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Huang K, Liu X, Zhang Z, Wang T, Xu H, Li Q, Jia Y, Huang L, Kim P, Zhou X. AgeAnnoMO: a knowledgebase of multi-omics annotation for animal aging. Nucleic Acids Res 2024; 52:D822-D834. [PMID: 37850649 PMCID: PMC10767957 DOI: 10.1093/nar/gkad884] [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: 08/17/2023] [Revised: 09/16/2023] [Accepted: 10/02/2023] [Indexed: 10/19/2023] Open
Abstract
Aging entails gradual functional decline influenced by interconnected factors. Multiple hallmarks proposed as common and conserved underlying denominators of aging on the molecular, cellular and systemic levels across multiple species. Thus, understanding the function of aging hallmarks and their relationships across species can facilitate the translation of anti-aging drug development from model organisms to humans. Here, we built AgeAnnoMO (https://relab.xidian.edu.cn/AgeAnnoMO/#/), a knowledgebase of multi-omics annotation for animal aging. AgeAnnoMO encompasses an extensive collection of 136 datasets from eight modalities, encompassing 8596 samples from 50 representative species, making it a comprehensive resource for aging and longevity research. AgeAnnoMO characterizes multiple aging regulators across species via multi-omics data, comprehensively annotating aging-related genes, proteins, metabolites, mitochondrial genes, microbiotas and age-specific TCR and BCR sequences tied to aging hallmarks for these species and tissues. AgeAnnoMO not only facilitates a deeper and more generalizable understanding of aging mechanisms, but also provides potential insights of the specificity across tissues and species in aging process, which is important to develop the effective anti-aging interventions for diverse populations. We anticipate that AgeAnnoMO will provide a valuable resource for comprehending and integrating the conserved driving hallmarks in aging biology and identifying the targetable biomarkers for aging research.
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Affiliation(s)
- Kexin Huang
- The Center of Gerontology and Geriatrics and West China Biomedical Big Data Centre, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Med-X Center for Informatics, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Xi Liu
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Zhaocan Zhang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Tiangang Wang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Haixia Xu
- The Center of Gerontology and Geriatrics and West China Biomedical Big Data Centre, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Qingxuan Li
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Yuhao Jia
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Liyu Huang
- School of Life Science and Technology, Xidian University, Xi’an, Shaanxi 710071, PR China
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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2
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Hernández CL. Mitochondrial DNA in Human Diversity and Health: From the Golden Age to the Omics Era. Genes (Basel) 2023; 14:1534. [PMID: 37628587 PMCID: PMC10453943 DOI: 10.3390/genes14081534] [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: 06/19/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is a small fraction of our hereditary material. However, this molecule has had an overwhelming presence in scientific research for decades until the arrival of high-throughput studies. Several appealing properties justify the application of mtDNA to understand how human populations are-from a genetic perspective-and how individuals exhibit phenotypes of biomedical importance. Here, I review the basics of mitochondrial studies with a focus on the dawn of the field, analysis methods and the connection between two sides of mitochondrial genetics: anthropological and biomedical. The particularities of mtDNA, with respect to inheritance pattern, evolutionary rate and dependence on the nuclear genome, explain the challenges of associating mtDNA composition and diseases. Finally, I consider the relevance of this single locus in the context of omics research. The present work may serve as a tribute to a tool that has provided important insights into the past and present of humankind.
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Affiliation(s)
- Candela L Hernández
- Department of Biodiversity, Ecology and Evolution, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
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3
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Mitochondrial Dysfunction in Cardiac Arrhythmias. Cells 2023; 12:cells12050679. [PMID: 36899814 PMCID: PMC10001005 DOI: 10.3390/cells12050679] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Electrophysiological and structural disruptions in cardiac arrhythmias are closely related to mitochondrial dysfunction. Mitochondria are an organelle generating ATP, thereby satisfying the energy demand of the incessant electrical activity in the heart. In arrhythmias, the homeostatic supply-demand relationship is impaired, which is often accompanied by progressive mitochondrial dysfunction leading to reduced ATP production and elevated reactive oxidative species generation. Furthermore, ion homeostasis, membrane excitability, and cardiac structure can be disrupted through pathological changes in gap junctions and inflammatory signaling, which results in impaired cardiac electrical homeostasis. Herein, we review the electrical and molecular mechanisms of cardiac arrhythmias, with a particular focus on mitochondrial dysfunction in ionic regulation and gap junction action. We provide an update on inherited and acquired mitochondrial dysfunction to explore the pathophysiology of different types of arrhythmias. In addition, we highlight the role of mitochondria in bradyarrhythmia, including sinus node dysfunction and atrioventricular node dysfunction. Finally, we discuss how confounding factors, such as aging, gut microbiome, cardiac reperfusion injury, and electrical stimulation, modulate mitochondrial function and cause tachyarrhythmia.
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4
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Summerhill VI, Sukhorukov VN, Eid AH, Nedosugova LV, Sobenin IA, Orekhov AN. Pathophysiological Aspects of the Development of Abdominal Aortic Aneurysm with a Special Focus on Mitochondrial Dysfunction and Genetic Associations. Biomol Concepts 2021; 12:55-67. [PMID: 34115932 DOI: 10.1515/bmc-2021-0007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 04/28/2021] [Indexed: 01/01/2023] Open
Abstract
Abdominal aortic aneurysm (AAA) is a complex degenerative vascular disease, with considerable morbidity and mortality rates among the elderly population. The mortality of AAA is related to aneurysm expansion (the enlargement of the aortic diameter up to 30 mm and above) and the subsequent rupture. The pathogenesis of AAA involves several biological processes, including aortic mural inflammation, oxidative stress, vascular smooth muscle cell apoptosis, elastin depletion, and degradation of the extracellular matrix. Mitochondrial dysfunction was also found to be associated with AAA formation. The evidence accumulated to date supports a close relationship between environmental and genetic factors in AAA initiation and progression. However, a comprehensive pathophysiological understanding of AAA formation remains incomplete. The open surgical repair of AAA is the only therapeutic option currently available, while a specific pharmacotherapy is still awaited. Therefore, there is a great need to clarify pathophysiological cellular and molecular mechanisms underlying AAA formation that would help to develop effective pharmacological therapies. In this review, pathophysiological aspects of AAA development with a special focus on mitochondrial dysfunction and genetic associations were discussed.
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Affiliation(s)
- Volha I Summerhill
- Department of Basic Research, Institute for Atherosclerosis Research, Moscow 121609, Russia
| | - Vasily N Sukhorukov
- Laboratory of Cellular and Molecular Pathology of Cardiovascular System, Research Institute of Human Morphology, 3 Tsyurupa Street, Moscow 117418, Russia
| | - Ali H Eid
- Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, PO Box 2713, Doha, Qatar.,Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, PO Box 2713, Doha, Qatar.,Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, PO Box 11-0236, Beirut-Lebanon
| | - Ludmila V Nedosugova
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 8/2 Trubenskaya Street, Moscow 119991, Russia
| | - Igor A Sobenin
- Laboratory of Cellular and Molecular Pathology of Cardiovascular System, Research Institute of Human Morphology, 3 Tsyurupa Street, Moscow 117418, Russia.,Laboratory of Medical Genetics, National Medical Research Center of Cardiology, 15A 3-rd Cherepkovskaya Street, Moscow 121552, Russia.,Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 8 Baltiiskaya Street, Moscow 125315, Russia
| | - Alexander N Orekhov
- Department of Basic Research, Institute for Atherosclerosis Research, Moscow 121609, Russia.,Laboratory of Cellular and Molecular Pathology of Cardiovascular System, Research Institute of Human Morphology, 3 Tsyurupa Street, Moscow 117418, Russia
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5
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Saadeh K, Fazmin IT. Mitochondrial Dysfunction Increases Arrhythmic Triggers and Substrates; Potential Anti-arrhythmic Pharmacological Targets. Front Cardiovasc Med 2021; 8:646932. [PMID: 33659284 PMCID: PMC7917191 DOI: 10.3389/fcvm.2021.646932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/26/2021] [Indexed: 12/31/2022] Open
Abstract
Incidence of cardiac arrhythmias increases significantly with age. In order to effectively stratify arrhythmic risk in the aging population it is crucial to elucidate the relevant underlying molecular mechanisms. The changes underlying age-related electrophysiological disruption appear to be closely associated with mitochondrial dysfunction. Thus, the present review examines the mechanisms by which age-related mitochondrial dysfunction promotes arrhythmic triggers and substrate. Namely, via alterations in plasmalemmal ionic currents (both sodium and potassium), gap junctions, cellular Ca2+ homeostasis, and cardiac fibrosis. Stratification of patients' mitochondrial function status permits application of appropriate anti-arrhythmic therapies. Here, we discuss novel potential anti-arrhythmic pharmacological interventions that specifically target upstream mitochondrial function and hence ameliorates the need for therapies targeting downstream changes which have constituted traditional antiarrhythmic therapy.
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Affiliation(s)
- Khalil Saadeh
- School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom.,Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Ibrahim Talal Fazmin
- School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom.,Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom.,Royal Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
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6
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Greenwell JC, Torres-Gonzalez E, Ritzenthaler JD, Roman J. Interplay between aging, lung inflammation/remodeling, and fibronectin EDA in lung cancer progression. Cancer Biol Ther 2020; 21:1109-1118. [PMID: 33222614 DOI: 10.1080/15384047.2020.1831372] [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: 10/22/2022] Open
Abstract
Lung cancer remains the leading cause of cancer death in the United States. Since most lung cancers occur in aged individuals with chronic lung disorders characterized by inflammation and/or fibrosis, we hypothesized that aging and tissue inflammation/remodeling act in concert to promote lung cancer progression. To test this, we engaged in studies using young and aged C57BL/6 mice in conjunction with bleomycin treatment in a syngeneic model of lung cancer. Wildtype young (3 months) and aged (9 months) C57BL/6 mice were injected with Lewis Lung Carcinoma (LLC) cells at day 14 after injection with phosphate-buffered saline or bleomycin. Untreated aged mice were found to develop more lung metastases than young mice. Bleomycin induced weight loss and lung inflammation/remodeling in both young and aged mice, and it increased the number of lung metastases in aged lungs, but not in young lungs. Since aged lungs show alterations in the expression of fibronectin EDA, we repeated studies in aged WT and aged FN EDA KO mice. In the absence of tissue remodeling/inflammation, WT and FN EDA KO mice developed the same number of metastases when injected with LLC cells. However, the increase in lung metastasis due to bleomycin treatment was abolished in FN EDA KO mice, but only in aged and injured lungs. Together, these studies show increased lung cancer metastasis in aging animals and point to the influence of FN EDA and injury in this process.
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Affiliation(s)
- John C Greenwell
- Department of Pharmacology & Toxicology, University of Louisville, Health Sciences Center , Louisville, KY, USA
| | - Edilson Torres-Gonzalez
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Disorders, University of Louisville Health Sciences Center , Louisville, KY, USA.,Department of Medicine, Division of Pulmonary, Allergy, and Critical Care and the Jane & Leonard Korman Respiratory Institute, Thomas Jefferson University , Philadelphia, PA, USA
| | - Jeffrey D Ritzenthaler
- Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Disorders, University of Louisville Health Sciences Center , Louisville, KY, USA.,Department of Medicine, Division of Pulmonary, Allergy, and Critical Care and the Jane & Leonard Korman Respiratory Institute, Thomas Jefferson University , Philadelphia, PA, USA
| | - Jesse Roman
- Department of Pharmacology & Toxicology, University of Louisville, Health Sciences Center , Louisville, KY, USA.,Department of Medicine, Division of Pulmonary, Critical Care, and Sleep Disorders, University of Louisville Health Sciences Center , Louisville, KY, USA.,Department of Medicine, Division of Pulmonary, Allergy, and Critical Care and the Jane & Leonard Korman Respiratory Institute, Thomas Jefferson University , Philadelphia, PA, USA.,Robley Rex VA Medical Center , Louisville, KY, USA
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7
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Edling C, Fazmin I, Saadeh K, Chadda K, Ahmad S, Valli H, Huang CH, Jeevaratnam K. Molecular basis of arrhythmic substrate in ageing murine peroxisome proliferator-activated receptor γ co-activator deficient hearts modelling mitochondrial dysfunction. Biosci Rep 2019; 39:BSR20190403. [PMID: 31778152 PMCID: PMC6911157 DOI: 10.1042/bsr20190403] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 11/19/2019] [Accepted: 11/26/2019] [Indexed: 12/19/2022] Open
Abstract
INTRODUCTION Ageing and chronic metabolic disorders are associated with mitochondrial dysfunction and cardiac pro-arrhythmic phenotypes which were recently attributed to slowed atrial and ventricular action potential (AP) conduction in peroxisome proliferator-activated receptor γ co-activator deficient (Pgc-1β-/-) mice. METHODS We compared expression levels of voltage-gated Na+ channel (NaV1.5) and gap junction channels, Connexins 40 and 43 (Cx40 and Cx43) in the hearts of young and old, and wild-type (WT) and Pgc-1β-/- mice. This employed Western blotting (WB) for NaV1.5, Cx40 and Cx43 in atrial/ventricular tissue lysates, and immunofluorescence (IF) from Cx43 was explored in tissue sections. Results were analysed using two-way analysis of variance (ANOVA) for independent/interacting effects of age and genotype. RESULTS In atria, increased age and Pgc-1β-/- genotype each independently decreased both Cx40 and Cx43 expression without interacting effects. In IF experiments, both age and Pgc-1β deletion independently reduced Cx43 expression. In ventricles, age and genotype exerted interacting effects in WB studies of NaV1.5 expression. Young Pgc-1β-/- then showed greater NaV1.5 expression than young WT ventricles. However, neither age nor Pgc-1β deletion affected Cx43 expression, independently or through interacting effects in both WB and IF studies. CONCLUSION Similar pro-arrhythmic atrial/ventricular phenotypes arise in aged/Pgc-1β-/- from differing contributions of altered protein expression and functional effects that may arise from multiple acute mechanisms.
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Affiliation(s)
- Charlotte E. Edling
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, United Kingdom
| | - Ibrahim T. Fazmin
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, United Kingdom
- Physiological Laboratory, University of Cambridge, Downing Street, Cambridge CB2 3EG, United Kingdom
| | - Khalil Saadeh
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, United Kingdom
- Physiological Laboratory, University of Cambridge, Downing Street, Cambridge CB2 3EG, United Kingdom
| | - Karan R. Chadda
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, United Kingdom
- Physiological Laboratory, University of Cambridge, Downing Street, Cambridge CB2 3EG, United Kingdom
| | - Shiraz Ahmad
- Physiological Laboratory, University of Cambridge, Downing Street, Cambridge CB2 3EG, United Kingdom
| | - Haseeb Valli
- Physiological Laboratory, University of Cambridge, Downing Street, Cambridge CB2 3EG, United Kingdom
| | - Christopher L.-H. Huang
- Physiological Laboratory, University of Cambridge, Downing Street, Cambridge CB2 3EG, United Kingdom
- Department of Biochemistry, Hopkins Building, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Kamalan Jeevaratnam
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, United Kingdom
- Department of Biochemistry, Hopkins Building, University of Cambridge, Cambridge CB2 1QW, United Kingdom
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8
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Systemic Lupus Erythematosus: Pathogenesis at the Functional Limit of Redox Homeostasis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:1651724. [PMID: 31885772 PMCID: PMC6899283 DOI: 10.1155/2019/1651724] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/15/2019] [Accepted: 09/09/2019] [Indexed: 12/14/2022]
Abstract
Systemic lupus erythematosus (SLE) is a disease characterized by the production of autoreactive antibodies and cytokines, which are thought to have a major role in disease activity and progression. Immune system exposure to excessive amounts of autoantigens that are not efficiently removed is reported to play a significant role in the generation of autoantibodies and the pathogenesis of SLE. While several mechanisms of cell death-based autoantigenic exposure and compromised autoantigen removal have been described in relation to disease onset, a significant association with the development of SLE can be attributed to increased apoptosis and impaired phagocytosis of apoptotic cells. Both apoptosis and impaired phagocytosis can be caused by hydrogen peroxide whose cellular production is enhanced by exposure to endogenous hormones or environmental chemicals, which have been implicated in the pathogenesis of SLE. Hydrogen peroxide can cause lymphocyte apoptosis and glutathione depletion, both of which are associated with the severity of SLE. The cellular accumulation of hydrogen peroxide is facilitated by the myriad of stimuli causing increased cellular bioenergetic activity that enhances metabolic production of this toxic oxidizing agent such as emotional stress and infection, which are recognized SLE exacerbating factors. When combined with impaired cellular hydrogen peroxide removal caused by xenobiotics and genetically compromised hydrogen peroxide elimination due to enzymatic polymorphic variation, a mechanism for cellular accumulation of hydrogen peroxide emerges, leading to hydrogen peroxide-induced apoptosis and impaired phagocytosis, enhanced autoantigen exposure, formation of autoantibodies, and development of SLE.
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9
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Edling CE, Fazmin IT, Chadda KR, Ahmad S, Valli H, Huang CLH, Jeevaratnam K. Atrial Transcriptional Profiles of Molecular Targets Mediating Electrophysiological Function in Aging and Pgc-1β Deficient Murine Hearts. Front Physiol 2019; 10:497. [PMID: 31068841 PMCID: PMC6491872 DOI: 10.3389/fphys.2019.00497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 04/08/2019] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Deficiencies in the transcriptional co-activator, peroxisome proliferative activated receptor, gamma, coactivator-1β are implicated in deficient mitochondrial function. The latter accompanies clinical conditions including aging, physical inactivity, obesity, and diabetes. Recent electrophysiological studies reported that Pgc-1β-/- mice recapitulate clinical age-dependent atrial pro-arrhythmic phenotypes. They implicated impaired chronotropic responses to adrenergic challenge, compromised action potential (AP) generation and conduction despite normal AP recovery timecourses and background resting potentials, altered intracellular Ca2+ homeostasis, and fibrotic change in the observed arrhythmogenicity. OBJECTIVE We explored the extent to which these age-dependent physiological changes correlated with alterations in gene transcription in murine Pgc-1β-/- atria. METHODS AND RESULTS RNA isolated from murine atrial tissue samples from young (12-16 weeks) and aged (>52 weeks of age), wild type (WT) and Pgc-1β-/- mice were studied by pre-probed quantitative PCR array cards. We examined genes encoding sixty ion channels and other strategic atrial electrophysiological proteins. Pgc-1β-/- genotype independently reduced gene transcription underlying Na+-K+-ATPase, sarcoplasmic reticular Ca2+-ATPase, background K+ channel and cholinergic receptor function. Age independently decreased Na+-K+-ATPase and fibrotic markers. Both factors interacted to alter Hcn4 channel activity underlying atrial automaticity. However, neither factor, whether independently or interactively, affected transcription of cardiac Na+, voltage-dependent K+ channels, surface or intracellular Ca2+ channels. Nor were gap junction channels, β-adrenergic receptors or transforming growth factor-β affected. CONCLUSION These findings limit the possible roles of gene transcriptional changes in previously reported age-dependent pro-arrhythmic electrophysiologial changes observed in Pgc-1β-/- atria to an altered Ca2+-ATPase (Atp2a2) expression. This directly parallels previously reported arrhythmic mechanism associated with p21-activated kinase type 1 deficiency. This could add to contributions from the direct physiological outcomes of mitochondrial dysfunction, whether through reactive oxygen species (ROS) production or altered Ca2+ homeostasis.
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Affiliation(s)
- Charlotte E. Edling
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Ibrahim T. Fazmin
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom,Physiological Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Karan R. Chadda
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom,Physiological Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Shiraz Ahmad
- Physiological Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Haseeb Valli
- Physiological Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Christopher L.-H. Huang
- Physiological Laboratory, University of Cambridge, Cambridge, United Kingdom,Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Kamalan Jeevaratnam
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom,Physiological Laboratory, University of Cambridge, Cambridge, United Kingdom,School of Medicine, Perdana University-Royal College of Surgeons in Ireland, Selangor, Malaysia,*Correspondence: Kamalan Jeevaratnam,
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10
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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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11
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Chadda KR, Edling CE, Valli H, Ahmad S, Huang CLH, Jeevaratnam K. Gene and Protein Expression Profile of Selected Molecular Targets Mediating Electrophysiological Function in Pgc-1α Deficient Murine Atria. Int J Mol Sci 2018; 19:ijms19113450. [PMID: 30400228 PMCID: PMC6274828 DOI: 10.3390/ijms19113450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 10/25/2018] [Accepted: 10/29/2018] [Indexed: 12/27/2022] Open
Abstract
Increases in the prevalence of obesity, insulin resistance, and metabolic syndrome has led to the increase of atrial fibrillation (AF) cases in the developed world. These AF risk factors are associated with mitochondrial dysfunction, previously modelled using peroxisome proliferator activated receptor-γ (PPARγ) coactivator-1 (Pgc-1)-deficient murine cardiac models. We explored gene and protein expression profiles of selected molecular targets related to electrophysiological function in murine Pgc-1α−/− atria. qPCR analysis surveyed genes related to Na+-K+-ATPase, K+ conductance, hyperpolarisation-activated cyclic nucleotide-gated (Hcn), Na+ channels, Ca2+ channels, and indicators for adrenergic and cholinergic receptor modulation. Western blot analysis for molecular targets specific to conduction velocity (Nav1.5 channel and gap junctions) was performed. Transcription profiles revealed downregulation of molecules related to Na+-K+-ATPase transport, Hcn-dependent pacemaker function, Na+ channel-dependent action potential activation and propagation, Ca2+ current generation, calsequestrin-2 dependent Ca2+ homeostasis, and adrenergic α1D dependent protection from hypertrophic change. Nav1.5 channel protein expression but not gap junction expression was reduced in Pgc-1α−/− atria compared to WT. Nav1.5 reduction reflects corresponding reduction in its gene expression profile. These changes, as well as the underlying Pgc-1α−/− alteration, suggest potential pharmacological targets directed towards either upstream PGC-1 signalling mechanisms or downstream ion channel changes.
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Affiliation(s)
- Karan R Chadda
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK.
- Physiological Laboratory, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK.
| | - Charlotte E Edling
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK.
| | - Haseeb Valli
- Physiological Laboratory, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK.
| | - Shiraz Ahmad
- Physiological Laboratory, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK.
| | - Christopher L-H Huang
- Physiological Laboratory, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK.
- Department of Biochemistry, Hopkins Building, University of Cambridge, Cambridge CB2 1QW, UK.
| | - Kamalan Jeevaratnam
- Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7AL, UK.
- Physiological Laboratory, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK.
- School of Medicine, Perdana University-Royal College of Surgeons Ireland, Serdang 43400, Malaysia.
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12
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Boucret L, Bris C, Seegers V, Goudenège D, Desquiret-Dumas V, Domin-Bernhard M, Ferré-L'Hotellier V, Bouet PE, Descamps P, Reynier P, Procaccio V, May-Panloup P. Deep sequencing shows that oocytes are not prone to accumulate mtDNA heteroplasmic mutations during ovarian ageing. Hum Reprod 2018; 32:2101-2109. [PMID: 28938736 DOI: 10.1093/humrep/dex268] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/28/2017] [Indexed: 12/30/2022] Open
Abstract
STUDY QUESTION Does ovarian ageing increase the number of heteroplasmic mitochondrial DNA (mtDNA) point mutations in oocytes? SUMMARY ANSWER Our results suggest that oocytes are not subject to the accumulation of mtDNA point mutations during ovarian ageing. WHAT IS KNOWN ALREADY Ageing is associated with the alteration of mtDNA integrity in various tissues. Primary oocytes, present in the ovary since embryonic life, may accumulate mtDNA mutations during the process of ovarian ageing. STUDY DESIGN, SIZE, DURATION This was an observational study of 53 immature oocyte-cumulus complexes retrieved from 35 women undergoing IVF at the University Hospital of Angers, France, from March 2013 to March 2014. The women were classified in two groups, one including 19 women showing signs of ovarian ageing objectified by a diminished ovarian reserve (DOR), and the other, including 16 women with a normal ovarian reserve (NOR), which served as a control group. PARTICIPANTS/MATERIALS, SETTING, METHODS mtDNA was extracted from isolated oocytes, and from their corresponding cumulus cells (CCs) considered as a somatic cell compartment. The average mtDNA content of each sample was assessed by using a quantitative real-time PCR technique. Deep sequencing was performed using the Ion Torrent Proton for Next-Generation Sequencing. Signal processing and base calling were done by the embedded pre-processing pipeline and the variants were analyzed using an in-house workflow. The distribution of the different variants between DOR and NOR patients, on one hand, and oocyte and CCs, on the other, was analyzed with the generalized mixed linear model to take into account the cluster of cells belonging to a given mother. MAIN RESULTS AND THE ROLE OF CHANCE There were no significant differences between the numbers of mtDNA variants between the DOR and the NOR patients, either in the oocytes (P = 0.867) or in the surrounding CCs (P = 0.154). There were also no differences in terms of variants with potential functional consequences. De-novo mtDNA variants were found in 28% of the oocytes and in 66% of the CCs with the mean number of variants being significantly different (respectively 0.321, SD = 0.547 and 1.075, SD = 1.158) (P < 0.0001). Variants with a potential functional consequence were also overrepresented in CCs compared with oocytes (P = 0.0019). LARGE SCALE DATA N/A. LIMITATIONS, REASONS FOR CAUTION Limitations may be due to the use of immature oocytes discarded during the assisted reproductive technology procedure, the small size of the sample, and the high-throughput sequencing technology that might not have detected heteroplasmy levels lower than 2%. WIDER IMPLICATIONS OF THE FINDINGS The alteration of mtDNA integrity in oocytes during ovarian ageing is a recurring question to which our pilot study suggests a reassuring answer. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the University Hospital of Angers, the University of Angers, France, and the French national research centers, INSERM and the CNRS. There are nocompeting interests.
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Affiliation(s)
- L Boucret
- Laboratoire de Biologie de la Reproduction, Centre Hospitalier Universitaire d'Angers, 49933 Angers cedex 9, France.,Institut MITOVASC, CNRS 6015, INSERM U1083, Université d'Angers, 49933 Angers, France
| | - C Bris
- Institut MITOVASC, CNRS 6015, INSERM U1083, Université d'Angers, 49933 Angers, France.,Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, 49933 Angers cedex 9, France
| | - V Seegers
- Département de Biométrie, Institut de Cancérologie de l'Ouest, CRCINA-Unité Inserm U1232-Equipe 7, 49100 Angers, France
| | - D Goudenège
- Institut MITOVASC, CNRS 6015, INSERM U1083, Université d'Angers, 49933 Angers, France.,Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, 49933 Angers cedex 9, France
| | - V Desquiret-Dumas
- Institut MITOVASC, CNRS 6015, INSERM U1083, Université d'Angers, 49933 Angers, France.,Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, 49933 Angers cedex 9, France
| | - M Domin-Bernhard
- Département de Gynécologie Obstétrique et Reproduction Humaine, CHU de Rennes, F-35033 Rennes, France
| | - V Ferré-L'Hotellier
- Laboratoire de Biologie de la Reproduction, Centre Hospitalier Universitaire d'Angers, 49933 Angers cedex 9, France
| | - P E Bouet
- Service de Gynécologie-Obstétrique, Centre Hospitalier Universitaire d'Angers, 49933 Angers cedex 9, France
| | - P Descamps
- Service de Gynécologie-Obstétrique, Centre Hospitalier Universitaire d'Angers, 49933 Angers cedex 9, France
| | - P Reynier
- Institut MITOVASC, CNRS 6015, INSERM U1083, Université d'Angers, 49933 Angers, France.,Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, 49933 Angers cedex 9, France
| | - V Procaccio
- Institut MITOVASC, CNRS 6015, INSERM U1083, Université d'Angers, 49933 Angers, France.,Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, 49933 Angers cedex 9, France
| | - P May-Panloup
- Laboratoire de Biologie de la Reproduction, Centre Hospitalier Universitaire d'Angers, 49933 Angers cedex 9, France.,Institut MITOVASC, CNRS 6015, INSERM U1083, Université d'Angers, 49933 Angers, France
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Antipova VN, Lomaeva MG, Zyrina NV. Mitochondrial DNA deletions in tissues of mice after ionizing radiation exposure. Int J Radiat Biol 2018; 94:282-288. [DOI: 10.1080/09553002.2018.1419299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Valeriya N. Antipova
- Laboratory of Biophysics of Active Media, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Milena G. Lomaeva
- Laboratory of Radiation Molecular Biology, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Nadezhda V. Zyrina
- Laboratory of Crystallophysics and X-ray Research, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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14
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Ren Q, Zhang F, Xu H. Proliferation Cycle Causes Age Dependent Mitochondrial Deficiencies and Contributes to the Aging of Stem Cells. Genes (Basel) 2017; 8:genes8120397. [PMID: 29257059 PMCID: PMC5748715 DOI: 10.3390/genes8120397] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/17/2017] [Accepted: 12/14/2017] [Indexed: 12/15/2022] Open
Abstract
In addition to chronological aging, stem cells are also subject to proliferative aging during the adult life span. However, the consequences of proliferative cycle and their contributions to stem cells aging have not been well investigated. Using Drosophila female germ line stem cells as a model, we found that the replication cycle leads to the age dependent decline of female fecundity, and is a major factor causing developmental abnormalities in the progeny of old females. The proliferative aging does not cause telomere shortening, but causes an accumulation of mitochondrial DNA (mtDNA) mutations or rearrangements at the control region. We propose that damaging mutations on mtDNA caused by accumulation of proliferation cycles in aged stem cells may disrupt mitochondrial respiration chain and impair mtDNA replication and represent a conserved mechanism underlying stem cell aging.
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Affiliation(s)
- Qiuting Ren
- Laboratory of Molecular Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Fan Zhang
- Laboratory of Molecular Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Hong Xu
- Laboratory of Molecular Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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15
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Kandola K, Bowman A, Birch-Machin MA. Oxidative stress - a key emerging impact factor in health, ageing, lifestyle and aesthetics. Int J Cosmet Sci 2015; 37 Suppl 2:1-8. [DOI: 10.1111/ics.12287] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/05/2015] [Indexed: 01/18/2023]
Affiliation(s)
- K. Kandola
- Dermatology; Medical School Newcastle University; Newcastle upon Tyne NE24HH U.K
| | - A. Bowman
- Dermatology; Medical School Newcastle University; Newcastle upon Tyne NE24HH U.K
| | - M. A. Birch-Machin
- Dermatology; Medical School Newcastle University; Newcastle upon Tyne NE24HH U.K
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16
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Casoli T, Spazzafumo L, Di Stefano G, Conti F. Role of diffuse low-level heteroplasmy of mitochondrial DNA in Alzheimer's disease neurodegeneration. Front Aging Neurosci 2015; 7:142. [PMID: 26257647 PMCID: PMC4511837 DOI: 10.3389/fnagi.2015.00142] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 07/10/2015] [Indexed: 01/08/2023] Open
Abstract
Alzheimer’s disease (AD) is the most common form of dementia in the elderly. The vast majority of cases are not linked to a known genetic defect and the molecular mechanisms underlying AD pathogenesis are still elusive. Evidence suggests that mitochondrial dysfunction is a prominent feature of the disease, and that mitochondrial DNA (mtDNA) alterations may represent a possible starting point of the pathophysiological cascade. Although specific mtDNA alterations have been reported in AD patients both in brain and peripheral tissues, such as D-loop mutations, 4977-bp deletion and poly-C tract D310 cytosine insertion, a generalized subtle allelic shift has also been demonstrated. This shift is significant for a few nucleotide positions (nps), but it is also detectable for most nps, although at a lower level. As single allelic substitutions can unlikely be determinant, it is proposed that the combination of all of them could lead to a less efficient oxidative phosphorylation, thus influencing AD development and course.
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Affiliation(s)
- Tiziana Casoli
- Center for Neurobiology of Aging, INRCA IRCCS Ancona, Italy
| | | | | | - Fiorenzo Conti
- Center for Neurobiology of Aging, INRCA IRCCS Ancona, Italy ; Department of Experimental and Clinical Medicine, Section of Neuroscience and Cell Biology, Università Politecnica delle Marche Ancona, Italy
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17
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McKenzie M, Chiotis M, Hroudová J, Lopez Sanchez MIG, Lim SC, Cook MJ, McKelvie P, Cotton RGH, Murphy M, St John JC, Trounce IA. Capture of somatic mtDNA point mutations with severe effects on oxidative phosphorylation in synaptosome cybrid clones from human brain. Hum Mutat 2015; 35:1476-84. [PMID: 25219341 DOI: 10.1002/humu.22694] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 09/03/2014] [Indexed: 01/13/2023]
Abstract
Mitochondrial DNA (mtDNA) is replicated throughout life in postmitotic cells, resulting in higher levels of somatic mutation than in nuclear genes. However, controversy remains as to the importance of low-level mtDNA somatic mutants in cancerous and normal human tissues. To capture somatic mtDNA mutations for functional analysis, we generated synaptosome cybrids from synaptic endings isolated from fresh hippocampus and cortex brain biopsies. We analyzed the whole mtDNA genome from 120 cybrid clones derived from four individual donors by chemical cleavage of mismatch and Sanger sequencing, scanning around two million base pairs. Seventeen different somatic point mutations were identified, including eight coding region mutations, four of which result in frameshifts. Examination of one cybrid clone with a novel m.2949_2953delCTATT mutation in MT-RNR2 (which encodes mitochondrial 16S rRNA) revealed a severe disruption of mtDNA-encoded protein translation. We also performed functional studies on a homoplasmic nonsense mutation in MT-ND1, previously reported in oncocytomas, and show that both ATP generation and the stability of oxidative phosphorylation complex I are disrupted. As the mtDNA remains locked against direct genetic manipulation, we demonstrate that the synaptosome cybrid approach can capture biologically relevant mtDNA mutants in vitro to study effects on mitochondrial respiratory chain function.
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Affiliation(s)
- Matthew McKenzie
- Centre for Genetic Diseases, MIMR-PHI Institute of Medical Research, Monash University, Clayton, Victoria, 3168, Australia; Monash University, Clayton, Victoria, 3168, Australia
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18
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Mitochondrial DNA: Radically free of free-radical driven mutations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1354-61. [PMID: 26050972 DOI: 10.1016/j.bbabio.2015.06.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 05/08/2015] [Accepted: 06/02/2015] [Indexed: 01/31/2023]
Abstract
Mitochondrial DNA has long been posited as a likely target of oxidative damage induced mutation during the ageing process. Research over the past decades has uncovered the accumulation of mitochondrial DNA mutations in association with a mosaic pattern of cells displaying mitochondrial dysfunction in ageing individuals. Unfortunately, the underlying mechanisms are far less straightforward than originally anticipated. Recent research on mitochondria reveals that these genomes are far less helpless than originally envisioned. Additionally, new technologies have allowed us to analyze the mutational signatures of many more somatic mitochondrial DNA mutations, revealing surprising patterns that are inconsistent with a DNA-oxidative damage based hypothesis. In this review, we will discuss these recent observations and new insights into the eccentricities of mitochondrial genetics, and their impact on our understanding of mitochondrial mutations and their role in the ageing process. This article is part of a Special Issue entitled: Mitochondrial Dysfunction in Aging.
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19
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Beekman M, Dowling DK, Aanen DK. The costs of being male: are there sex-specific effects of uniparental mitochondrial inheritance? Philos Trans R Soc Lond B Biol Sci 2015; 369:20130440. [PMID: 24864311 DOI: 10.1098/rstb.2013.0440] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Eukaryotic cells typically contain numerous mitochondria, each with multiple copies of their own genome, the mtDNA. Uniparental transmission of mitochondria, usually via the mother, prevents the mixing of mtDNA from different individuals. While on the one hand, this should resolve the potential for selection for fast-replicating mtDNA variants that reduce organismal fitness, maternal inheritance will, in theory, come with another set of problems that are specifically relevant to males. Maternal inheritance implies that the mitochondrial genome is never transmitted through males, and thus selection can target only the mtDNA sequence when carried by females. A consequence is that mtDNA mutations that confer male-biased phenotypic expression will be prone to evade selection, and accumulate. Here, we review the evidence from the ecological, evolutionary and medical literature for male specificity of mtDNA mutations affecting fertility, health and ageing. While such effects have been discovered experimentally in the laboratory, their relevance to natural populations--including the human population--remains unclear. We suggest that the existence of male expression-biased mtDNA mutations is likely to be a broad phenomenon, but that these mutations remain cryptic owing to the presence of counter-adapted nuclear compensatory modifier mutations, which offset their deleterious effects.
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Affiliation(s)
- Madeleine Beekman
- School of Biological Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Duur K Aanen
- Laboratory of Genetics, Wageningen University, 6708 PB Wageningen, The Netherlands
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20
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The Emerging Role of MitomiRs in the Pathophysiology of Human Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 888:123-54. [DOI: 10.1007/978-3-319-22671-2_8] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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21
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Levin L, Mishmar D. A Genetic View of the Mitochondrial Role in Ageing: Killing Us Softly. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 847:89-106. [DOI: 10.1007/978-1-4939-2404-2_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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22
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Wahlestedt M, Ameur A, Moraghebi R, Norddahl GL, Sten G, Woods NB, Bryder D. Somatic cells with a heavy mitochondrial DNA mutational load render induced pluripotent stem cells with distinct differentiation defects. Stem Cells 2014; 32:1173-82. [PMID: 24446123 DOI: 10.1002/stem.1630] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 12/27/2013] [Indexed: 01/19/2023]
Abstract
It has become increasingly clear that several age-associated pathologies associate with mutations in the mitochondrial genome. Experimental modeling of such events has revealed that acquisition of mitochondrial DNA (mtDNA) damage can impair respiratory function and, as a consequence, can lead to widespread decline in cellular function. This includes premature aging syndromes. By taking advantage of a mutator mouse model with an error-prone mtDNA polymerase, we here investigated the impact of an established mtDNA mutational load with regards to the generation, maintenance, and differentiation of induced pluripotent stem (iPS) cells. We demonstrate that somatic cells with a heavy mtDNA mutation burden were amenable for reprogramming into iPS cells. However, mutator iPS cells displayed delayed proliferation kinetics and harbored extensive differentiation defects. While mutator iPS cells had normal ATP levels and glycolytic activity, the induction of differentiation coincided with drastic decreases in ATP production and a hyperactive glycolysis. These data demonstrate the differential requirements of mitochondrial integrity for pluripotent stem cell self-renewal versus differentiation and highlight the relevance of assessing the mitochondrial genome when aiming to generate iPS cells with robust differentiation potential.
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Affiliation(s)
- Martin Wahlestedt
- Medical Faculty, Institution for Experimental Medical Science, Immunology Section, Lund Stem Cell Center, Lund University, Lund, Sweden
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23
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Duarte FV, Palmeira CM, Rolo AP. The Role of microRNAs in Mitochondria: Small Players Acting Wide. Genes (Basel) 2014; 5:865-86. [PMID: 25264560 PMCID: PMC4276918 DOI: 10.3390/genes5040865] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 09/05/2014] [Accepted: 09/05/2014] [Indexed: 01/17/2023] Open
Abstract
MicroRNAs (miRNAs) are short, single-stranded, non-coding RNA molecules that act as post-transcriptional gene regulators. They can inhibit target protein-coding genes, through repressing messenger RNA (mRNA) translation or promoting their degradation. miRNAs were initially found to be originated from nuclear genome and exported to cytosol; where they exerted most of their actions. More recently, miRNAs were found to be present specifically in mitochondria; even originated there from mitochondrial DNA, regulating in a direct manner genes coding for mitochondrial proteins, and consequently mitochondrial function. Since miRNAs are recognized as major players in several biological processes, they are being considered as a key to better understand, explain, and probably prevent/cure not only the pathogenesis of multifactorial diseases but also mitochondrial dysfunction and associated diseases. Here we review some of the molecular mechanisms purported for miRNA actions in several biological processes, particularly the miRNAs acting in mitochondria or in mitochondria-related mechanisms.
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Affiliation(s)
- Filipe V Duarte
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra 3004-504, Portugal.
| | - Carlos M Palmeira
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra 3004-504, Portugal.
| | - Anabela P Rolo
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra 3004-504, Portugal.
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24
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Aanen DK, Spelbrink JN, Beekman M. What cost mitochondria? The maintenance of functional mitochondrial DNA within and across generations. Philos Trans R Soc Lond B Biol Sci 2014; 369:20130438. [PMID: 24864309 PMCID: PMC4032515 DOI: 10.1098/rstb.2013.0438] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The peculiar biology of mitochondrial DNA (mtDNA) potentially has detrimental consequences for organismal health and lifespan. Typically, eukaryotic cells contain multiple mitochondria, each with multiple mtDNA genomes. The high copy number of mtDNA implies that selection on mtDNA functionality is relaxed. Furthermore, because mtDNA replication is not strictly regulated, within-cell selection may favour mtDNA variants with a replication advantage, but a deleterious effect on cell fitness. The opportunities for selfish mtDNA mutations to spread are restricted by various organism-level adaptations, such as uniparental transmission, germline mtDNA bottlenecks, germline selection and, during somatic growth, regular alternation between fusion and fission of mitochondria. These mechanisms are all hypothesized to maintain functional mtDNA. However, the strength of selection for maintenance of functional mtDNA progressively declines with age, resulting in age-related diseases. Furthermore, organismal adaptations that most probably evolved to restrict the opportunities for selfish mtDNA create secondary problems. Owing to predominantly maternal mtDNA transmission, recombination among mtDNA from different individuals is highly restricted or absent, reducing the scope for repair. Moreover, maternal inheritance precludes selection against mtDNA variants with male-specific effects. We finish by discussing the consequences of life-history differences among taxa with respect to mtDNA evolution and make a case for the use of microorganisms to experimentally manipulate levels of selection.
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Affiliation(s)
- Duur K Aanen
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, PO Box 309, 6700 AH Wageningen, The Netherlands
| | - Johannes N Spelbrink
- Department of Pediatrics, Nijmegen Centre for Mitochondrial Disorders, Radboud University Medical Centre, Geert Grooteplein 10, PO Box 9101, 6500 HB Nijmegen, The Netherlands FinMIT Centre of Excellence, BioMediTech and Tampere University Hospital, Pirkanmaa Hospital District, 33014 Tampere, Finland
| | - Madeleine Beekman
- Behaviour and Genetics of Social Insects Lab, The University of Sydney, Sydney NSW 2006, Australia
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25
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26
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Dhillon VS, Fenech M. Mutations that affect mitochondrial functions and their association with neurodegenerative diseases. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2013; 759:1-13. [PMID: 24055911 DOI: 10.1016/j.mrrev.2013.09.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 09/05/2013] [Accepted: 09/08/2013] [Indexed: 12/20/2022]
Abstract
Mitochondria are essential for mammalian and human cell function as they generate ATP via aerobic respiration. The proteins required in the electron transport chain are mainly encoded by the circular mitochondrial genome but other essential mitochondrial proteins such as DNA repair genes, are coded in the nuclear genome and require transport into the mitochondria. In this review we summarize current knowledge on the association of point mutations and deletions in the mitochondrial genome that are detrimental to mitochondrial function and are associated with accelerated ageing and neurological disorders including Alzheimer's, Parkinson's, Huntington's and Amyotrophic lateral sclerosis (ALS). Mutations in the nuclear encoded genes that disrupt mitochondrial functions are also discussed. It is evident that a greater understanding of the causes of mutations that adversely affect mitochondrial metabolism is required to develop preventive measures against accelerated ageing and neurological disorders caused by mitochondrial dysfunction.
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Affiliation(s)
- Varinderpal S Dhillon
- Preventative-Health Flagship, Gate 13, Kintore Avenue, Adelaide, SA 5000, Australia; CSIRO Animal, Food and Health Sciences, Gate 13, Kintore Avenue, Adelaide, SA 5000, Australia.
| | - Michael Fenech
- Preventative-Health Flagship, Gate 13, Kintore Avenue, Adelaide, SA 5000, Australia; CSIRO Animal, Food and Health Sciences, Gate 13, Kintore Avenue, Adelaide, SA 5000, Australia
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27
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Bouhlal Y, Martinez S, Gong H, Dumas K, Shieh JTC. Twin Mitochondrial Sequence Analysis. Mol Genet Genomic Med 2013; 1:174-186. [PMID: 24040623 PMCID: PMC3768015 DOI: 10.1002/mgg3.20] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
When applying genome-wide sequencing technologies to disease investigation, it is increasingly important to resolve sequence variation in regions of the genome that may have homologous sequences. The human mitochondrial genome challenges interpretation given the potential for heteroplasmy, somatic variation, and homologous nuclear mitochondrial sequences (numts). Identical twins share the same mitochondrial DNA (mtDNA) from early life, but whether the mitochondrial sequence remains similar is unclear. We compared an adult monozygotic twin pair using high-throughput sequencing and evaluated variants with primer extension and mitochondrial preenrichment. Thirty-seven variants were shared between the twin individuals, and the variants were verified on the original genomic DNA. These studies support highly identical genetic sequence in this case. Certain low-level variant calls were of high quality and homology to the mtDNA, and they were further evaluated. When we assessed calls in preenriched mtDNA templates, we found that these may represent numts, which can be differentiated from mtDNA variation. We conclude that twin identity extends to mtDNA, and it is critical to differentiate between numts and mtDNA in genome sequencing, particularly as significant heteroplasmy could influence genome interpretation. Further studies on mtDNA and numts will aid in understanding how variation occurs and persists.
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Affiliation(s)
- Yosr Bouhlal
- Division of Medical Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
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28
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Terzioglu M, Ruzzenente B, Harmel J, Mourier A, Jemt E, López MD, Kukat C, Stewart JB, Wibom R, Meharg C, Habermann B, Falkenberg M, Gustafsson CM, Park CB, Larsson NG. MTERF1 binds mtDNA to prevent transcriptional interference at the light-strand promoter but is dispensable for rRNA gene transcription regulation. Cell Metab 2013; 17:618-26. [PMID: 23562081 DOI: 10.1016/j.cmet.2013.03.006] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 01/22/2013] [Accepted: 03/12/2013] [Indexed: 11/30/2022]
Abstract
Mitochondrial transcription termination factor 1, MTERF1, has been reported to couple rRNA gene transcription initiation with termination and is therefore thought to be a key regulator of mammalian mitochondrial ribosome biogenesis. The prevailing model is based on a series of observations published over the last two decades, but no in vivo evidence exists to show that MTERF1 regulates transcription of the heavy-strand region of mtDNA containing the rRNA genes. Here, we demonstrate that knockout of Mterf1 in mice has no effect on mitochondrial rRNA levels or mitochondrial translation. Instead, loss of Mterf1 influences transcription initiation at the light-strand promoter, resulting in a decrease of de novo transcription manifested as reduced 7S RNA levels. Based on these observations, we suggest that MTERF1 does not regulate heavy-strand transcription, but rather acts to block transcription on the opposite strand of mtDNA to prevent transcription interference at the light-strand promoter.
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Affiliation(s)
- Mügen Terzioglu
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
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29
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Raap AK, Jahangir Tafrechi RS, van de Rijke FM, Pyle A, Wählby C, Szuhai K, Ravelli RBG, de Coo RFM, Rajasimha HK, Nilsson M, Chinnery PF, Samuels DC, Janssen GMC. Non-random mtDNA segregation patterns indicate a metastable heteroplasmic segregation unit in m.3243A>G cybrid cells. PLoS One 2012; 7:e52080. [PMID: 23272214 PMCID: PMC3525564 DOI: 10.1371/journal.pone.0052080] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 11/08/2012] [Indexed: 01/07/2023] Open
Abstract
Many pathogenic mitochondrial DNA mutations are heteroplasmic, with a mixture of mutated and wild-type mtDNA present within individual cells. The severity and extent of the clinical phenotype is largely due to the distribution of mutated molecules between cells in different tissues, but mechanisms underpinning segregation are not fully understood. To facilitate mtDNA segregation studies we developed assays that measure m.3243A>G point mutation loads directly in hundreds of individual cells to determine the mechanisms of segregation over time. In the first study of this size, we observed a number of discrete shifts in cellular heteroplasmy between periods of stable heteroplasmy. The observed patterns could not be parsimoniously explained by random mitotic drift of individual mtDNAs. Instead, a genetically metastable, heteroplasmic mtDNA segregation unit provides the likely explanation, where stable heteroplasmy is maintained through the faithful replication of segregating units with a fixed wild-type/m.3243A>G mutant ratio, and shifts occur through the temporary disruption and re-organization of the segregation units. While the nature of the physical equivalent of the segregation unit remains uncertain, the factors regulating its organization are of major importance for the pathogenesis of mtDNA diseases.
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Affiliation(s)
- Anton K. Raap
- Department of Molecular Cell Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | | | - Frans M. van de Rijke
- Department of Molecular Cell Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Angela Pyle
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Carolina Wählby
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Centre for Image Analysis, Uppsala University, Uppsala, Sweden
| | - Karoly Szuhai
- Department of Molecular Cell Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Raimond B. G. Ravelli
- Department of Molecular Cell Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - René F. M. de Coo
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Harsha K. Rajasimha
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Mats Nilsson
- Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Patrick F. Chinnery
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David C. Samuels
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - George M. C. Janssen
- Department of Molecular Cell Biology, Leiden University Medical Centre, Leiden, The Netherlands
- * E-mail:
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30
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Elstner M, Turnbull DM. Transcriptome analysis in mitochondrial disorders. Brain Res Bull 2012; 88:285-93. [DOI: 10.1016/j.brainresbull.2011.07.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 07/24/2011] [Indexed: 12/21/2022]
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Mitochondrial DNA damage and its consequences for mitochondrial gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:979-91. [PMID: 22728831 DOI: 10.1016/j.bbagrm.2012.06.002] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 06/06/2012] [Accepted: 06/14/2012] [Indexed: 12/11/2022]
Abstract
How mitochondria process DNA damage and whether a change in the steady-state level of mitochondrial DNA damage (mtDNA) contributes to mitochondrial dysfunction are questions that fuel burgeoning areas of research into aging and disease pathogenesis. Over the past decade, researchers have identified and measured various forms of endogenous and environmental mtDNA damage and have elucidated mtDNA repair pathways. Interestingly, mitochondria do not appear to contain the full range of DNA repair mechanisms that operate in the nucleus, although mtDNA contains types of damage that are targets of each nuclear DNA repair pathway. The reduced repair capacity may, in part, explain the high mutation frequency of the mitochondrial chromosome. Since mtDNA replication is dependent on transcription, mtDNA damage may alter mitochondrial gene expression at three levels: by causing DNA polymerase γ nucleotide incorporation errors leading to mutations, by interfering with the priming of mtDNA replication by the mitochondrial RNA polymerase, or by inducing transcriptional mutagenesis or premature transcript termination. This review summarizes our current knowledge of mtDNA damage, its repair, and its effects on mtDNA integrity and gene expression. This article is part of a special issue entitled: Mitochondrial Gene Expression.
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Guja KE, Garcia-Diaz M. Hitting the brakes: termination of mitochondrial transcription. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:939-47. [PMID: 22137970 DOI: 10.1016/j.bbagrm.2011.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 11/07/2011] [Accepted: 11/15/2011] [Indexed: 10/15/2022]
Abstract
Deficiencies in mitochondrial protein production are associated with human disease and aging. Given the central role of transcription in gene expression, recent years have seen a renewed interest in understanding the molecular mechanisms controlling this process. In this review, we have focused on the mostly uncharacterized process of transcriptional termination. We review how several recent breakthroughs have provided insight into our understanding of the termination mechanism, the protein factors that mediate termination, and the functional relevance of different termination events. Furthermore, the identification of termination defects resulting from a number of mtDNA mutations has led to the suggestion that this could be a common mechanism influencing pathogenesis in a number of mitochondrial diseases, highlighting the importance of understanding the processes that regulate transcription in human mitochondria. We discuss how these recent findings set the stage for future studies on this important regulatory mechanism. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
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Affiliation(s)
- Kip E Guja
- Medical Scientist Training Program, Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Stony Brook, NY 11794, USA.
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Mitochondrial transcription: lessons from mouse models. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:961-9. [PMID: 22120174 DOI: 10.1016/j.bbagrm.2011.11.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 11/09/2011] [Accepted: 11/10/2011] [Indexed: 11/22/2022]
Abstract
Mammalian mitochondrial DNA (mtDNA) is a circular double-stranded DNA genome of ~16.5 kilobase pairs (kb) that encodes 13 catalytic proteins of the ATP-producing oxidative phosphorylation system (OXPHOS), and the rRNAs and tRNAs required for the translation of the mtDNA transcripts. All the components needed for transcription and replication of the mtDNA are, therefore, encoded in the nuclear genome, as are the remaining components of the OXPHOS system and the mitochondrial translation machinery. Regulation of mtDNA gene expression is very important for modulating the OXPHOS capacity in response to metabolic requirements and in pathological processes. The combination of in vitro and in vivo studies has allowed the identification of the core machinery required for basal mtDNA transcription in mammals and a few proteins that regulate mtDNA transcription. Specifically, the generation of knockout mouse strains in the last several years, has been key to understanding the basis of mtDNA transcription in vivo. However, it is well accepted that many components of the transcription machinery are still unknown and little is known about mtDNA gene expression regulation under different metabolic requirements or disease processes. In this review we will focus on how the creation of knockout mouse models and the study of their phenotypes have contributed to the understanding of mitochondrial transcription in mammals. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
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Aanen DK, Maas MFPM. Recruitment of healthy mitochondria fuels transmissible cancers. Trends Genet 2011; 28:1-6. [PMID: 22030339 DOI: 10.1016/j.tig.2011.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 10/03/2011] [Accepted: 10/03/2011] [Indexed: 02/07/2023]
Abstract
The replication of mitochondrial DNA (mtDNA) is not under strict control of the nucleus. Therefore, within-cell selection can favour mtDNA variants with a replication or survival advantage even if deleterious for the cell. Here, we consider how the balance between selection within and among cells is shifted in cancer cell lineages, and how this affects the somatic evolution of mitochondria. Cancer cell lineages are known to be prone to mitochondrial genetic erosion. Nevertheless, some cancer lineages are long lived and a few exceptional lineages even can survive their host because of horizontal transmission to other individuals. Recent work now shows that such transmissible cancer cell lineages occasionally secondarily recruit the mitochondrial genome of their host, which we propose as a means to replace genetically eroded mitochondrial genomes. Studying the dynamics of the horizontal exchange of mtDNA between somatic cells may provide important insight into the evolution of mitochondria during somatic growth and in mitochondrial diseases.
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Affiliation(s)
- Duur K Aanen
- Laboratory of Genetics, Wageningen University, The Netherlands.
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35
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Impaired mitochondrial transport and Parkin-independent degeneration of respiratory chain-deficient dopamine neurons in vivo. Proc Natl Acad Sci U S A 2011; 108:12937-42. [PMID: 21768369 DOI: 10.1073/pnas.1103295108] [Citation(s) in RCA: 226] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Mitochondrial dysfunction is heavily implicated in Parkinson disease (PD) as exemplified by the finding of an increased frequency of respiratory chain-deficient dopamine (DA) neurons in affected patients. An inherited form of PD is caused by impaired function of Parkin, an E3 ubiquitin ligase reported to translocate to defective mitochondria in vitro to facilitate their clearance. We have developed a reporter mouse to assess mitochondrial morphology in DA neurons in vivo and show here that respiratory chain deficiency leads to fragmentation of the mitochondrial network and to the formation of large cytoplasmic bodies derived from mitochondria. Surprisingly, the dysfunctional mitochondria do not recruit Parkin in vivo, and neither the clearance of defective mitochondria nor the neurodegeneration phenotype is affected by the absence of Parkin. We also show that anterograde axonal transport of mitochondria is impaired in respiratory chain-deficient DA neurons, leading to a decreased supply of mitochondria to the axonal terminals.
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Antipova VN, Malakhova LV, Bezlepkin VG. Detection of large deletions of mitochondrial DNA in tissues of mice exposed to X-rays. Biophysics (Nagoya-shi) 2011. [DOI: 10.1134/s0006350911030031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Abstract
The small mammalian mitochondrial DNA (mtDNA) is very gene dense and encodes factors critical for oxidative phosphorylation. Mutations of mtDNA cause a variety of human mitochondrial diseases and are also heavily implicated in age-associated disease and aging. There has been considerable progress in our understanding of the role for mtDNA mutations in human pathology during the last two decades, but important mechanisms in mitochondrial genetics remain to be explained at the molecular level. In addition, mounting evidence suggests that most mtDNA mutations may be generated by replication errors and not by accumulated damage.
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Affiliation(s)
- Chan Bae Park
- Institute for Medical Sciences, Ajou University School of Medicine, Suwon 443-721, Korea
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MTERF4 regulates translation by targeting the methyltransferase NSUN4 to the mammalian mitochondrial ribosome. Cell Metab 2011; 13:527-39. [PMID: 21531335 DOI: 10.1016/j.cmet.2011.04.002] [Citation(s) in RCA: 205] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 01/27/2011] [Accepted: 02/25/2011] [Indexed: 02/05/2023]
Abstract
Precise control of mitochondrial DNA gene expression is critical for regulation of oxidative phosphorylation capacity in mammals. The MTERF protein family plays a key role in this process, and its members have been implicated in regulation of transcription initiation and site-specific transcription termination. We now demonstrate that a member of this family, MTERF4, directly controls mitochondrial ribosomal biogenesis and translation. MTERF4 forms a stoichiometric complex with the ribosomal RNA methyltransferase NSUN4 and is necessary for recruitment of this factor to the large ribosomal subunit. Loss of MTERF4 leads to defective ribosomal assembly and a drastic reduction in translation. Our results thus show that MTERF4 is an important regulator of translation in mammalian mitochondria.
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Ameur A, Stewart JB, Freyer C, Hagström E, Ingman M, Larsson NG, Gyllensten U. Ultra-deep sequencing of mouse mitochondrial DNA: mutational patterns and their origins. PLoS Genet 2011; 7:e1002028. [PMID: 21455489 PMCID: PMC3063763 DOI: 10.1371/journal.pgen.1002028] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 02/01/2011] [Indexed: 01/12/2023] Open
Abstract
Somatic mutations of mtDNA are implicated in the aging process, but there is no universally accepted method for their accurate quantification. We have used ultra-deep sequencing to study genome-wide mtDNA mutation load in the liver of normally- and prematurely-aging mice. Mice that are homozygous for an allele expressing a proof-reading–deficient mtDNA polymerase (mtDNA mutator mice) have 10-times-higher point mutation loads than their wildtype siblings. In addition, the mtDNA mutator mice have increased levels of a truncated linear mtDNA molecule, resulting in decreased sequence coverage in the deleted region. In contrast, circular mtDNA molecules with large deletions occur at extremely low frequencies in mtDNA mutator mice and can therefore not drive the premature aging phenotype. Sequence analysis shows that the main proportion of the mutation load in heterozygous mtDNA mutator mice and their wildtype siblings is inherited from their heterozygous mothers consistent with germline transmission. We found no increase in levels of point mutations or deletions in wildtype C57Bl/6N mice with increasing age, thus questioning the causative role of these changes in aging. In addition, there was no increased frequency of transversion mutations with time in any of the studied genotypes, arguing against oxidative damage as a major cause of mtDNA mutations. Our results from studies of mice thus indicate that most somatic mtDNA mutations occur as replication errors during development and do not result from damage accumulation in adult life. Mitochondria represent the powerhouses of cells and have their own DNA. Mutations in the mitochondrial genome are associated with a range of human diseases and have also been implicated as a driving force behind the aging process. We have used ultra-deep sequencing to study the genome-wide mutation load in the mitochondrial DNA (mtDNA) of liver from normal inbred mice and mice that express a proof-reading–deficient mtDNA polymerase (mtDNA mutator mice) that cause premature aging. The mtDNA mutator mice show a dramatic increase of point mutations with age and have 10-times-higher point mutation levels than wildtype siblings or normal C57Bl/6N mice. Circular mtDNA molecules with large deletions occur at very low frequencies in mtDNA mutator mice and are therefore unlikely to contribute to the premature aging phenotype. We found no increase in levels of point mutations or deletions in normal mice with increasing age, arguing against the accumulation of mtDNA mutations as contributing to aging. Our results indicate that most somatic mtDNA mutations occur as replication errors during the rapid amplification of mtDNA during embryogenesis and do not result from damage accumulation in adult life.
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Affiliation(s)
- Adam Ameur
- Department of Immunology, Genetics, and Pathology, SciLifeLab Uppsala, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | | | | | - Erik Hagström
- Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Max Ingman
- Department of Immunology, Genetics, and Pathology, SciLifeLab Uppsala, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Nils-Göran Larsson
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ulf Gyllensten
- Department of Immunology, Genetics, and Pathology, SciLifeLab Uppsala, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
- * E-mail:
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40
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Czarnecka AM, Bartnik E. The role of the mitochondrial genome in ageing and carcinogenesis. J Aging Res 2011; 2011:136435. [PMID: 21403887 PMCID: PMC3042732 DOI: 10.4061/2011/136435] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 01/03/2011] [Indexed: 01/01/2023] Open
Abstract
Mitochondrial DNA mutations and polymorphisms have been the focus of intensive investigations for well over a decade in an attempt to understand how they affect fundamental processes such as cancer and aging. Initial interest in mutations occurring in mitochondrial DNA of cancer cells diminished when most were found to be the same mutations which occurred during the evolution of human mitochondrial haplogroups. However, increasingly correlations are being found between various mitochondrial haplogroups and susceptibility to cancer or diseases in some cases and successful aging in others.
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Affiliation(s)
- Anna M. Czarnecka
- Laboratory of Molecular Oncology, Department of Oncology, Military Institute of Medicine, ul. Szaserów 128, 01-141 Warsaw, Poland
| | - Ewa Bartnik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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Campbell GR, Ziabreva I, Reeve AK, Krishnan KJ, Reynolds R, Howell O, Lassmann H, Turnbull DM, Mahad DJ. Mitochondrial DNA deletions and neurodegeneration in multiple sclerosis. Ann Neurol 2010; 69:481-92. [PMID: 21446022 PMCID: PMC3580047 DOI: 10.1002/ana.22109] [Citation(s) in RCA: 257] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2010] [Revised: 05/26/2010] [Accepted: 05/28/2010] [Indexed: 01/07/2023]
Abstract
Objective Cerebral atrophy is a correlate of clinical progression in multiple sclerosis (MS). Mitochondria are now established to play a part in the pathogenesis of MS. Uniquely, mitochondria harbor their own mitochondrial DNA (mtDNA), essential for maintaining a healthy central nervous system. We explored mitochondrial respiratory chain activity and mtDNA deletions in single neurons from secondary progressive MS (SPMS) cases. Methods Ninety-eight snap-frozen brain blocks from 13 SPMS cases together with complex IV/complex II histochemistry, immunohistochemistry, laser dissection microscopy, long-range and real-time PCR and sequencing were used to identify and analyze respiratory-deficient neurons devoid of complex IV and with complex II activity. Results The density of respiratory-deficient neurons in SPMS was strikingly in excess of aged controls. The majority of respiratory-deficient neurons were located in layer VI and immediate subcortical white matter (WM) irrespective of lesions. Multiple deletions of mtDNA were apparent throughout the gray matter (GM) in MS. The respiratory-deficient neurons harbored high levels of clonally expanded mtDNA deletions at a single-cell level. Furthermore, there were neurons lacking mtDNA-encoded catalytic subunits of complex IV. mtDNA deletions sufficiently explained the biochemical defect in the majority of respiratory-deficient neurons. Interpretation These findings provide evidence that neurons in MS are respiratory-deficient due to mtDNA deletions, which are extensive in GM and may be induced by inflammation. We propose induced multiple deletions of mtDNA as an important contributor to neurodegeneration in MS.
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Affiliation(s)
- Graham R Campbell
- Institute of Ageing and Health, Mitochondrial Research Group, Newcastle University, Newcastle upon Tyne, UK
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Somatic point mutations in mtDNA control region are influenced by genetic background and associated with healthy aging: a GEHA study. PLoS One 2010; 5:e13395. [PMID: 20976236 PMCID: PMC2954809 DOI: 10.1371/journal.pone.0013395] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 09/18/2010] [Indexed: 02/02/2023] Open
Abstract
Tissue specific somatic mutations occurring in the mtDNA control region have been proposed to provide a survival advantage. Data on twins and on relatives of long-lived subjects suggested that the occurrence/accumulation of these mutations may be genetically influenced. To further investigate control region somatic heteroplasmy in the elderly, we analyzed the segment surrounding the nt 150 position (previously reported as specific of Leukocytes) in various types of leukocytes obtained from 195 ultra-nonagenarians sib-pairs of Italian or Finnish origin collected in the frame of the GEHA Project. We found a significant correlation of the mtDNA control region heteroplasmy between sibs, confirming a genetic influence on this phenomenon. Furthermore, many subjects showed heteroplasmy due to mutations different from the C150T transition. In these cases heteroplasmy was correlated within sibpairs in Finnish and northern Italian samples, but not in southern Italians. This suggested that the genetic contribution to control region mutations may be population specific. Finally, we observed a possible correlation between heteroplasmy and Hand Grip strength, one of the best markers of physical performance and of mortality risk in the elderly. Our study provides new evidence on the relevance of mtDNA somatic mutations in aging and longevity and confirms that the occurrence of specific point mutations in the mtDNA control region may represent a strategy for the age-related remodelling of organismal functions.
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Jobson RW, Dehne-Garcia A, Galtier N. Apparent longevity-related adaptation of mitochondrial amino acid content is due to nucleotide compositional shifts. Mitochondrion 2010; 10:540-7. [PMID: 20594973 DOI: 10.1016/j.mito.2010.05.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 05/24/2010] [Accepted: 05/28/2010] [Indexed: 10/19/2022]
Abstract
Recent studies across animal phyla have suggested a possible link between amino acid compositional shifts and adaptive evolution across mitochondrial proteomes enabling longer lifespans. These studies examined associations of a gradual loss of cysteine (Cys) residues, increased usage of methionine (Met), and increased usage of threonine (Thr), with the evolution of longevity. Here, we examine all three hypotheses in a framework that considers nucleotide composition. We find that nucleotide composition is strongly correlated across codon positions, and with the above amino acid frequency patterns. We also find that the ND6 gene, which in vertebrates is the only mitochondrial gene situated on the "light-strand" shows no significant pattern for any of the amino acid associations. We also reasoned that if the mitochondrially-encoded proteins of oxidative phosphorylation (OXPHOS) were under selection for such shifts, then nuclear-encoded components should also reflect such pressure. However, we found non-correspondence of these patterns in the nuclear genes when compared to the mitochondrial genes previously associated with positive selection. These results are strongly suggestive of mutational bias, or less efficient purifying selection, as the primary driver of whole proteome shifts in amino acid composition.
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Affiliation(s)
- Richard W Jobson
- Institut des Sciences de l'Evolution, CNRS UMR 5554, Université Montpellier 2, Place E. Bataillon, 34095 Montpellier, France.
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Abstract
Mitochondrial dysfunction is heavily implicated in the multifactorial aging process. Aging humans have increased levels of somatic mtDNA mutations that tend to undergo clonal expansion to cause mosaic respiratory chain deficiency in various tissues, such as heart, brain, skeletal muscle, and gut. Genetic mouse models have shown that somatic mtDNA mutations and cell type-specific respiratory chain dysfunction can cause a variety of phenotypes associated with aging and age-related disease. There is thus strong observational and experimental evidence to implicate somatic mtDNA mutations and mosaic respiratory chain dysfunction in the mammalian aging process. The hypothesis that somatic mtDNA mutations are generated by oxidative damage has not been conclusively proven. Emerging data instead suggest that the inherent error rate of mitochondrial DNA (mtDNA) polymerase gamma (Pol gamma) may be responsible for the majority of somatic mtDNA mutations. The roles for mtDNA damage and replication errors in aging need to be further experimentally addressed.
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Lee YH, Lin Q, Boelsterli UA, Chung MCM. The Sod2 mutant mouse as a model for oxidative stress: a functional proteomics perspective. MASS SPECTROMETRY REVIEWS 2010; 29:179-196. [PMID: 19294730 DOI: 10.1002/mas.20226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Oxidative stress has been implicated in the pathogenesis of numerous human diseases and disorders, but the mechanistic basis often remains enigmatic. The Sod2 mutant mouse, which is sensitized to mitochondrial stress, is an ideal mutant model for studying the role of oxidative stress in a diverse range of complications arising from mitochondrial dysfunction and diminished antioxidant defense. To fully appreciate the widespread molecular consequences under increased oxidative stress, a systems approach utilizing proteomics is able to provide a global overview of the complex biological changes, which a targeted single biomolecular approach cannot address fully. This review focuses on the applications of mass spectrometry and functional proteomics in the Sod2 mouse. The combinatorial approach provides novel insights into the interplay of chemistry and biology, free radicals and proteins, thereby augmenting our understanding of how redox perturbations influence protein dynamics. Ultimately, this knowledge can lead to the development of free radical-targeted therapies.
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Affiliation(s)
- Yie Hou Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, Singapore 117597, Singapore
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46
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Yu-Wai-Man P, Lai-Cheong J, Borthwick GM, He L, Taylor GA, Greaves LC, Taylor RW, Griffiths PG, Turnbull DM. Somatic mitochondrial DNA deletions accumulate to high levels in aging human extraocular muscles. Invest Ophthalmol Vis Sci 2010; 51:3347-53. [PMID: 20164450 DOI: 10.1167/iovs.09-4660] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
PURPOSE. Mitochondrial function and the presence of somatic mitochondrial DNA (mtDNA) defects were investigated in extraocular muscles (EOMs) collected from individuals covering a wide age range, to document the changes seen with normal aging. METHODS. Cytochrome c oxidase (COX) and succinate dehydrogenase (SDH) histochemistry was performed on 46 EOM samples to determine the level of COX deficiency in serial cryostat muscle sections (mean age, 42.6 years; range, 3.0-96.0 years). Competitive three-primer and real-time PCR were performed on single-fiber lysates to detect and quantify mtDNA deletions. Whole-genome mitochondrial sequencing was also performed to evaluate the contribution of mtDNA point mutations to the overall mutational load. RESULTS. COX-negative fibers were seen in EOMs beginning in the third decade of life, and there was a significant age-related increase: <30 years, 0.05% (n = 17); 30 to 60 years, 1.94% (n = 13); and >60 years, 3.34% (n = 16, P = 0.0001). Higher levels of COX deficiency were also present in EOM than in skeletal muscle in all three age groups (P < 0.0001). Most of the COX-negative fibers harbored high levels (>70%) of mtDNA deletions (206/284, 72.54%) and the mean deletion level was 66.64% (SD 36.45%). The mutational yield from whole mitochondrial genome sequencing was relatively low (1/19, 5.3%), with only a single mtDNA point mutation identified among COX-negative fibers with low deletion levels < or =70%. CONCLUSIONS. The results show an exponential increase in COX deficiency in EOMs beginning in early adulthood, which suggests an accelerated aging process compared with other postmitotic tissues.
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Affiliation(s)
- Patrick Yu-Wai-Man
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle-upon-Tyne, United Kingdom.
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Greaves LC, Barron MJ, Plusa S, Kirkwood TB, Mathers JC, Taylor RW, Turnbull DM. Defects in multiple complexes of the respiratory chain are present in ageing human colonic crypts. Exp Gerontol 2010; 45:573-9. [PMID: 20096767 PMCID: PMC2887930 DOI: 10.1016/j.exger.2010.01.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Revised: 01/12/2010] [Accepted: 01/14/2010] [Indexed: 01/21/2023]
Abstract
Mitochondrial DNA (mtDNA) mutations accumulate in a number of ageing tissues and are proposed to play a role in the ageing process. We have previously shown that colonic crypt stem cells accumulate somatic mtDNA point mutations during ageing. These mtDNA mutations result in the loss of the activity of complex IV (cytochrome c oxidase (COX)) of the respiratory chain in the stem cells and their progeny, producing colonic crypts which are entirely COX deficient. However it is not known whether the other complexes of the respiratory chain are similarly affected during ageing. Here we have used antibodies to individual subunits of complexes I–IV to investigate their expression in the colonic epithelium from human subjects aged 18–84. We show that in ∼50% of crypts with any form of respiratory chain deficiency, decreased expression of subunits of multiple complexes is observed. Furthermore we have sequenced the entire mitochondrial genome of a number of cells with multiple complex defects and have found a wide variety of point mutations in these cells affecting a number of different protein encoding and RNA encoding genes. Finally we discuss the possible mechanisms by which multiple respiratory chain complex defects may occur in these cells.
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Affiliation(s)
- Laura C Greaves
- Mitochondrial Research Group, Institute for Ageing and Health, Medical School, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne, UK
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Krishnan KJ, Blackwood JK, Reeve AK, Turnbull DM, Taylor RW. Detection of mitochondrial DNA variation in human cells. Methods Mol Biol 2010; 628:227-257. [PMID: 20238085 DOI: 10.1007/978-1-60327-367-1_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The ability to detect mitochondrial DNA (mtDNA) variation within human cells is important not only to identify mutations causing mtDNA disease, but also as mtDNA mutations are being increasingly described in many ageing tissues and in complex diseases such as diabetes, neurodegeneration and cancer. In this review, we discuss the main molecular genetic techniques that can be applied to study the two main types of mtDNA mutation: point mutations and large-scale mtDNA rearrangements. We then describe in detail protocols routinely used within our laboratory to analyse mtDNA mutations in individual human cells such as single muscle fibres and individual neurons to study the relationship between mtDNA mutation load and respiratory chain dysfunction.
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Affiliation(s)
- Kim J Krishnan
- Mitochondrial Research Group, Newcastle University, Newcastle upon Tyne, Tyne and Wear, UK
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49
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Birch-Machin MA, Swalwell H. How mitochondria record the effects of UV exposure and oxidative stress using human skin as a model tissue. Mutagenesis 2009; 25:101-7. [DOI: 10.1093/mutage/gep061] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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50
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Schiff M, Loublier S, Coulibaly A, Bénit P, Ogier de Baulny H, Rustin P. Mitochondria and diabetes mellitus: untangling a conflictive relationship? J Inherit Metab Dis 2009; 32:684-698. [PMID: 19821144 DOI: 10.1007/s10545-009-1263-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 08/19/2009] [Accepted: 08/25/2009] [Indexed: 01/19/2023]
Abstract
Diabetes mellitus is occasionally observed in patients with skeletal muscle respiratory chain deficiency, suggesting that skeletal muscle mitochondrial dysfunction might play a pathogenic role in type 2 diabetes (T2D). In support of this hypothesis, decreased muscle mitochondrial activity has been reported in T2D patients and in mouse models of diabetes. However, recent work by several groups suggests that decreased muscle mitochondrial function may be a consequence rather than a cause of diabetes, since decreased mitochondrial function in mice affords protection from diabetes and obesity. We review the data on this controversial but important issue of potential links between mitochondrial dysfunction and diabetes.
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Affiliation(s)
- M Schiff
- Hôpital Robert Debré, Paris, France
- Université Paris 7, Faculté de médecine Denis Diderot, IFR02, Paris, France
- Centre de référence Maladies Métaboliques, Hôpital Robert Debré, APHP, Paris, France
| | - S Loublier
- Hôpital Robert Debré, Paris, France
- Université Paris 7, Faculté de médecine Denis Diderot, IFR02, Paris, France
| | - A Coulibaly
- Hôpital Robert Debré, Paris, France
- Université Paris 7, Faculté de médecine Denis Diderot, IFR02, Paris, France
| | - P Bénit
- Hôpital Robert Debré, Paris, France
- Université Paris 7, Faculté de médecine Denis Diderot, IFR02, Paris, France
| | - H Ogier de Baulny
- Centre de référence Maladies Métaboliques, Hôpital Robert Debré, APHP, Paris, France
| | - P Rustin
- Hôpital Robert Debré, Paris, France.
- Université Paris 7, Faculté de médecine Denis Diderot, IFR02, Paris, France.
- INSERM U676, Bâtiment Ecran, Hôpital Robert Debré, 48, boulevard Sérurier, 75019, Paris, France.
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