1
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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 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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2
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Zhuang F, Huang S, Liu L. PYCR3 modulates mtDNA copy number to drive proliferation and doxorubicin resistance in triple-negative breast cancer. Int J Biochem Cell Biol 2024; 171:106581. [PMID: 38642827 DOI: 10.1016/j.biocel.2024.106581] [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: 01/08/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
Triple-negative breast cancer (TNBC) poses significant challenges in treatment due to its aggressive nature and limited therapeutic targets. Understanding the underlying molecular mechanisms driving TNBC progression and chemotherapy resistance is imperative for developing effective therapeutic strategies. Thus, in this study, we aimed to elucidate the role of pyrroline-5-carboxylate reductase 3 (PYCR3) in TNBC pathogenesis and therapeutic response. We observed that PYCR3 is significantly upregulated in TNBC specimens compared to normal breast tissues, correlating with a poorer prognosis in TNBC patients. Knockdown of PYCR3 not only suppresses TNBC cell proliferation but also reverses acquired resistance of TNBC cells to doxorubicin, a commonly used chemotherapeutic agent. Mechanistically, we identified the mitochondrial localization of PYCR3 in TNBC cells and demonstrated its impact on TNBC cell proliferation and sensitivity to doxorubicin through the regulation of mtDNA copy number and mitochondrial respiration. Importantly, Selective reduction of mtDNA copy number using the mtDNA replication inhibitor 2', 3'-dideoxycytidine effectively recapitulates the phenotypic effects observed in PYCR3 knockout, resulting in decreased TNBC cell proliferation and the reversal of doxorubicin resistance through apoptosis induction. Thus, our study underscores the clinical relevance of PYCR3 and highlight its potential as a therapeutic target in TNBC management. By elucidating the functional significance of PYCR3 in TNBC, our findings contribute to a deeper understanding of TNBC biology and provide a foundation for developing novel therapeutic strategies aimed at improving patient outcomes.
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Affiliation(s)
- Feifei Zhuang
- Department of Medical Oncology, Yantaishan Hospital, Yantai, Shandong, China
| | - Shaoyan Huang
- Department of Medical Oncology, Yantaishan Hospital, Yantai, Shandong, China
| | - Lei Liu
- Department of Medical Oncology, Yantaishan Hospital, Yantai, Shandong, China.
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3
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Isaac RS, Tullius TW, Hansen KG, Dubocanin D, Couvillion M, Stergachis AB, Churchman LS. Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA. Nat Struct Mol Biol 2024; 31:568-577. [PMID: 38347148 DOI: 10.1038/s41594-024-01225-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/09/2024] [Indexed: 03/03/2024]
Abstract
Cellular metabolism relies on the regulation and maintenance of mitochondrial DNA (mtDNA). Hundreds to thousands of copies of mtDNA exist in each cell, yet because mitochondria lack histones or other machinery important for nuclear genome compaction, it remains unresolved how mtDNA is packaged into individual nucleoids. In this study, we used long-read single-molecule accessibility mapping to measure the compaction of individual full-length mtDNA molecules at near single-nucleotide resolution. We found that, unlike the nuclear genome, human mtDNA largely undergoes all-or-none global compaction, with most nucleoids existing in an inaccessible, inactive state. Highly accessible mitochondrial nucleoids are co-occupied by transcription and replication components and selectively form a triple-stranded displacement loop structure. In addition, we showed that the primary nucleoid-associated protein TFAM directly modulates the fraction of inaccessible nucleoids both in vivo and in vitro, acting consistently with a nucleation-and-spreading mechanism to coat and compact mitochondrial nucleoids. Together, these findings reveal the primary architecture of mtDNA packaging and regulation in human cells.
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Affiliation(s)
- R Stefan Isaac
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Thomas W Tullius
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Katja G Hansen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Danilo Dubocanin
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Mary Couvillion
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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4
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Gao Y, Guo L, Wang F, Wang Y, Li P, Zhang D. Development of mitochondrial gene-editing strategies and their potential applications in mitochondrial hereditary diseases: a review. Cytotherapy 2024; 26:11-24. [PMID: 37930294 DOI: 10.1016/j.jcyt.2023.10.004] [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: 06/08/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/07/2023]
Abstract
Mitochondrial DNA (mtDNA) is a critical genome contained within the mitochondria of eukaryotic cells, with many copies present in each mitochondrion. Mutations in mtDNA often are inherited and can lead to severe health problems, including various inherited diseases and premature aging. The lack of efficient repair mechanisms and the susceptibility of mtDNA to damage exacerbate the threat to human health. Heteroplasmy, the presence of different mtDNA genotypes within a single cell, increases the complexity of these diseases and requires an effective editing method for correction. Recently, gene-editing techniques, including programmable nucleases such as restriction endonuclease, zinc finger nuclease, transcription activator-like effector nuclease, clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeats-associated 9 and base editors, have provided new tools for editing mtDNA in mammalian cells. Base editors are particularly promising because of their high efficiency and precision in correcting mtDNA mutations. In this review, we discuss the application of these techniques in mitochondrial gene editing and their limitations. We also explore the potential of base editors for mtDNA modification and discuss the opportunities and challenges associated with their application in mitochondrial gene editing. In conclusion, this review highlights the advancements, limitations and opportunities in current mitochondrial gene-editing technologies and approaches. Our insights aim to stimulate the development of new editing strategies that can ultimately alleviate the adverse effects of mitochondrial hereditary diseases.
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Affiliation(s)
- Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Linlin Guo
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
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5
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Wu H, Zhang W, Xu F, Peng K, Liu X, Ding W, Ma Q, Cheng H, Wang X. C17orf80 binds the mitochondrial genome to promote its replication. J Cell Biol 2023; 222:e202302037. [PMID: 37676315 PMCID: PMC10484793 DOI: 10.1083/jcb.202302037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/26/2023] [Accepted: 07/17/2023] [Indexed: 09/08/2023] Open
Abstract
Serving as the power plant and signaling hub of a cell, mitochondria contain their own genome which encodes proteins essential for energy metabolism and forms DNA-protein assemblies called nucleoids. Mitochondrial DNA (mtDNA) exists in multiple copies within each cell ranging from hundreds to tens of thousands. Maintaining mtDNA homeostasis is vital for healthy cells, and its dysregulation causes multiple human diseases. However, the players involved in regulating mtDNA maintenance are largely unknown though the core components of its replication machinery have been characterized. Here, we identify C17orf80, a functionally uncharacterized protein, as a critical player in maintaining mtDNA homeostasis. C17orf80 primarily localizes to mitochondrial nucleoid foci and exhibits robust double-stranded DNA binding activity throughout the mitochondrial genome, thus constituting a bona fide new mitochondrial nucleoid protein. It controls mtDNA levels by promoting mtDNA replication and plays important roles in mitochondrial metabolism and cell proliferation. Our findings provide a potential target for therapeutics of human diseases associated with defective mtDNA control.
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Affiliation(s)
- Hao Wu
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Academy of Advanced Interdisciplinary Study, Peking University, Beijing, China
| | - Wenshuo Zhang
- Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing, China
| | - Fengli Xu
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Kun Peng
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Xiaoyu Liu
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Wanqiu Ding
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Qi Ma
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Heping Cheng
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Research Unit of Mitochondria in Brain Diseases, Chinese Academy of Medical Sciences, PKU-Nanjing Institute of Translational Medicine, Nanjing, China
| | - Xianhua Wang
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Research Unit of Mitochondria in Brain Diseases, Chinese Academy of Medical Sciences, PKU-Nanjing Institute of Translational Medicine, Nanjing, China
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6
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Potter A, Hangas A, Goffart S, Huynen MA, Cabrera-Orefice A, Spelbrink JN. Uncharacterized protein C17orf80 - a novel interactor of human mitochondrial nucleoids. J Cell Sci 2023; 136:jcs260822. [PMID: 37401363 PMCID: PMC10445727 DOI: 10.1242/jcs.260822] [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: 11/23/2022] [Accepted: 06/26/2023] [Indexed: 07/05/2023] Open
Abstract
Molecular functions of many human proteins remain unstudied, despite the demonstrated association with diseases or pivotal molecular structures, such as mitochondrial DNA (mtDNA). This small genome is crucial for the proper functioning of mitochondria, the energy-converting organelles. In mammals, mtDNA is arranged into macromolecular complexes called nucleoids that serve as functional stations for its maintenance and expression. Here, we aimed to explore an uncharacterized protein C17orf80, which was previously detected close to the nucleoid components by proximity labelling mass spectrometry. To investigate the subcellular localization and function of C17orf80, we took advantage of immunofluorescence microscopy, interaction proteomics and several biochemical assays. We demonstrate that C17orf80 is a mitochondrial membrane-associated protein that interacts with nucleoids even when mtDNA replication is inhibited. In addition, we show that C17orf80 is not essential for mtDNA maintenance and mitochondrial gene expression in cultured human cells. These results provide a basis for uncovering the molecular function of C17orf80 and the nature of its association with nucleoids, possibly leading to new insights about mtDNA and its expression.
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Affiliation(s)
- Alisa Potter
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Anu Hangas
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, 80101, Finland
| | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, 80101, Finland
| | - Martijn A. Huynen
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Alfredo Cabrera-Orefice
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Johannes N. Spelbrink
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
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7
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Functional Assessment of Mitochondrial DNA Maintenance by Depletion and Repopulation Using 2',3'-Dideoxycytidine in Cultured Cells. Methods Mol Biol 2023; 2615:229-240. [PMID: 36807796 DOI: 10.1007/978-1-0716-2922-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The manipulation of mitochondrial DNA (mtDNA) copy number in cultured cells, using substances that interfere with DNA replication, is a useful tool to investigate various aspects of mtDNA maintenance. Here we describe the use of 2',3'-dideoxycytidine (ddC) to induce a reversible reduction of mtDNA copy number in human primary fibroblasts and human embryonic kidney (HEK293) cells. Once the application of ddC is stopped, cells depleted for mtDNA attempt to recover normal mtDNA copy numbers. The dynamics of repopulation of mtDNA provide a valuable measure for the enzymatic activity of the mtDNA replication machinery.
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8
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Burgstaller JP, Chiaratti MR. Mitochondrial Inheritance Following Nuclear Transfer: From Cloned Animals to Patients with Mitochondrial Disease. Methods Mol Biol 2023; 2647:83-104. [PMID: 37041330 DOI: 10.1007/978-1-0716-3064-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Mitochondria are indispensable power plants of eukaryotic cells that also act as a major biochemical hub. As such, mitochondrial dysfunction, which can originate from mutations in the mitochondrial genome (mtDNA), may impair organism fitness and lead to severe diseases in humans. MtDNA is a multi-copy, highly polymorphic genome that is uniparentally transmitted through the maternal line. Several mechanisms act in the germline to counteract heteroplasmy (i.e., coexistence of two or more mtDNA variants) and prevent expansion of mtDNA mutations. However, reproductive biotechnologies such as cloning by nuclear transfer can disrupt mtDNA inheritance, resulting in new genetic combinations that may be unstable and have physiological consequences. Here, we review the current understanding of mitochondrial inheritance, with emphasis on its pattern in animals and human embryos generated by nuclear transfer.
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Affiliation(s)
- Jörg P Burgstaller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Marcos R Chiaratti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil.
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9
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Al Khatib I, Deng J, Symes A, Kerr M, Zhang H, Huang SYN, Pommier Y, Khan A, Shutt TE. Functional characterization of two variants of mitochondrial topoisomerase TOP1MT that impact regulation of the mitochondrial genome. J Biol Chem 2022; 298:102420. [PMID: 36030054 PMCID: PMC9513266 DOI: 10.1016/j.jbc.2022.102420] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/21/2022] Open
Abstract
TOP1MT encodes a mitochondrial topoisomerase that is important for mtDNA regulation and is involved in mitochondrial replication, transcription, and translation. Two variants predicted to affect TOP1MT function (V1 - R198C and V2 - V338L) were identified by exome sequencing of a newborn with hypertrophic cardiomyopathy. As no pathogenic TOP1MT variants had been confirmed previously, we characterized these variants for their ability to rescue several TOP1MT functions in KO cells. Consistent with these TOP1MT variants contributing to the patient phenotype, our comprehensive characterization suggests that both variants had impaired activity. Critically, we determined neither variant was able to restore steady state levels of mitochondrial-encoded proteins nor to rescue oxidative phosphorylation when re-expressed in TOP1MT KO cells. However, we found the two variants behaved differently in some respects; while the V1 variant was more efficient in restoring transcript levels, the V2 variant showed better rescue of mtDNA copy number and replication. These findings suggest that the different TOP1MT variants affect distinct TOP1MT functions. Altogether, these findings begin to provide insight into the many roles that TOP1MT plays in the maintenance and expression of the mitochondrial genome and how impairments in this important protein may lead to human pathology.
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Affiliation(s)
- Iman Al Khatib
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jingti Deng
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Andrew Symes
- Department of Geomatics Engineering, Schulich School of Engineering, University of Calgary, Calgary, Alberta, Canada
| | | | - Hongliang Zhang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Shar-Yin Naomi Huang
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland, USA
| | - Aneal Khan
- Discovery DNA, Calgary, Alberta, Canada; M.A.G.I.C. Clinic Ltd (Metabolics and Genetics in Calgary), Department of Pediatrics, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Timothy E Shutt
- Departments of Biochemistry & Molecular Biology and Medical Genetics, Cumming School of Medicine, Alberta Children's Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada.
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10
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Mehmedović M, Martucci M, Spåhr H, Ishak L, Mishra A, Sanchez-Sandoval ME, Pardo-Hernández C, Peter B, van den Wildenberg SM, Falkenberg M, Farge G. Disease causing mutation (P178L) in mitochondrial transcription factor A results in impaired mitochondrial transcription initiation. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166467. [PMID: 35716868 DOI: 10.1016/j.bbadis.2022.166467] [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: 03/13/2022] [Revised: 05/31/2022] [Accepted: 06/09/2022] [Indexed: 10/18/2022]
Abstract
Mitochondrial transcription factor A (TFAM) is essential for the maintenance, expression, and packaging of mitochondrial DNA (mtDNA). Recently, a pathogenic homozygous variant in TFAM (P178L) has been associated with a severe mtDNA depletion syndrome leading to neonatal liver failure and early death. We have performed a biochemical characterization of the TFAM variant P178L in order to understand the molecular basis for the pathogenicity of this mutation. We observe no effects on DNA binding, and compaction of DNA is only mildly affected by the P178L amino acid change. Instead, the mutation severely impairs mtDNA transcription initiation at the mitochondrial heavy and light strand promoters. Molecular modeling suggests that the P178L mutation affects promoter sequence recognition and the interaction between TFAM and the tether helix of POLRMT, thus explaining transcription initiation deficiency.
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Affiliation(s)
- Majda Mehmedović
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Martial Martucci
- Université Clermont Auvergne, CNRS, Laboratoire de Physique de Clermont, F-63000 Clermont-Ferrand, France
| | - Henrik Spåhr
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden; Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm 17177, Sweden
| | - Layal Ishak
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Anup Mishra
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Maria Eugenia Sanchez-Sandoval
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Carlos Pardo-Hernández
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Bradley Peter
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Siet M van den Wildenberg
- Université Clermont Auvergne, CNRS, Laboratoire de Physique de Clermont, F-63000 Clermont-Ferrand, France; Université Clermont Auvergne, CNRS, IRD, Université Jean Monnet Saint Etienne, LMV, F-63000 Clermont-Ferrand, France
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden.
| | - Geraldine Farge
- Université Clermont Auvergne, CNRS, Laboratoire de Physique de Clermont, F-63000 Clermont-Ferrand, France.
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11
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Silva-Pinheiro P, Minczuk M. The potential of mitochondrial genome engineering. Nat Rev Genet 2022; 23:199-214. [PMID: 34857922 DOI: 10.1038/s41576-021-00432-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2021] [Indexed: 12/19/2022]
Abstract
Mitochondria are subject to unique genetic control by both nuclear DNA and their own genome, mitochondrial DNA (mtDNA), of which each mitochondrion contains multiple copies. In humans, mutations in mtDNA can lead to devastating, heritable, multi-system diseases that display different tissue-specific presentation at any stage of life. Despite rapid advances in nuclear genome engineering, for years, mammalian mtDNA has remained resistant to genetic manipulation, hampering our ability to understand the mechanisms that underpin mitochondrial disease. Recent developments in the genetic modification of mammalian mtDNA raise the possibility of using genome editing technologies, such as programmable nucleases and base editors, for the treatment of hereditary mitochondrial disease.
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Affiliation(s)
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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12
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Kuthethur R, Shukla V, Mallya S, Adiga D, Kabekkodu SP, Ramachandra L, Saxena Pu P, Satyamoorthy K, Chakrabarty S. Expression analysis and function of mitochondrial genome-encoded microRNAs. J Cell Sci 2022; 135:274749. [PMID: 35297485 DOI: 10.1242/jcs.258937] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 03/11/2022] [Indexed: 11/20/2022] Open
Abstract
MicroRNAs play a significant role in nuclear and mitochondrial anterograde and retrograde signaling. Most of the miRNAs found inside mitochondria are nuclear genome encoded, with few mitochondrial genome encoded non-coding RNAs have been reported. In this study, we have identified 13 mitochondrial genome-encoded microRNAs (mitomiRs), which were differentially expressed in breast cancer cell lines (MCF-7, MDA-MB-468, and MDA-MB-231), non-malignant breast epithelial cell line (MCF-10A), and normal and breast cancer tissue specimens. We found that mitochondrial DNA depletion and inhibition of mitochondrial transcription leads to reduced expression of mitomiRs in breast cancer cells. MitomiRs physically interact with Ago2, an RNA-induced silencing complex (RISC) protein, in the cytoplasm and inside mitochondria. MitomiRs regulate the expression of both nuclear and mitochondrial transcripts in breast cancer cells. We showed that mitomiR-5 targets PPARGC1A and regulates mtDNA copy number in breast cancer cells. MitomiRs identified in the present study may be a promising tool for expression and functional analysis in patients with a defective mitochondrial phenotype, including cancer and metabolic syndromes.
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Affiliation(s)
- Raviprasad Kuthethur
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Vaibhav Shukla
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sandeep Mallya
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Lingadakai Ramachandra
- Department of Surgery, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Prakash Saxena Pu
- Department of Radiation Oncology, Kasturba Medical College, Manipal Academy of Higher Education, Mangalore, Karnataka, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
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13
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Nomiyama T, Setoyama D, Yasukawa T, Kang D. Mitochondria Metabolomics Reveals a Role of β-Nicotinamide Mononucleotide Metabolism in Mitochondrial DNA Replication. J Biochem 2021; 171:325-338. [PMID: 34865026 DOI: 10.1093/jb/mvab136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/30/2021] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial DNA (mtDNA) replication is tightly regulated and necessary for cellular homeostasis; however, its relationship with mitochondrial metabolism remains unclear. Advances in metabolomics integrated with the rapid isolation of mitochondria will allow for remarkable progress in analyzing mitochondrial metabolism. Here, we propose a novel methodology for mitochondria-targeted metabolomics, which employs a quick isolation procedure using a hemolytic toxin from Streptococcus pyogenes streptolysin O (SLO). SLO-isolation of mitochondria from cultured HEK293 cells is time- and labor-saving for simultaneous multi-sample processing and has been applied to various other cell lines in this study. Furthermore, our method can detect the time-dependent reduction in mitochondrial ATP in response to a glycolytic inhibitor 2-deoxyglucose, indicating the suitability to prepare metabolite analysis-competent mitochondria. Using this methodology, we searched for specific mitochondrial metabolites associated with mtDNA replication activation, and nucleotides and NAD+ were identified to be prominently altered. Most notably, treatment of β-Nicotinamide Mononucleotide (β-NMN), a precursor of NAD+, to HEK293 cells activated and improved the rate of mtDNA replication by increasing nucleotides in mitochondria and decreasing their degradation products: nucleosides. Our results suggest that β-NMN metabolism play a role in supporting mtDNA replication by maintaining the nucleotide pool balance in the mitochondria.
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Affiliation(s)
- Tomoko Nomiyama
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Fukuoka, Japan.,Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, 3-1-1 Maidashi, Fukuoka, Japan
| | - Daiki Setoyama
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Fukuoka, Japan.,Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, 3-1-1 Maidashi, Fukuoka, Japan
| | - Takehiro Yasukawa
- Department of Pathology and Oncology, Juntendo University School of Medicine, 2-1-1 Hongo, Tokyo, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Fukuoka, Japan.,Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, 3-1-1 Maidashi, Fukuoka, Japan
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14
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Emerging methods for and novel insights gained by absolute quantification of mitochondrial DNA copy number and its clinical applications. Pharmacol Ther 2021; 232:107995. [PMID: 34592204 DOI: 10.1016/j.pharmthera.2021.107995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 02/07/2023]
Abstract
The past thirty years have seen a surge in interest in pathophysiological roles of mitochondria, and the accurate quantification of mitochondrial DNA copy number (mCN) in cells and tissue samples is a fundamental aspect of assessing changes in mitochondrial health and biogenesis. Quantification of mCN between studies is surprisingly variable due to a combination of physiological variability and diverse protocols being used to measure this endpoint. The advent of novel methods to quantify nucleic acids like digital polymerase chain reaction (dPCR) and high throughput sequencing offer the ability to measure absolute values of mCN. We conducted an in-depth survey of articles published between 1969 -- 2020 to create an overview of mCN values, to assess consensus values of tissue-specific mCN, and to evaluate consistency between methods of assessing mCN. We identify best practices for methods used to assess mCN, and we address the impact of using specific loci on the mitochondrial genome to determine mCN. Current data suggest that clinical measurement of mCN can provide diagnostic and prognostic value in a range of diseases and health conditions, with emphasis on cancer and cardiovascular disease, and the advent of means to measure absolute mCN should improve future clinical applications of mCN measurements.
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15
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Cheng AN, Cheng LC, Kuo CL, Lo YK, Chou HY, Chen CH, Wang YH, Chuang TH, Cheng SJ, Lee AYL. Mitochondrial Lon-induced mtDNA leakage contributes to PD-L1-mediated immunoescape via STING-IFN signaling and extracellular vesicles. J Immunother Cancer 2020; 8:e001372. [PMID: 33268351 PMCID: PMC7713199 DOI: 10.1136/jitc-2020-001372] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Mitochondrial Lon is a chaperone and DNA-binding protein that functions in protein quality control and stress response pathways. The level of Lon regulates mitochondrial DNA (mtDNA) metabolism and the production of mitochondrial reactive oxygen species (ROS). However, there is little information in detail on how mitochondrial Lon regulates ROS-dependent cancer immunoescape through mtDNA metabolism in the tumor microenvironment (TME). METHODS We explored the understanding of the intricate interplay between mitochondria and the innate immune response in the inflammatory TME. RESULTS We found that oxidized mtDNA is released into the cytosol when Lon is overexpressed and then it induces interferon (IFN) signaling via cGAS-STING-TBK1, which upregulates PD-L1 and IDO-1 expression to inhibit T-cell activation. Unexpectedly, upregulation of Lon also induces the secretion of extracellular vehicles (EVs), which carry mtDNA and PD-L1. Lon-induced EVs further induce the production of IFN and IL-6 from macrophages, which attenuates T-cell immunity in the TME. CONCLUSIONS The levels of mtDNA and PD-L1 in EVs in patients with oral cancer function as a potential diagnostic biomarker for anti-PD-L1 immunotherapy. Our studies provide an insight into the immunosuppression on mitochondrial stress and suggest a therapeutic synergy between anti-inflammation therapy and immunotherapy in cancer.
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Affiliation(s)
- An Ning Cheng
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Li-Chun Cheng
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Cheng-Liang Kuo
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Yu Kang Lo
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Han-Yu Chou
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Chung-Hsing Chen
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Yi-Hao Wang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Tsung-Hsien Chuang
- Immunology Research Center, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Shih-Jung Cheng
- School of Dentistry, National Taiwan University, Taipei, Taiwan
- Department of Dentistry, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Alan Yueh-Luen Lee
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Miaoli, Taiwan
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
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16
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Chen J, Zheng Q, Peiffer LB, Hicks JL, Haffner MC, Rosenberg AZ, Levi M, Wang XX, Ozbek B, Baena-Del Valle J, Yegnasubramanian S, De Marzo AM. An in Situ Atlas of Mitochondrial DNA in Mammalian Tissues Reveals High Content in Stem and Proliferative Compartments. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:1565-1579. [PMID: 32304697 PMCID: PMC7338910 DOI: 10.1016/j.ajpath.2020.03.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 02/25/2020] [Accepted: 03/19/2020] [Indexed: 02/07/2023]
Abstract
Mitochondria regulate ATP production, metabolism, and cell death. Alterations in mitochondrial DNA (mtDNA) sequence and copy number are implicated in aging and organ dysfunction in diverse inherited and sporadic diseases. Because most measurements of mtDNA use homogenates of complex tissues, little is known about cell-type-specific mtDNA copy number heterogeneity in normal physiology, aging, and disease. Thus, the precise cell types whose loss of mitochondrial activity and altered mtDNA copy number that result in organ dysfunction in aging and disease have often not been clarified. Here, an in situ hybridization approach to generate a single-cell-resolution atlas of mtDNA content in mammalian tissues was validated. In hierarchically organized self-renewing tissues, higher levels of mtDNA were observed in stem/proliferative compartments compared with differentiated compartments. Striking zonal patterns of mtDNA levels in the liver reflected the known oxygen tension gradient. In the kidney, proximal and distal tubules had markedly higher mtDNA levels compared with cells within glomeruli and collecting duct epithelial cells. In mice, decreased mtDNA levels were visualized in renal tubules as a function of aging, which was prevented by calorie restriction. This study provides a novel approach for quantifying species- and cell-type-specific mtDNA copy number and dynamics in any normal or diseased tissue that can be used for monitoring the effects of interventions in animal and human studies.
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Affiliation(s)
- Jiayu Chen
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Qizhi Zheng
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lauren B Peiffer
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jessica L Hicks
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Michael C Haffner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Moshe Levi
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC
| | - Xiaoxin X Wang
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC
| | - Busra Ozbek
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Javier Baena-Del Valle
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Srinivasan Yegnasubramanian
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Urology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Angelo M De Marzo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Urology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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17
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Takishita Y, Yasuda H, Shimizu M, Matsuo A, Morita A, Tsutsumi T, Tsuchiya M, Sato EF. Formation of neutrophil extracellular traps in mitochondrial DNA-deficient cells. J Clin Biochem Nutr 2019; 66:15-23. [PMID: 32001952 PMCID: PMC6983440 DOI: 10.3164/jcbn.19-77] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 09/05/2019] [Indexed: 12/22/2022] Open
Abstract
Neutrophil extracellular trap (NET) formation plays an important role in inflammatory diseases. Although it is known that NET formation occurs via NADPH oxidase (NOX)-dependent and NOX-independent pathways, the detailed mechanism remains unknown. Therefore, in this study, we aimed to elucidate the role of mitochondria in NOX-dependent and NOX-independent NET formation. We generated mitochondrial DNA-deficient cells (ρ0 cells) by treating HL-60 cells with dideoxycytidine and differentiated them to neutrophil-like cells. These neutrophil-like ρ0 cells showed markedly reduced NOX-independent NET formation but not NOX-dependent NET formation. However, NET-associated intracellular histone citrullination was not inhibited in ρ0 cells. Furthermore, cells membrane disruption in NOX-dependent NET formation occurred in a Myeloperoxidase (MPO) and mixed lineage kinase domain like pseudokinase (MLKL)-dependent manner; however, cell membrane disruption in NOX-independent NET formation partially occurred in an MLKL-dependent manner. These results highlight the importance of mitochondria in NOX-independent NET formation.
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Affiliation(s)
- Yutaka Takishita
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minamitamagaki, Suzuka-city, Mie 513-8670, Japan
| | - Hiroyuki Yasuda
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minamitamagaki, Suzuka-city, Mie 513-8670, Japan
| | - Mio Shimizu
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minamitamagaki, Suzuka-city, Mie 513-8670, Japan
| | - Akane Matsuo
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minamitamagaki, Suzuka-city, Mie 513-8670, Japan
| | - Akihiro Morita
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minamitamagaki, Suzuka-city, Mie 513-8670, Japan
| | - Tomonari Tsutsumi
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minamitamagaki, Suzuka-city, Mie 513-8670, Japan
| | - Masahiko Tsuchiya
- Department of Anesthesiology, Osaka City University Medical School, 1-5-7 Asahi-machi, Abeno, Osaka 545-8586, Japan
| | - Eisuke F Sato
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minamitamagaki, Suzuka-city, Mie 513-8670, Japan
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18
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Srirattana K, St John JC. Transmission of Dysfunctional Mitochondrial DNA and Its Implications for Mammalian Reproduction. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2019; 231:75-103. [PMID: 30617719 DOI: 10.1007/102_2018_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondrial DNA (mtDNA) encodes proteins for the electron transport chain which produces the vast majority of cellular energy. MtDNA has its own replication and transcription machinery that relies on nuclear-encoded transcription and replication factors. MtDNA is inherited in a non-Mendelian fashion as maternal-only mtDNA is passed onto the next generation. Mutation to mtDNA can cause mitochondrial dysfunction, which affects energy production and tissue and organ function. In somatic cell nuclear transfer (SCNT), there is an issue with the mixing of two populations of mtDNA, namely from the donor cell and recipient oocyte. This review focuses on the transmission of mtDNA in SCNT embryos and offspring. The transmission of donor cell mtDNA can be prevented by depleting the donor cell of its mtDNA using mtDNA depletion agents prior to SCNT. As a result, SCNT embryos harbour oocyte-only mtDNA. Moreover, culturing SCNT embryos derived from mtDNA depleted cells in media supplemented with a nuclear reprograming agent can increase the levels of expression of genes related to embryo development when compared with non-depleted cell-derived embryos. Furthermore, we have reviewed how mitochondrial supplementation in oocytes can have beneficial effects for SCNT embryos by increasing mtDNA copy number and the levels of expression of genes involved in energy production and decreasing the levels of expression of genes involved in embryonic cell death. Notably, there are beneficial effects of mtDNA supplementation over the use of nuclear reprograming agents in terms of regulating gene expression in embryos. Taken together, manipulating mtDNA in donor cells and/or oocytes prior to SCNT could enhance embryo production efficiency.
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Affiliation(s)
- Kanokwan Srirattana
- Mitochondrial Genetics Group, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Justin C St John
- Mitochondrial Genetics Group, Hudson Institute of Medical Research, Clayton, VIC, Australia. .,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia.
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19
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Srirattana K, St John JC. Additional mitochondrial DNA influences the interactions between the nuclear and mitochondrial genomes in a bovine embryo model of nuclear transfer. Sci Rep 2018; 8:7246. [PMID: 29740154 PMCID: PMC5940817 DOI: 10.1038/s41598-018-25516-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 04/24/2018] [Indexed: 01/13/2023] Open
Abstract
We generated cattle embryos using mitochondrial supplementation and somatic cell nuclear transfer (SCNT), named miNT, to determine how additional mitochondrial DNA (mtDNA) modulates the nuclear genome. To eliminate any confounding effects from somatic cell mtDNA in intraspecies SCNT, donor cell mtDNA was depleted prior to embryo production. Additional oocyte mtDNA did not affect embryo development rates but increased mtDNA copy number in blastocyst stage embryos. Moreover, miNT-derived blastocysts had different gene expression profiles when compared with SCNT-derived blastocysts. Additional mtDNA increased expression levels of genes involved in oxidative phosphorylation, cell cycle and DNA repair. Supplementing the embryo culture media with a histone deacetylase inhibitor, Trichostatin A (TSA), had no beneficial effects on the development of miNT-derived embryos, unlike SCNT-derived embryos. When compared with SCNT-derived blastocysts cultured in the presence of TSA, additional mtDNA alone had beneficial effects as the activity of glycolysis may increase and embryonic cell death may decrease. However, these beneficial effects were not found with additional mtDNA and TSA together, suggesting that additional mtDNA alone enhances reprogramming. In conclusion, additional mtDNA increased mtDNA copy number and expression levels of genes involved in energy production and embryo development in blastocyst stage embryos emphasising the importance of nuclear-mitochondrial interactions.
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Affiliation(s)
- Kanokwan Srirattana
- Centre for Genetic Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Justin C St John
- Centre for Genetic Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia.
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3168, Australia.
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20
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Wiehe RS, Gole B, Chatre L, Walther P, Calzia E, Ricchetti M, Wiesmüller L. Endonuclease G promotes mitochondrial genome cleavage and replication. Oncotarget 2018; 9:18309-18326. [PMID: 29719607 PMCID: PMC5915074 DOI: 10.18632/oncotarget.24822] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/12/2018] [Indexed: 12/26/2022] Open
Abstract
Endonuclease G (EndoG) is a nuclear-encoded endonuclease, mostly localised in mitochondria. In the nucleus EndoG participates in site-specific cleavage during replication stress and genome-wide DNA degradation during apoptosis. However, the impact of EndoG on mitochondrial DNA (mtDNA) metabolism is poorly understood. Here, we investigated whether EndoG is involved in the regulation of mtDNA replication and removal of aberrant copies. We applied the single-cell mitochondrial Transcription and Replication Imaging Protocol (mTRIP) and PCR-based strategies on human cells after knockdown/knockout and re-expression of EndoG. Our analysis revealed that EndoG stimulates both mtDNA replication initiation and mtDNA depletion, the two events being interlinked and dependent on EndoG's nuclease activity. Stimulation of mtDNA replication by EndoG was independent of 7S DNA processing at the replication origin. Importantly, both mtDNA-directed activities of EndoG were promoted by oxidative stress. Inhibition of base excision repair (BER) that repairs oxidative stress-induced DNA damage unveiled a pronounced effect of EndoG on mtDNA removal, reminiscent of recently discovered links between EndoG and BER in the nucleus. Altogether with the downstream effects on mitochondrial transcription, protein expression, redox status and morphology, this study demonstrates that removal of damaged mtDNA by EndoG and compensatory replication play a critical role in mitochondria homeostasis.
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Affiliation(s)
| | - Boris Gole
- Department of Obstetrics and Gynecology, Ulm University, Ulm, 89075, Germany
- Present address: Centre for Human Molecular Genetics and Pharmacogenomics, Medical Faculty, University of Maribor, Maribor, SI-2000, Slovenia
| | - Laurent Chatre
- Department of Developmental and Stem Cell Biology, Institute Pasteur, Stem Cells and Development, 75724 Cedex 15, Paris, France
- Team Stability of Nuclear and Mitochondrial DNA, Unit of Stem Cells and Development, CNRS UMR 3738, 75724 Cedex 15, Paris, France
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, Ulm, 89081, Germany
| | - Enrico Calzia
- Institute of Anesthesiological Pathophysiology and Process Engineering, Ulm University Hospital, Ulm, 89081, Germany
| | - Miria Ricchetti
- Department of Developmental and Stem Cell Biology, Institute Pasteur, Stem Cells and Development, 75724 Cedex 15, Paris, France
- Team Stability of Nuclear and Mitochondrial DNA, Unit of Stem Cells and Development, CNRS UMR 3738, 75724 Cedex 15, Paris, France
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, Ulm, 89075, Germany
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21
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Young MJ. Off-Target Effects of Drugs that Disrupt Human Mitochondrial DNA Maintenance. Front Mol Biosci 2017; 4:74. [PMID: 29214156 PMCID: PMC5702650 DOI: 10.3389/fmolb.2017.00074] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 10/31/2017] [Indexed: 12/17/2022] Open
Abstract
Nucleoside reverse transcriptase inhibitors (NRTIs) were the first drugs used to treat human immunodeficiency virus (HIV) the cause of acquired immunodeficiency syndrome. Development of severe mitochondrial toxicity has been well documented in patients infected with HIV and administered NRTIs. In vitro biochemical experiments have demonstrated that the replicative mitochondrial DNA (mtDNA) polymerase gamma, Polg, is a sensitive target for inhibition by metabolically active forms of NRTIs, nucleotide reverse transcriptase inhibitors (NtRTIs). Once incorporated into newly synthesized daughter strands NtRTIs block further DNA polymerization reactions. Human cell culture and animal studies have demonstrated that cell lines and mice exposed to NRTIs display mtDNA depletion. Further complicating NRTI off-target effects on mtDNA maintenance, two additional DNA polymerases, Pol beta and PrimPol, were recently reported to localize to mitochondria as well as the nucleus. Similar to Polg, in vitro work has demonstrated both Pol beta and PrimPol incorporate NtRTIs into nascent DNA. Cell culture and biochemical experiments have also demonstrated that antiviral ribonucleoside drugs developed to treat hepatitis C infection act as off-target substrates for POLRMT, the mitochondrial RNA polymerase and primase. Accompanying the above-mentioned topics, this review examines: (1) mtDNA maintenance in human health and disease, (2) reports of DNA polymerases theta and zeta (Rev3) localizing to mitochondria, and (3) additional drugs with off-target effects on mitochondrial function. Lastly, mtDNA damage may induce cell death; therefore, the possibility of utilizing compounds that disrupt mtDNA maintenance to kill cancer cells is discussed.
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Affiliation(s)
- Matthew J Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL, United States
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22
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Vaghjiani V, Cain JE, Lee W, Vaithilingam V, Tuch BE, St John JC. Modulation of Mitochondrial DNA Copy Number to Induce Hepatocytic Differentiation of Human Amniotic Epithelial Cells. Stem Cells Dev 2017; 26:1505-1519. [PMID: 28756741 DOI: 10.1089/scd.2017.0041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial deoxyribonucleic acid (mtDNA) copy number is tightly regulated during pluripotency and differentiation. There is increased demand of cellular adenosine triphosphate (ATP) during differentiation for energy-intensive cell types such as hepatocytes and neurons to meet the cell's functional requirements. During hepatocyte differentiation, mtDNA copy number should be synchronously increased to generate sufficient ATP through oxidative phosphorylation. Unlike bone marrow mesenchymal cells, mtDNA copy number failed to increase by 28 days of differentiation of human amniotic epithelial cells (hAEC) into hepatocyte-like cells (HLC) despite their expression of some end-stage hepatic markers. This was due to higher levels of DNA methylation at exon 2 of POLGA, the mtDNA-specific replication factor. Treatment with a DNA demethylation agent, 5-azacytidine, resulted in increased mtDNA copy number, reduced DNA methylation at exon 2 of POLGA, and reduced hepatic gene expression. Depletion of mtDNA followed by subsequent differentiation did not increase mtDNA copy number, but reduced DNA methylation at exon 2 of POLGA and increased expression of hepatic and pluripotency genes. We encapsulated hAEC in barium alginate microcapsules and subsequently differentiated them into HLC. Encapsulation resulted in no net increase of mtDNA copy number but a significant reduction in DNA methylation of POLGA. RNAseq analysis showed that differentiated HLC express hepatocyte-specific genes but also increased expression of inflammatory interferon genes. Differentiation in encapsulated cells showed suppression of inflammatory genes as well as increased expression of genes associated with hepatocyte function pathways and networks. This study demonstrates that an increase in classical hepatic gene expression can be achieved in HLC through encapsulation, although they fail to effectively regulate mtDNA copy number.
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Affiliation(s)
- Vijesh Vaghjiani
- 1 Centre for Genetic Diseases, Hudson Institute of Medical Research , Clayton, Australia .,2 Department of Molecular and Translational Science, Monash University , Clayton, Australia
| | - Jason E Cain
- 2 Department of Molecular and Translational Science, Monash University , Clayton, Australia .,3 Centre for Cancer Research, Hudson Institute of Medical Research , Clayton, Australia
| | - William Lee
- 1 Centre for Genetic Diseases, Hudson Institute of Medical Research , Clayton, Australia .,2 Department of Molecular and Translational Science, Monash University , Clayton, Australia
| | - Vijayaganapathy Vaithilingam
- 4 Future Manufacturing Flagship, Commonwealth Scientific and Industrial Research Organisation , North Ryde, Australia
| | - Bernard E Tuch
- 4 Future Manufacturing Flagship, Commonwealth Scientific and Industrial Research Organisation , North Ryde, Australia .,5 School of Biomedical Science, Discipline Physiology, University of Sydney , Sydney, Australia
| | - Justin C St John
- 1 Centre for Genetic Diseases, Hudson Institute of Medical Research , Clayton, Australia .,2 Department of Molecular and Translational Science, Monash University , Clayton, Australia
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23
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Manipulating the Mitochondrial Genome To Enhance Cattle Embryo Development. G3-GENES GENOMES GENETICS 2017; 7:2065-2080. [PMID: 28500053 PMCID: PMC5499117 DOI: 10.1534/g3.117.042655] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mixing of mitochondrial DNA (mtDNA) from the donor cell and the recipient oocyte in embryos and offspring derived from somatic cell nuclear transfer (SCNT) compromises genetic integrity and affects embryo development. We set out to generate SCNT embryos that inherited their mtDNA from the recipient oocyte only, as is the case following natural conception. While SCNT blastocysts produced from Holstein (Bos taurus) fibroblasts were depleted of their mtDNA, and oocytes derived from Angus (Bos taurus) cattle possessed oocyte mtDNA only, the coexistence of donor cell and oocyte mtDNA resulted in blastocysts derived from nondepleted cells. Moreover, the use of the reprogramming agent, Trichostatin A (TSA), further improved the development of embryos derived from depleted cells. RNA-seq analysis highlighted 35 differentially expressed genes from the comparison between blastocysts generated from nondepleted cells and blastocysts from depleted cells, both in the presence of TSA. The only differences between these two sets of embryos were the presence of donor cell mtDNA, and a significantly higher mtDNA copy number for embryos derived from nondepleted cells. Furthermore, the use of TSA on embryos derived from depleted cells positively modulated the expression of CLDN8, TMEM38A, and FREM1, which affect embryonic development. In conclusion, SCNT embryos produced by mtDNA depleted donor cells have the same potential to develop to the blastocyst stage without the presumed damaging effect resulting from the mixture of donor and recipient mtDNA.
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Tetramethylpyrazine blocks TFAM degradation and up-regulates mitochondrial DNA copy number by interacting with TFAM. Biosci Rep 2017; 37:BSR20170319. [PMID: 28465355 PMCID: PMC5434891 DOI: 10.1042/bsr20170319] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 04/25/2017] [Accepted: 05/02/2017] [Indexed: 01/26/2023] Open
Abstract
The natural small molecule compound: 2,3,5,6-tetramethylpyrazine (TMP), is a major component of the Chinese medicine Chuanxiong, which has wide clinical applications in dilating blood vessels, inhibiting platelet aggregation and treating thrombosis. Recent work suggests that TMP is also an antitumour agent. Despite its chemotherapeutic potential, the mechanism(s) underlying TMP action are unknown. Herein, we demonstrate that TMP binds to mitochondrial transcription factor A (TFAM) and blocks its degradation by the mitochondrial Lon protease. TFAM is a key regulator of mtDNA replication, transcription and transmission. Our previous work showed that when TFAM is not bound to DNA, it is rapidly degraded by the ATP-dependent Lon protease, which is essential for mitochondrial proteostasis. In cultured cells, TMP specifically blocks Lon-mediated degradation of TFAM, leading to TFAM accumulation and subsequent up-regulation of mtDNA content in cells with substantially low levels of mtDNA. In vitro protease assays show that TMP does not directly inhibit mitochondrial Lon, rather interacts with TFAM and blocks degradation. Pull-down assays show that biotinylated TMP interacts with TFAM. These findings suggest a novel mechanism whereby TMP stabilizes TFAM and confers resistance to Lon-mediated degradation, thereby promoting mtDNA up-regulation in cells with low mtDNA content.
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Manio MCC, Inoue K, Fujitani M, Matsumura S, Fushiki T. Combined pharmacological activation of AMPK and PPARδ potentiates the effects of exercise in trained mice. Physiol Rep 2016; 4:4/5/e12625. [PMID: 26997622 PMCID: PMC4823600 DOI: 10.14814/phy2.12625] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The combined activation of the cellular energy sensor AMP‐activated protein kinase (AMPK) and the nuclear transcription factor peroxisome proliferator‐activated receptor delta (PPARδ) has been demonstrated to improve endurance and muscle function by mimicking the effects of exercise training. However, their combined pharmacological activation with exercise training has not been explored. Balb/c mice were trained on a treadmill and administered both the AMPK activator AICAR and the PPARδ agonist GW0742 for 4 weeks. AICAR treatment potentiated endurance, but the combination of AICAR and GW0742 further potentiated endurance and increased all running parameters significantly relative to exercised and nonexercised groups (138–179% and 355% increase in running time, respectively). Despite the lack of change in basal whole‐body metabolism, a significant shift to fat as the main energy source with a decline in carbohydrate utilization was observed upon indirect calorimetry analysis at the period near exhaustion. Increased energy substrates before exercise, and elevated muscle nonesterified fatty acids (NEFA) and elevated muscle glycogen at exhaustion were observed together with increased PDK4 mRNA expression. Citrate synthase activity was elevated in AICAR‐treated groups, while PGC‐1α protein level tended to be increased in GW0742‐treated groups. At exhaustion, Pgc1a was robustly upregulated together with Pdk4, Cd36, and Lpl in the muscle. A robust upregulation of Pgc1a and a downregulation in Chrebp were observed in the liver. Our data show that combined pharmacological activation of AMPK and PPARδ potentiates endurance in trained mice by transcriptional changes in muscle and liver, increased available energy substrates, delayed hypoglycemia through glycogen sparing accompanied by increased NEFA availability, and improved substrate shift from carbohydrate to fat.
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Affiliation(s)
- Mark Christian C Manio
- Graduate School of Agriculture, Division of Food Science and Biotechnology, Laboratory of Nutrition Chemistry, Kyoto University, Kyoto, Japan
| | - Kazuo Inoue
- Graduate School of Agriculture, Division of Food Science and Biotechnology, Laboratory of Nutrition Chemistry, Kyoto University, Kyoto, Japan
| | - Mina Fujitani
- Graduate School of Agriculture, Division of Food Science and Biotechnology, Laboratory of Nutrition Chemistry, Kyoto University, Kyoto, Japan
| | - Shigenobu Matsumura
- Graduate School of Agriculture, Division of Food Science and Biotechnology, Laboratory of Nutrition Chemistry, Kyoto University, Kyoto, Japan
| | - Tohru Fushiki
- Graduate School of Agriculture, Division of Food Science and Biotechnology, Laboratory of Nutrition Chemistry, Kyoto University, Kyoto, Japan
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Abstract
Mammalian mitochondrial DNA (mtDNA) encodes 13 proteins that are essential for the function of the oxidative phosphorylation system, which is composed of four respiratory-chain complexes and adenosine triphosphate (ATP) synthase. Remarkably, the maintenance and expression of mtDNA depend on the mitochondrial import of hundreds of nuclear-encoded proteins that control genome maintenance, replication, transcription, RNA maturation, and mitochondrial translation. The importance of this complex regulatory system is underscored by the identification of numerous mutations of nuclear genes that impair mtDNA maintenance and expression at different levels, causing human mitochondrial diseases with pleiotropic clinical manifestations. The basic scientific understanding of the mechanisms controlling mtDNA function has progressed considerably during the past few years, thanks to advances in biochemistry, genetics, and structural biology. The challenges for the future will be to understand how mtDNA maintenance and expression are regulated and to what extent direct intramitochondrial cross talk between different processes, such as transcription and translation, is important.
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Affiliation(s)
- Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 405 30 Gothenburg, Sweden; ,
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 405 30 Gothenburg, Sweden; ,
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany; .,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
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Bianchessi V, Vinci MC, Nigro P, Rizzi V, Farina F, Capogrossi MC, Pompilio G, Gualdi V, Lauri A. Methylation profiling by bisulfite sequencing analysis of the mtDNA Non-Coding Region in replicative and senescent Endothelial Cells. Mitochondrion 2016; 27:40-7. [PMID: 26910457 DOI: 10.1016/j.mito.2016.02.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 02/19/2016] [Accepted: 02/19/2016] [Indexed: 12/21/2022]
Abstract
The regulation and function of Mitochondrial DNA (mtDNA) cytosine methylation (5 mC) are largely unexplored. Mitochondria, Endothelial Cell (EC) senescence, and cardiovascular dysfunction are closely related. We extensively investigated the mtDNA Non-Coding Region (NCR) methylation pattern and its variations in EC replicative senescence. We observed previously undescribed 5 mC clusters and a biased distribution of 5 mC among DNA sites and throughout the NCR. The methylation pattern in senescent EC showed non-random variations, including the hypo-methylation of mtDNA replication regulatory sites. Additional experiments opened to a possible role for 5 mC in D-loop formation, rather than in mitochondrial gene expression.
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Affiliation(s)
- Valentina Bianchessi
- Unit of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino (CCM), IRCCS, Milano, Italy
| | | | - Patrizia Nigro
- Unit of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino (CCM), IRCCS, Milano, Italy
| | - Valeria Rizzi
- Genomics Core, Parco Tecnologico Padano, Lodi, Italy
| | - Floriana Farina
- Unit of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino (CCM), IRCCS, Milano, Italy
| | - Maurizio C Capogrossi
- Laboratory of Vascular Pathology, Istituto Dermopatico dell'Immacolata (IDI), IRCCS, Roma, Italy
| | - Giulio Pompilio
- Unit of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino (CCM), IRCCS, Milano, Italy
| | | | - Andrea Lauri
- Unit of Vascular Biology and Regenerative Medicine, Centro Cardiologico Monzino (CCM), IRCCS, Milano, Italy.
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Grünewald A, Rygiel KA, Hepplewhite PD, Morris CM, Picard M, Turnbull DM. Mitochondrial DNA Depletion in Respiratory Chain-Deficient Parkinson Disease Neurons. Ann Neurol 2016; 79:366-78. [PMID: 26605748 PMCID: PMC4819690 DOI: 10.1002/ana.24571] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/24/2015] [Indexed: 12/11/2022]
Abstract
Objective To determine the extent of respiratory chain abnormalities and investigate the contribution of mtDNA to the loss of respiratory chain complexes (CI–IV) in the substantia nigra (SN) of idiopathic Parkinson disease (IPD) patients at the single‐neuron level. Methods Multiple‐label immunofluorescence was applied to postmortem sections of 10 IPD patients and 10 controls to quantify the abundance of CI–IV subunits (NDUFB8 or NDUFA13, SDHA, UQCRC2, and COXI) and mitochondrial transcription factors (TFAM and TFB2M) relative to mitochondrial mass (porin and GRP75) in dopaminergic neurons. To assess the involvement of mtDNA in respiratory chain deficiency in IPD, SN neurons, isolated with laser‐capture microdissection, were assayed for mtDNA deletions, copy number, and presence of transcription/replication‐associated 7S DNA employing a triplex real‐time polymerase chain reaction (PCR) assay. Results Whereas mitochondrial mass was unchanged in single SN neurons from IPD patients, we observed a significant reduction in the abundances of CI and II subunits. At the single‐cell level, CI and II deficiencies were correlated in patients. The CI deficiency concomitantly occurred with low abundances of the mtDNA transcription factors TFAM and TFB2M, which also initiate transcription‐primed mtDNA replication. Consistent with this, real‐time PCR analysis revealed fewer transcription/replication‐associated mtDNA molecules and an overall reduction in mtDNA copy number in patients. This effect was more pronounced in single IPD neurons with severe CI deficiency. Interpretation Respiratory chain dysfunction in IPD neurons not only involves CI, but also extends to CII. These deficiencies are possibly a consequence of the interplay between nDNA and mtDNA‐encoded factors mechanistically connected via TFAM. ANN NEUROL 2016;79:366–378
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Affiliation(s)
- Anne Grünewald
- Wellcome Trust Centre for Mitochondrial Research and Medical Research Council/Biotechnology and Biological Sciences Research Council Centre for Ageing and Vitality, Institute of Neurosciences, Newcastle University, Newcastle upon Tyne, United Kingdom.,Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.,Molecular and Functional Neurobiology Group, Luxembourg Center for Systems Biomedicine, University of Luxembourg, Campus Belval, Belvaux, Luxembourg
| | - Karolina A Rygiel
- Wellcome Trust Centre for Mitochondrial Research and Medical Research Council/Biotechnology and Biological Sciences Research Council Centre for Ageing and Vitality, Institute of Neurosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Philippa D Hepplewhite
- Wellcome Trust Centre for Mitochondrial Research and Medical Research Council/Biotechnology and Biological Sciences Research Council Centre for Ageing and Vitality, Institute of Neurosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Christopher M Morris
- Newcastle Brain Tissue Resource, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Martin Picard
- Division of Behavioral Medicine, Department of Psychiatry and Department of Neurology, College of Physicians and Surgeons, Columbia University, Columbia University Medical Center, New York, NY
| | - Doug M Turnbull
- Wellcome Trust Centre for Mitochondrial Research and Medical Research Council/Biotechnology and Biological Sciences Research Council Centre for Ageing and Vitality, Institute of Neurosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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29
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Brown TA, Tkachuk AN, Clayton DA. Mitochondrial Transcription Factor A (TFAM) Binds to RNA Containing 4-Way Junctions and Mitochondrial tRNA. PLoS One 2015; 10:e0142436. [PMID: 26545237 PMCID: PMC4636309 DOI: 10.1371/journal.pone.0142436] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/21/2015] [Indexed: 11/26/2022] Open
Abstract
Mitochondrial DNA (mtDNA) is maintained within nucleoprotein complexes known as nucleoids. These structures are highly condensed by the DNA packaging protein, mitochondrial Transcription Factor A (TFAM). Nucleoids also include RNA, RNA:DNA hybrids, and are associated with proteins involved with RNA processing and mitochondrial ribosome biogenesis. Here we characterize the ability of TFAM to bind various RNA containing substrates in order to determine their role in TFAM distribution and function within the nucleoid. We find that TFAM binds to RNA-containing 4-way junctions but does not bind appreciably to RNA hairpins, internal loops, or linear RNA:DNA hybrids. Therefore the RNA within nucleoids largely excludes TFAM, and its distribution is not grossly altered with removal of RNA. Within the cell, TFAM binds to mitochondrial tRNAs, consistent with our RNA 4-way junction data. Kinetic binding assays and RNase-insensitive TFAM distribution indicate that DNA remains the preferred substrate within the nucleoid. However, TFAM binds to tRNA with nanomolar affinity and these complexes are not rare. TFAM-immunoprecipitated tRNAs have processed ends, suggesting that binding is not specific to RNA precursors. The amount of each immunoprecipitated tRNA is not well correlated with tRNA celluar abundance, indicating unequal TFAM binding preferences. TFAM-mt-tRNA interaction suggests potentially new functions for this protein.
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Affiliation(s)
- Timothy A. Brown
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
- * E-mail:
| | - Ariana N. Tkachuk
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - David A. Clayton
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
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30
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Jemt E, Persson Ö, Shi Y, Mehmedovic M, Uhler JP, Dávila López M, Freyer C, Gustafsson CM, Samuelsson T, Falkenberg M. Regulation of DNA replication at the end of the mitochondrial D-loop involves the helicase TWINKLE and a conserved sequence element. Nucleic Acids Res 2015; 43:9262-75. [PMID: 26253742 PMCID: PMC4627069 DOI: 10.1093/nar/gkv804] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 07/28/2015] [Indexed: 11/12/2022] Open
Abstract
The majority of mitochondrial DNA replication events are terminated prematurely. The nascent DNA remains stably associated with the template, forming a triple-stranded displacement loop (D-loop) structure. However, the function of the D-loop region of the mitochondrial genome remains poorly understood. Using a comparative genomics approach we here identify two closely related 15 nt sequence motifs of the D-loop, strongly conserved among vertebrates. One motif is at the D-loop 5'-end and is part of the conserved sequence block 1 (CSB1). The other motif, here denoted coreTAS, is at the D-loop 3'-end. Both these sequences may prevent transcription across the D-loop region, since light and heavy strand transcription is terminated at CSB1 and coreTAS, respectively. Interestingly, the replication of the nascent D-loop strand, occurring in a direction opposite to that of heavy strand transcription, is also terminated at coreTAS, suggesting that coreTAS is involved in termination of both transcription and replication. Finally, we demonstrate that the loading of the helicase TWINKLE at coreTAS is reversible, implying that this site is a crucial component of a switch between D-loop formation and full-length mitochondrial DNA replication.
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Affiliation(s)
- Elisabeth Jemt
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Örjan Persson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Yonghong Shi
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Majda Mehmedovic
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Jay P Uhler
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Marcela Dávila López
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Christoph Freyer
- Department of Laboratory Medicine, Karolinska Institutet, Retzius väg 8, 171 77 Stockholm, Sweden
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Tore Samuelsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
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31
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MUNTEAN BRIANS, JIN XINGJIAN, WILLIAMS FREDERICKE, NAULI SURYAM. Primary cilium regulates CaV1.2 expression through Wnt signaling. J Cell Physiol 2014; 229:1926-34. [PMID: 24700505 PMCID: PMC11036877 DOI: 10.1002/jcp.24642] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 04/01/2014] [Indexed: 12/27/2022]
Abstract
Primary cilia are sensory organelles that provide a feedback mechanism to restrict Wnt signaling in the absence of endogenous Wnt activators. Abnormal Wnt signaling has been shown to result in polycystic kidney disease (PKD) although the exact mechanism has been debated. Previously, we reported that the calcium channel CaV1.2 functions in primary cilia. In this study, we show that CaV1.2 expression level is regulated by Wnt signaling. This occurs through modulation of mitochondrial mass and activity resulting in increased reactive oxygen species which generate oxidative DNA lesions. We found that the subsequent cellular DNA damage response triggers increased CaV1.2 expression. In the absence of primary cilia where Wnt signaling is upregulated, we found that CaV1.2 is overexpressed as a compensatory mechanism. We show for the first time that CaV1.2 knockdown in zebrafish results in classic primary cilia defects including renal cyst formation, hydrocephalus, and left-right asymmetry defects. Our study shows that suppressed Wnt signaling prevents CaV1.2 expression ultimately resulting in PKD phenotypes. Thus, CaV1.2 expression is tightly regulated through Wnt signaling and plays an essential sensory role in primary cilia necessary for cellular homeostasis.
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Affiliation(s)
- BRIAN S. MUNTEAN
- Department of Medicinal and Biological Chemistry, The University of Toledo, Toledo, Ohio
| | - XINGJIAN JIN
- Department of Pharmacology, The University of Toledo, Toledo, Ohio
| | | | - SURYA M. NAULI
- Department of Medicinal and Biological Chemistry, The University of Toledo, Toledo, Ohio
- Department of Pharmacology, The University of Toledo, Toledo, Ohio
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32
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Abstract
Understanding regulation of mitochondrial DNA (mtDNA) expression is of considerable interest given that mitochondrial dysfunction is important in human pathology and aging. Similar to the situation in bacteria, there is no compartmentalization between transcription and translation in mitochondria; hence, both processes are likely to have a direct molecular crosstalk. Accumulating evidence suggests that there are important mechanisms for regulation of mammalian mtDNA expression at the posttranscriptional level. Regulation of mRNA maturation, mRNA stability, translational coordination, ribosomal biogenesis, and translation itself all form the basis for controlling oxidative phosphorylation capacity. Consequently, a wide variety of inherited human mitochondrial diseases are caused by mutations of nuclear genes regulating various aspects of mitochondrial translation. Furthermore, mutations of mtDNA, associated with human disease and aging, often affect tRNA genes critical for mitochondrial translation. Recent advances in molecular understanding of mitochondrial translation regulation will most likely provide novel avenues for modulating mitochondrial function for treating human disease.
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Affiliation(s)
- B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Röntgen-Ångström-Cluster, Karolinska Institutet Outstation, Centre for Structural Systems Biology, DESY Campus, 22603 Hamburg, Germany; European Molecular Biology Laboratory, Hamburg Unit, 22603 Hamburg, Germany.
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 509 31 Cologne, Germany; Department of Laboratory Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden.
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33
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Chen X, Peng X, Huang X, Xiang D. Complete mitochondrial genome of the Zebra bullhead shark Heterodontus zebra (Heterodontiformes: Heterodontidae). ACTA ACUST UNITED AC 2014; 25:280-1. [PMID: 25023667 DOI: 10.3109/19401736.2013.796514] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of the Zebra bullhead shark Heterodontus zebra was first presented in this study. It was 16,720 bp in length, encoding 37 genes and one control region. The gene order and translate orientation were identical to most vertebrates. Overall nucleotide base composition of H. zebra mitogenome was 31.6% A; 26.8% C; 13.1% G and 28.4% T. Total 27 bp overlaps and 20 bp short intergenic spaces were found in 17 gene junctions in the genome. Two start codons (ATG and GTG) and three terminate codons (TAG, TAA and T) were found in 13 protein-coding genes. Except for tRNA-Ser2, which lost the dihydrouridine (DHU) arm and formed one simple loop, the remaining tRNAs could fold into the typical clover-leaf secondary structures. The termination-associated sequences and three short conserved blocks (CBS I-III) were identified in the control region.
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Affiliation(s)
- Xiao Chen
- Department of Marine Science, Wenzhou Medical College , Wenzhou , PR China and
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34
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Sun Y, Wei T, Su X, Li T. The complete mitochondrial genome of Grammistes sexlineatus (Perciformes, Serranidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:821-3. [PMID: 24845444 DOI: 10.3109/19401736.2014.919458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitochondrial genome of Grammistes sexlineatus was first determined and studied in the present study. The mitochondrial genome was 16,502 nucleotides that contained 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and one putative control region. The overall base composition of G. sexlineatus was T 23.74%, C 31.05%, A 28.79%, and G 16.42%, with a slight A + T bias of 52.53%. The gene order and composition of G. sexlineatus mitogenome was similar to the most vertebrate. Meanwhile, a termination-associated sequence (TAS) and the conserved sequence blocks (CSB-2 and CSB-3) were determined in G. sexlineatus control region. The mitochondrial genome would play key role in phylogenetics analysis of the Serranidae.
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Affiliation(s)
- Yuena Sun
- a School of Marine Sciences, Ningbo University , Ningbo , Zhejiang Province , China
| | - Tao Wei
- b College of Marine Science, Zhejiang Ocean University , Zhoushan , Zhejiang Province , China , and
| | - Xiurong Su
- a School of Marine Sciences, Ningbo University , Ningbo , Zhejiang Province , China
| | - Taiwu Li
- a School of Marine Sciences, Ningbo University , Ningbo , Zhejiang Province , China .,c Ningbo City College of Vocational Technology , Ningbo , Zhejiang Province , China
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35
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In D-loop: 40 years of mitochondrial 7S DNA. Exp Gerontol 2014; 56:175-81. [PMID: 24709344 DOI: 10.1016/j.exger.2014.03.027] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/27/2014] [Accepted: 03/28/2014] [Indexed: 11/23/2022]
Abstract
Given the tiny size of the mammalian mitochondrial genome, at only 16.5 kb, it is often surprising how little we know about some of its molecular features, and the molecular mechanisms governing its maintenance. One such conundrum is the biogenesis and function of the mitochondrial displacement loop (D-loop). The mitochondrial D-loop is a triple-stranded region found in the major non-coding region (NCR) of many mitochondrial genomes, and is formed by stable incorporation of a third, short DNA strand known as 7S DNA. In this article we review the current affairs regarding the main features of the D-loop structure, the diverse frequency of D-loops in the mtDNAs of various species and tissues, and also the mechanisms of its synthesis and turnover. This is followed by an account of the possible functions of the mitochondrial D-loop that have been proposed over the last four decades. In the last section, we discuss the potential links of the D-loop with mammalian ageing.
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36
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Xiang D, Ai W, Peng X, Qiu J, Chen S. Complete mitogenome of Hemiculter leucisculus (Cyprinidae: Cultrinae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:145-6. [PMID: 24450718 DOI: 10.3109/19401736.2013.878916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitogenome was first determined for a minnow Hemiculter leucisculus in this study. It is 16,622 bp in length and has 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region. Overall nucleotide base composition is 30.4% A, 27.10% C, 17.10% G and 25.40% T. All the tRNA genes can fold into the typical clover-leaf secondary structures, except the tRNA-Ser2 which loses the dihydrouridine arm and is replaced with one 11 bp loop. The origin of light-strand replication (OL) was found between the tRNA-Asn and tRNA-Cys genes while the termination associated sequence (TAS) and the conserved sequence blocks (CSB1-3) were found in the control region.
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Affiliation(s)
- Dan Xiang
- a Department of Marine Science , Wenzhou Medical University , Wenzhou , PR China and.,b Zhejiang Mariculture Research Institute , Wenzhou , PR China
| | - Weiming Ai
- a Department of Marine Science , Wenzhou Medical University , Wenzhou , PR China and
| | - Xin Peng
- b Zhejiang Mariculture Research Institute , Wenzhou , PR China
| | - Jianbiao Qiu
- b Zhejiang Mariculture Research Institute , Wenzhou , PR China
| | - Shaobo Chen
- a Department of Marine Science , Wenzhou Medical University , Wenzhou , PR China and.,b Zhejiang Mariculture Research Institute , Wenzhou , PR China
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37
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Xiang D, Ai W, Chen X, Chen Y, Chen S. Complete mitogenome of Pseudohemiculter dispar (Cyprinidae: Cultrinae). MITOCHONDRIAL DNA 2013; 24:356-8. [PMID: 23617372 DOI: 10.3109/19401736.2012.760557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete mitogenome was first determined for a minnow Pseudohemiculter dispar in this study. It is 16,621 bp in length, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region. Overall nucleotide base composition is 30.30% A, 27.10% C, 17.10% G, and 25.50% T, with a A+T bias. Except for the tRNA-Ser2 that lost the dihydrouridine arm and replaced with one 11-bp loop, the other 22 tRNA genes can fold into the typical cloverleaf secondary structures. The origin of light-strand replication (OL) was found between the tRNA-Asn and tRNA-Cys genes, while the termination-associated sequence (TAS) was found in the control region. Both OL and TAS can form the hairpin structure that acts as the signals participated in the mitochondrial DNA replication.
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Affiliation(s)
- Dan Xiang
- Department of Marine Science, Wenzhou Medical College, Wenzhou 325035, PR China
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38
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Sage JM, Knight KL. Human Rad51 promotes mitochondrial DNA synthesis under conditions of increased replication stress. Mitochondrion 2013; 13:350-6. [PMID: 23591384 DOI: 10.1016/j.mito.2013.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Revised: 03/26/2013] [Accepted: 04/04/2013] [Indexed: 01/05/2023]
Abstract
Homologous recombination is essential for productive DNA replication particularly under stress conditions. We previously demonstrated a stress-induced recruitment of Rad51 to mitochondria and a critical need for its activity in the maintenance of mitochondrial DNA (mtDNA) copy number. Using the human osteosarcoma cell line U20S, we show in the present study that recruitment of Rad51 to mitochondria under stress conditions requires ongoing mtDNA replication. Additionally, Rad51 levels in mitochondria increase in cells recovering from mtDNA depletion. Our findings highlight an important new role for Rad51 in supporting mtDNA replication, and further promote the idea that recombination is indispensable for sustaining DNA synthesis under conditions of replication stress.
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Affiliation(s)
- Jay M Sage
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655-4321, USA
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Darrin Hulsey C, Keck BP, Alamillo H, O'Meara BC. Mitochondrial genome primers for Lake Malawi cichlids. Mol Ecol Resour 2013; 13:347-53. [PMID: 23347464 DOI: 10.1111/1755-0998.12066] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 12/11/2012] [Accepted: 12/12/2012] [Indexed: 11/28/2022]
Abstract
Resolving the evolutionary history of rapidly diversifying lineages like the Lake Malawi Cichlid Flock demands powerful phylogenetic tools. Although this clade of over 500 species of fish likely diversified in less than two million years, the availability of extensive sequence data sets, such as complete mitochondrial genomes, could help resolve evolutionary patterns in this group. Using a large number of newly developed primers, we generated whole mitochondrial genome sequences for 14 Lake Malawi cichlids. We compared sequence divergence across protein-coding regions of the mitochondrial genome and also compared divergence in the mitochondrial loci to divergence at two nuclear protein-coding loci, Mitfb and Dlx2. Despite the widespread sharing of haplotypes of identical sequences at individual loci, the combined use of all protein-coding mitochondrial loci provided a bifurcating phylogenetic hypothesis for the exemplars of major lineages within the Lake Malawi cichlid radiation. The primers presented here could have substantial utility for evolutionary analyses of mitochondrial evolution and hybridization within this diverse clade.
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Affiliation(s)
- C Darrin Hulsey
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA.
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40
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Loss-of-function mutations in MGME1 impair mtDNA replication and cause multisystemic mitochondrial disease. Nat Genet 2013; 45:214-9. [PMID: 23313956 DOI: 10.1038/ng.2501] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 11/28/2012] [Indexed: 12/17/2022]
Abstract
Known disease mechanisms in mitochondrial DNA (mtDNA) maintenance disorders alter either the mitochondrial replication machinery (POLG, POLG2 and C10orf2) or the biosynthesis pathways of deoxyribonucleoside 5'-triphosphates for mtDNA synthesis. However, in many of these disorders, the underlying genetic defect has yet to be discovered. Here, we identify homozygous nonsense and missense mutations in the orphan gene C20orf72 in three families with a mitochondrial syndrome characterized by external ophthalmoplegia, emaciation and respiratory failure. Muscle biopsies showed mtDNA depletion and multiple mtDNA deletions. C20orf72, hereafter MGME1 (mitochondrial genome maintenance exonuclease 1), encodes a mitochondrial RecB-type exonuclease belonging to the PD-(D/E)XK nuclease superfamily. We show that MGME1 cleaves single-stranded DNA and processes DNA flap substrates. Fibroblasts from affected individuals do not repopulate after chemically induced mtDNA depletion. They also accumulate intermediates of stalled replication and show increased levels of 7S DNA, as do MGME1-depleted cells. Thus, we show that MGME1-mediated mtDNA processing is essential for mitochondrial genome maintenance.
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41
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Wan X, Gupta S, Zago MP, Davidson MM, Dousset P, Amoroso A, Garg NJ. Defects of mtDNA replication impaired mitochondrial biogenesis during Trypanosoma cruzi infection in human cardiomyocytes and chagasic patients: the role of Nrf1/2 and antioxidant response. J Am Heart Assoc 2012; 1:e003855. [PMID: 23316324 PMCID: PMC3540675 DOI: 10.1161/jaha.112.003855] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/09/2012] [Indexed: 01/05/2023]
Abstract
BACKGROUND Mitochondrial dysfunction is a key determinant in chagasic cardiomyopathy development in mice; however, its relevance in human Chagas disease is not known. We determined if defects in mitochondrial biogenesis and dysregulation of peroxisome proliferator-activated receptor gamma (PPARγ) coactivator-1 (PGC-1)-regulated transcriptional pathways constitute a mechanism or mechanisms underlying mitochondrial oxidative-phosphorylation (OXPHOS) deficiency in human Chagas disease. METHODS AND RESULTS We utilized human cardiomyocytes and left-ventricular tissue from chagasic and other cardiomyopathy patients and healthy donors (n>6/group). We noted no change in citrate synthase activity, yet mRNA and/or protein levels of subunits of the respiratory complexes were significantly decreased in Trypanosoma cruzi-infected cardiomyocytes (0 to 24 hours) and chagasic hearts. We observed increased mRNA and decreased nuclear localization of PGC-1-coactivated transcription factors, yet the expression of genes for PPARγ-regulated fatty acid oxidation and nuclear respiratory factor (NRF1/2)-regulated mtDNA replication and transcription machinery was enhanced in infected cardiomyocytes and chagasic hearts. The D-loop formation was normal or higher, but mtDNA replication and mtDNA content were decreased by 83% and 40% to 65%, respectively. Subsequently, we noted that reactive oxygen species (ROS), oxidative stress, and mtDNA oxidation were significantly increased, yet NRF1/2-regulated antioxidant gene expression remained compromised in infected cardiomyocytes and chagasic hearts. CONCLUSIONS The replication of mtDNA was severely compromised, resulting in a significant loss of mtDNA and expression of OXPHOS genes in T cruzi-infected cardiomyocytes and chagasic hearts. Our data suggest increased ROS generation and selective functional incapacity of NRF2-mediated antioxidant gene expression played a role in the defects in mtDNA replication and unfitness of mtDNA for replication and gene expression in Chagas disease.
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Affiliation(s)
- Xianxiu Wan
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555-1070, USA
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42
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Terencio ML, Schneider CH, Gross MC, Feldberg E, Porto JIR. Structure and organization of the mitochondrial DNA control region with tandemly repeated sequence in the Amazon ornamental fish. ACTA ACUST UNITED AC 2012; 24:74-82. [PMID: 22954310 DOI: 10.3109/19401736.2012.717934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Tandemly repeated sequences are a common feature of vertebrate mitochondrial DNA control regions. However, questions still remain about their mode of evolution and function. To better understand patterns of variation in length and to explore the existence of previously described domain, we have characterized the control region structure of the Amazonian ornamental fish Nannostomus eques and Nannostomus unifasciatus. The control region ranged from 1121 to 1142 bp in length and could be separated into three domains: the domain associated with the extended terminal associated sequences, the central conserved domain, and the conserved sequence blocks domain. In the first domain, we encountered a sequence repeated 10 times in tandem (variable number tandem repeat (VNTR)) that could adopt an "inverted repetitions" type structural conformation. The results suggest that the VNTR pattern encountered in both N. eques and N. unifasciatus is consistent with the prerequisites of the illegitimate elongation model in which the unequal pairing of the chains near the 5'-end of the control region favors the formation of repetitions.
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Affiliation(s)
- Maria Leandra Terencio
- Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Coordenação de Pesquisas em Biologia Aquática, Av. André Araújo, 2936, Petrópolis, 69011-970 Manaus, AM, Brazil.
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43
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Iyer S, Xiao E, Alsayegh K, Eroshenko N, Riggs MJ, Bennett JP, Rao RR. Mitochondrial gene replacement in human pluripotent stem cell-derived neural progenitors. Gene Ther 2012; 19:469-75. [PMID: 21918550 PMCID: PMC11071659 DOI: 10.1038/gt.2011.134] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 07/13/2011] [Accepted: 08/05/2011] [Indexed: 12/22/2022]
Abstract
Human pluripotent stem cell-derived neural progenitor (hNP) cells are an excellent resource for understanding early neural development and neurodegenerative disorders. Given that many neurodegenerative disorders can be correlated with defects in the mitochondrial genome, optimal utilization of hNP cells requires an ability to manipulate and monitor changes in the mitochondria. Here, we describe a novel approach that uses recombinant human mitochondrial transcription factor A (rhTFAM) protein to transfect and express a pathogenic mitochondrial genome (mtDNA) carrying the G11778A mutation associated with Leber's hereditary optic neuropathy (LHON) disease, into dideoxycytidine (ddC)-treated hNPs. Treatment with ddC reduced endogenous mtDNA and gene expression, without loss of hNP phenotypic markers. Entry of G11778A mtDNA complexed with the rhTFAM was observed in mitochondria of ddC-hNPs. Expression of the pathogenic RNA was confirmed by restriction enzyme analysis of the SfaN1-digested cDNA. On the basis of the expression of neuron-specific class III beta-tubulin, neuronal differentiation occurred. Our results show for the first time that pathogenic mtDNA can be introduced and expressed into hNPs without loss of phenotype or neuronal differentiation potential. This mitochondrial gene replacement technology allows for creation of in vitro stem cell-based models useful for understanding neuronal development and treatment of neurodegenerative disorders.
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Affiliation(s)
- S Iyer
- Center for the Study of Biological Complexity, Life Sciences Program, Virginia Commonwealth University, Richmond, VA, USA
| | - E Xiao
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA, USA
- Current address: Neuroimaging Core; Genes, Cognition, and Psychosis Program, National Institute of Mental Health, Bethesda, MD, USA
| | - K Alsayegh
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - N Eroshenko
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA, USA
- School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA
| | - MJ Riggs
- Integrated Life Sciences Program, Virginia Commonwealth University, Richmond, VA, USA
| | - JP Bennett
- Parkinson’s Disease Center, Virginia Commonwealth University, Richmond, VA, USA
- Department of Neurology, Virginia Commonwealth University, Richmond, VA, USA
| | - RR Rao
- Center for the Study of Biological Complexity, Life Sciences Program, Virginia Commonwealth University, Richmond, VA, USA
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA, USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
- Integrated Life Sciences Program, Virginia Commonwealth University, Richmond, VA, USA
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Villa AM, Fusi P, Pastori V, Amicarelli G, Pozzi C, Adlerstein D, Doglia SM. Ethidium bromide as a marker of mtDNA replication in living cells. JOURNAL OF BIOMEDICAL OPTICS 2012; 17:046001. [PMID: 22559680 DOI: 10.1117/1.jbo.17.4.046001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Mitochondrial DNA (mtDNA) in tumor cells was found to play an important role in maintaining the malignant phenotype. Using laser scanning confocal fluorescence microscopy (LSCFM) in a recent work, we reported a variable fluorescence intensity of ethidium bromide (EB) in mitochondria nucleoids of living carcinoma cells. Since when EB is bound to nucleic acids its fluorescence is intensified; a higher EB fluorescence intensity could reflect a higher DNA accessibility to EB, suggesting a higher mtDNA replication activity. To prove this hypothesis, in the present work we studied, by LSCFM, the EB fluorescence in mitochondria nucleoids of living neuroblastoma cells, a model system in which differentiation affects the level of mtDNA replication. A drastic decrease of fluorescence was observed after differentiation. To correlate EB fluorescence intensity to the mtDNA replication state, we evaluated the mtDNA nascent strands content by ligation-mediated real-time PCR, and we found a halved amount of replicating mtDNA molecules in differentiating cells. A similar result was obtained by BrdU incorporation. These results indicate that the low EB fluorescence of nucleoids in differentiated cells is correlated to a low content of replicating mtDNA, suggesting that EB may be used as a marker of mtDNA replication in living cells.
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Affiliation(s)
- Anna Maria Villa
- University of Milano-Bicocca, Department of Biotechnology e Biosciences, P.za della Scienza 2, 20126 Milan, Italy.
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Superresolution fluorescence imaging of mitochondrial nucleoids reveals their spatial range, limits, and membrane interaction. Mol Cell Biol 2011; 31:4994-5010. [PMID: 22006021 DOI: 10.1128/mcb.05694-11] [Citation(s) in RCA: 178] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A fundamental objective in molecular biology is to understand how DNA is organized in concert with various proteins, RNA, and biological membranes. Mitochondria maintain and express their own DNA (mtDNA), which is arranged within structures called nucleoids. Their functions, dimensions, composition, and precise locations relative to other mitochondrial structures are poorly defined. Superresolution fluorescence microscopy techniques that exceed the previous limits of imaging within the small and highly compartmentalized mitochondria have been recently developed. We have improved and employed both two- and three-dimensional applications of photoactivated localization microscopy (PALM and iPALM, respectively) to visualize the core dimensions and relative locations of mitochondrial nucleoids at an unprecedented resolution. PALM reveals that nucleoids differ greatly in size and shape. Three-dimensional volumetric analysis indicates that, on average, the mtDNA within ellipsoidal nucleoids is extraordinarily condensed. Two-color PALM shows that the freely diffusible mitochondrial matrix protein is largely excluded from the nucleoid. In contrast, nucleoids are closely associated with the inner membrane and often appear to be wrapped around cristae or crista-like inner membrane invaginations. Determinations revealing high packing density, separation from the matrix, and tight association with the inner membrane underscore the role of mechanisms that regulate access to mtDNA and that remain largely unknown.
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Ruhanen H, Ushakov K, Yasukawa T. Involvement of DNA ligase III and ribonuclease H1 in mitochondrial DNA replication in cultured human cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1813:2000-7. [PMID: 21878356 PMCID: PMC3223524 DOI: 10.1016/j.bbamcr.2011.08.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Revised: 07/29/2011] [Accepted: 08/01/2011] [Indexed: 12/05/2022]
Abstract
Recent evidence suggests that coupled leading and lagging strand DNA synthesis operates in mammalian mitochondrial DNA (mtDNA) replication, but the factors involved in lagging strand synthesis are largely uncharacterised. We investigated the effect of knockdown of the candidate proteins in cultured human cells under conditions where mtDNA appears to replicate chiefly via coupled leading and lagging strand DNA synthesis to restore the copy number of mtDNA to normal levels after transient mtDNA depletion. DNA ligase III knockdown attenuated the recovery of mtDNA copy number and appeared to cause single strand nicks in replicating mtDNA molecules, suggesting the involvement of DNA ligase III in Okazaki fragment ligation in human mitochondria. Knockdown of ribonuclease (RNase) H1 completely prevented the mtDNA copy number restoration, and replication intermediates with increased single strand nicks were readily observed. On the other hand, knockdown of neither flap endonuclease 1 (FEN1) nor DNA2 affected mtDNA replication. These findings imply that RNase H1 is indispensable for the progression of mtDNA synthesis through removing RNA primers from Okazaki fragments. In the nucleus, Okazaki fragments are ligated by DNA ligase I, and the RNase H2 is involved in Okazaki fragment processing. This study thus proposes that the mitochondrial replication system utilises distinct proteins, DNA ligase III and RNase H1, for Okazaki fragment maturation.
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Affiliation(s)
- Heini Ruhanen
- The Wolfson Institute for Biomedical Research, University College London, Gower Street, London, UK
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Karamanlidis G, Bautista-Hernandez V, Fynn-Thompson F, Del Nido P, Tian R. Impaired mitochondrial biogenesis precedes heart failure in right ventricular hypertrophy in congenital heart disease. Circ Heart Fail 2011; 4:707-13. [PMID: 21840936 DOI: 10.1161/circheartfailure.111.961474] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND The outcome of the surgical repair in congenital heart disease correlates with the degree of myocardial damage. In this study, we determined whether mitochondrial DNA depletion is a sensitive marker of right ventricular (RV) damage and whether impaired mitochondrial DNA (mtDNA) replication contributes to the transition from compensated hypertrophy to failure. METHODS AND RESULTS RV samples obtained from 31 patients undergoing cardiac surgery were compared with 5 RV samples from nonfailing hearts (control). Patients were divided into compensated hypertrophy and failure groups, based on preoperative echocardiography, catheterization, and/or MRI data. Mitochondrial enzyme activities (citrate synthase and succinate dehydrogenase) were maintained during hypertrophy and decreased by ≈40% (P<0.05 versus control) at the stage of failure. In contrast, mtDNA content was progressively decreased in the hypertrophied RV through failure (by 28±8% and 67±11%, respectively, P<0.05 for both), whereas mtDNA-encoded gene expression was sustained by increased transcriptional activity during compensated hypertrophy but not in failure. Mitochondrial DNA depletion was attributed to reduced mtDNA replication in both hypertrophied and failing RV, and it was independent of PGC-1 downregulation but was accompanied by reduced expression of proteins constituting the mtDNA replication fork. Decreased mtDNA content in compensated hypertrophy was also associated with pathological changes of mitochondria ultrastructure. CONCLUSIONS Impaired mtDNA replication causes early and progressive depletion of mtDNA in the RV of the patients with congenital heart disease during the transition from hypertrophy to failure. Decreased mtDNA content probably is a sensitive marker of mitochondrial injury in this patient population.
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Affiliation(s)
- Georgios Karamanlidis
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, USA
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48
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Ruhanen H, Borrie S, Szabadkai G, Tyynismaa H, Jones AW, Kang D, Taanman JW, Yasukawa T. Mitochondrial single-stranded DNA binding protein is required for maintenance of mitochondrial DNA and 7S DNA but is not required for mitochondrial nucleoid organisation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:931-9. [DOI: 10.1016/j.bbamcr.2010.04.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 03/31/2010] [Accepted: 04/20/2010] [Indexed: 01/19/2023]
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Intraspecific variation in the mitochondrial genome among local populations of Medaka Oryzias latipes. Gene 2010; 457:13-24. [DOI: 10.1016/j.gene.2010.02.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 02/19/2010] [Accepted: 02/23/2010] [Indexed: 11/30/2022]
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Karamanlidis G, Nascimben L, Couper GS, Shekar PS, del Monte F, Tian R. Defective DNA replication impairs mitochondrial biogenesis in human failing hearts. Circ Res 2010; 106:1541-8. [PMID: 20339121 DOI: 10.1161/circresaha.109.212753] [Citation(s) in RCA: 172] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
RATIONALE Mitochondrial dysfunction plays a pivotal role in the development of heart failure. Animal studies suggest that impaired mitochondrial biogenesis attributable to downregulation of the peroxisome proliferator-activated receptor gamma coactivator (PGC)-1 transcriptional pathway is integral of mitochondrial dysfunction in heart failure. OBJECTIVE The study sought to define mechanisms underlying the impaired mitochondrial biogenesis and function in human heart failure. METHODS AND RESULTS We collected left ventricular tissue from end-stage heart failure patients and from nonfailing hearts (n=23, and 19, respectively). The mitochondrial DNA (mtDNA) content was decreased by >40% in the failing hearts, after normalization for a moderate decrease in citrate synthase activity (P<0.05). This was accompanied by reductions in mtDNA-encoded proteins (by 25% to 80%) at both mRNA and protein level (P<0.05). The mRNA levels of PGC-1alpha/beta and PRC (PGC-1-related coactivator) were unchanged, whereas PGC-1alpha protein increased by 58% in the failing hearts. Among the PGC-1 coactivating targets, the expression of estrogen-related receptor alpha and its downstream genes decreased by up to 50% (P<0.05), whereas peroxisome proliferator-activated receptor alpha and its downstream gene expression were unchanged in the failing hearts. The formation of D-loop in the mtDNA was normal but D-loop extension, which dictates the replication process of mtDNA, was decreased by 75% in the failing hearts. Furthermore, DNA oxidative damage was increased by 50% in the failing hearts. CONCLUSIONS Mitochondrial biogenesis is severely impaired as evidenced by reduced mtDNA replication and depletion of mtDNA in the human failing heart. These defects are independent of the downregulation of the PGC-1 expression suggesting novel mechanisms for mitochondrial dysfunction in heart failure.
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