtDNA.
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Affiliation(s)
- Yi Wang
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Jing-Song Yang
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Min Zhao
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Jia-Qi Chen
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Hai-Xin Xie
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Hao-Yuan Yu
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Na-Hui Liu
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Zi-Juan Yi
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Hui-Lin Liang
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Xing
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Hu-Lin Jiang
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China; College of Pharmacy, Yanbian University, Yanji 133002, China.
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3
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Yu Y, Martins LM. Mitochondrial One-Carbon Metabolism and Alzheimer's Disease. Int J Mol Sci 2024; 25:6302. [PMID: 38928008 PMCID: PMC11203557 DOI: 10.3390/ijms25126302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 06/28/2024] Open
Abstract
Mitochondrial one-carbon metabolism provides carbon units to several pathways, including nucleic acid synthesis, mitochondrial metabolism, amino acid metabolism, and methylation reactions. Late-onset Alzheimer's disease is the most common age-related neurodegenerative disease, characterised by impaired energy metabolism, and is potentially linked to mitochondrial bioenergetics. Here, we discuss the intersection between the molecular pathways linked to both mitochondrial one-carbon metabolism and Alzheimer's disease. We propose that enhancing one-carbon metabolism could promote the metabolic processes that help brain cells cope with Alzheimer's disease-related injuries. We also highlight potential therapeutic avenues to leverage one-carbon metabolism to delay Alzheimer's disease pathology.
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Affiliation(s)
- Yizhou Yu
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
| | - L. Miguel Martins
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
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4
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Bernardino Gomes TM, Vincent AE, Menger KE, Stewart JB, Nicholls TJ. Mechanisms and pathologies of human mitochondrial DNA replication and deletion formation. Biochem J 2024; 481:683-715. [PMID: 38804971 PMCID: PMC11346376 DOI: 10.1042/bcj20230262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
Human mitochondria possess a multi-copy circular genome, mitochondrial DNA (mtDNA), that is essential for cellular energy metabolism. The number of copies of mtDNA per cell, and their integrity, are maintained by nuclear-encoded mtDNA replication and repair machineries. Aberrant mtDNA replication and mtDNA breakage are believed to cause deletions within mtDNA. The genomic location and breakpoint sequences of these deletions show similar patterns across various inherited and acquired diseases, and are also observed during normal ageing, suggesting a common mechanism of deletion formation. However, an ongoing debate over the mechanism by which mtDNA replicates has made it difficult to develop clear and testable models for how mtDNA rearrangements arise and propagate at a molecular and cellular level. These deletions may impair energy metabolism if present in a high proportion of the mtDNA copies within the cell, and can be seen in primary mitochondrial diseases, either in sporadic cases or caused by autosomal variants in nuclear-encoded mtDNA maintenance genes. These mitochondrial diseases have diverse genetic causes and multiple modes of inheritance, and show notoriously broad clinical heterogeneity with complex tissue specificities, which further makes establishing genotype-phenotype relationships challenging. In this review, we aim to cover our current understanding of how the human mitochondrial genome is replicated, the mechanisms by which mtDNA replication and repair can lead to mtDNA instability in the form of large-scale rearrangements, how rearranged mtDNAs subsequently accumulate within cells, and the pathological consequences when this occurs.
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Affiliation(s)
- Tiago M. Bernardino Gomes
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- NHS England Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4HH, U.K
| | - Amy E. Vincent
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Katja E. Menger
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - James B. Stewart
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Thomas J. Nicholls
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
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5
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Saha LK, Pommier Y. TOP3A coupling with replication forks and repair of TOP3A cleavage complexes. Cell Cycle 2024; 23:115-130. [PMID: 38341866 PMCID: PMC11037291 DOI: 10.1080/15384101.2024.2314440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/08/2024] [Indexed: 02/13/2024] Open
Abstract
Humans have two Type IA topoisomerases, topoisomerase IIIα (TOP3A) and topoisomerase IIIβ (TOP3B). In this review, we focus on the role of human TOP3A in DNA replication and highlight the recent progress made in understanding TOP3A in the context of replication. Like other topoisomerases, TOP3A acts by a reversible mechanism of cleavage and rejoining of DNA strands allowing changes in DNA topology. By cleaving and resealing single-stranded DNA, it generates TOP3A-linked single-strand breaks as TOP3A cleavage complexes (TOP3Accs) with a TOP3A molecule covalently bound to the 5´-end of the break. TOP3A is critical for both mitochondrial and for nuclear DNA replication. Here, we discuss the formation and repair of irreversible TOP3Accs, as their presence compromises genome integrity as they form TOP3A DNA-protein crosslinks (TOP3A-DPCs) associated with DNA breaks. We discuss the redundant pathways that repair TOP3A-DPCs, and how their defects are a source of DNA damage leading to neurological diseases and mitochondrial disorders.
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Affiliation(s)
- Liton Kumar Saha
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
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6
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Sallmyr A, Bhandari SK, Naila T, Tomkinson AE. Mammalian DNA ligases; roles in maintaining genome integrity. J Mol Biol 2024; 436:168276. [PMID: 37714297 PMCID: PMC10843057 DOI: 10.1016/j.jmb.2023.168276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
The joining of breaks in the DNA phosphodiester backbone is essential for genome integrity. Breaks are generated during normal processes such as DNA replication, cytosine demethylation during differentiation, gene rearrangement in the immune system and germ cell development. In addition, they are generated either directly by a DNA damaging agent or indirectly due to damage excision during repair. Breaks are joined by a DNA ligase that catalyzes phosphodiester bond formation at DNA nicks with 3' hydroxyl and 5' phosphate termini. Three human genes encode ATP-dependent DNA ligases. These enzymes have a conserved catalytic core consisting of three subdomains that encircle nicked duplex DNA during ligation. The DNA ligases are targeted to different nuclear DNA transactions by specific protein-protein interactions. Both DNA ligase IIIα and DNA ligase IV form stable complexes with DNA repair proteins, XRCC1 and XRCC4, respectively. There is functional redundancy between DNA ligase I and DNA ligase IIIα in DNA replication, excision repair and single-strand break repair. Although DNA ligase IV is a core component of the major double-strand break repair pathway, non-homologous end joining, the other enzymes participate in minor, alternative double-strand break repair pathways. In contrast to the nucleus, only DNA ligase IIIα is present in mitochondria and is essential for maintaining the mitochondrial genome. Human immunodeficiency syndromes caused by mutations in either LIG1 or LIG4 have been described. Preclinical studies with DNA ligase inhibitors have identified potentially targetable abnormalities in cancer cells and evidence that DNA ligases are potential targets for cancer therapy.
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Affiliation(s)
- Annahita Sallmyr
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States
| | - Seema Khattri Bhandari
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States
| | - Tasmin Naila
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States
| | - Alan E Tomkinson
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States.
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7
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Xu D, Huang Y, Luo L, Tang L, Lu M, Cao H, Wang F, Diao Y, Lyubchenko L, Kapranov P. Genome-Wide Profiling of Endogenous Single-Stranded DNA Using the SSiNGLe-P1 Method. Int J Mol Sci 2023; 24:12062. [PMID: 37569439 PMCID: PMC10418711 DOI: 10.3390/ijms241512062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Endogenous single-stranded DNA (essDNA) can form in a mammalian genome as the result of a variety of molecular processes and can both play important roles inside the cell as well as have detrimental consequences to genome integrity, much of which remains to be fully understood. Here, we established the SSiNGLe-P1 approach based on limited digestion by P1 endonuclease for high-throughput genome-wide identification of essDNA regions. We applied this method to profile essDNA in both human mitochondrial and nuclear genomes. In the mitochondrial genome, the profiles of essDNA provide new evidence to support the strand-displacement model of mitochondrial DNA replication. In the nuclear genome, essDNA regions were found to be enriched in certain types of functional genomic elements, particularly, the origins of DNA replication, R-loops, and to a lesser degree, in promoters. Furthermore, interestingly, many of the essDNA regions identified by SSiNGLe-P1 have not been annotated and thus could represent yet unknown functional elements.
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Affiliation(s)
- Dongyang Xu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Yu Huang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Lingcong Luo
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Lu Tang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Meng Lu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Huifen Cao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Fang Wang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Yong Diao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
| | - Liudmila Lyubchenko
- National Medical Research Center for Radiology, Ministry of Health of Russia, 125284 Moscow, Russia
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China; (D.X.)
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
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8
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Xu D, Luo L, Huang Y, Lu M, Tang L, Diao Y, Kapranov P. Dynamic Patterns of Mammalian Mitochondrial DNA Replication Uncovered Using SSiNGLe-5'ES. Int J Mol Sci 2023; 24:ijms24119711. [PMID: 37298662 DOI: 10.3390/ijms24119711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
The proper replication of mitochondrial DNA is key to the maintenance of this crucial organelle. Multiple studies aimed at understanding the mechanisms of replication of the mitochondrial genome have been conducted in the past several decades; however, while highly informative, they were conducted using relatively low-sensitivity techniques. Here, we established a high-throughput approach based on next-generation sequencing to identify replication start sites with nucleotide-level resolution and applied it to the genome of mitochondria from different human and mouse cell types. We found complex and highly reproducible patterns of mitochondrial initiation sites, both previously annotated and newly discovered in this work, that showed differences among different cell types and species. These results suggest that the patterns of the replication initiation sites are dynamic and might reflect, in some yet unknown ways, the complexities of mitochondrial and cellular physiology. Overall, this work suggests that much remains unknown about the details of mitochondrial DNA replication in different biological states, and the method established here opens up a new avenue in the study of the replication of mitochondrial and potentially other genomes.
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Affiliation(s)
- Dongyang Xu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
| | - Lingcong Luo
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
| | - Yu Huang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
| | - Meng Lu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
| | - Lu Tang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
| | - Yong Diao
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
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9
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Bi C, Wang L, Fan Y, Yuan B, Alsolami S, Zhang Y, Zhang PY, Huang Y, Yu Y, Izpisua Belmonte J, Li M. Quantitative haplotype-resolved analysis of mitochondrial DNA heteroplasmy in Human single oocytes, blastoids, and pluripotent stem cells. Nucleic Acids Res 2023; 51:3793-3805. [PMID: 37014011 PMCID: PMC10164563 DOI: 10.1093/nar/gkad209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 04/05/2023] Open
Abstract
Maternal mitochondria are the sole source of mtDNA for every cell of the offspring. Heteroplasmic mtDNA mutations inherited from the oocyte are a common cause of metabolic diseases and associated with late-onset diseases. However, the origin and dynamics of mtDNA heteroplasmy remain unclear. We used our individual Mitochondrial Genome sequencing (iMiGseq) technology to study mtDNA heterogeneity, quantitate single nucleotide variants (SNVs) and large structural variants (SVs), track heteroplasmy dynamics, and analyze genetic linkage between variants at the individual mtDNA molecule level in single oocytes and human blastoids. Our study presented the first single-mtDNA analysis of the comprehensive heteroplasmy landscape in single human oocytes. Unappreciated levels of rare heteroplasmic variants well below the detection limit of conventional methods were identified in healthy human oocytes, of which many are reported to be deleterious and associated with mitochondrial disease and cancer. Quantitative genetic linkage analysis revealed dramatic shifts of variant frequency and clonal expansions of large SVs during oogenesis in single-donor oocytes. iMiGseq of a single human blastoid suggested stable heteroplasmy levels during early lineage differentiation of naïve pluripotent stem cells. Therefore, our data provided new insights of mtDNA genetics and laid a foundation for understanding mtDNA heteroplasmy at early stages of life.
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Affiliation(s)
- Chongwei Bi
- Bioscience program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Lin Wang
- Bioscience program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Yong Fan
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, 510150 Guangzhou, China
| | - Baolei Yuan
- Bioscience program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Samhan Alsolami
- Bioscience program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Yingzi Zhang
- Bioscience program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Pu-Yao Zhang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing100191, China
| | - Yanyi Huang
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, College of Chemistry, College of Engineering, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, China
| | - Yang Yu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing100191, China
- Stem Cell Research Center, Peking University Third Hospital, Beijing100191, China
| | - Juan Carlos Izpisua Belmonte
- Bioscience program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- Altos Labs, Inc., San Diego, CA92121, USA
| | - Mo Li
- Bioscience program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- Bioengineering program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Guangzhou, Saudi Arabia
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10
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Loureiro D, Tout I, Narguet S, Bed CM, Roinard M, Sleiman A, Boyer N, Pons‐Kerjean N, Castelnau C, Giuly N, Tonui D, Soumelis V, El Benna J, Soussan P, Moreau R, Paradis V, Mansouri A, Asselah T. Mitochondrial stress in advanced fibrosis and cirrhosis associated with chronic hepatitis B, chronic hepatitis C, or nonalcoholic steatohepatitis. Hepatology 2023; 77:1348-1365. [PMID: 35971873 PMCID: PMC10026976 DOI: 10.1002/hep.32731] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 07/20/2022] [Accepted: 08/08/2022] [Indexed: 12/08/2022]
Abstract
BACKGROUND AND AIMS Hepatitis B virus (HBV) infection causes oxidative stress (OS) and alters mitochondria in experimental models. Our goal was to investigate whether HBV might alter liver mitochondria also in humans, and the resulting mitochondrial stress might account for the progression of fibrosis in chronic hepatitis B (CHB). APPROACH AND RESULTS The study included 146 treatment-naïve CHB mono-infected patients. Patients with CHB and advanced fibrosis (AF) or cirrhosis (F3-F4) were compared to patients with no/mild-moderate fibrosis (F0-F2). Patients with CHB were further compared to patients with chronic hepatitis C (CHC; n = 33), nonalcoholic steatohepatatis (NASH; n = 12), and healthy controls ( n = 24). We detected oxidative damage to mitochondrial DNA (mtDNA), including mtDNA strand beaks, and identified multiple mtDNA deletions in patients with F3-F4 as compared to patients with F0-F2. Alterations in mitochondrial function, mitochondrial unfolded protein response, biogenesis, mitophagy, and liver inflammation were observed in patients with AF or cirrhosis associated with CHB, CHC, and NASH. In vitro , significant increases of the mitochondrial formation of superoxide and peroxynitrite as well as mtDNA damage, nitration of the mitochondrial respiratory chain complexes, and impairment of complex I occurred in HepG2 cells replicating HBV or transiently expressing hepatitits B virus X protein. mtDNA damage and complex I impairment were prevented with the superoxide-scavenging Mito-Tempo or with inducible nitric oxide synthase (iNOS)-specific inhibitor 1400 W. CONCLUSIONS Our results emphasized the importance of mitochondrial OS, mtDNA damage, and associated alterations in mitochondrial function and dynamics in AF or cirrhosis in CHB and NASH. Mitochondria might be a target in drug development to stop fibrosis progression.
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Affiliation(s)
- Dimitri Loureiro
- Université Paris Cité, Centre de Recherche sur l'Inflammation, INSERM U1149, CNRS ERL8252, Paris, France
- Assistance Publique‐Hôpitaux de Paris (AP‐HP), Department of Hepatology, Hôpital Beaujon, Clichy, France
| | - Issam Tout
- Université Paris Cité, Centre de Recherche sur l'Inflammation, INSERM U1149, CNRS ERL8252, Paris, France
- Assistance Publique‐Hôpitaux de Paris (AP‐HP), Department of Hepatology, Hôpital Beaujon, Clichy, France
| | - Stéphanie Narguet
- Université Paris Cité, Centre de Recherche sur l'Inflammation, INSERM U1149, CNRS ERL8252, Paris, France
- Assistance Publique‐Hôpitaux de Paris (AP‐HP), Department of Hepatology, Hôpital Beaujon, Clichy, France
| | - Cheikh Mohamed Bed
- Université Paris Cité, Centre de Recherche sur l'Inflammation, INSERM U1149, CNRS ERL8252, Paris, France
- Assistance Publique‐Hôpitaux de Paris (AP‐HP), Department of Hepatology, Hôpital Beaujon, Clichy, France
| | - Morgane Roinard
- Université Paris Cité, Centre de Recherche sur l'Inflammation, INSERM U1149, CNRS ERL8252, Paris, France
- Assistance Publique‐Hôpitaux de Paris (AP‐HP), Department of Hepatology, Hôpital Beaujon, Clichy, France
| | - Ahmad Sleiman
- Université Paris Cité, Centre de Recherche sur l'Inflammation, INSERM U1149, CNRS ERL8252, Paris, France
- Assistance Publique‐Hôpitaux de Paris (AP‐HP), Department of Hepatology, Hôpital Beaujon, Clichy, France
| | - Nathalie Boyer
- Université Paris Cité, Centre de Recherche sur l'Inflammation, INSERM U1149, CNRS ERL8252, Paris, France
- Assistance Publique‐Hôpitaux de Paris (AP‐HP), Department of Hepatology, Hôpital Beaujon, Clichy, France
| | - Nathalie Pons‐Kerjean
- Assistance Publique‐Hôpitaux de Paris (AP‐HP), Department of Pharmacy, Hôpital Beaujon, Clichy, France
| | - Corinne Castelnau
- Université Paris Cité, Centre de Recherche sur l'Inflammation, INSERM U1149, CNRS ERL8252, Paris, France
- Assistance Publique‐Hôpitaux de Paris (AP‐HP), Department of Hepatology, Hôpital Beaujon, Clichy, France
| | - Nathalie Giuly
- Université Paris Cité, Centre de Recherche sur l'Inflammation, INSERM U1149, CNRS ERL8252, Paris, France
- Assistance Publique‐Hôpitaux de Paris (AP‐HP), Department of Hepatology, Hôpital Beaujon, Clichy, France
| | - Dorothy Tonui
- Université Paris Cité, Centre de Recherche sur l'Inflammation, INSERM U1149, CNRS ERL8252, Paris, France
- Assistance Publique‐Hôpitaux de Paris (AP‐HP), Department of Hepatology, Hôpital Beaujon, Clichy, France
| | - Vassili Soumelis
- Université de Paris Cité, INSERM U976 HIPI Unit, Paris, France
- Assistance Publique‐Hôpitaux de Paris (AP‐HP), Laboratoire d'Immunologie et Histocompatibilité, Hôpital Saint‐Louis, Paris, France
| | - Jamel El Benna
- Université Paris Cité, Centre de Recherche sur l'Inflammation, INSERM U1149, CNRS ERL8252, Paris, France
| | | | - Richard Moreau
- Université Paris Cité, Centre de Recherche sur l'Inflammation, INSERM U1149, CNRS ERL8252, Paris, France
- Assistance Publique‐Hôpitaux de Paris (AP‐HP), Department of Hepatology, Hôpital Beaujon, Clichy, France
| | - Valérie Paradis
- Université Paris Cité, Centre de Recherche sur l'Inflammation, INSERM U1149, CNRS ERL8252, Paris, France
- Assistance Publique‐Hôpitaux de Paris (AP‐HP), Department of Hepatology, Hôpital Beaujon, Clichy, France
| | - Abdellah Mansouri
- Université Paris Cité, Centre de Recherche sur l'Inflammation, INSERM U1149, CNRS ERL8252, Paris, France
- Assistance Publique‐Hôpitaux de Paris (AP‐HP), Department of Hepatology, Hôpital Beaujon, Clichy, France
| | - Tarik Asselah
- Université Paris Cité, Centre de Recherche sur l'Inflammation, INSERM U1149, CNRS ERL8252, Paris, France
- Assistance Publique‐Hôpitaux de Paris (AP‐HP), Department of Hepatology, Hôpital Beaujon, Clichy, France
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11
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The N-terminal domain of human mitochondrial helicase Twinkle has DNA-binding activity crucial for supporting processive DNA synthesis by polymerase γ. J Biol Chem 2022; 299:102797. [PMID: 36528058 PMCID: PMC9860392 DOI: 10.1016/j.jbc.2022.102797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 12/15/2022] Open
Abstract
Twinkle is the ring-shaped replicative helicase within the human mitochondria with high homology to bacteriophage T7 gp4 helicase-primase. Unlike many orthologs of Twinkle, the N-terminal domain (NTD) of human Twinkle has lost its primase activity through evolutionarily acquired mutations. The NTD has no demonstrated activity thus far; its role has remained unclear. Here, we biochemically characterize the isolated NTD and C-terminal domain (CTD) with linker to decipher their contributions to full-length Twinkle activities. This novel CTD construct hydrolyzes ATP, has weak DNA unwinding activity, and assists DNA polymerase γ (Polγ)-catalyzed strand-displacement synthesis on short replication forks. However, CTD fails to promote multikilobase length product formation by Polγ in rolling-circle DNA synthesis. Thus, CTD retains all the motor functions but struggles to implement them for processive translocation. We show that NTD has DNA-binding activity, and its presence stabilizes Twinkle oligomerization. CTD oligomerizes on its own, but the loss of NTD results in heterogeneously sized oligomeric species. The CTD also exhibits weaker and salt-sensitive DNA binding compared with full-length Twinkle. Based on these results, we propose that NTD directly contributes to DNA binding and holds the DNA in place behind the central channel of the CTD like a "doorstop," preventing helicase slippages and sustaining processive unwinding. Consistent with this model, mitochondrial single-stranded DNA-binding protein (mtSSB) compensate for the NTD loss and partially restore kilobase length DNA synthesis by CTD and Polγ. The implications of our studies are foundational for understanding the mechanisms of disease-causing Twinkle mutants that lie in the NTD.
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12
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Akbari M, Nilsen HL, Montaldo NP. Dynamic features of human mitochondrial DNA maintenance and transcription. Front Cell Dev Biol 2022; 10:984245. [PMID: 36158192 PMCID: PMC9491825 DOI: 10.3389/fcell.2022.984245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/02/2022] [Indexed: 12/03/2022] Open
Abstract
Mitochondria are the primary sites for cellular energy production and are required for many essential cellular processes. Mitochondrial DNA (mtDNA) is a 16.6 kb circular DNA molecule that encodes only 13 gene products of the approximately 90 different proteins of the respiratory chain complexes and an estimated 1,200 mitochondrial proteins. MtDNA is, however, crucial for organismal development, normal function, and survival. MtDNA maintenance requires mitochondrially targeted nuclear DNA repair enzymes, a mtDNA replisome that is unique to mitochondria, and systems that control mitochondrial morphology and quality control. Here, we provide an overview of the current literature on mtDNA repair and transcription machineries and discuss how dynamic functional interactions between the components of these systems regulate mtDNA maintenance and transcription. A profound understanding of the molecular mechanisms that control mtDNA maintenance and transcription is important as loss of mtDNA integrity is implicated in normal process of aging, inflammation, and the etiology and pathogenesis of a number of diseases.
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Affiliation(s)
- Mansour Akbari
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Hilde Loge Nilsen
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Unit for precision medicine, Akershus University Hospital, Nordbyhagen, Norway
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Nicola Pietro Montaldo
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- *Correspondence: Nicola Pietro Montaldo,
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13
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Meng F, Jia Z, Zheng J, Ji Y, Wang J, Xiao Y, Fu Y, Wang M, Ling F, Guan MX. A deafness-associated mitochondrial DNA mutation caused pleiotropic effects on DNA replication and tRNA metabolism. Nucleic Acids Res 2022; 50:9453-9469. [PMID: 36039763 PMCID: PMC9458427 DOI: 10.1093/nar/gkac720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/09/2022] [Indexed: 12/24/2022] Open
Abstract
In this report, we investigated the molecular mechanism underlying a deafness-associated m.5783C > T mutation that affects the canonical C50-G63 base-pairing of TΨC stem of tRNACys and immediately adjacent to 5' end of light-strand origin of mitochondrial DNA (mtDNA) replication (OriL). Two dimensional agarose gel electrophoresis revealed marked decreases in the replication intermediates including ascending arm of Y-fork arcs spanning OriL in the mutant cybrids bearing m.5783C > T mutation. mtDNA replication alterations were further evidenced by decreased levels of PolγA, Twinkle and SSBP1, newly synthesized mtDNA and mtDNA contents in the mutant cybrids. The m.5783C > T mutation altered tRNACys structure and function, including decreased melting temperature, conformational changes, instability and deficient aminoacylation of mutated tRNACys. The m.5783C > T mutation impaired the 5' end processing efficiency of tRNACys precursors and reduced the levels of tRNACys and downstream tRNATyr. The aberrant tRNA metabolism impaired mitochondrial translation, which was especially pronounced effects in the polypeptides harboring higher numbers of cysteine and tyrosine codons. These alterations led to deficient oxidative phosphorylation including instability and reduced activities of the respiratory chain enzyme complexes I, III, IV and intact supercomplexes overall. Our findings highlight the impact of mitochondrial dysfunction on deafness arising from defects in mitochondrial DNA replication and tRNA metabolism.
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Affiliation(s)
| | | | - Jing Zheng
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China,Zhejiang Provincial Key Lab of Genetic and Developmental Disorder, Hangzhou, Zhejiang, China
| | - Yanchun Ji
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China,Zhejiang Provincial Key Lab of Genetic and Developmental Disorder, Hangzhou, Zhejiang, China
| | - Jing Wang
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yun Xiao
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yong Fu
- Division of Otolaryngology-Head and Neck Surgery, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Meng Wang
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China,Zhejiang Provincial Key Lab of Genetic and Developmental Disorder, Hangzhou, Zhejiang, China
| | - Feng Ling
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Hirosawa 2-1, Wako, Saitama, Japan
| | - Min-Xin Guan
- To whom correspondence should be addressed. Tel: +86 571 88206916; Fax: +86 571 88982377;
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14
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Abd Radzak SM, Mohd Khair SZN, Ahmad F, Patar A, Idris Z, Mohamed Yusoff AA. Insights regarding mitochondrial DNA copy number alterations in human cancer (Review). Int J Mol Med 2022; 50:104. [PMID: 35713211 PMCID: PMC9304817 DOI: 10.3892/ijmm.2022.5160] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/26/2022] [Indexed: 11/25/2022] Open
Abstract
Mitochondria are the critical organelles involved in various cellular functions. Mitochondrial biogenesis is activated by multiple cellular mechanisms which require a synchronous regulation between mitochondrial DNA (mtDNA) and nuclear DNA (nDNA). The mitochondrial DNA copy number (mtDNA-CN) is a proxy indicator for mitochondrial activity, and its alteration reflects mitochondrial biogenesis and function. Despite the precise mechanisms that modulate the amount and composition of mtDNA, which have not been fully elucidated, mtDNA-CN is known to influence numerous cellular pathways that are associated with cancer and as well as multiple other diseases. In addition, the utility of current technology in measuring mtDNA-CN contributes to its extensive assessment of diverse traits and tumorigenesis. The present review provides an overview of mtDNA-CN variations across human cancers and an extensive summary of the existing knowledge on the regulation and machinery of mtDNA-CN. The current information on the advanced methods used for mtDNA-CN assessment is also presented.
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Affiliation(s)
- Siti Muslihah Abd Radzak
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia
| | - Siti Zulaikha Nashwa Mohd Khair
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia
| | - Farizan Ahmad
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia
| | - Azim Patar
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia
| | - Zamzuri Idris
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia
| | - Abdul Aziz Mohamed Yusoff
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia
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15
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Roy A, Kandettu A, Ray S, Chakrabarty S. Mitochondrial DNA replication and repair defects: Clinical phenotypes and therapeutic interventions. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148554. [PMID: 35341749 DOI: 10.1016/j.bbabio.2022.148554] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 03/06/2022] [Accepted: 03/16/2022] [Indexed: 12/15/2022]
Abstract
Mitochondria is a unique cellular organelle involved in multiple cellular processes and is critical for maintaining cellular homeostasis. This semi-autonomous organelle contains its circular genome - mtDNA (mitochondrial DNA), that undergoes continuous cycles of replication and repair to maintain the mitochondrial genome integrity. The majority of the mitochondrial genes, including mitochondrial replisome and repair genes, are nuclear-encoded. Although the repair machinery of mitochondria is quite efficient, the mitochondrial genome is highly susceptible to oxidative damage and other types of exogenous and endogenous agent-induced DNA damage, due to the absence of protective histones and their proximity to the main ROS production sites. Mutations in replication and repair genes of mitochondria can result in mtDNA depletion and deletions subsequently leading to mitochondrial genome instability. The combined action of mutations and deletions can result in compromised mitochondrial genome maintenance and lead to various mitochondrial disorders. Here, we review the mechanism of mitochondrial DNA replication and repair process, key proteins involved, and their altered function in mitochondrial disorders. The focus of this review will be on the key genes of mitochondrial DNA replication and repair machinery and the clinical phenotypes associated with mutations in these genes.
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Affiliation(s)
- Abhipsa Roy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Amoolya Kandettu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Swagat Ray
- Department of Life Sciences, School of Life and Environmental Sciences, University of Lincoln, Lincoln LN6 7TS, United Kingdom
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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16
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Mitochondria homeostasis: Biology and involvement in hepatic steatosis to NASH. Acta Pharmacol Sin 2022; 43:1141-1155. [PMID: 35105958 PMCID: PMC9061859 DOI: 10.1038/s41401-022-00864-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/09/2022] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial biology and behavior are central to the physiology of liver. Multiple mitochondrial quality control mechanisms remodel mitochondrial homeostasis under physiological and pathological conditions. Mitochondrial dysfunction and damage induced by overnutrition lead to oxidative stress, inflammation, liver cell death, and collagen production, which advance hepatic steatosis to nonalcoholic steatohepatitis (NASH). Accumulating evidence suggests that specific interventions that target mitochondrial homeostasis, including energy metabolism, antioxidant effects, and mitochondrial quality control, have emerged as promising strategies for NASH treatment. However, clinical translation of these findings is challenging due to the complex and unclear mechanisms of mitochondrial homeostasis in the pathophysiology of NASH.
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17
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Kumar R, Harilal S, Thomas Parambi DG, Kanthlal S, Rahman MA, Alexiou A, Batiha GES, Mathew B. The Role of Mitochondrial Genes in Neurodegenerative Disorders. Curr Neuropharmacol 2022; 20:824-835. [PMID: 34503413 PMCID: PMC9881096 DOI: 10.2174/1570159x19666210908163839] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 07/09/2021] [Accepted: 09/07/2021] [Indexed: 11/22/2022] Open
Abstract
Mitochondrial disorders are clinically heterogeneous, resulting from nuclear gene and mitochondrial mutations that disturb the mitochondrial functions and dynamics. There is a lack of evidence linking mtDNA mutations to neurodegenerative disorders, mainly due to the absence of noticeable neuropathological lesions in postmortem samples. This review describes various gene mutations in Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, multiple sclerosis, and stroke. These abnormalities, including PINK1, Parkin, and SOD1 mutations, seem to reveal mitochondrial dysfunctions due to either mtDNA mutation or deletion, the mechanism of which remains unclear in depth.
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Affiliation(s)
- Rajesh Kumar
- Department of Pharmacy, Kerala University of Health Sciences, Thrissur, Kerala, India
| | - Seetha Harilal
- Department of Pharmacy, Kerala University of Health Sciences, Thrissur, Kerala, India
| | - Della Grace Thomas Parambi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Al Jouf-2014, Saudi Arabia
| | - S.K. Kanthlal
- Department of Pharmacology, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi-682 041, India
| | - Md Atiar Rahman
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong, Bangladesh
| | - Athanasios Alexiou
- Novel Global Community Educational Foundation, Hebersham, Australia;,AFNP Med Austria, Wien, Austria
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, AlBeheira, Egypt
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi-682 041, India,Address correspondence to this author at the Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Sciences Campus, Kochi-682 041, India; E-mails: ;
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18
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Arbeithuber B, Cremona MA, Hester J, Barrett A, Higgins B, Anthony K, Chiaromonte F, Diaz FJ, Makova KD. Advanced age increases frequencies of de novo mitochondrial mutations in macaque oocytes and somatic tissues. Proc Natl Acad Sci U S A 2022; 119:e2118740119. [PMID: 35394879 PMCID: PMC9169796 DOI: 10.1073/pnas.2118740119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/25/2022] [Indexed: 12/18/2022] Open
Abstract
Mutations in mitochondrial DNA (mtDNA) contribute to multiple diseases. However, how new mtDNA mutations arise and accumulate with age remains understudied because of the high error rates of current sequencing technologies. Duplex sequencing reduces error rates by several orders of magnitude via independently tagging and analyzing each of the two template DNA strands. Here, using duplex sequencing, we obtained high-quality mtDNA sequences for somatic tissues (liver and skeletal muscle) and single oocytes of 30 unrelated rhesus macaques, from 1 to 23 y of age. Sequencing single oocytes minimized effects of natural selection on germline mutations. In total, we identified 17,637 tissue-specific de novo mutations. Their frequency increased ∼3.5-fold in liver and ∼2.8-fold in muscle over the ∼20 y assessed. Mutation frequency in oocytes increased ∼2.5-fold until the age of 9 y, but did not increase after that, suggesting that oocytes of older animals maintain the quality of their mtDNA. We found the light-strand origin of replication (OriL) to be a hotspot for mutation accumulation with aging in liver. Indeed, the 33-nucleotide-long OriL harbored 12 variant hotspots, 10 of which likely disrupt its hairpin structure and affect replication efficiency. Moreover, in somatic tissues, protein-coding variants were subject to positive selection (potentially mitigating toxic effects of mitochondrial activity), the strength of which increased with the number of macaques harboring variants. Our work illuminates the origins and accumulation of somatic and germline mtDNA mutations with aging in primates and has implications for delayed reproduction in modern human societies.
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Affiliation(s)
- Barbara Arbeithuber
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Experimental Gynaecology, Obstetrics and Gynaecological Endocrinology, Kepler University Hospital Linz, Johannes Kepler University Linz, 4020 Linz, Austria
| | - Marzia A. Cremona
- Department of Operations and Decision Systems, Université Laval, Québec, QC G1V0A6, Canada
- Population Health and Optimal Health Practices, CHU de Québec - Université Laval Research Center, Québec, QC G1V4G2, Canada
- Center for Medical Genomics, The Pennsylvania State University, University Park, PA 16802
| | - James Hester
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802
| | - Alison Barrett
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - Bonnie Higgins
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - Kate Anthony
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - Francesca Chiaromonte
- Center for Medical Genomics, The Pennsylvania State University, University Park, PA 16802
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802
- Institute of Economics and EMbeDS, Sant'Anna School of Advanced Studies, Pisa 56127, Italy
| | - Francisco J. Diaz
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802
| | - Kateryna D. Makova
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Center for Medical Genomics, The Pennsylvania State University, University Park, PA 16802
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19
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Silva-Pinheiro P, Minczuk M. The potential of mitochondrial genome engineering. Nat Rev Genet 2022; 23:199-214. [PMID: 34857922 DOI: 10.1038/s41576-021-00432-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2021] [Indexed: 12/19/2022]
Abstract
Mitochondria are subject to unique genetic control by both nuclear DNA and their own genome, mitochondrial DNA (mtDNA), of which each mitochondrion contains multiple copies. In humans, mutations in mtDNA can lead to devastating, heritable, multi-system diseases that display different tissue-specific presentation at any stage of life. Despite rapid advances in nuclear genome engineering, for years, mammalian mtDNA has remained resistant to genetic manipulation, hampering our ability to understand the mechanisms that underpin mitochondrial disease. Recent developments in the genetic modification of mammalian mtDNA raise the possibility of using genome editing technologies, such as programmable nucleases and base editors, for the treatment of hereditary mitochondrial disease.
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Affiliation(s)
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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20
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Kosar M, Piccini D, Foiani M, Giannattasio M. A rapid method to visualize human mitochondrial DNA replication through rotary shadowing and transmission electron microscopy. Nucleic Acids Res 2021; 49:e121. [PMID: 34500456 PMCID: PMC8643652 DOI: 10.1093/nar/gkab770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 08/15/2021] [Accepted: 08/26/2021] [Indexed: 11/21/2022] Open
Abstract
We report a rapid experimental procedure based on high-density in vivo psoralen inter-strand DNA cross-linking coupled to spreading of naked purified DNA, positive staining, low-angle rotary shadowing, and transmission electron microscopy (TEM) that allows quick visualization of the dynamic of heavy strand (HS) and light strand (LS) human mitochondrial DNA replication. Replication maps built on linearized mitochondrial genomes and optimized rotary shadowing conditions enable clear visualization of the progression of the mitochondrial DNA synthesis and visualization of replication intermediates carrying long single-strand DNA stretches. One variant of this technique, called denaturing spreading, allowed the inspection of the fine chromatin structure of the mitochondrial genome and was applied to visualize the in vivo three-strand DNA structure of the human mitochondrial D-loop intermediate with unprecedented clarity.
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Affiliation(s)
- Martin Kosar
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milano, Italy
| | - Daniele Piccini
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milano, Italy
| | - Marco Foiani
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milano, Italy.,Dipartimento di Oncologia & Emato-Oncologia, Università degli Studi di Milano, Milano, Italy
| | - Michele Giannattasio
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milano, Italy.,Dipartimento di Oncologia & Emato-Oncologia, Università degli Studi di Milano, Milano, Italy
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21
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Sanchez-Contreras M, Sweetwyne MT, Kohrn BF, Tsantilas KA, Hipp MJ, Schmidt EK, Fredrickson J, Whitson JA, Campbell MD, Rabinovitch PS, Marcinek DJ, Kennedy SR. A replication-linked mutational gradient drives somatic mutation accumulation and influences germline polymorphisms and genome composition in mitochondrial DNA. Nucleic Acids Res 2021; 49:11103-11118. [PMID: 34614167 PMCID: PMC8565317 DOI: 10.1093/nar/gkab901] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/10/2021] [Accepted: 09/22/2021] [Indexed: 11/22/2022] Open
Abstract
Mutations in mitochondrial DNA (mtDNA) cause maternally inherited diseases, while somatic mutations are linked to common diseases of aging. Although mtDNA mutations impact health, the processes that give rise to them are under considerable debate. To investigate the mechanism by which de novo mutations arise, we analyzed the distribution of naturally occurring somatic mutations across the mouse and human mtDNA obtained by Duplex Sequencing. We observe distinct mutational gradients in G→A and T→C transitions delimited by the light-strand origin and the mitochondrial Control Region (mCR). The gradient increases unequally across the mtDNA with age and is lost in the absence of DNA polymerase γ proofreading activity. In addition, high-resolution analysis of the mCR shows that important regulatory elements exhibit considerable variability in mutation frequency, consistent with them being mutational ‘hot-spots’ or ‘cold-spots’. Collectively, these patterns support genome replication via a deamination prone asymmetric strand-displacement mechanism as the fundamental driver of mutagenesis in mammalian DNA. Moreover, the distribution of mtDNA single nucleotide polymorphisms in humans and the distribution of bases in the mtDNA across vertebrate species mirror this gradient, indicating that replication-linked mutations are likely the primary source of inherited polymorphisms that, over evolutionary timescales, influences genome composition during speciation.
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Affiliation(s)
- Monica Sanchez-Contreras
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Mariya T Sweetwyne
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Brendan F Kohrn
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | | | - Michael J Hipp
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth K Schmidt
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jeanne Fredrickson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jeremy A Whitson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Matthew D Campbell
- Department of Radiology, University of Washington, Seattle, WA 98195, USA
| | - Peter S Rabinovitch
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - David J Marcinek
- Department of Radiology, University of Washington, Seattle, WA 98195, USA
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
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22
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Inatomi T, Matsuda S, Ishiuchi T, Do Y, Nakayama M, Abe S, Kasho K, Wanrooij S, Nakada K, Ichiyanagi K, Sasaki H, Yasukawa T, Kang D. TFB2M and POLRMT are essential for mammalian mitochondrial DNA replication. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119167. [PMID: 34744028 DOI: 10.1016/j.bbamcr.2021.119167] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 10/13/2021] [Accepted: 10/13/2021] [Indexed: 12/24/2022]
Abstract
Two classes of replication intermediates have been observed from mitochondrial DNA (mtDNA) in many mammalian tissue and cells with two-dimensional agarose gel electrophoresis. One is assigned to leading-strand synthesis in the absence of synchronous lagging-strand synthesis (strand-asynchronous replication), and the other has properties of coupled leading- and lagging-strand synthesis (strand-coupled replication). While strand-asynchronous replication is primed by long noncoding RNA synthesized from a defined transcription initiation site, little is known about the commencement of strand-coupled replication. To investigate it, we attempted to abolish strand-asynchronous replication in cultured human cybrid cells by knocking out the components of the transcription initiation complexes, mitochondrial transcription factor B2 (TFB2M/mtTFB2) and mitochondrial RNA polymerase (POLRMT/mtRNAP). Unexpectedly, removal of either protein resulted in complete mtDNA loss, demonstrating for the first time that TFB2M and POLRMT are indispensable for the maintenance of human mtDNA. Moreover, a lack of TFB2M could not be compensated for by mitochondrial transcription factor B1 (TFB1M/mtTFB1). These findings indicate that TFB2M and POLRMT are crucial for the priming of not only strand-asynchronous but also strand-coupled replication, providing deeper insights into the molecular basis of mtDNA replication initiation.
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Affiliation(s)
- Teppei Inatomi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Shigeru Matsuda
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan; Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryocho, Aoba-ku, Sendai-shi, Miyagi 980-8575, Japan
| | - Takashi Ishiuchi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Yura Do
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Masunari Nakayama
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Shusaku Abe
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Kazutoshi Kasho
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Kazuto Nakada
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba-shi, Ibaraki 305-8572, Japan
| | - Kenji Ichiyanagi
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya-shi, Aichi 464-8601, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Takehiro Yasukawa
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan; Department of Pathology and Oncology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan.
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
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23
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Menger KE, Rodríguez-Luis A, Chapman J, Nicholls TJ. Controlling the topology of mammalian mitochondrial DNA. Open Biol 2021; 11:210168. [PMID: 34547213 PMCID: PMC8455175 DOI: 10.1098/rsob.210168] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genome of mitochondria, called mtDNA, is a small circular DNA molecule present at thousands of copies per human cell. MtDNA is packaged into nucleoprotein complexes called nucleoids, and the density of mtDNA packaging affects mitochondrial gene expression. Genetic processes such as transcription, DNA replication and DNA packaging alter DNA topology, and these topological problems are solved by a family of enzymes called topoisomerases. Within mitochondria, topoisomerases are involved firstly in the regulation of mtDNA supercoiling and secondly in disentangling interlinked mtDNA molecules following mtDNA replication. The loss of mitochondrial topoisomerase activity leads to defects in mitochondrial function, and variants in the dual-localized type IA topoisomerase TOP3A have also been reported to cause human mitochondrial disease. We review the current knowledge on processes that alter mtDNA topology, how mtDNA topology is modulated by the action of topoisomerases, and the consequences of altered mtDNA topology for mitochondrial function and human health.
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Affiliation(s)
- Katja E. Menger
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Alejandro Rodríguez-Luis
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - James Chapman
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Thomas J. Nicholls
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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24
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Jakovlić I, Zou H, Zhao XM, Zhang J, Wang GT, Zhang D. Evolutionary History of Inversions in Directional Mutational Pressures in Crustacean Mitochondrial Genomes: Implications for Evolutionary Studies. Mol Phylogenet Evol 2021; 164:107288. [PMID: 34365015 DOI: 10.1016/j.ympev.2021.107288] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 01/29/2023]
Abstract
Inversions of the origin of replication (ORI) in mitochondrial genomes produce asymmetrical mutational pressures that can cause strong base composition skews. Due to skews often being overlooked, the total number of crustacean lineages that underwent ORI events remains unknown. We analysed skews, cumulative skew plots, conserved sequence motifs, and mitochondrial architecture of all 965 available crustacean mitogenomes (699 unique species). We found indications of an ORI in 159 (22.7%) species, and mapped these to 23 ORI events: 16 identified with confidence and 7 putative (13 newly proposed, and for 5 we improved the resolution). Two ORIs occurred at or above the order level: Isopoda and Copepoda. Shifts in skew plots are not a precise tool for identifying the replication mechanism. We discuss how ORIs can produce mutational bursts in mitogenomes and show how these can interfere with various types of evolutionary studies. Phylogenetic analyses were plagued by artefactual clustering, and ORI lineages exhibited longer branches, a higher number of synonymous substitutions, higher mutational saturation, and higher compositional heterogeneity. ORI events also affected codon usage and protein properties. We discuss how this may have caused erroneous interpretation of data in previous studies that did not account for skew patterns.
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Affiliation(s)
- Ivan Jakovlić
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, 730000 Lanzhou, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xu-Mao Zhao
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, 730000 Lanzhou, China
| | - Jin Zhang
- Bio-Transduction Lab, Wuhan 430075, China
| | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, 730000 Lanzhou, China.
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25
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Renaudin X, Lee M, Shehata M, Surmann EM, Venkitaraman AR. BRCA2 deficiency reveals that oxidative stress impairs RNaseH1 function to cripple mitochondrial DNA maintenance. Cell Rep 2021; 36:109478. [PMID: 34348152 PMCID: PMC8356021 DOI: 10.1016/j.celrep.2021.109478] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 06/16/2021] [Accepted: 07/13/2021] [Indexed: 01/07/2023] Open
Abstract
Oxidative stress is a ubiquitous cellular challenge implicated in aging, neurodegeneration, and cancer. By studying pathogenic mutations in the tumor suppressor BRCA2, we identify a general mechanism by which oxidative stress restricts mitochondrial (mt)DNA replication. BRCA2 inactivation induces R-loop accumulation in the mtDNA regulatory region and diminishes mtDNA replication initiation. In BRCA2-deficient cells, intracellular reactive oxygen species (ROS) are elevated, and ROS scavengers suppress the mtDNA defects. Conversely, wild-type cells exposed to oxidative stress by pharmacologic or genetic manipulation phenocopy these defects. Mechanistically, we find that 8-oxoguanine accumulation in mtDNA caused by oxidative stress suffices to impair recruitment of the mitochondrial enzyme RNaseH1 to sites of R-loop accrual, restricting mtDNA replication initiation. Thus, oxidative stress impairs RNaseH1 function to cripple mtDNA maintenance. Our findings highlight a molecular mechanism that links oxidative stress to mitochondrial dysfunction and is elicited by the inactivation of genes implicated in neurodegeneration and cancer. BRCA2-deficient cells accumulate mtDNA R-loops due to oxidative stress This stress creates 8-oxoguanine lesions impairing RNaseH1 recruitment to mtDNA RNaseH1 impairment triggers R-loop formation and restricts mtDNA replication Other sources of oxidative stress also cripple mtDNA maintenance via this mechanism
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Affiliation(s)
- Xavier Renaudin
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
| | - Miyoung Lee
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
| | - Mona Shehata
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
| | - Eva-Maria Surmann
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
| | - Ashok R Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK.
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26
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Fu L, Luo YX, Liu Y, Liu H, Li HZ, Yu Y. Potential of Mitochondrial Genome Editing for Human Fertility Health. Front Genet 2021; 12:673951. [PMID: 34354734 PMCID: PMC8329452 DOI: 10.3389/fgene.2021.673951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 06/28/2021] [Indexed: 12/21/2022] Open
Abstract
Mitochondrial DNA (mtDNA) encodes vital proteins and RNAs for the normal functioning of the mitochondria. Mutations in mtDNA leading to mitochondrial dysfunction are relevant to a large spectrum of diseases, including fertility disorders. Since mtDNA undergoes rather complex processes during gametogenesis and fertilization, clarification of the changes and functions of mtDNA and its essential impact on gamete quality and fertility during this process is of great significance. Thanks to the emergence and rapid development of gene editing technology, breakthroughs have been made in mitochondrial genome editing (MGE), offering great potential for the treatment of mtDNA-related diseases. In this review, we summarize the features of mitochondria and their unique genome, emphasizing their inheritance patterns; illustrate the role of mtDNA in gametogenesis and fertilization; and discuss potential therapies based on MGE as well as the outlook in this field.
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Affiliation(s)
- Lin Fu
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Yu-Xin Luo
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Ying Liu
- Food Inspection and Quarantine Technology Center of Shenzhen Customs District, FICS, Shenzhen, China
| | - Hui Liu
- Stem Cell Research Center, Peking University Third Hospital, Beijing, China
| | - Hong-Zhen Li
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Yang Yu
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology and Key Laboratory of Assisted Reproduction, Ministry of Education, Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.,Stem Cell Research Center, Peking University Third Hospital, Beijing, China
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27
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Mitochondrial genome stability in human: understanding the role of DNA repair pathways. Biochem J 2021; 478:1179-1197. [DOI: 10.1042/bcj20200920] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 11/17/2022]
Abstract
Mitochondria are semiautonomous organelles in eukaryotic cells and possess their own genome that replicates independently. Mitochondria play a major role in oxidative phosphorylation due to which its genome is frequently exposed to oxidative stress. Factors including ionizing radiation, radiomimetic drugs and replication fork stalling can also result in different types of mutations in mitochondrial DNA (mtDNA) leading to genome fragility. Mitochondria from myopathies, dystonia, cancer patient samples show frequent mtDNA mutations such as point mutations, insertions and large-scale deletions that could account for mitochondria-associated disease pathogenesis. The mechanism by which such mutations arise following exposure to various DNA-damaging agents is not well understood. One of the well-studied repair pathways in mitochondria is base excision repair. Other repair pathways such as mismatch repair, homologous recombination and microhomology-mediated end joining have also been reported. Interestingly, nucleotide excision repair and classical nonhomologous DNA end joining are not detected in mitochondria. In this review, we summarize the potential causes of mitochondrial genome fragility, their implications as well as various DNA repair pathways that operate in mitochondria.
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28
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Fontana GA, Gahlon HL. Mechanisms of replication and repair in mitochondrial DNA deletion formation. Nucleic Acids Res 2020; 48:11244-11258. [PMID: 33021629 PMCID: PMC7672454 DOI: 10.1093/nar/gkaa804] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/07/2020] [Accepted: 09/25/2020] [Indexed: 02/06/2023] Open
Abstract
Deletions in mitochondrial DNA (mtDNA) are associated with diverse human pathologies including cancer, aging and mitochondrial disorders. Large-scale deletions span kilobases in length and the loss of these associated genes contributes to crippled oxidative phosphorylation and overall decline in mitochondrial fitness. There is not a united view for how mtDNA deletions are generated and the molecular mechanisms underlying this process are poorly understood. This review discusses the role of replication and repair in mtDNA deletion formation as well as nucleic acid motifs such as repeats, secondary structures, and DNA damage associated with deletion formation in the mitochondrial genome. We propose that while erroneous replication and repair can separately contribute to deletion formation, crosstalk between these pathways is also involved in generating deletions.
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Affiliation(s)
- Gabriele A Fontana
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland
| | - Hailey L Gahlon
- To whom correspondence should be addressed. Tel: +41 44 632 3731;
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29
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In Vivo Analysis of mtDNA Replication at the Single Molecule Level and with High Resolution. Methods Mol Biol 2020. [PMID: 33230762 DOI: 10.1007/978-1-0716-0834-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Single molecule analysis of replicating DNA (SMARD) is a powerful methodology that allows in vivo analysis of replicating DNA; identification of origins of replication, assessment of fork directionality, and measurement of replication fork speed. SMARD, which has been extensively used to study replication of nuclear DNA, involves incorporation of thymidine analogs to nascent DNA chains and their subsequent visualization through immune detection. Here, we adapt and fine-tune the SMARD technique to the specifics of human and mouse mitochondrial DNA. The mito-SMARD protocol allows researchers to gain in vivo insight into mitochondrial DNA (mtDNA) replication at the single molecule level and with high resolution.
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30
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Falkenberg M, Gustafsson CM. Mammalian mitochondrial DNA replication and mechanisms of deletion formation. Crit Rev Biochem Mol Biol 2020; 55:509-524. [DOI: 10.1080/10409238.2020.1818684] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Claes M. Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
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31
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Lujan SA, Longley MJ, Humble MH, Lavender CA, Burkholder A, Blakely EL, Alston CL, Gorman GS, Turnbull DM, McFarland R, Taylor RW, Kunkel TA, Copeland WC. Ultrasensitive deletion detection links mitochondrial DNA replication, disease, and aging. Genome Biol 2020; 21:248. [PMID: 32943091 PMCID: PMC7500033 DOI: 10.1186/s13059-020-02138-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/07/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Acquired human mitochondrial genome (mtDNA) deletions are symptoms and drivers of focal mitochondrial respiratory deficiency, a pathological hallmark of aging and late-onset mitochondrial disease. RESULTS To decipher connections between these processes, we create LostArc, an ultrasensitive method for quantifying deletions in circular mtDNA molecules. LostArc reveals 35 million deletions (~ 470,000 unique spans) in skeletal muscle from 22 individuals with and 19 individuals without pathogenic variants in POLG. This nuclear gene encodes the catalytic subunit of replicative mitochondrial DNA polymerase γ. Ablation, the deleted mtDNA fraction, suffices to explain skeletal muscle phenotypes of aging and POLG-derived disease. Unsupervised bioinformatic analyses reveal distinct age- and disease-correlated deletion patterns. CONCLUSIONS These patterns implicate replication by DNA polymerase γ as the deletion driver and suggest little purifying selection against mtDNA deletions by mitophagy in postmitotic muscle fibers. Observed deletion patterns are best modeled as mtDNA deletions initiated by replication fork stalling during strand displacement mtDNA synthesis.
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Affiliation(s)
- Scott A Lujan
- Genome Integrity and Structural Biology Laboratory, DNA Replication Fidelity Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Matthew J Longley
- Genome Integrity and Structural Biology Laboratory, Mitochondrial DNA Replication Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Margaret H Humble
- Genome Integrity and Structural Biology Laboratory, Mitochondrial DNA Replication Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Christopher A Lavender
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Adam Burkholder
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Emma L Blakely
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK
| | - Charlotte L Alston
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK
| | - Grainne S Gorman
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Doug M Turnbull
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, DNA Replication Fidelity Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, Mitochondrial DNA Replication Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
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32
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Chapman J, Ng YS, Nicholls TJ. The Maintenance of Mitochondrial DNA Integrity and Dynamics by Mitochondrial Membranes. Life (Basel) 2020; 10:life10090164. [PMID: 32858900 PMCID: PMC7555930 DOI: 10.3390/life10090164] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/20/2020] [Accepted: 08/23/2020] [Indexed: 12/18/2022] Open
Abstract
Mitochondria are complex organelles that harbour their own genome. Mitochondrial DNA (mtDNA) exists in the form of a circular double-stranded DNA molecule that must be replicated, segregated and distributed around the mitochondrial network. Human cells typically possess between a few hundred and several thousand copies of the mitochondrial genome, located within the mitochondrial matrix in close association with the cristae ultrastructure. The organisation of mtDNA around the mitochondrial network requires mitochondria to be dynamic and undergo both fission and fusion events in coordination with the modulation of cristae architecture. The dysregulation of these processes has profound effects upon mtDNA replication, manifesting as a loss of mtDNA integrity and copy number, and upon the subsequent distribution of mtDNA around the mitochondrial network. Mutations within genes involved in mitochondrial dynamics or cristae modulation cause a wide range of neurological disorders frequently associated with defects in mtDNA maintenance. This review aims to provide an understanding of the biological mechanisms that link mitochondrial dynamics and mtDNA integrity, as well as examine the interplay that occurs between mtDNA, mitochondrial dynamics and cristae structure.
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Affiliation(s)
- James Chapman
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK;
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Correspondence: (J.C.); (T.J.N.)
| | - Yi Shiau Ng
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK;
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Thomas J. Nicholls
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK;
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Correspondence: (J.C.); (T.J.N.)
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33
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Zheng L, Meng Y, Campbell JL, Shen B. Multiple roles of DNA2 nuclease/helicase in DNA metabolism, genome stability and human diseases. Nucleic Acids Res 2020; 48:16-35. [PMID: 31754720 PMCID: PMC6943134 DOI: 10.1093/nar/gkz1101] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/23/2019] [Accepted: 11/12/2019] [Indexed: 12/25/2022] Open
Abstract
DNA2 nuclease/helicase is a structure-specific nuclease, 5'-to-3' helicase, and DNA-dependent ATPase. It is involved in multiple DNA metabolic pathways, including Okazaki fragment maturation, replication of 'difficult-to-replicate' DNA regions, end resection, stalled replication fork processing, and mitochondrial genome maintenance. The participation of DNA2 in these different pathways is regulated by its interactions with distinct groups of DNA replication and repair proteins and by post-translational modifications. These regulatory mechanisms induce its recruitment to specific DNA replication or repair complexes, such as DNA replication and end resection machinery, and stimulate its efficient cleavage of various structures, for example, to remove RNA primers or to produce 3' overhangs at telomeres or double-strand breaks. Through these versatile activities at replication forks and DNA damage sites, DNA2 functions as both a tumor suppressor and promoter. In normal cells, it suppresses tumorigenesis by maintaining the genomic integrity. Thus, DNA2 mutations or functional deficiency may lead to cancer initiation. However, DNA2 may also function as a tumor promoter, supporting cancer cell survival by counteracting replication stress. Therefore, it may serve as an ideal target to sensitize advanced DNA2-overexpressing cancers to current chemo- and radiotherapy regimens.
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Affiliation(s)
- Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Yuan Meng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Judith L Campbell
- Divisions of Chemistry and Chemical Engineering and Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
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Patient-specific neural progenitor cells derived from induced pluripotent stem cells offer a promise of good models for mitochondrial disease. Cell Tissue Res 2020; 380:15-30. [PMID: 31925525 DOI: 10.1007/s00441-019-03164-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 12/19/2019] [Indexed: 02/06/2023]
Abstract
Mitochondria are the primary generators of ATP in eukaryotic cells through the process of oxidative phosphorylation. Mitochondria are also involved in several other important cellular functions including regulation of intracellular Ca2+, cell signaling and apoptosis. Mitochondrial dysfunction causes disease and since it is not possible to perform repeated studies in humans, models are essential to enable us to investigate the mechanisms involved. Recently, the discovery of induced pluripotent stem cells (iPSCs), made by reprogramming adult somatic cells (Takahashi and Yamanaka 2006; Yamanaka and Blau 2010), has provided a unique opportunity for studying aspects of disease mechanisms in patient-specific cells and tissues. Reprogramming cells to neuronal lineage such as neural progenitor cells (NPCs) generated from the neural induction of reprogrammed iPSCs can thus provide a useful model for investigating neurological disease mechanisms including those caused by mitochondrial dysfunction. In addition, NPCs display a huge clinical potential in drug screening and therapeutics.
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Matkarimov BT, Saparbaev MK. DNA Repair and Mutagenesis in Vertebrate Mitochondria: Evidence for Asymmetric DNA Strand Inheritance. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1241:77-100. [DOI: 10.1007/978-3-030-41283-8_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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36
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Abstract
DNA replication in human mitochondria has been studied for several decades; however, its mechanism still remains unclear. During the last 15 years, many new experimental data on the mitochondrial replication have appeared, although extremely contradictory. Two asynchronous (strand displacement and RITOLS) and one synchronous (strand-coupled) replication models have been proposed. In the asynchronous models, replication from the origin in the H-chain starts earlier, so that the replication of the two chains ends at different times. The synchronous model is more traditional and implies two replication forks with leading and lagging strands initiated at the same origin. For each of the three models, both confirming and contradicting experimental data exist. Most likely, there is no single model of mitochondrial replication. It is possible that the unique mitochondrial replication machinery that has originated as a results of endosymbiosis has an unexpected variety of replication strategies to maintain the mitochondrial genome. An unusual combination of enzymes of different origin (phage, bacterial, eukaryotic) and unique features of the mitochondrial genome (existance of heavy and light chains, insertions of ribonucleotides, a variety of origins) can allow replication through different mechanisms. In human mitochondria, asynchronous replication seems to dominate; however, synchronous replication is also possible under certain conditions. In the human heart mitochondria, circular mitochondrial DNA (mtDNA) molecules can rearrange in a network of rapidly replicating linear genomes, thereby suggesting possible existence of a wide range of replication mechanisms in the mitochondria. The review describes the main stages of mtDNA replication and enzymes involved in this process, as well as discusses the prospects of mitochondrial replication studies.
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Affiliation(s)
- L A Zinovkina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119234, Russia.
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Brieba LG. Structure-Function Analysis Reveals the Singularity of Plant Mitochondrial DNA Replication Components: A Mosaic and Redundant System. PLANTS 2019; 8:plants8120533. [PMID: 31766564 PMCID: PMC6963530 DOI: 10.3390/plants8120533] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 02/06/2023]
Abstract
Plants are sessile organisms, and their DNA is particularly exposed to damaging agents. The integrity of plant mitochondrial and plastid genomes is necessary for cell survival. During evolution, plants have evolved mechanisms to replicate their mitochondrial genomes while minimizing the effects of DNA damaging agents. The recombinogenic character of plant mitochondrial DNA, absence of defined origins of replication, and its linear structure suggest that mitochondrial DNA replication is achieved by a recombination-dependent replication mechanism. Here, I review the mitochondrial proteins possibly involved in mitochondrial DNA replication from a structural point of view. A revision of these proteins supports the idea that mitochondrial DNA replication could be replicated by several processes. The analysis indicates that DNA replication in plant mitochondria could be achieved by a recombination-dependent replication mechanism, but also by a replisome in which primers are synthesized by three different enzymes: Mitochondrial RNA polymerase, Primase-Helicase, and Primase-Polymerase. The recombination-dependent replication model and primers synthesized by the Primase-Polymerase may be responsible for the presence of genomic rearrangements in plant mitochondria.
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Affiliation(s)
- Luis Gabriel Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 629, Irapuato, Guanajuato C.P. 36821, Mexico
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Melchinger H, Jain K, Tyagi T, Hwa J. Role of Platelet Mitochondria: Life in a Nucleus-Free Zone. Front Cardiovasc Med 2019; 6:153. [PMID: 31737646 PMCID: PMC6828734 DOI: 10.3389/fcvm.2019.00153] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 10/08/2019] [Indexed: 12/19/2022] Open
Abstract
Platelets are abundant, small, anucleate circulating cells, serving many emerging pathophysiological roles beyond hemostasis; including active critical roles in thrombosis, injury response, and immunoregulation. In the absence of genomic DNA transcriptional regulation (no nucleus), platelets require strategic prepackaging of all the needed RNA and organelles from megakaryocytes, to sense stress (e.g., hyperglycemia), to protect themselves from stress (e.g., mitophagy), and to communicate a stress response to other cells (e.g., granule and microparticle release). Distinct from avian thrombocytes that have a nucleus, the absence of a nucleus allows the mammalian platelet to maintain its small size, permits morphological flexibility, and may improve speed and efficiency of protein expression in response to stress. In the absence of a nucleus, platelet lifespan of 7–10 days, is largely determined by the mitochondria. The packaging of 5–8 mitochondria is critical in aerobic respiration and yielding metabolic substrates needed for function and survival. Mitochondria damage or dysfunction, as observed with several disease processes, results in greatly attenuated platelet survival and increased risk for thrombovascular events. Here we provide insights into the emerging roles of platelets despite the lack of a nucleus, and the key role played by mitochondria in platelet function and survival both in health and disease.
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Affiliation(s)
- Hannah Melchinger
- Department of Internal Medicine, Yale Cardiovascular Research Center, Yale School of Medicine, New Haven, CT, United States
| | - Kanika Jain
- Department of Internal Medicine, Yale Cardiovascular Research Center, Yale School of Medicine, New Haven, CT, United States
| | - Tarun Tyagi
- Department of Internal Medicine, Yale Cardiovascular Research Center, Yale School of Medicine, New Haven, CT, United States
| | - John Hwa
- Department of Internal Medicine, Yale Cardiovascular Research Center, Yale School of Medicine, New Haven, CT, United States
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Mackiewicz P, Urantówka AD, Kroczak A, Mackiewicz D. Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications. Genome Biol Evol 2019; 11:2824-2849. [PMID: 31580435 PMCID: PMC6795242 DOI: 10.1093/gbe/evz209] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2019] [Indexed: 12/29/2022] Open
Abstract
Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.
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Affiliation(s)
- Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
| | - Adam Dawid Urantówka
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Aleksandra Kroczak
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
- Department of Genetics, Wroclaw University of Environmental and Life Sciences, Poland
| | - Dorota Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wrocław, Poland
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40
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Plant Organelle Genome Replication. PLANTS 2019; 8:plants8100358. [PMID: 31546578 PMCID: PMC6843274 DOI: 10.3390/plants8100358] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/14/2019] [Accepted: 09/18/2019] [Indexed: 12/21/2022]
Abstract
Mitochondria and chloroplasts perform essential functions in respiration, ATP production, and photosynthesis, and both organelles contain genomes that encode only some of the proteins that are required for these functions. The proteins and mechanisms for organelle DNA replication are very similar to bacterial or phage systems. The minimal replisome may consist of DNA polymerase, a primase/helicase, and a single-stranded DNA binding protein (SSB), similar to that found in bacteriophage T7. In Arabidopsis, there are two genes for organellar DNA polymerases and multiple potential genes for SSB, but there is only one known primase/helicase protein to date. Genome copy number varies widely between type and age of plant tissues. Replication mechanisms are only poorly understood at present, and may involve multiple processes, including recombination-dependent replication (RDR) in plant mitochondria and perhaps also in chloroplasts. There are still important questions remaining as to how the genomes are maintained in new organelles, and how genome copy number is determined. This review summarizes our current understanding of these processes.
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41
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Cluett TJ, Akman G, Reyes A, Kazak L, Mitchell A, Wood SR, Spinazzola A, Spelbrink JN, Holt IJ. Transcript availability dictates the balance between strand-asynchronous and strand-coupled mitochondrial DNA replication. Nucleic Acids Res 2019; 46:10771-10781. [PMID: 30239839 PMCID: PMC6237803 DOI: 10.1093/nar/gky852] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 09/12/2018] [Indexed: 11/15/2022] Open
Abstract
Mammalian mitochondria operate multiple mechanisms of DNA replication. In many cells and tissues a strand-asynchronous mechanism predominates over coupled leading and lagging-strand DNA synthesis. However, little is known of the factors that control or influence the different mechanisms of replication, and the idea that strand-asynchronous replication entails transient incorporation of transcripts (aka bootlaces) is controversial. A firm prediction of the bootlace model is that it depends on mitochondrial transcripts. Here, we show that elevated expression of Twinkle DNA helicase in human mitochondria induces bidirectional, coupled leading and lagging-strand DNA synthesis, at the expense of strand-asynchronous replication; and this switch is accompanied by decreases in the steady-state level of some mitochondrial transcripts. However, in the so-called minor arc of mitochondrial DNA where transcript levels remain high, the strand-asynchronous replication mechanism is instated. Hence, replication switches to a strand-coupled mechanism only where transcripts are scarce, thereby establishing a direct correlation between transcript availability and the mechanism of replication. Thus, these findings support a critical role of mitochondrial transcripts in the strand-asynchronous mechanism of mitochondrial DNA replication; and, as a corollary, mitochondrial RNA availability and RNA/DNA hybrid formation offer means of regulating the mechanisms of DNA replication in the organelle.
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Affiliation(s)
- Tricia J Cluett
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB1 9SY, UK
| | | | - Aurelio Reyes
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB1 9SY, UK
| | - Lawrence Kazak
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB1 9SY, UK
| | - Alice Mitchell
- Department of Clinical Movement Neurosciences, Institute of Neurology, Royal Free Campus, University College London, London NW3 2PF, UK
| | - Stuart R Wood
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB1 9SY, UK
| | - Antonella Spinazzola
- Department of Clinical Movement Neurosciences, Institute of Neurology, Royal Free Campus, University College London, London NW3 2PF, UK.,MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, London, UK
| | - Johannes N Spelbrink
- Department of Pediatrics, Radboud Centre for Mitochondrial Medicine, Radboud University Medical Centre, Geert Grooteplein 10, 6500 HB, Nijmegen, The Netherlands
| | - Ian J Holt
- Department of Clinical Movement Neurosciences, Institute of Neurology, Royal Free Campus, University College London, London NW3 2PF, UK.,Biodonostia Health Research Institute, 20014 San Sebastián, Spain and IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
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42
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Mitochondrial Homeostasis and Cellular Senescence. Cells 2019; 8:cells8070686. [PMID: 31284597 PMCID: PMC6678662 DOI: 10.3390/cells8070686] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 07/02/2019] [Accepted: 07/05/2019] [Indexed: 01/07/2023] Open
Abstract
Cellular senescence refers to a stress response aiming to preserve cellular and, therefore, organismal homeostasis. Importantly, deregulation of mitochondrial homeostatic mechanisms, manifested as impaired mitochondrial biogenesis, metabolism and dynamics, has emerged as a hallmark of cellular senescence. On the other hand, impaired mitostasis has been suggested to induce cellular senescence. This review aims to provide an overview of homeostatic mechanisms operating within mitochondria and a comprehensive insight into the interplay between cellular senescence and mitochondrial dysfunction.
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43
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Abstract
Replication stalling has been associated with the formation of pathological mitochondrial DNA (mtDNA) rearrangements. Yet, almost nothing is known about the fate of stalled replication intermediates in mitochondria. We show here that replication stalling in mitochondria leads to replication fork regression and mtDNA double-strand breaks. The resulting mtDNA fragments are normally degraded by a mechanism involving the mitochondrial exonuclease MGME1, and the loss of this enzyme results in accumulation of linear and recombining mtDNA species. Additionally, replication stress promotes the initiation of alternative replication origins as an apparent means of rescue by fork convergence. Besides demonstrating an interplay between two major mechanisms rescuing stalled replication forks – mtDNA degradation and homology-dependent repair – our data provide evidence that mitochondria employ similar mechanisms to cope with replication stress as known from other genetic systems.
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44
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Wanrooij PH, Chabes A. Ribonucleotides in mitochondrial DNA. FEBS Lett 2019; 593:1554-1565. [PMID: 31093968 DOI: 10.1002/1873-3468.13440] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/09/2019] [Accepted: 05/09/2019] [Indexed: 01/05/2023]
Abstract
The incorporation of ribonucleotides (rNMPs) into DNA during genome replication has gained substantial attention in recent years and has been shown to be a significant source of genomic instability. Studies in yeast and mammals have shown that the two genomes, the nuclear DNA (nDNA) and the mitochondrial DNA (mtDNA), differ with regard to their rNMP content. This is largely due to differences in rNMP repair - whereas rNMPs are efficiently removed from the nuclear genome, mitochondria lack robust mechanisms for removal of single rNMPs incorporated during DNA replication. In this minireview, we describe the processes that determine the frequency of rNMPs in the mitochondrial genome and summarise recent findings regarding the effect of incorporated rNMPs on mtDNA stability and function.
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Affiliation(s)
- Paulina H Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, Sweden
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45
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Degtyareva NP, Saini N, Sterling JF, Placentra VC, Klimczak LJ, Gordenin DA, Doetsch PW. Mutational signatures of redox stress in yeast single-strand DNA and of aging in human mitochondrial DNA share a common feature. PLoS Biol 2019; 17:e3000263. [PMID: 31067233 PMCID: PMC6527239 DOI: 10.1371/journal.pbio.3000263] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 05/20/2019] [Accepted: 04/25/2019] [Indexed: 11/18/2022] Open
Abstract
Redox stress is a major hallmark of cancer. Analysis of thousands of sequenced cancer exomes and whole genomes revealed distinct mutational signatures that can be attributed to specific sources of DNA lesions. Clustered mutations discovered in several cancer genomes were linked to single-strand DNA (ssDNA) intermediates in various processes of DNA metabolism. Previously, only one clustered mutational signature had been clearly associated with a subclass of ssDNA-specific apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) cytidine deaminases. Others remain to be elucidated. We report here deciphering of the mutational spectra and mutational signature of redox stress in ssDNA of budding yeast and the signature of aging in human mitochondrial DNA. We found that the predominance of C to T substitutions is a common feature of both signatures. Measurements of the frequencies of hydrogen peroxide-induced mutations in proofreading-defective yeast mutants supported the conclusion that hydrogen peroxide-induced mutagenesis is not the result of increased DNA polymerase misincorporation errors but rather is caused by direct damage to DNA. Proteins involved in modulation of chromatin status play a significant role in prevention of redox stress-induced mutagenesis, possibly by facilitating protection through modification of chromatin structure. These findings provide an opportunity for the search and identification of the mutational signature of redox stress in cancers and in other pathological conditions and could potentially be used for informing therapeutic decisions. In addition, the discovery of such signatures that may be present in related organisms should also advance our understanding of evolution.
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Affiliation(s)
- Natalya P. Degtyareva
- Mutagenesis and DNA Repair Regulation Group, Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina, United States of America
| | - Natalie Saini
- Mechanisms of Genome Dynamics Group, Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina, United States of America
| | - Joan F. Sterling
- Mechanisms of Genome Dynamics Group, Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina, United States of America
| | - Victoria C. Placentra
- Mutagenesis and DNA Repair Regulation Group, Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina, United States of America
| | - Leszek J. Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina, United States of America
| | - Dmitry A. Gordenin
- Mechanisms of Genome Dynamics Group, Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina, United States of America
| | - Paul W. Doetsch
- Mutagenesis and DNA Repair Regulation Group, Laboratory of Genome Integrity and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina, United States of America
- * E-mail:
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46
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Xia X. Is there a mutation gradient along vertebrate mitochondrial genome mediated by genome replication? Mitochondrion 2019; 46:30-40. [DOI: 10.1016/j.mito.2018.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 05/07/2018] [Accepted: 06/13/2018] [Indexed: 11/29/2022]
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47
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Yusoff AAM, Abdullah WSW, Khair SZNM, Radzak SMA. A comprehensive overview of mitochondrial DNA 4977-bp deletion in cancer studies. Oncol Rev 2019; 13:409. [PMID: 31044027 PMCID: PMC6478002 DOI: 10.4081/oncol.2019.409] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 02/19/2019] [Indexed: 01/04/2023] Open
Abstract
Mitochondria are cellular machines essential for energy production. The biogenesis of mitochondria is a highly complex and it depends on the coordination of the nuclear and mitochondrial genome. Mitochondrial DNA (mtDNA) mutations and deletions are suspected to be associated with carcinogenesis. The most described mtDNA deletion in various human cancers is called the 4977-bp common deletion (mDNA4977) and it has been explored since two decades. In spite of that, its implication in carcinogenesis still unknown and its predictive and prognostic impact remains controversial. This review article provides an overview of some of the cellular and molecular mechanisms underlying mDNA4977 formation and a detailed summary about mDNA4977 reported in various types of cancers. The current knowledges of mDNA4977 as a prognostic and predictive marker are also discussed.
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Affiliation(s)
- Abdul Aziz Mohamed Yusoff
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Wan Salihah Wan Abdullah
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | | | - Siti Muslihah Abd Radzak
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
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48
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Chen Z, Zhang F, Xu H. Human mitochondrial DNA diseases and Drosophila models. J Genet Genomics 2019; 46:201-212. [DOI: 10.1016/j.jgg.2019.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 03/05/2019] [Accepted: 03/25/2019] [Indexed: 01/06/2023]
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49
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Nissanka N, Minczuk M, Moraes CT. Mechanisms of Mitochondrial DNA Deletion Formation. Trends Genet 2019; 35:235-244. [PMID: 30691869 DOI: 10.1016/j.tig.2019.01.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 02/02/2023]
Abstract
Mitochondrial DNA (mtDNA) encodes a subset of genes which are essential for oxidative phosphorylation. Deletions in the mtDNA can ablate a number of these genes and result in mitochondrial dysfunction, which is associated with bona fide mitochondrial disorders. Although mtDNA deletions are thought to occur as a result of replication errors or following double-strand breaks, the exact mechanism(s) behind deletion formation have yet to be determined. In this review we discuss the current knowledge about the fate of mtDNA following double-strand breaks, including the molecular players which mediate the degradation of linear mtDNA fragments and possible mechanisms of recircularization. We propose that mtDNA deletions formed from replication errors versus following double-strand breaks can be mediated by separate pathways.
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Affiliation(s)
- Nadee Nissanka
- Department of Neurology, University of Miami, Miller School of Medicine, FL 33136, USA
| | - Michal Minczuk
- Medical Research Council (MRC) Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Carlos T Moraes
- Department of Neurology, University of Miami, Miller School of Medicine, FL 33136, USA.
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50
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Mitochondrial DNA Integrity: Role in Health and Disease. Cells 2019; 8:cells8020100. [PMID: 30700008 PMCID: PMC6406942 DOI: 10.3390/cells8020100] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 01/06/2023] Open
Abstract
As the primary cellular location for respiration and energy production, mitochondria serve in a critical capacity to the cell. Yet, by virtue of this very function of respiration, mitochondria are subject to constant oxidative stress that can damage one of the unique features of this organelle, its distinct genome. Damage to mitochondrial DNA (mtDNA) and loss of mitochondrial genome integrity is increasingly understood to play a role in the development of both severe early-onset maladies and chronic age-related diseases. In this article, we review the processes by which mtDNA integrity is maintained, with an emphasis on the repair of oxidative DNA lesions, and the cellular consequences of diminished mitochondrial genome stability.
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