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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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Tan K, Tse-Dinh YC. Variation of Structure and Cellular Functions of Type IA Topoisomerases across the Tree of Life. Cells 2024; 13:553. [PMID: 38534397 DOI: 10.3390/cells13060553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/12/2024] [Accepted: 03/19/2024] [Indexed: 03/28/2024] Open
Abstract
Topoisomerases regulate the topological state of cellular genomes to prevent impediments to vital cellular processes, including replication and transcription from suboptimal supercoiling of double-stranded DNA, and to untangle topological barriers generated as replication or recombination intermediates. The subfamily of type IA topoisomerases are the only topoisomerases that can alter the interlinking of both DNA and RNA. In this article, we provide a review of the mechanisms by which four highly conserved N-terminal protein domains fold into a toroidal structure, enabling cleavage and religation of a single strand of DNA or RNA. We also explore how these conserved domains can be combined with numerous non-conserved protein sequences located in the C-terminal domains to form a diverse range of type IA topoisomerases in Archaea, Bacteria, and Eukarya. There is at least one type IA topoisomerase present in nearly every free-living organism. The variation in C-terminal domain sequences and interacting partners such as helicases enable type IA topoisomerases to conduct important cellular functions that require the passage of nucleic acids through the break of a single-strand DNA or RNA that is held by the conserved N-terminal toroidal domains. In addition, this review will exam a range of human genetic disorders that have been linked to the malfunction of type IA topoisomerase.
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Affiliation(s)
- Kemin Tan
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Avenue, Lemont, IL 60439, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
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Ali A, Esmaeil A, Behbehani R. Mitochondrial Chronic Progressive External Ophthalmoplegia. Brain Sci 2024; 14:135. [PMID: 38391710 PMCID: PMC10887352 DOI: 10.3390/brainsci14020135] [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: 12/25/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND Chronic progressive external ophthalmoplegia (CPEO) is a rare disorder that can be at the forefront of several mitochondrial diseases. This review overviews mitochondrial CPEO encephalomyopathies to enhance accurate recognition and diagnosis for proper management. METHODS This study is conducted based on publications and guidelines obtained by selective review in PubMed. Randomized, double-blind, placebo-controlled trials, Cochrane reviews, and literature meta-analyses were particularly sought. DISCUSSION CPEO is a common presentation of mitochondrial encephalomyopathies, which can result from alterations in mitochondrial or nuclear DNA. Genetic sequencing is the gold standard for diagnosing mitochondrial encephalomyopathies, preceded by non-invasive tests such as fibroblast growth factor-21 and growth differentiation factor-15. More invasive options include a muscle biopsy, which can be carried out after uncertain diagnostic testing. No definitive treatment option is available for mitochondrial diseases, and management is mainly focused on lifestyle risk modification and supplementation to reduce mitochondrial load and symptomatic relief, such as ptosis repair in the case of CPEO. Nevertheless, various clinical trials and endeavors are still at large for achieving beneficial therapeutic outcomes for mitochondrial encephalomyopathies. KEY MESSAGES Understanding the varying presentations and genetic aspects of mitochondrial CPEO is crucial for accurate diagnosis and management.
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Affiliation(s)
- Ali Ali
- Neuro-Ophthalmology Unit, Ibn Sina Hospital, Al-Bahar Ophthalmology Center, Kuwait City 70035, Kuwait
| | - Ali Esmaeil
- Neuro-Ophthalmology Unit, Ibn Sina Hospital, Al-Bahar Ophthalmology Center, Kuwait City 70035, Kuwait
| | - Raed Behbehani
- Neuro-Ophthalmology Unit, Ibn Sina Hospital, Al-Bahar Ophthalmology Center, Kuwait City 70035, Kuwait
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Saha LK, Pommier Y. TOP3A coupling with replication forks and repair of TOP3A cleavage complexes. Cell Cycle 2024; 23:115-130. [PMID: 38341866 PMCID: PMC11037291 DOI: 10.1080/15384101.2024.2314440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/08/2024] [Indexed: 02/13/2024] Open
Abstract
Humans have two Type IA topoisomerases, topoisomerase IIIα (TOP3A) and topoisomerase IIIβ (TOP3B). In this review, we focus on the role of human TOP3A in DNA replication and highlight the recent progress made in understanding TOP3A in the context of replication. Like other topoisomerases, TOP3A acts by a reversible mechanism of cleavage and rejoining of DNA strands allowing changes in DNA topology. By cleaving and resealing single-stranded DNA, it generates TOP3A-linked single-strand breaks as TOP3A cleavage complexes (TOP3Accs) with a TOP3A molecule covalently bound to the 5´-end of the break. TOP3A is critical for both mitochondrial and for nuclear DNA replication. Here, we discuss the formation and repair of irreversible TOP3Accs, as their presence compromises genome integrity as they form TOP3A DNA-protein crosslinks (TOP3A-DPCs) associated with DNA breaks. We discuss the redundant pathways that repair TOP3A-DPCs, and how their defects are a source of DNA damage leading to neurological diseases and mitochondrial disorders.
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Affiliation(s)
- Liton Kumar Saha
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
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Erdinc D, Rodríguez‐Luis A, Fassad MR, Mackenzie S, Watson CM, Valenzuela S, Xie X, Menger KE, Sergeant K, Craig K, Hopton S, Falkous G, Poulton J, Garcia‐Moreno H, Giunti P, de Moura Aschoff CA, Morales Saute JA, Kirby AJ, Toro C, Wolfe L, Novacic D, Greenbaum L, Eliyahu A, Barel O, Anikster Y, McFarland R, Gorman GS, Schaefer AM, Gustafsson CM, Taylor RW, Falkenberg M, Nicholls TJ. Pathological variants in TOP3A cause distinct disorders of mitochondrial and nuclear genome stability. EMBO Mol Med 2023; 15:e16775. [PMID: 37013609 PMCID: PMC10165364 DOI: 10.15252/emmm.202216775] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 03/10/2023] [Accepted: 03/14/2023] [Indexed: 04/05/2023] Open
Abstract
Topoisomerase 3α (TOP3A) is an enzyme that removes torsional strain and interlinks between DNA molecules. TOP3A localises to both the nucleus and mitochondria, with the two isoforms playing specialised roles in DNA recombination and replication respectively. Pathogenic variants in TOP3A can cause a disorder similar to Bloom syndrome, which results from bi-allelic pathogenic variants in BLM, encoding a nuclear-binding partner of TOP3A. In this work, we describe 11 individuals from 9 families with an adult-onset mitochondrial disease resulting from bi-allelic TOP3A gene variants. The majority of patients have a consistent clinical phenotype characterised by bilateral ptosis, ophthalmoplegia, myopathy and axonal sensory-motor neuropathy. We present a comprehensive characterisation of the effect of TOP3A variants, from individuals with mitochondrial disease and Bloom-like syndrome, upon mtDNA maintenance and different aspects of enzyme function. Based on these results, we suggest a model whereby the overall severity of the TOP3A catalytic defect determines the clinical outcome, with milder variants causing adult-onset mitochondrial disease and more severe variants causing a Bloom-like syndrome with mitochondrial dysfunction in childhood.
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Affiliation(s)
- Direnis Erdinc
- Department of Medical Biochemistry and Cell BiologyUniversity of GothenburgGothenburgSweden
| | - Alejandro Rodríguez‐Luis
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Mahmoud R Fassad
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Sarah Mackenzie
- The Newcastle Upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Christopher M Watson
- North East and Yorkshire Genomic Laboratory Hub, Central LabSt. James's University HospitalLeedsUK
- Leeds Institute of Medical ResearchUniversity of Leeds, St. James's University HospitalLeedsUK
| | - Sebastian Valenzuela
- Department of Medical Biochemistry and Cell BiologyUniversity of GothenburgGothenburgSweden
| | - Xie Xie
- Department of Medical Biochemistry and Cell BiologyUniversity of GothenburgGothenburgSweden
| | - Katja E Menger
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Kate Sergeant
- Oxford Genetics LaboratoriesOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Kate Craig
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Service for Rare Mitochondrial DisordersNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Sila Hopton
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Service for Rare Mitochondrial DisordersNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Gavin Falkous
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Service for Rare Mitochondrial DisordersNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | | | - Joanna Poulton
- Nuffield Department of Women's & Reproductive Health, The Women's CentreUniversity of OxfordOxfordUK
| | - Hector Garcia‐Moreno
- Department of Clinical and Movement Neurosciences, Ataxia CentreUCL Queen Square Institute of NeurologyLondonUK
| | - Paola Giunti
- Department of Clinical and Movement Neurosciences, Ataxia CentreUCL Queen Square Institute of NeurologyLondonUK
| | | | - Jonas A Morales Saute
- Medical Genetics ServiceHospital de Clínicas de Porto Alegre (HCPA)Porto AlegreBrazil
- Department of Internal MedicineUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
- Graduate Program in Medicine: Medical SciencesUniversidade Federal do Rio Grande do SulPorto AlegreBrazil
| | - Amelia J Kirby
- Department of PediatricsWake Forest School of MedicineWinston‐SalemNCUSA
| | - Camilo Toro
- Undiagnosed Diseases ProgramNational Human Genome Research Institute, National Institutes of HealthBethesdaMDUSA
| | - Lynne Wolfe
- Undiagnosed Diseases ProgramNational Human Genome Research Institute, National Institutes of HealthBethesdaMDUSA
| | - Danica Novacic
- Undiagnosed Diseases ProgramNational Human Genome Research Institute, National Institutes of HealthBethesdaMDUSA
| | - Lior Greenbaum
- The Danek Gertner Institute of Human GeneticsSheba Medical CenterTel HashomerIsrael
- The Joseph Sagol Neuroscience Center, Sheba Medical CenterTel HashomerIsrael
- Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Aviva Eliyahu
- The Danek Gertner Institute of Human GeneticsSheba Medical CenterTel HashomerIsrael
- Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Ortal Barel
- Genomics UnitThe Center for Cancer Research, Sheba Medical CenterTel HashomerIsrael
| | - Yair Anikster
- Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
- Metabolic Disease UnitEdmond and Lily Safra Children's Hospital, Sheba Medical CenterTel HashomerIsrael
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Gráinne S Gorman
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Andrew M Schaefer
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Service for Rare Mitochondrial DisordersNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell BiologyUniversity of GothenburgGothenburgSweden
- Department of Clinical ChemistrySahlgrenska University HospitalGothenburgSweden
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Service for Rare Mitochondrial DisordersNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell BiologyUniversity of GothenburgGothenburgSweden
| | - Thomas J Nicholls
- Wellcome Centre for Mitochondrial Research, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
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