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Ayala DA, Matarazzo A, Seaberg BL, Patel M, Tijerina E, Matthews C, Bizi G, Brown A, Ta A, Rimer M, Srinivasan R. Heterogeneous brain region-specific responses to astrocytic mitochondrial DNA damage in mice. Sci Rep 2024; 14:18586. [PMID: 39127716 PMCID: PMC11316820 DOI: 10.1038/s41598-024-69499-w] [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: 06/04/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024] Open
Abstract
Astrocytes display context-specific diversity in their functions and respond to noxious stimuli between brain regions. Astrocytic mitochondria have emerged as key players in governing astrocytic functional heterogeneity, given their ability to dynamically adapt their morphology to regional demands on ATP generation and Ca2+ buffering functions. Although there is reciprocal regulation between mitochondrial dynamics and mitochondrial Ca2+ signaling in astrocytes, the extent of this regulation in astrocytes from different brain regions remains unexplored. Brain-wide, experimentally induced mitochondrial DNA (mtDNA) loss in astrocytes showed that mtDNA integrity is critical for astrocyte function, however, possible diverse responses to this noxious stimulus between brain areas were not reported in these experiments. To selectively damage mtDNA in astrocytes in a brain-region-specific manner, we developed a novel adeno-associated virus (AAV)-based tool, Mito-PstI expressing the restriction enzyme PstI, specifically in astrocytic mitochondria. Here, we applied Mito-PstI to two brain regions, the dorsolateral striatum and dentate gyrus, and we show that Mito-PstI induces astrocytic mtDNA loss in vivo, but with remarkable brain-region-dependent differences on mitochondrial dynamics, Ca2+ fluxes, and astrocytic and microglial reactivity. Thus, AAV-Mito-PstI is a novel tool to explore the relationship between astrocytic mitochondrial network dynamics and astrocytic mitochondrial Ca2+ signaling in a brain-region-selective manner.
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Affiliation(s)
- Daniela A Ayala
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, 77843, USA
- Graduate Program in Medical Sciences, Texas A&M University, Bryan, TX, 77843, USA
| | - Anthony Matarazzo
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, 77843, USA
- Graduate Program in Genetics and Genomics, Texas A&M University, Bryan, TX, 77843, USA
| | - Bonnie L Seaberg
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, 77843, USA
| | - Misha Patel
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, 77843, USA
| | - Eliana Tijerina
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, 77843, USA
| | - Camryn Matthews
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, 77843, USA
| | - Gabriel Bizi
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, 77843, USA
| | - Ashton Brown
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, 77843, USA
| | - Alan Ta
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, 77843, USA
| | - Mendell Rimer
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, 77843, USA.
- Graduate Program in Genetics and Genomics, Texas A&M University, Bryan, TX, 77843, USA.
- Texas A&M Institute for Neuroscience, Texas A&M University, Bryan, TX, 77843, USA.
| | - Rahul Srinivasan
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, 77843, USA.
- Graduate Program in Medical Sciences, Texas A&M University, Bryan, TX, 77843, USA.
- Texas A&M Institute for Neuroscience, Texas A&M University, Bryan, TX, 77843, USA.
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2
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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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3
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Ayala DA, Matarazzo A, Seaberg BL, Patel M, Tijerina E, Matthews C, Bizi G, Brown A, Ta A, Rimer M, Srinivasan R. Heterogeneous brain region-specific responses to astrocytic mitochondrial DNA damage in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596517. [PMID: 38853966 PMCID: PMC11160752 DOI: 10.1101/2024.05.29.596517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Astrocytes use Ca 2+ signals to regulate multiple aspects of normal and pathological brain function. Astrocytes display context-specific diversity in their functions, and in their response to noxious stimuli between brain regions. Indeed, astrocytic mitochondria have emerged as key players in governing astrocytic functional heterogeneity, given their ability to dynamically adapt their morphology to regional demands on their ATP generation and Ca 2+ buffering functions. Although there is reciprocal regulation between mitochondrial dynamics and mitochondrial Ca 2+ signaling in astrocytes, the extent of this regulation into the rich diversity of astrocytes in different brain regions remains largely unexplored. Brain-wide, experimentally induced mitochondrial DNA (mtDNA) loss in astrocytes showed that mtDNA integrity is critical for proper astrocyte function, however, few insights into possible diverse responses to this noxious stimulus from astrocytes in different brain areas were reported in these experiments. To selectively damage mtDNA in astrocytes in a brain-region-specific manner, we developed a novel adeno-associated virus (AAV)-based tool, Mito-PstI, which expresses the restriction enzyme PstI, specifically in astrocytic mitochondria. Here, we applied Mito-PstI to two distinct brain regions, the dorsolateral striatum, and the hippocampal dentate gyrus, and we show that Mito-PstI can induce astrocytic mtDNA loss in vivo , but with remarkable brain-region-dependent differences on mitochondrial dynamics, spontaneous Ca 2+ fluxes and astrocytic as well as microglial reactivity. Thus, AAV-Mito-PstI is a novel tool to explore the relationship between astrocytic mitochondrial network dynamics and astrocytic mitochondrial Ca 2+ signaling in a brain-region-selective manner.
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4
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Yu C, Asadian S, Tigano M. Molecular and cellular consequences of mitochondrial DNA double-stranded breaks. Hum Mol Genet 2024; 33:R12-R18. [PMID: 38779775 PMCID: PMC11112379 DOI: 10.1093/hmg/ddae048] [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: 02/12/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 05/25/2024] Open
Abstract
Mitochondria are subcellular organelles essential for life. Beyond their role in producing energy, mitochondria govern various physiological mechanisms, encompassing energy generation, metabolic processes, apoptotic events, and immune responses. Mitochondria also contain genetic material that is susceptible to various forms of damage. Mitochondrial double-stranded breaks (DSB) are toxic lesions that the nucleus repairs promptly. Nevertheless, the significance of DSB repair in mammalian mitochondria is controversial. This review presents an updated view of the available research on the consequences of mitochondrial DNA DSB from the molecular to the cellular level. We discuss the crucial function of mitochondrial DNA damage in regulating processes such as senescence, integrated stress response, and innate immunity. Lastly, we discuss the potential role of mitochondrial DNA DSB in mediating the cellular consequences of ionizing radiations, the standard of care in treating solid tumors.
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Affiliation(s)
- Chenxiao Yu
- Department of Pathology and Genomic Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia 19107, United States
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, 199 Renai Road, Suzhou 215123, China
| | - Samieh Asadian
- Tehran University of Medical Sciences, Pour Sina St, Tehran 1416634793, Iran
| | - Marco Tigano
- Department of Pathology and Genomic Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia 19107, United States
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5
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Nikitchina N, Ulashchik E, Shmanai V, Heckel AM, Tarassov I, Mazunin I, Entelis N. Targeting of CRISPR-Cas12a crRNAs into human mitochondria. Biochimie 2024; 217:74-85. [PMID: 37690471 DOI: 10.1016/j.biochi.2023.09.006] [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: 05/15/2023] [Revised: 08/10/2023] [Accepted: 09/04/2023] [Indexed: 09/12/2023]
Abstract
Mitochondrial gene editing holds great promise as a therapeutic approach for mitochondrial diseases caused by mutations in the mitochondrial DNA (mtDNA). Current strategies focus on reducing mutant mtDNA heteroplasmy levels through targeted cleavage or base editing. However, the delivery of editing components into mitochondria remains a challenge. Here we investigate the import of CRISPR-Cas12a system guide RNAs (crRNAs) into human mitochondria and study the structural requirements for this process by northern blot analysis of RNA isolated from nucleases-treated mitoplasts. To investigate whether the fusion of crRNA with known RNA import determinants (MLS) improve its mitochondrial targeting, we added MLS hairpin structures at 3'-end of crRNA and demonstrated that this did not impact crRNA ability to program specific cleavage of DNA in lysate of human cells expressing AsCas12a nuclease. Surprisingly, mitochondrial localization of the fused crRNA molecules was not improved compared to non-modified version, indicating that structured scaffold domain of crRNA can probably function as MLS, assuring crRNA mitochondrial import. Then, we designed a series of crRNAs targeting different regions of mtDNA and demonstrated their ability to program specific cleavage of mtDNA fragments in cell lysate and their partial localization in mitochondrial matrix in human cells transfected with these RNA molecules. We hypothesize that mitochondrial import of crRNAs may depend on their secondary structure/sequence. We presume that imported crRNA allow reconstituting the active crRNA/Cas12a system in human mitochondria, which can contribute to the development of effective strategies for mitochondrial gene editing and potential future treatment of mitochondrial diseases.
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Affiliation(s)
- Natalia Nikitchina
- UMR7156 - Molecular Genetics, Genomics, Microbiology, University of Strasbourg, Strasbourg, 67000, France
| | - Egor Ulashchik
- Institute of Physical Organic Chemistry, National Academy of Science of Belarus, Minsk, 220072, Belarus
| | - Vadim Shmanai
- Institute of Physical Organic Chemistry, National Academy of Science of Belarus, Minsk, 220072, Belarus
| | - Anne-Marie Heckel
- UMR7156 - Molecular Genetics, Genomics, Microbiology, University of Strasbourg, Strasbourg, 67000, France
| | - Ivan Tarassov
- UMR7156 - Molecular Genetics, Genomics, Microbiology, University of Strasbourg, Strasbourg, 67000, France
| | - Ilya Mazunin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, 143026, Russia
| | - Nina Entelis
- UMR7156 - Molecular Genetics, Genomics, Microbiology, University of Strasbourg, Strasbourg, 67000, France.
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6
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Shammas MK, Nie Y, Gilsrud A, Huang X, Narendra DP, Chinnery PF. CHCHD10 mutations induce tissue-specific mitochondrial DNA deletions with a distinct signature. Hum Mol Genet 2023; 33:91-101. [PMID: 37815936 PMCID: PMC10729859 DOI: 10.1093/hmg/ddad161] [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: 06/19/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 10/12/2023] Open
Abstract
Mutations affecting the mitochondrial intermembrane space protein CHCHD10 cause human disease, but it is not known why different amino acid substitutions cause markedly different clinical phenotypes, including amyotrophic lateral sclerosis-frontotemporal dementia, spinal muscular atrophy Jokela-type, isolated autosomal dominant mitochondrial myopathy and cardiomyopathy. CHCHD10 mutations have been associated with deletions of mitochondrial DNA (mtDNA deletions), raising the possibility that these explain the clinical variability. Here, we sequenced mtDNA obtained from hearts, skeletal muscle, livers and spinal cords of WT and Chchd10 G58R or S59L knockin mice to characterise the mtDNA deletion signatures of the two mutant lines. We found that the deletion levels were higher in G58R and S59L mice than in WT mice in some tissues depending on the Chchd10 genotype, and the deletion burden increased with age. Furthermore, we observed that the spinal cord was less prone to the development of mtDNA deletions than the other tissues examined. Finally, in addition to accelerating the rate of naturally occurring deletions, Chchd10 mutations also led to the accumulation of a novel set of deletions characterised by shorter direct repeats flanking the deletion breakpoints. Our results indicate that Chchd10 mutations in mice induce tissue-specific deletions which may also contribute to the clinical phenotype associated with these mutations in humans.
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Affiliation(s)
- Mario K Shammas
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, United Kingdom
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 35 Convent Drive, Bethesda, MD 20892, United States
| | - Yu Nie
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, United Kingdom
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Alexandra Gilsrud
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 35 Convent Drive, Bethesda, MD 20892, United States
| | - Xiaoping Huang
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 35 Convent Drive, Bethesda, MD 20892, United States
| | - Derek P Narendra
- Inherited Movement Disorders Unit, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 35 Convent Drive, Bethesda, MD 20892, United States
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, United Kingdom
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom
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7
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Wang X, Lu H, Li M, Zhang Z, Wei Z, Zhou P, Cao Y, Ji D, Zou W. Research development and the prospect of animal models of mitochondrial DNA-related mitochondrial diseases. Anal Biochem 2023; 669:115122. [PMID: 36948236 DOI: 10.1016/j.ab.2023.115122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/19/2023] [Accepted: 03/19/2023] [Indexed: 03/24/2023]
Abstract
Mitochondrial diseases (MDs) are genetic and clinical heterogeneous diseases caused by mitochondrial oxidative phosphorylation defects. It is not only one of the most common genetic diseases, but also the only genetic disease involving two different genomes in humans. As a result of the complicated genetic condition, the pathogenesis of MDs is not entirely elucidated at present, and there is a lack of effective treatment in the clinic. Establishing the ideal animal models is the critical preclinical platform to explore the pathogenesis of MDs and to verify new therapeutic strategies. However, the development of animal modeling of mitochondrial DNA (mtDNA)-related MDs is time-consuming due to the limitations of physiological structure and technology. A small number of animal models of mtDNA mutations have been constructed using cell hybridization and other methods. However, the diversity of mtDNA mutation sites and clinical phenotypes make establishing relevant animal models tricky. The development of gene editing technology has become a new hope for establishing animal models of mtDNA-related mitochondrial diseases.
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Affiliation(s)
- Xiaolei Wang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University, Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Hedong Lu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University, Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Min Li
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University, Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Zhiguo Zhang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University, Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Zhaolian Wei
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University, Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Ping Zhou
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China; Anhui Province Key Laboratory of Reproductive Health and Genetics, No 81 Meishan Road, Hefei, 230032, Anhui, China; Biopreservation and Artificial Organs, Anhui Provincial Engineering Research Center, Anhui Medical University, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Yunxia Cao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University, Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China.
| | - Dongmei Ji
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China; Anhui Province Key Laboratory of Reproductive Health and Genetics, No 81 Meishan Road, Hefei, 230032, Anhui, China; Biopreservation and Artificial Organs, Anhui Provincial Engineering Research Center, Anhui Medical University, No 81 Meishan Road, Hefei, 230032, Anhui, China.
| | - Weiwei Zou
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), No 81 Meishan Road, Hefei, 230032, Anhui, China; Key Laboratory of Population Health Across Life Cycle (Anhui Medical University, Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China.
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8
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Dahal S, Siddiqua H, Sharma S, Babu RK, Rathore D, Sharma S, Raghavan SC. Unleashing a novel function of Endonuclease G in mitochondrial genome instability. eLife 2022; 11:e69916. [PMID: 36394256 PMCID: PMC9711528 DOI: 10.7554/elife.69916] [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: 04/29/2021] [Accepted: 11/16/2022] [Indexed: 11/18/2022] Open
Abstract
Having its genome makes the mitochondrion a unique and semiautonomous organelle within cells. Mammalian mitochondrial DNA (mtDNA) is a double-stranded closed circular molecule of about 16 kb coding for 37 genes. Mutations, including deletions in the mitochondrial genome, can culminate in different human diseases. Mapping the deletion junctions suggests that the breakpoints are generally seen at hotspots. '9 bp deletion' (8271-8281), seen in the intergenic region of cytochrome c oxidase II/tRNALys, is the most common mitochondrial deletion. While it is associated with several diseases like myopathy, dystonia, and hepatocellular carcinoma, it has also been used as an evolutionary marker. However, the mechanism responsible for its fragility is unclear. In the current study, we show that Endonuclease G, a mitochondrial nuclease responsible for nonspecific cleavage of nuclear DNA during apoptosis, can induce breaks at sequences associated with '9 bp deletion' when it is present on a plasmid or in the mitochondrial genome. Through a series of in vitro and intracellular studies, we show that Endonuclease G binds to G-quadruplex structures formed at the hotspot and induces DNA breaks. Therefore, we uncover a new role for Endonuclease G in generating mtDNA deletions, which depends on the formation of G4 DNA within the mitochondrial genome. In summary, we identify a novel property of Endonuclease G, besides its role in apoptosis and the recently described 'elimination of paternal mitochondria during fertilisation.
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Affiliation(s)
- Sumedha Dahal
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Humaira Siddiqua
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Shivangi Sharma
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Ravi K Babu
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Diksha Rathore
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Sheetal Sharma
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
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9
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Dogan SA, Giacchin G, Zito E, Viscomi C. Redox Signaling and Stress in Inherited Myopathies. Antioxid Redox Signal 2022; 37:301-323. [PMID: 35081731 DOI: 10.1089/ars.2021.0266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Significance: Reactive oxygen species (ROS) are highly reactive compounds that behave like a double-edged sword; they damage cellular structures and act as second messengers in signal transduction. Mitochondria and endoplasmic reticulum (ER) are interconnected organelles with a central role in ROS production, detoxification, and oxidative stress response. Skeletal muscle is the most abundant tissue in mammals and one of the most metabolically active ones and thus relies mainly on oxidative phosphorylation (OxPhos) to synthesize adenosine triphosphate. The impairment of OxPhos leads to myopathy and increased ROS production, thus affecting both redox poise and signaling. In addition, ROS enter the ER and trigger ER stress and its maladaptive response, which also lead to a myopathic phenotype with mitochondrial involvement. Here, we review the role of ROS signaling in myopathies due to either mitochondrial or ER dysfunction. Recent Advances: Relevant advances have been evolving over the last 10 years on the intricate ROS-dependent pathways that act as modifiers of the disease course in several myopathies. To this end, pathways related to mitochondrial biogenesis, satellite cell differentiation, and ER stress have been studied extensively in myopathies. Critical Issues: The analysis of the chemistry and the exact quantitation, as well as the localization of ROS, are still challenging due to the intrinsic labile nature of ROS and the technical limitations of their sensors. Future Directions: The mechanistic studies of the pathogenesis of mitochondrial and ER-related myopathies offer a unique possibility to discover novel ROS-dependent pathways. Antioxid. Redox Signal. 37, 301-323.
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Affiliation(s)
- Sukru Anil Dogan
- Department of Molecular Biology and Genetics, Center for Life Sciences and Technologies, Bogazici University, Istanbul, Turkey
| | - Giacomo Giacchin
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Ester Zito
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy.,Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Carlo Viscomi
- Department of Biomedical Sciences, University of Padova, Padova, Italy
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10
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Sabharwal A, Campbell JM, Schwab TL, WareJoncas Z, Wishman MD, Ata H, Liu W, Ichino N, Hunter DE, Bergren JD, Urban MD, Urban RM, Holmberg SR, Kar B, Cook A, Ding Y, Xu X, Clark KJ, Ekker SC. A Primer Genetic Toolkit for Exploring Mitochondrial Biology and Disease Using Zebrafish. Genes (Basel) 2022; 13:1317. [PMID: 35893052 PMCID: PMC9331066 DOI: 10.3390/genes13081317] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/14/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023] Open
Abstract
Mitochondria are a dynamic eukaryotic innovation that play diverse roles in biology and disease. The mitochondrial genome is remarkably conserved in all vertebrates, encoding the same 37-gene set and overall genomic structure, ranging from 16,596 base pairs (bp) in the teleost zebrafish (Danio rerio) to 16,569 bp in humans. Mitochondrial disorders are amongst the most prevalent inherited diseases, affecting roughly 1 in every 5000 individuals. Currently, few effective treatments exist for those with mitochondrial ailments, representing a major unmet patient need. Mitochondrial dysfunction is also a common component of a wide variety of other human illnesses, ranging from neurodegenerative disorders such as Huntington's disease and Parkinson's disease to autoimmune illnesses such as multiple sclerosis and rheumatoid arthritis. The electron transport chain (ETC) component of mitochondria is critical for mitochondrial biology and defects can lead to many mitochondrial disease symptoms. Here, we present a publicly available collection of genetic mutants created in highly conserved, nuclear-encoded mitochondrial genes in Danio rerio. The zebrafish system represents a potentially powerful new opportunity for the study of mitochondrial biology and disease due to the large number of orthologous genes shared with humans and the many advanced features of this model system, from genetics to imaging. This collection includes 15 mutant lines in 13 different genes created through locus-specific gene editing to induce frameshift or splice acceptor mutations, leading to predicted protein truncation during translation. Additionally, included are 11 lines created by the random insertion of the gene-breaking transposon (GBT) protein trap cassette. All these targeted mutant alleles truncate conserved domains of genes critical to the proper function of the ETC or genes that have been implicated in human mitochondrial disease. This collection is designed to accelerate the use of zebrafish to study many different aspects of mitochondrial function to widen our understanding of their role in biology and human disease.
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Affiliation(s)
- Ankit Sabharwal
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Jarryd M. Campbell
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Tanya L. Schwab
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Zachary WareJoncas
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Mark D. Wishman
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Hirotaka Ata
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Wiebin Liu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
- Division of Cardiovascular Diseases, Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Noriko Ichino
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Danielle E. Hunter
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Jake D. Bergren
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Mark D. Urban
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Rhianna M. Urban
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Shannon R. Holmberg
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Bibekananda Kar
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Alex Cook
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Yonghe Ding
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
- Division of Cardiovascular Diseases, Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaolei Xu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
- Division of Cardiovascular Diseases, Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Karl J. Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Stephen C. Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
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11
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Nadalutti CA, Ayala-Peña S, Santos JH. Mitochondrial DNA damage as driver of cellular outcomes. Am J Physiol Cell Physiol 2022; 322:C136-C150. [PMID: 34936503 PMCID: PMC8799395 DOI: 10.1152/ajpcell.00389.2021] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Mitochondria are primarily involved in energy production through the process of oxidative phosphorylation (OXPHOS). Increasing evidence has shown that mitochondrial function impacts a plethora of different cellular activities, including metabolism, epigenetics, and innate immunity. Like the nucleus, mitochondria own their genetic material, but this organellar genome is circular, present in multiple copies, and maternally inherited. The mitochondrial DNA (mtDNA) encodes 37 genes that are solely involved in OXPHOS. Maintenance of mtDNA, through replication and repair, requires the import of nuclear DNA-encoded proteins. Thus, mitochondria completely rely on the nucleus to prevent mitochondrial genetic alterations. As most cells contain hundreds to thousands of mitochondria, it follows that the shear number of organelles allows for the buffering of dysfunction-at least to some extent-before tissue homeostasis becomes impaired. Only red blood cells lack mitochondria entirely. Impaired mitochondrial function is a hallmark of aging and is involved in a number of different disorders, including neurodegenerative diseases, diabetes, cancer, and autoimmunity. Although alterations in mitochondrial processes unrelated to OXPHOS, such as fusion and fission, contribute to aging and disease, maintenance of mtDNA integrity is critical for proper organellar function. Here, we focus on how mtDNA damage contributes to cellular dysfunction and health outcomes.
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Affiliation(s)
- Cristina A. Nadalutti
- 1Mechanistic Toxicology Branch, Division of the National Toxicology
Program (DNTP), National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Research Triangle Park, North Carolina
| | - Sylvette Ayala-Peña
- 2Department of Pharmacology and Toxicology, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - Janine H. Santos
- 1Mechanistic Toxicology Branch, Division of the National Toxicology
Program (DNTP), National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Research Triangle Park, North Carolina
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12
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Liang H, Liu J, Su S, Zhao Q. Mitochondrial noncoding RNAs: new wine in an old bottle. RNA Biol 2021; 18:2168-2182. [PMID: 34110970 DOI: 10.1080/15476286.2021.1935572] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial noncoding RNAs (mt-ncRNAs) include noncoding RNAs inside the mitochondria that are transcribed from the mitochondrial genome or nuclear genome, and noncoding RNAs transcribed from the mitochondrial genome that are transported to the cytosol or nucleus. Recent findings have revealed that mt-ncRNAs play important roles in not only mitochondrial functions, but also other cellular activities. This review proposes a classification of mt-ncRNAs and outlines the emerging understanding of mitochondrial circular RNAs (mt-circRNAs), mitochondrial microRNAs (mitomiRs), and mitochondrial long noncoding RNAs (mt-lncRNAs), with an emphasis on their identification and functions.
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Affiliation(s)
- Huixin Liang
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Jiayu Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Shicheng Su
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Department of Immunology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Qiyi Zhao
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
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13
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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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14
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Lakshmanan LN, Yee Z, Halliwell B, Gruber J, Gunawan R. Thermodynamic analysis of DNA hybridization signatures near mitochondrial DNA deletion breakpoints. iScience 2021; 24:102138. [PMID: 33665557 PMCID: PMC7900216 DOI: 10.1016/j.isci.2021.102138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/14/2021] [Accepted: 01/29/2021] [Indexed: 11/17/2022] Open
Abstract
Broad evidence in the literature supports double-strand breaks (DSBs) as initiators of mitochondrial DNA (mtDNA) deletion mutations. While DNA misalignment during DSB repair is commonly proposed as the mechanism by which DSBs cause deletion mutations, details such as the specific DNA repair errors are still lacking. Here, we used DNA hybridization thermodynamics to infer the sequence lengths of mtDNA misalignments that are associated with mtDNA deletions. We gathered and analyzed 9,921 previously reported mtDNA deletion breakpoints in human, rhesus monkey, mouse, rat, and Caenorhabditis elegans. Our analysis shows that a large fraction of mtDNA breakpoint positions can be explained by the thermodynamics of short ≤ 5-nt misalignments. The significance of short DNA misalignments supports an important role for erroneous non-homologous and micro-homology-dependent DSB repair in mtDNA deletion formation. The consistency of the results of our analysis across species further suggests a shared mode of mtDNA deletion mutagenesis.
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Affiliation(s)
- Lakshmi Narayanan Lakshmanan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Zhuangli Yee
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Barry Halliwell
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jan Gruber
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Ageing Research Laboratory, Science Division, Yale-NUS College, Singapore, Singapore
| | - Rudiyanto Gunawan
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, NY, USA
- Corresponding author
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15
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Stewart JB. Current progress with mammalian models of mitochondrial DNA disease. J Inherit Metab Dis 2021; 44:325-342. [PMID: 33099782 DOI: 10.1002/jimd.12324] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 12/16/2022]
Abstract
Mitochondrial disorders make up a large class of heritable diseases that cause a broad array of different human pathologies. They can affect many different organ systems, or display very specific tissue presentation, and can lead to illness either in childhood or later in life. While the over 1200 genes encoded in the nuclear DNA play an important role in human mitochondrial disease, it has been known for over 30 years that mutations of the mitochondria's own small, multicopy DNA chromosome (mtDNA) can lead to heritable human diseases. Unfortunately, animal mtDNA has resisted transgenic and directed genome editing technologies until quite recently. As such, animal models to aid in our understanding of these diseases, and to explore preclinical therapeutic research have been quite rare. This review will discuss the unusual properties of animal mitochondria that have hindered the generation of animal models. It will also discuss the existing mammalian models of human mtDNA disease, describe the methods employed in their generation, and will discuss recent advances in the targeting of DNA-manipulating enzymes to the mitochondria and how these may be employed to generate new models.
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Affiliation(s)
- James Bruce Stewart
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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16
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Zakirova EG, Muzyka VV, Mazunin IO, Orishchenko KE. Natural and Artificial Mechanisms of Mitochondrial Genome Elimination. Life (Basel) 2021; 11:life11020076. [PMID: 33498399 PMCID: PMC7909434 DOI: 10.3390/life11020076] [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: 12/18/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 01/11/2023] Open
Abstract
The generally accepted theory of the genetic drift of mitochondrial alleles during mammalian ontogenesis is based on the presence of a selective bottleneck in the female germline. However, there is a variety of different theories on the pathways of genetic regulation of mitochondrial DNA (mtDNA) dynamics in oogenesis and adult somatic cells. The current review summarizes present knowledge on the natural mechanisms of mitochondrial genome elimination during mammalian development. We also discuss the variety of existing and developing methodologies for artificial manipulation of the mtDNA heteroplasmy level. Understanding of the basics of mtDNA dynamics will shed the light on the pathogenesis and potential therapies of human diseases associated with mitochondrial dysfunction.
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Affiliation(s)
- Elvira G. Zakirova
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.G.Z.); (V.V.M.)
| | - Vladimir V. Muzyka
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.G.Z.); (V.V.M.)
- Department of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Ilya O. Mazunin
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Russia;
| | - Konstantin E. Orishchenko
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.G.Z.); (V.V.M.)
- Department of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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p53 is required for nuclear but not mitochondrial DNA damage-induced degeneration. Cell Death Dis 2021; 12:104. [PMID: 33473103 PMCID: PMC7817838 DOI: 10.1038/s41419-020-03373-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 12/18/2022]
Abstract
While the consequences of nuclear DNA damage have been well studied, the exact consequences of acute and selective mitochondrial DNA (mtDNA) damage are less understood. DNA damaging chemotherapeutic drugs are known to activate p53-dependent apoptosis in response to sustained nuclear DNA damage. While it is recognized that whole-cell exposure to these drugs also damages mtDNA, the specific contribution of mtDNA damage to cellular degeneration is less clear. To examine this, we induced selective mtDNA damage in neuronal axons using microfluidic chambers that allow for the spatial and fluidic isolation of neuronal cell bodies (containing nucleus and mitochondria) from the axons (containing mitochondria). Exposure of the DNA damaging drug cisplatin selectively to only the axons induced mtDNA damage in axonal mitochondria, without nuclear damage. We found that this resulted in the selective degeneration of only the targeted axons that were exposed to DNA damage, where ROS was induced but mitochondria were not permeabilized. mtDNA damage-induced axon degeneration was not mediated by any of the three known axon degeneration pathways: apoptosis, axon pruning, and Wallerian degeneration, as Bax-deficiency, or Casp3-deficiency, or Sarm1-deficiency failed to protect the degenerating axons. Strikingly, p53, which is essential for degeneration after nuclear DNA damage, was also not required for degeneration induced with mtDNA damage. This was most evident when the p53-deficient neurons were globally exposed to cisplatin. While the cell bodies of p53-deficient neurons were protected from degeneration in this context, the axons farthest from the cell bodies still underwent degeneration. These results highlight how whole cell exposure to DNA damage activates two pathways of degeneration; a faster, p53-dependent apoptotic degeneration that is triggered in the cell bodies with nuclear DNA damage, and a slower, p53-independent degeneration that is induced with mtDNA damage.
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18
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Wang B, Lv X, Wang Y, Wang Z, Liu Q, Lu B, Liu Y, Gu F. CRISPR/Cas9-mediated mutagenesis at microhomologous regions of human mitochondrial genome. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1463-1472. [PMID: 33420919 DOI: 10.1007/s11427-020-1819-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/04/2020] [Indexed: 12/21/2022]
Abstract
Genetic manipulation of mitochondrial DNA (mtDNA) could be harnessed for deciphering the gene function of mitochondria; it also acts as a promising approach for the therapeutic correction of pathogenic mutation in mtDNA. However, there is still a lack of direct evidence showing the edited mutagenesis within human mtDNA by clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9). Here, using engineered CRISPR/Cas9, we observed numerous insertion/deletion (InDel) events at several mtDNA microhomologous regions, which were triggered specifically by double-strand break (DSB) lesions within mtDNA. InDel mutagenesis was significantly improved by sgRNA multiplexing and a DSB repair inhibitor, iniparib, demonstrating the evidence of rewiring DSB repair status to manipulate mtDNA using CRISPR/Cas9. These findings would provide novel insights into mtDNA mutagenesis and mitochondrial gene therapy for diseases involving pathogenic mtDNA.
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Affiliation(s)
- Bang Wang
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory of Ophthalmology, Optometry and Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Xiujuan Lv
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory of Ophthalmology, Optometry and Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Yufei Wang
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory of Ophthalmology, Optometry and Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhibo Wang
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory of Ophthalmology, Optometry and Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Qi Liu
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 200092, China
| | - Bin Lu
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Yong Liu
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory of Ophthalmology, Optometry and Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Feng Gu
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory of Ophthalmology, Optometry and Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, 325027, China.
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19
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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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20
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Chesner LN, Essawy M, Warner C, Campbell C. DNA-protein crosslinks are repaired via homologous recombination in mammalian mitochondria. DNA Repair (Amst) 2020; 97:103026. [PMID: 33316746 PMCID: PMC7855827 DOI: 10.1016/j.dnarep.2020.103026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/24/2020] [Accepted: 11/12/2020] [Indexed: 11/19/2022]
Abstract
While mammalian mitochondria are known to possess a robust base excision repair system, direct evidence for the existence of additional mitochondrial DNA repair pathways is elusive. Herein a PCR-based assay was employed to demonstrate that plasmids containing DNA-protein crosslinks are rapidly repaired following electroporation into isolated mammalian mitochondria. Several lines of evidence argue that this repair occurs via homologous recombination. First, DNA-protein crosslinks present on plasmid DNA homologous to the mitochondrial genome were efficiently repaired (21 % repair in three hours), whereas a DNA-protein crosslink present on DNA that lacked homology to the mitochondrial genome remained unrepaired. Second, DNA-protein crosslinks present on plasmid DNA lacking homology to the mitochondrial genome were repaired when they were co-electroporated into mitochondria with an undamaged, homologous plasmid DNA molecule. Third, no repair was observed when DNA-protein crosslink-containing plasmids were electroporated into mitochondria isolated from cells pre-treated with the Rad51 inhibitor B02. These findings suggest that mitochondria utilize homologous recombination to repair endogenous and xenobiotic-induced DNA-protein crosslinks. Consistent with this interpretation, cisplatin-induced mitochondrial DNA-protein crosslinks accumulated to higher levels in cells pre-treated with B02 than in control cisplatin-treated cells. These results represent the first evidence of how spontaneous and xenobiotic-induced DNA-protein crosslinks are removed from mitochondrial DNA.
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Affiliation(s)
- Lisa N Chesner
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Maram Essawy
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Cecilia Warner
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Colin Campbell
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455, USA.
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21
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Bagge EK, Fujimori-Tonou N, Kubota-Sakashita M, Kasahara T, Kato T. Unbiased PCR-free spatio-temporal mapping of the mtDNA mutation spectrum reveals brain region-specific responses to replication instability. BMC Biol 2020; 18:150. [PMID: 33097039 PMCID: PMC7585204 DOI: 10.1186/s12915-020-00890-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/06/2020] [Indexed: 12/24/2022] Open
Abstract
Background The accumulation of mtDNA mutations in different tissues from various mouse models has been widely studied especially in the context of mtDNA mutation-driven ageing but has been confounded by the inherent limitations of the most widely used approaches. By implementing a method to sequence mtDNA without PCR amplification prior to library preparation, we map the full unbiased mtDNA mutation spectrum across six distinct brain regions from mice. Results We demonstrate that ageing-induced levels of mtDNA mutations (single nucleotide variants and deletions) reach stable levels at 50 weeks of age but can be further elevated specifically in the cortex, nucleus accumbens (NAc), and paraventricular thalamic nucleus (PVT) by expression of a proof-reading-deficient mitochondrial DNA polymerase, PolgD181A. The increase in single nucleotide variants increases the fraction of shared SNVs as well as their frequency, while characteristics of deletions remain largely unaffected. In addition, PolgD181A also induces an ageing-dependent accumulation of non-coding control-region multimers in NAc and PVT, a feature that appears almost non-existent in wild-type mice. Conclusions Our data provide a novel view of the spatio-temporal accumulation of mtDNA mutations using very limited tissue input. The differential response of brain regions to a state of replication instability provides insight into a possible heterogenic mitochondrial landscape across the brain that may be involved in the ageing phenotype and mitochondria-associated disorders.
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Affiliation(s)
- Emilie Kristine Bagge
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Noriko Fujimori-Tonou
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, Japan.,Current address: Support Unit for Bio-Material Analysis, Research Resources Division, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Mie Kubota-Sakashita
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Takaoki Kasahara
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, Japan.,Current address: Career Development Program, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, Japan. .,Department of Psychiatry and Behavioral Science, Juntendo University, Graduate School of Medicine, Hongo 2-1-1, Bunkyo, Tokyo 113-8421, Japan.
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22
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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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23
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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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24
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Fu Y, Tigano M, Sfeir A. Safeguarding mitochondrial genomes in higher eukaryotes. Nat Struct Mol Biol 2020; 27:687-695. [PMID: 32764737 DOI: 10.1038/s41594-020-0474-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/02/2020] [Indexed: 12/20/2022]
Abstract
Mitochondria respond to DNA damage and preserve their own genetic material in a manner distinct from that of the nucleus but that requires organized mito-nuclear communication. Failure to resolve mtDNA breaks leads to mitochondrial dysfunction and affects host cells and tissues. Here, we review the pathways that safeguard mitochondrial genomes and examine the insights gained from studies of cellular and tissue-wide responses to mtDNA damage and mito-nuclear genome incompatibility.
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Affiliation(s)
- Yi Fu
- Skirball Institute of Biomolecular Medicine, Cell Biology Department, NYU Grossman School of Medicine, New York, NY, USA
| | - Marco Tigano
- Skirball Institute of Biomolecular Medicine, Cell Biology Department, NYU Grossman School of Medicine, New York, NY, USA
| | - Agnel Sfeir
- Skirball Institute of Biomolecular Medicine, Cell Biology Department, NYU Grossman School of Medicine, New York, NY, USA.
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25
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Oliveira MT, Pontes CDB, Ciesielski GL. Roles of the mitochondrial replisome in mitochondrial DNA deletion formation. Genet Mol Biol 2020; 43:e20190069. [PMID: 32141473 PMCID: PMC7197994 DOI: 10.1590/1678-4685-gmb-2019-0069] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 08/12/2019] [Indexed: 01/07/2023] Open
Abstract
Mitochondrial DNA (mtDNA) deletions are a common cause of human mitochondrial
diseases. Mutations in the genes encoding components of the mitochondrial
replisome, such as DNA polymerase gamma (Pol γ) and the mtDNA helicase Twinkle,
have been associated with the accumulation of such deletions and the development
of pathological conditions in humans. Recently, we demonstrated that changes in
the level of wild-type Twinkle promote mtDNA deletions, which implies that not
only mutations in, but also dysregulation of the stoichiometry between the
replisome components is potentially pathogenic. The mechanism(s) by which
alterations to the replisome function generate mtDNA deletions is(are) currently
under debate. It is commonly accepted that stalling of the replication fork at
sites likely to form secondary structures precedes the deletion formation. The
secondary structural elements can be bypassed by the replication-slippage
mechanism. Otherwise, stalling of the replication fork can generate single- and
double-strand breaks, which can be repaired through recombination leading to the
elimination of segments between the recombination sites. Here, we discuss
aberrances of the replisome in the context of the two debated outcomes, and
suggest new mechanistic explanations based on replication restart and template
switching that could account for all the deletion types reported for
patients.
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Affiliation(s)
- Marcos T Oliveira
- Universidade Estadual Paulista Júlio de Mesquita Filho, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil
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26
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Nissanka N, Moraes CT. Mitochondrial DNA heteroplasmy in disease and targeted nuclease-based therapeutic approaches. EMBO Rep 2020; 21:e49612. [PMID: 32073748 DOI: 10.15252/embr.201949612] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/11/2019] [Accepted: 01/29/2020] [Indexed: 12/31/2022] Open
Abstract
Mitochondrial DNA (mtDNA) encodes a subset of the genes which are responsible for oxidative phosphorylation. Pathogenic mutations in the human mtDNA are often heteroplasmic, where wild-type mtDNA species co-exist with the pathogenic mtDNA and a bioenergetic defect is only seen when the pathogenic mtDNA percentage surpasses a threshold for biochemical manifestations. mtDNA segregation during germline development can explain some of the extreme variation in heteroplasmy from one generation to the next. Patients with high heteroplasmy for deleterious mtDNA species will likely suffer from bona-fide mitochondrial diseases, which currently have no cure. Shifting mtDNA heteroplasmy toward the wild-type mtDNA species could provide a therapeutic option to patients. Mitochondrially targeted engineered nucleases, such as mitoTALENs and mitoZFNs, have been used in vitro in human cells harboring pathogenic patient-derived mtDNA mutations and more recently in vivo in a mouse model of a pathogenic mtDNA point mutation. These gene therapy tools for shifting mtDNA heteroplasmy can also be used in conjunction with other therapies aimed at eliminating and/or preventing the transfer of pathogenic mtDNA from mother to child.
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Affiliation(s)
- Nadee Nissanka
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Carlos T Moraes
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
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27
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Bacman SR, Gammage P, Minczuk M, Moraes CT. Manipulation of mitochondrial genes and mtDNA heteroplasmy. Methods Cell Biol 2020; 155:441-487. [DOI: 10.1016/bs.mcb.2019.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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28
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Kotrys AV, Szczesny RJ. Mitochondrial Gene Expression and Beyond-Novel Aspects of Cellular Physiology. Cells 2019; 9:cells9010017. [PMID: 31861673 PMCID: PMC7017415 DOI: 10.3390/cells9010017] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 02/06/2023] Open
Abstract
Mitochondria are peculiar organelles whose proper function depends on the crosstalk between two genomes, mitochondrial and nuclear. The human mitochondrial genome (mtDNA) encodes only 13 proteins; nevertheless, its proper expression is essential for cellular homeostasis, as mtDNA-encoded proteins are constituents of mitochondrial respiratory complexes. In addition, mtDNA expression results in the production of RNA molecules, which influence cell physiology once released from the mitochondria into the cytoplasm. As a result, dysfunctions of mtDNA expression may lead to pathologies in humans. Here, we review the mechanisms of mitochondrial gene expression with a focus on recent findings in the field. We summarize the complex turnover of mitochondrial transcripts and present an increasing body of evidence indicating new functions of mitochondrial transcripts. We discuss mitochondrial gene regulation in different cellular contexts, focusing on stress conditions. Finally, we highlight the importance of emerging aspects of mitochondrial gene regulation in human health and disease.
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29
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Wallis CP, Scott LH, Filipovska A, Rackham O. Manipulating and elucidating mitochondrial gene expression with engineered proteins. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190185. [PMID: 31787043 DOI: 10.1098/rstb.2019.0185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many conventional, modern genome engineering tools cannot be used to study mitochondrial genetics due to the unusual structure and physiology of the mitochondrial genome. Here, we review a number of newly developed, synthetic biology-based approaches for altering levels of mutant mammalian mitochondrial DNA and mitochondrial RNAs, including transcription activator-like effector nucleases, zinc finger nucleases and engineered RNA-binding proteins. These approaches allow researchers to manipulate and visualize mitochondrial processes and may provide future therapeutics. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
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Affiliation(s)
- Christopher P Wallis
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,The University of Western Australia Centre for Medical Research, Crawley, Western Australia 6009, Australia
| | - Louis H Scott
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,The University of Western Australia Centre for Medical Research, Crawley, Western Australia 6009, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,The University of Western Australia Centre for Medical Research, Crawley, Western Australia 6009, Australia.,School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Western Australia 6102, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia 6102, Australia
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30
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Bahhir D, Yalgin C, Ots L, Järvinen S, George J, Naudí A, Krama T, Krams I, Tamm M, Andjelković A, Dufour E, González de Cózar JM, Gerards M, Parhiala M, Pamplona R, Jacobs HT, Jõers P. Manipulating mtDNA in vivo reprograms metabolism via novel response mechanisms. PLoS Genet 2019; 15:e1008410. [PMID: 31584940 PMCID: PMC6795474 DOI: 10.1371/journal.pgen.1008410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 10/16/2019] [Accepted: 09/10/2019] [Indexed: 11/18/2022] Open
Abstract
Mitochondria have been increasingly recognized as a central regulatory nexus for multiple metabolic pathways, in addition to ATP production via oxidative phosphorylation (OXPHOS). Here we show that inducing mitochondrial DNA (mtDNA) stress in Drosophila using a mitochondrially-targeted Type I restriction endonuclease (mtEcoBI) results in unexpected metabolic reprogramming in adult flies, distinct from effects on OXPHOS. Carbohydrate utilization was repressed, with catabolism shifted towards lipid oxidation, accompanied by elevated serine synthesis. Cleavage and translocation, the two modes of mtEcoBI action, repressed carbohydrate rmetabolism via two different mechanisms. DNA cleavage activity induced a type II diabetes-like phenotype involving deactivation of Akt kinase and inhibition of pyruvate dehydrogenase, whilst translocation decreased post-translational protein acetylation by cytonuclear depletion of acetyl-CoA (AcCoA). The associated decrease in the concentrations of ketogenic amino acids also produced downstream effects on physiology and behavior, attributable to decreased neurotransmitter levels. We thus provide evidence for novel signaling pathways connecting mtDNA to metabolism, distinct from its role in supporting OXPHOS. Mitochondria, subcellular compartments (organelles) found in virtually all eukaryotes, contain DNA which is believed to be a remnant of an ancestral bacterial genome. They are best known for the synthesis of the universal energy carrier ATP, but also serve as the hub of various metabolic and signalling pathways. We report here that mtDNA integrity is linked to a signaling system that influences metabolic fuel selection between fats and sugars. By disrupting mtDNA in the fruit fly we induced a strong shift towards lipid catabolism. This was caused both by a widespread decrease in post-translational acetylation of proteins, as well as specific inhibition of the machinery that transports glucose into cells across the plasma membrane. This phenomenon is very similar to the pathophysiology of diabetes, where the inability to transport glucose to cells is considered the main hallmark of the disease. Moreover, decreased protein acetylation was associated with lower levels of certain neurotransmitters, causing various effects on feeding and fertility. Our discovery reveals an unexpected role for mtDNA stability in regulating global metabolic balance and suggests that it could be instrumental in pandemic metabolic disorders such as diabetes and obesity.
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Affiliation(s)
- Diana Bahhir
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Cagri Yalgin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Liina Ots
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Sampsa Järvinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jack George
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Alba Naudí
- Experimental Medicine Department, University of Lleida-Institute for Research in Biomedicine of Lleida (UdL-IRBLLEIDA), Lleida, Spain
| | - Tatjana Krama
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Department of Plant Health, Institute of Agricultural and Environmental Sciences, Estonian University of Life Science, Tartu, Estonia
| | - Indrikis Krams
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Department of Zoology and Animal Ecology, Faculty of Biology, University of Latvia, Rīga, Latvia
- Department of Biotechnology, Daugavpils University, Daugavpils, Latvia
| | - Mairi Tamm
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Ana Andjelković
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Eric Dufour
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | - Mike Gerards
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
| | - Mikael Parhiala
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Reinald Pamplona
- Experimental Medicine Department, University of Lleida-Institute for Research in Biomedicine of Lleida (UdL-IRBLLEIDA), Lleida, Spain
| | - Howard T. Jacobs
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Priit Jõers
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- * E-mail:
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31
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Kauppila JHK, Bonekamp NA, Mourier A, Isokallio MA, Just A, Kauppila TES, Stewart JB, Larsson NG. Base-excision repair deficiency alone or combined with increased oxidative stress does not increase mtDNA point mutations in mice. Nucleic Acids Res 2019; 46:6642-6669. [PMID: 29860357 PMCID: PMC6061787 DOI: 10.1093/nar/gky456] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 05/11/2018] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial DNA (mtDNA) mutations become more prevalent with age and are postulated to contribute to the ageing process. Point mutations of mtDNA have been suggested to originate from two main sources, i.e. replicative errors and oxidative damage, but the contribution of each of these processes is much discussed. To elucidate the origin of mtDNA mutations, we measured point mutation load in mice with deficient mitochondrial base-excision repair (BER) caused by knockout alleles preventing mitochondrial import of the DNA repair glycosylases OGG1 and MUTYH (Ogg1 dMTS, Mutyh dMTS). Surprisingly, we detected no increase in the mtDNA mutation load in old Ogg1 dMTS mice. As DNA repair is especially important in the germ line, we bred the BER deficient mice for five consecutive generations but found no increase in the mtDNA mutation load in these maternal lineages. To increase reactive oxygen species (ROS) levels and oxidative damage, we bred the Ogg1 dMTS mice with tissue specific Sod2 knockout mice. Although increased superoxide levels caused a plethora of changes in mitochondrial function, we did not detect any changes in the mutation load of mtDNA or mtRNA. Our results show that the importance of oxidative damage as a contributor of mtDNA mutations should be re-evaluated.
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Affiliation(s)
- Johanna H K Kauppila
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Nina A Bonekamp
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Arnaud Mourier
- Université de Bordeaux and the Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires UMR 5095, Saint-Saëns, Bordeaux, France
| | - Marita A Isokallio
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Alexandra Just
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Timo E S Kauppila
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - James B Stewart
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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32
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Ciesielski GL, Nadalutti CA, Oliveira MT, Jacobs HT, Griffith JD, Kaguni LS. Structural rearrangements in the mitochondrial genome of Drosophila melanogaster induced by elevated levels of the replicative DNA helicase. Nucleic Acids Res 2019; 46:3034-3046. [PMID: 29432582 PMCID: PMC5887560 DOI: 10.1093/nar/gky094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/02/2018] [Indexed: 01/10/2023] Open
Abstract
Pathological conditions impairing functions of mitochondria often lead to compensatory upregulation of the mitochondrial DNA (mtDNA) replisome machinery, and the replicative DNA helicase appears to be a key factor in regulating mtDNA copy number. Moreover, mtDNA helicase mutations have been associated with structural rearrangements of the mitochondrial genome. To evaluate the effects of elevated levels of the mtDNA helicase on the integrity and replication of the mitochondrial genome, we overexpressed the helicase in Drosophila melanogaster Schneider cells and analyzed the mtDNA by two-dimensional neutral agarose gel electrophoresis and electron microscopy. We found that elevation of mtDNA helicase levels increases the quantity of replication intermediates and alleviates pausing at the replication slow zones. Though we did not observe a concomitant alteration in mtDNA copy number, we observed deletions specific to the segment of repeated elements in the immediate vicinity of the origin of replication, and an accumulation of species characteristic of replication fork stalling. We also found elevated levels of RNA that are retained in the replication intermediates. Together, our results suggest that upregulation of mtDNA helicase promotes the process of mtDNA replication but also results in genome destabilization.
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Affiliation(s)
- Grzegorz L Ciesielski
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, USA.,Institute of Biosciences and Medical Technology, University of Tampere, FI-33014 Tampere, Finland
| | - Cristina A Nadalutti
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Marcos T Oliveira
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, USA
| | - Howard T Jacobs
- Institute of Biosciences and Medical Technology, University of Tampere, FI-33014 Tampere, Finland.,Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laurie S Kaguni
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, USA.,Institute of Biosciences and Medical Technology, University of Tampere, FI-33014 Tampere, Finland
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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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MitoTALEN reduces mutant mtDNA load and restores tRNA Ala levels in a mouse model of heteroplasmic mtDNA mutation. Nat Med 2018; 24:1696-1700. [PMID: 30250143 DOI: 10.1038/s41591-018-0166-8] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/26/2018] [Indexed: 11/08/2022]
Abstract
Mutations in the mitochondrial DNA (mtDNA) are responsible for several metabolic disorders, commonly involving muscle and the central nervous system1. Because of the critical role of mtDNA in oxidative phosphorylation, the majority of pathogenic mtDNA mutations are heteroplasmic, co-existing with wild-type molecules1. Using a mouse model with a heteroplasmic mtDNA mutation2, we tested whether mitochondrial-targeted TALENs (mitoTALENs)3,4 could reduce the mutant mtDNA load in muscle and heart. AAV9-mitoTALEN was administered via intramuscular, intravenous, and intraperitoneal injections. Muscle and heart were efficiently transduced and showed a robust reduction in mutant mtDNA, which was stable over time. The molecular defect, namely a decrease in transfer RNAAla levels, was restored by the treatment. These results showed that mitoTALENs, when expressed in affected tissues, could revert disease-related phenotypes in mice.
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Pohjoismäki JLO, Forslund JME, Goffart S, Torregrosa-Muñumer R, Wanrooij S. Known Unknowns of Mammalian Mitochondrial DNA Maintenance. Bioessays 2018; 40:e1800102. [DOI: 10.1002/bies.201800102] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 06/18/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Jaakko L. O. Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland; 80101 Joensuu Finland
| | | | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland; 80101 Joensuu Finland
| | - Rubén Torregrosa-Muñumer
- Department of Environmental and Biological Sciences, University of Eastern Finland; 80101 Joensuu Finland
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University; 90187 Umeå Sweden
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Peralta S, Goffart S, Williams SL, Diaz F, Garcia S, Nissanka N, Area-Gomez E, Pohjoismäki J, Moraes CT. ATAD3 controls mitochondrial cristae structure in mouse muscle, influencing mtDNA replication and cholesterol levels. J Cell Sci 2018; 131:jcs217075. [PMID: 29898916 PMCID: PMC6051345 DOI: 10.1242/jcs.217075] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/30/2018] [Indexed: 01/01/2023] Open
Abstract
Mutations in the mitochondrial inner membrane ATPase ATAD3A result in neurological syndromes in humans. In mice, the ubiquitous disruption of Atad3 (also known as Atad3a) was embryonic lethal, but a skeletal muscle-specific conditional knockout (KO) was viable. At birth, ATAD3 muscle KO mice had normal weight, but from 2 months onwards they showed progressive motor-impaired coordination and weakness. Loss of ATAD3 caused early and severe mitochondrial structural abnormalities, mitochondrial proliferation and muscle atrophy. There was dramatic reduction in mitochondrial cristae junctions and overall cristae morphology. The lack of mitochondrial cristae was accompanied by a reduction in high molecular weight mitochondrial contact site and cristae organizing system (MICOS) complexes, and to a lesser extent in OPA1. Moreover, muscles lacking ATAD3 showed altered cholesterol metabolism, accumulation of mitochondrial DNA (mtDNA) replication intermediates, progressive mtDNA depletion and deletions. Unexpectedly, decreases in the levels of some OXPHOS components occurred after cristae destabilization, indicating that ATAD3 is not crucial for mitochondrial translation, as previously suggested. Our results show a critical early role of ATAD3 in regulating mitochondrial inner membrane structure, leading to secondary defects in mtDNA replication and complex V and cholesterol levels in postmitotic tissue.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Susana Peralta
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu 80101, Finland
| | - Sion L Williams
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Francisca Diaz
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Sofia Garcia
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Nadee Nissanka
- Neuroscience Graduate Program, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Estela Area-Gomez
- Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA
| | - Jaakko Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu 80101, Finland
| | - Carlos T Moraes
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Neuroscience Graduate Program, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Department of Cell Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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Nissanka N, Bacman SR, Plastini MJ, Moraes CT. The mitochondrial DNA polymerase gamma degrades linear DNA fragments precluding the formation of deletions. Nat Commun 2018; 9:2491. [PMID: 29950568 PMCID: PMC6021392 DOI: 10.1038/s41467-018-04895-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 05/25/2018] [Indexed: 02/03/2023] Open
Abstract
Double-strand breaks in the mitochondrial DNA (mtDNA) result in the formation of linear fragments that are rapidly degraded. However, the identity of the nuclease(s) performing this function is not known. We found that the exonuclease function of the mtDNA polymerase gamma (POLG) is required for this rapid degradation of mtDNA fragments. POLG is recruited to linearized DNA fragments in an origin of replication-independent manner. Moreover, in the absence of POLG exonuclease activity, the prolonged existence of mtDNA linear fragments leads to increased levels of mtDNA deletions, which have been previously identified in the mutator mouse, patients with POLG mutations and normal aging. Mitochondrial DNA fragments are rapidly degraded when double strand breaks occur. Here the authors reveal that the exonuclease activity of polymerase gamma is important for efficient degradation of these fragments and to avoid formation of large deletions.
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Affiliation(s)
- Nadee Nissanka
- Neuroscience Graduate Program, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Sandra R Bacman
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Melanie J Plastini
- Neuroscience Graduate Program, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Carlos T Moraes
- Neuroscience Graduate Program, University of Miami Miller School of Medicine, Miami, FL, 33136, USA. .,Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
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Verechshagina N, Nikitchina N, Yamada Y, Harashima Н, Tanaka M, Orishchenko K, Mazunin I. Future of human mitochondrial DNA editing technologies. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:214-221. [PMID: 29764251 DOI: 10.1080/24701394.2018.1472773] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
ATP and other metabolites, which are necessary for the development, maintenance, and functioning of bodily cells are all synthesized in the mitochondria. Multiple copies of the genome, present within the mitochondria, together with its maternal inheritance, determine the clinical manifestation and spreading of mutations in mitochondrial DNA (mtDNA). The main obstacle in the way of thorough understanding of mitochondrial biology and the development of gene therapy methods for mitochondrial diseases is the absence of systems that allow to directly change mtDNA sequence. Here, we discuss existing methods of manipulating the level of mtDNA heteroplasmy, as well as the latest systems, that could be used in the future as tools for human mitochondrial genome editing.
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Affiliation(s)
- N Verechshagina
- a Laboratory of Molecular Genetics Technologies , Immanuel Kant Baltic Federal University , Kaliningrad , Russia
| | - N Nikitchina
- a Laboratory of Molecular Genetics Technologies , Immanuel Kant Baltic Federal University , Kaliningrad , Russia
| | - Y Yamada
- b Faculty of Pharmaceutical Sciences, Laboratory for Molecular Design of Pharmaceutics , Hokkaido University , Sapporo , Japan
| | - Н Harashima
- b Faculty of Pharmaceutical Sciences, Laboratory for Molecular Design of Pharmaceutics , Hokkaido University , Sapporo , Japan
| | - M Tanaka
- c Department for Health and Longevity Research , National Institutes of Biomedical Innovation, Health and Nutrition , Ibaraki City, Osaka , Japan.,d Department of Neurology , Juntendo University Graduate School of Medicine , Tokyo , Japan
| | - K Orishchenko
- a Laboratory of Molecular Genetics Technologies , Immanuel Kant Baltic Federal University , Kaliningrad , Russia.,e Laboratory of Cell Technologies , Institute of Cytology and Genetics SB RAS , Novosibirsk , Russia
| | - I Mazunin
- a Laboratory of Molecular Genetics Technologies , Immanuel Kant Baltic Federal University , Kaliningrad , Russia
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Peeva V, Blei D, Trombly G, Corsi S, Szukszto MJ, Rebelo-Guiomar P, Gammage PA, Kudin AP, Becker C, Altmüller J, Minczuk M, Zsurka G, Kunz WS. Linear mitochondrial DNA is rapidly degraded by components of the replication machinery. Nat Commun 2018; 9:1727. [PMID: 29712893 PMCID: PMC5928156 DOI: 10.1038/s41467-018-04131-w] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 04/04/2018] [Indexed: 02/02/2023] Open
Abstract
Emerging gene therapy approaches that aim to eliminate pathogenic mutations of mitochondrial DNA (mtDNA) rely on efficient degradation of linearized mtDNA, but the enzymatic machinery performing this task is presently unknown. Here, we show that, in cellular models of restriction endonuclease-induced mtDNA double-strand breaks, linear mtDNA is eliminated within hours by exonucleolytic activities. Inactivation of the mitochondrial 5'-3'exonuclease MGME1, elimination of the 3'-5'exonuclease activity of the mitochondrial DNA polymerase POLG by introducing the p.D274A mutation, or knockdown of the mitochondrial DNA helicase TWNK leads to severe impediment of mtDNA degradation. We do not observe similar effects when inactivating other known mitochondrial nucleases (EXOG, APEX2, ENDOG, FEN1, DNA2, MRE11, or RBBP8). Our data suggest that rapid degradation of linearized mtDNA is performed by the same machinery that is responsible for mtDNA replication, thus proposing novel roles for the participating enzymes POLG, TWNK, and MGME1.
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Affiliation(s)
- Viktoriya Peeva
- 0000 0001 2240 3300grid.10388.32Institute of Experimental Epileptology and Cognition Research, University of Bonn, Sigmund-Freud-Str. 25, D-53105 Bonn, Germany
| | - Daniel Blei
- 0000 0001 2240 3300grid.10388.32Institute of Experimental Epileptology and Cognition Research, University of Bonn, Sigmund-Freud-Str. 25, D-53105 Bonn, Germany
| | - Genevieve Trombly
- 0000 0001 2240 3300grid.10388.32Institute of Experimental Epileptology and Cognition Research, University of Bonn, Sigmund-Freud-Str. 25, D-53105 Bonn, Germany
| | - Sarah Corsi
- 0000 0001 2240 3300grid.10388.32Institute of Experimental Epileptology and Cognition Research, University of Bonn, Sigmund-Freud-Str. 25, D-53105 Bonn, Germany ,0000 0001 0462 7212grid.1006.7Present Address: Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH UK
| | - Maciej J. Szukszto
- 0000000121885934grid.5335.0MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY UK
| | - Pedro Rebelo-Guiomar
- 0000000121885934grid.5335.0MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY UK ,0000 0001 1503 7226grid.5808.5Graduate Program in Areas of Basic and Applied Biology (GABBA), University of Porto, Porto, 4200-135 Portugal
| | - Payam A. Gammage
- 0000000121885934grid.5335.0MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY UK
| | - Alexei P. Kudin
- 0000 0001 2240 3300grid.10388.32Institute of Experimental Epileptology and Cognition Research, University of Bonn, Sigmund-Freud-Str. 25, D-53105 Bonn, Germany
| | - Christian Becker
- 0000 0000 8580 3777grid.6190.eCologne Center for Genomics, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Weyertal 115b, Cologne, D-50931 Germany
| | - Janine Altmüller
- 0000 0000 8580 3777grid.6190.eCologne Center for Genomics, Center for Molecular Medicine Cologne (CMMC), University of Cologne, Weyertal 115b, Cologne, D-50931 Germany ,0000 0000 8580 3777grid.6190.eInstitute of Human Genetics, University of Cologne, Kerpener Str. 34, Cologne, D-50931 Germany
| | - Michal Minczuk
- 0000000121885934grid.5335.0MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY UK
| | - Gábor Zsurka
- 0000 0001 2240 3300grid.10388.32Institute of Experimental Epileptology and Cognition Research, University of Bonn, Sigmund-Freud-Str. 25, D-53105 Bonn, Germany ,0000 0001 2240 3300grid.10388.32Department of Epileptology and Life & Brain Center, University of Bonn, Sigmund-Freud-Str. 25, Bonn, D-53105 Germany
| | - Wolfram S. Kunz
- 0000 0001 2240 3300grid.10388.32Institute of Experimental Epileptology and Cognition Research, University of Bonn, Sigmund-Freud-Str. 25, D-53105 Bonn, Germany ,0000 0001 2240 3300grid.10388.32Department of Epileptology and Life & Brain Center, University of Bonn, Sigmund-Freud-Str. 25, Bonn, D-53105 Germany
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40
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Zsurka G, Peeva V, Kotlyar A, Kunz WS. Is There Still Any Role for Oxidative Stress in Mitochondrial DNA-Dependent Aging? Genes (Basel) 2018; 9:genes9040175. [PMID: 29561808 PMCID: PMC5924517 DOI: 10.3390/genes9040175] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/09/2018] [Accepted: 03/16/2018] [Indexed: 11/21/2022] Open
Abstract
Recent deep sequencing data has provided compelling evidence that the spectrum of somatic point mutations in mitochondrial DNA (mtDNA) in aging tissues lacks G > T transversion mutations. This fact cannot, however, be used as an argument for the missing contribution of reactive oxygen species (ROS) to mitochondria-related aging because it is probably caused by the nucleotide selectivity of mitochondrial DNA polymerase γ (POLG). In contrast to point mutations, the age-dependent accumulation of mitochondrial DNA deletions is, in light of recent experimental data, still explainable by the segregation of mutant molecules generated by the direct mutagenic effects of ROS (in particular, of HO· radicals formed from H2O2 by a Fenton reaction). The source of ROS remains controversial, because the mitochondrial contribution to tissue ROS production is probably lower than previously thought. Importantly, in the discussion about the potential role of oxidative stress in mitochondria-dependent aging, ROS generated by inflammation-linked processes and the distribution of free iron also require careful consideration.
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Affiliation(s)
- Gábor Zsurka
- Institute of Experimental Epileptology and Neurocognition, University Bonn Medical Center, 53105 Bonn, Germany.
- Department of Epileptology, University Bonn Medical Center, 53105 Bonn, Germany.
| | - Viktoriya Peeva
- Institute of Experimental Epileptology and Neurocognition, University Bonn Medical Center, 53105 Bonn, Germany.
| | - Alexander Kotlyar
- Department of Biochemistry & Molecular Biology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Wolfram S Kunz
- Institute of Experimental Epileptology and Neurocognition, University Bonn Medical Center, 53105 Bonn, Germany.
- Department of Epileptology, University Bonn Medical Center, 53105 Bonn, Germany.
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41
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Gammage PA, Moraes CT, Minczuk M. Mitochondrial Genome Engineering: The Revolution May Not Be CRISPR-Ized. Trends Genet 2018; 34:101-110. [PMID: 29179920 PMCID: PMC5783712 DOI: 10.1016/j.tig.2017.11.001] [Citation(s) in RCA: 212] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/28/2017] [Accepted: 11/02/2017] [Indexed: 12/17/2022]
Abstract
In recent years mitochondrial DNA (mtDNA) has transitioned to greater prominence across diverse areas of biology and medicine. The recognition of mitochondria as a major biochemical hub, contributions of mitochondrial dysfunction to various diseases, and several high-profile attempts to prevent hereditary mtDNA disease through mitochondrial replacement therapy have roused interest in the organellar genome. Subsequently, attempts to manipulate mtDNA have been galvanized, although with few robust advances and much controversy. Re-engineered protein-only nucleases such as mtZFN and mitoTALEN function effectively in mammalian mitochondria, although efficient delivery of nucleic acids into the organelle remains elusive. Such an achievement, in concert with a mitochondria-adapted CRISPR/Cas9 platform, could prompt a revolution in mitochondrial genome engineering and biological understanding. However, the existence of an endogenous mechanism for nucleic acid import into mammalian mitochondria, a prerequisite for mitochondrial CRISPR/Cas9 gene editing, remains controversial.
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Affiliation(s)
- Payam A Gammage
- Medical Research Council (MRC) Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
| | - Carlos T Moraes
- Miller School of Medicine, University of Miami, Miami, FL, USA.
| | - Michal Minczuk
- Medical Research Council (MRC) Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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42
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Nissanka N, Moraes CT. Mitochondrial DNA damage and reactive oxygen species in neurodegenerative disease. FEBS Lett 2018; 592:728-742. [PMID: 29281123 DOI: 10.1002/1873-3468.12956] [Citation(s) in RCA: 252] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 12/06/2017] [Accepted: 12/19/2017] [Indexed: 12/12/2022]
Abstract
Mitochondria are essential organelles within the cell where most ATP is produced through oxidative phosphorylation (OXPHOS). A subset of the genes needed for this process are encoded by the mitochondrial DNA (mtDNA). One consequence of OXPHOS is the production of mitochondrial reactive oxygen species (ROS), whose role in mediating cellular damage, particularly in damaging mtDNA during ageing, has been controversial. There are subsets of neurons that appear to be more sensitive to ROS-induced damage, and mitochondrial dysfunction has been associated with several neurodegenerative disorders. In this review, we will discuss the current knowledge in the field of mtDNA and neurodegeneration, the debate about ROS as a pathological or beneficial contributor to neuronal function, bona fide mtDNA diseases, and insights from mouse models of mtDNA defects affecting the central nervous system.
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Affiliation(s)
- Nadee Nissanka
- Neuroscience Graduate Program, University of Miami Miller School of Medicine, FL, USA
| | - Carlos T Moraes
- Neuroscience Graduate Program, University of Miami Miller School of Medicine, FL, USA.,Department of Neurology, University of Miami Miller School of Medicine, FL, USA
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43
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McCann BJ, Cox A, Gammage PA, Stewart JB, Zernicka-Goetz M, Minczuk M. Delivery of mtZFNs into Early Mouse Embryos. Methods Mol Biol 2018; 1867:215-228. [PMID: 30155826 DOI: 10.1007/978-1-4939-8799-3_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mitochondrial diseases often result from mutations in the mitochondrial genome (mtDNA). In most cases, mutant mtDNA coexists with wild-type mtDNA, resulting in heteroplasmy. One potential future approach to treat heteroplasmic mtDNA diseases is the specific elimination of pathogenic mtDNA mutations, lowering the level of mutant mtDNA below pathogenic thresholds. Mitochondrially targeted zinc-finger nucleases (mtZFNs) have been demonstrated to specifically target and introduce double-strand breaks in mutant mtDNA, facilitating substantial shifts in heteroplasmy. One application of mtZFN technology, in the context of heteroplasmic mtDNA disease, is delivery into the heteroplasmic oocyte or early embryo to eliminate mutant mtDNA, preventing transmission of mitochondrial diseases through the germline. Here we describe a protocol for efficient production of mtZFN mRNA in vitro, and delivery of these into 0.5 dpc mouse embryos to elicit shifts of mtDNA heteroplasmy.
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Affiliation(s)
- Beverly J McCann
- Mitochondrial Genetics Group, MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Andy Cox
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Payam A Gammage
- Mitochondrial Genetics Group, MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - James B Stewart
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Magdalena Zernicka-Goetz
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Michal Minczuk
- Mitochondrial Genetics Group, MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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Lack of Parkin Anticipates the Phenotype and Affects Mitochondrial Morphology and mtDNA Levels in a Mouse Model of Parkinson's Disease. J Neurosci 2017; 38:1042-1053. [PMID: 29222404 DOI: 10.1523/jneurosci.1384-17.2017] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/24/2017] [Accepted: 10/03/2017] [Indexed: 02/08/2023] Open
Abstract
PARK2 is the most common gene mutated in monogenic recessive familial cases of Parkinson's disease (PD). Pathogenic mutations cause a loss of function of the encoded protein Parkin. ParkinKO mice, however, poorly represent human PD symptoms as they only exhibit mild motor phenotypes, minor dopamine metabolism abnormalities, and no signs of dopaminergic neurodegeneration. Parkin has been shown to participate in mitochondrial turnover, by targeting damaged mitochondria with low membrane potential to mitophagy. We studied the role of Parkin on mitochondrial quality control in vivo by knocking out Parkin in the PD-mito-PstI mouse (males), where the mitochondrial DNA (mtDNA) undergoes double-strand breaks only in dopaminergic neurons. The lack of Parkin promoted earlier onset of dopaminergic neurodegeneration and motor defects in the PD-mito-PstI mice, but it did not worsen the pathology. The lack of Parkin affected mitochondrial morphology in dopaminergic axons and was associated with an increase in mtDNA levels (mutant and wild type). Unexpectedly, it did not cause a parallel increase in mitochondrial mass or mitophagy. Our results suggest that Parkin affects mtDNA levels in a mitophagy-independent manner.SIGNIFICANCE STATEMENT Parkinson's disease is characterized by progressive motor symptoms due to the selective loss of dopaminergic neurons in the substantia nigra. Loss-of-function mutations of Parkin cause some monogenic forms of Parkinson's disease, possibly through its role in mitochondrial turnover and quality control. To study whether Parkin has a role in vivo in the context of mitochondrial damage, we knocked out Parkin in a mouse model in which the mitochondrial DNA is damaged in dopaminergic neurons. We found that the loss of Parkin did not exacerbate the parkinsonian pathology already present in the mice, but it was associated with an increase in mtDNA levels (mutant and wild-type) without altering mitochondrial mass. These results shed new light on the function of Parkin in vivo.
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45
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Khan FA, Ali SO. Physiological Roles of DNA Double-Strand Breaks. J Nucleic Acids 2017; 2017:6439169. [PMID: 29181194 PMCID: PMC5664317 DOI: 10.1155/2017/6439169] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 09/24/2017] [Indexed: 12/20/2022] Open
Abstract
Genomic integrity is constantly threatened by sources of DNA damage, internal and external alike. Among the most cytotoxic lesions is the DNA double-strand break (DSB) which arises from the cleavage of both strands of the double helix. Cells boast a considerable set of defences to both prevent and repair these breaks and drugs which derail these processes represent an important category of anticancer therapeutics. And yet, bizarrely, cells deploy this very machinery for the intentional and calculated disruption of genomic integrity, harnessing potentially destructive DSBs in delicate genetic transactions. Under tight spatiotemporal regulation, DSBs serve as a tool for genetic modification, widely used across cellular biology to generate diverse functionalities, ranging from the fundamental upkeep of DNA replication, transcription, and the chromatin landscape to the diversification of immunity and the germline. Growing evidence points to a role of aberrant DSB physiology in human disease and an understanding of these processes may both inform the design of new therapeutic strategies and reduce off-target effects of existing drugs. Here, we review the wide-ranging roles of physiological DSBs and the emerging network of their multilateral regulation to consider how the cell is able to harness DNA breaks as a critical biochemical tool.
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Affiliation(s)
- Farhaan A. Khan
- School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge CB2 0SP, UK
| | - Syed O. Ali
- School of Clinical Medicine, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge CB2 0SP, UK
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46
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Moretton A, Morel F, Macao B, Lachaume P, Ishak L, Lefebvre M, Garreau-Balandier I, Vernet P, Falkenberg M, Farge G. Selective mitochondrial DNA degradation following double-strand breaks. PLoS One 2017; 12:e0176795. [PMID: 28453550 PMCID: PMC5409072 DOI: 10.1371/journal.pone.0176795] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 04/17/2017] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial DNA (mtDNA) can undergo double-strand breaks (DSBs), caused by defective replication, or by various endogenous or exogenous sources, such as reactive oxygen species, chemotherapeutic agents or ionizing radiations. MtDNA encodes for proteins involved in ATP production, and maintenance of genome integrity following DSBs is thus of crucial importance. However, the mechanisms involved in mtDNA maintenance after DSBs remain unknown. In this study, we investigated the consequences of the production of mtDNA DSBs using a human inducible cell system expressing the restriction enzyme PstI targeted to mitochondria. Using this system, we could not find any support for DSB repair of mtDNA. Instead we observed a loss of the damaged mtDNA molecules and a severe decrease in mtDNA content. We demonstrate that none of the known mitochondrial nucleases are involved in the mtDNA degradation and that the DNA loss is not due to autophagy, mitophagy or apoptosis. Our study suggests that a still uncharacterized pathway for the targeted degradation of damaged mtDNA in a mitophagy/autophagy-independent manner is present in mitochondria, and might provide the main mechanism used by the cells to deal with DSBs.
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Affiliation(s)
- Amandine Moretton
- Université Clermont Auvergne, CNRS/IN2P3, Laboratoire de Physique de Clermont, BP 10448, F-63000 Clermont-Ferrand, France
| | - Frédéric Morel
- Université Clermont Auvergne, CNRS/IN2P3, Laboratoire de Physique de Clermont, BP 10448, F-63000 Clermont-Ferrand, France
| | - Bertil Macao
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30, Gothenburg, Sweden
| | - Philippe Lachaume
- Université Clermont Auvergne, CNRS/IN2P3, Laboratoire de Physique de Clermont, BP 10448, F-63000 Clermont-Ferrand, France
| | - Layal Ishak
- Université Clermont Auvergne, CNRS/IN2P3, Laboratoire de Physique de Clermont, BP 10448, F-63000 Clermont-Ferrand, France
| | - Mathilde Lefebvre
- Université Clermont Auvergne, CNRS/IN2P3, Laboratoire de Physique de Clermont, BP 10448, F-63000 Clermont-Ferrand, France
| | - Isabelle Garreau-Balandier
- Université Clermont Auvergne, CNRS/IN2P3, Laboratoire de Physique de Clermont, BP 10448, F-63000 Clermont-Ferrand, France
| | - Patrick Vernet
- Université Clermont Auvergne, CNRS/IN2P3, Laboratoire de Physique de Clermont, BP 10448, F-63000 Clermont-Ferrand, France
| | - Maria Falkenberg
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30, Gothenburg, Sweden
| | - Géraldine Farge
- Université Clermont Auvergne, CNRS/IN2P3, Laboratoire de Physique de Clermont, BP 10448, F-63000 Clermont-Ferrand, France
- * E-mail:
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47
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Phillips AF, Millet AR, Tigano M, Dubois SM, Crimmins H, Babin L, Charpentier M, Piganeau M, Brunet E, Sfeir A. Single-Molecule Analysis of mtDNA Replication Uncovers the Basis of the Common Deletion. Mol Cell 2017; 65:527-538.e6. [PMID: 28111015 DOI: 10.1016/j.molcel.2016.12.014] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 10/04/2016] [Accepted: 12/16/2016] [Indexed: 11/30/2022]
Abstract
Mutations in mtDNA lead to muscular and neurological diseases and are linked to aging. The most frequent aberrancy is the "common deletion" that involves a 4,977-bp region flanked by 13-bp repeats. To investigate the basis of this deletion, we developed a single-molecule mtDNA combing method. The analysis of replicating mtDNA molecules provided in vivo evidence in support of the asymmetric mode of replication. Furthermore, we observed frequent fork stalling at the junction of the common deletion, suggesting that impaired replication triggers the formation of this toxic lesion. In parallel experiments, we employed mito-TALENs to induce breaks in distinct loci of the mitochondrial genome and found that breaks adjacent to the 5' repeat trigger the common deletion. Interestingly, this process was mediated by the mitochondrial replisome independent of canonical DSB repair. Altogether, our data underscore a unique replication-dependent repair pathway that leads to the mitochondrial common deletion.
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Affiliation(s)
- Aaron F Phillips
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Armêl R Millet
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 75005 Paris, France; Genome Dynamics in the Immune System Laboratory, INSERM, UMR 1163, Institut Imagine, 75015 Paris, France
| | - Marco Tigano
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Sonia M Dubois
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 75005 Paris, France
| | - Hannah Crimmins
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Loelia Babin
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 75005 Paris, France; Genome Dynamics in the Immune System Laboratory, INSERM, UMR 1163, Institut Imagine, 75015 Paris, France
| | - Marine Charpentier
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 75005 Paris, France
| | - Marion Piganeau
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 75005 Paris, France
| | - Erika Brunet
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 75005 Paris, France; Genome Dynamics in the Immune System Laboratory, INSERM, UMR 1163, Institut Imagine, 75015 Paris, France.
| | - Agnel Sfeir
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA.
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48
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Neuhaus JFG, Baris OR, Kittelmann A, Becker K, Rothschild MA, Wiesner RJ. Catecholamine Metabolism Induces Mitochondrial DNA Deletions and Leads to Severe Adrenal Degeneration during Aging. Neuroendocrinology 2017; 104:72-84. [PMID: 26895241 DOI: 10.1159/000444680] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 02/12/2016] [Indexed: 11/19/2022]
Abstract
BACKGROUND Aging is a multifactorial process characterized by organ loss of function and degeneration, but the mechanisms involved remain elusive. We have shown recently that catecholamine metabolism drives the accumulation of mitochondrial DNA (mtDNA) deletions in dopaminergic cells, which likely contribute to their degeneration during aging. Here we investigated whether the well-documented degeneration and altered function of adrenals during aging is linked to catecholamine production in the medulla followed by accumulation of mtDNA deletions. MATERIAL AND METHODS We analyzed adrenal medullary and cortical samples of both murine and human origin covering a wide range of ages for mtDNA deletion content, mtDNA copy number, mitochondrial and cellular integrity as well as aging-related tissue changes such as fibrosis. RESULTS Indeed, we demonstrate in mice and humans that the adrenal medulla accumulates a strikingly high amount of mtDNA deletions with age, causing mitochondrial dysfunction in the adrenal medulla, but also in the cortex, accompanied by apoptosis and, more importantly, by severe inflammation and remarkable fibrosis. Additionally, a concomitant and dramatic loss of medullary and cortical cells is observed in old animals. CONCLUSION Our results show that accumulation of mtDNA deletions, and the ensuing mitochondrial dysfunction, is a hallmark of adrenal aging, further strengthening the hypothesis that catecholamine metabolism is detrimental to mtDNA integrity, mitochondrial function and cell survival. Moreover, the cell loss potentially induced by mitochondrial dysfunction could explain the decline in adrenal hormonal and steroidal secretion during aging.
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Affiliation(s)
- Johannes Friedrich Georg Neuhaus
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, Cologne, Germany
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49
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Gammage PA, Gaude E, Van Haute L, Rebelo-Guiomar P, Jackson CB, Rorbach J, Pekalski ML, Robinson AJ, Charpentier M, Concordet JP, Frezza C, Minczuk M. Near-complete elimination of mutant mtDNA by iterative or dynamic dose-controlled treatment with mtZFNs. Nucleic Acids Res 2016; 44:7804-16. [PMID: 27466392 PMCID: PMC5027515 DOI: 10.1093/nar/gkw676] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 07/20/2016] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial diseases are frequently associated with mutations in mitochondrial DNA (mtDNA). In most cases, mutant and wild-type mtDNAs coexist, resulting in heteroplasmy. The selective elimination of mutant mtDNA, and consequent enrichment of wild-type mtDNA, can rescue pathological phenotypes in heteroplasmic cells. Use of the mitochondrially targeted zinc finger-nuclease (mtZFN) results in degradation of mutant mtDNA through site-specific DNA cleavage. Here, we describe a substantial enhancement of our previous mtZFN-based approaches to targeting mtDNA, allowing near-complete directional shifts of mtDNA heteroplasmy, either by iterative treatment or through finely controlled expression of mtZFN, which limits off-target catalysis and undesired mtDNA copy number depletion. To demonstrate the utility of this improved approach, we generated an isogenic distribution of heteroplasmic cells with variable mtDNA mutant level from the same parental source without clonal selection. Analysis of these populations demonstrated an altered metabolic signature in cells harbouring decreased levels of mutant m.8993T>G mtDNA, associated with neuropathy, ataxia, and retinitis pigmentosa (NARP). We conclude that mtZFN-based approaches offer means for mtDNA heteroplasmy manipulation in basic research, and may provide a strategy for therapeutic intervention in selected mitochondrial diseases.
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Affiliation(s)
| | | | | | - Pedro Rebelo-Guiomar
- MRC Mitochondrial Biology Unit, Cambridge, UK GABBA, University of Porto, Portugal
| | | | | | - Marcin L Pekalski
- JDRF/Wellcome Trust DIL, Cambridge Institute for Medical Research, University of Cambridge, UK
| | | | - Marine Charpentier
- INSERM U1154, CNRS UMR 7196, Muséum National d'Histoire Naturelle, Paris, France
| | - Jean-Paul Concordet
- INSERM U1154, CNRS UMR 7196, Muséum National d'Histoire Naturelle, Paris, France
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50
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Fernández del Río L, Gutiérrez-Casado E, Varela-López A, Villalba JM. Olive Oil and the Hallmarks of Aging. Molecules 2016; 21:163. [PMID: 26840281 PMCID: PMC6273542 DOI: 10.3390/molecules21020163] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 01/20/2016] [Accepted: 01/22/2016] [Indexed: 12/30/2022] Open
Abstract
Aging is a multifactorial and tissue-specific process involving diverse alterations regarded as the "hallmarks of aging", which include genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion and altered intracellular communication. Virtually all these hallmarks are targeted by dietary olive oil, particularly by virgin olive oil, since many of its beneficial effects can be accounted not only for the monounsaturated nature of its predominant fatty acid (oleic acid), but also for the bioactivity of its minor compounds, which can act on cells though both direct and indirect mechanisms due to their ability to modulate gene expression. Among the minor constituents of virgin olive oil, secoiridoids stand out for their capacity to modulate many pathways that are relevant for the aging process. Attenuation of aging-related alterations by olive oil or its minor compounds has been observed in cellular, animal and human models. How olive oil targets the hallmarks of aging could explain the improvement of health, reduced risk of aging-associated diseases, and increased longevity which have been associated with consumption of a typical Mediterranean diet containing this edible oil as the predominant fat source.
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Affiliation(s)
- Lucía Fernández del Río
- Department of Cell Biology, Physiology and Immunology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, Campus Rabanales, Severo Ochoa Building, 14014 Córdoba, Spain.
| | - Elena Gutiérrez-Casado
- Department of Cell Biology, Physiology and Immunology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, Campus Rabanales, Severo Ochoa Building, 14014 Córdoba, Spain.
| | - Alfonso Varela-López
- Department of Physiology, Institute of Nutrition and Food Technology "José Mataix", Biomedical Research Center (CIBM), University of Granada, Avda. del Conocimiento s.n., Armilla, 18100 Granada, Spain.
| | - José M Villalba
- Department of Cell Biology, Physiology and Immunology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, Campus Rabanales, Severo Ochoa Building, 14014 Córdoba, Spain.
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