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Akbari M, Nilsen HL, Montaldo NP. Dynamic features of human mitochondrial DNA maintenance and transcription. Front Cell Dev Biol 2022; 10:984245. [PMID: 36158192 PMCID: PMC9491825 DOI: 10.3389/fcell.2022.984245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/02/2022] [Indexed: 12/03/2022] Open
Abstract
Mitochondria are the primary sites for cellular energy production and are required for many essential cellular processes. Mitochondrial DNA (mtDNA) is a 16.6 kb circular DNA molecule that encodes only 13 gene products of the approximately 90 different proteins of the respiratory chain complexes and an estimated 1,200 mitochondrial proteins. MtDNA is, however, crucial for organismal development, normal function, and survival. MtDNA maintenance requires mitochondrially targeted nuclear DNA repair enzymes, a mtDNA replisome that is unique to mitochondria, and systems that control mitochondrial morphology and quality control. Here, we provide an overview of the current literature on mtDNA repair and transcription machineries and discuss how dynamic functional interactions between the components of these systems regulate mtDNA maintenance and transcription. A profound understanding of the molecular mechanisms that control mtDNA maintenance and transcription is important as loss of mtDNA integrity is implicated in normal process of aging, inflammation, and the etiology and pathogenesis of a number of diseases.
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Affiliation(s)
- Mansour Akbari
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Hilde Loge Nilsen
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Unit for precision medicine, Akershus University Hospital, Nordbyhagen, Norway
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Nicola Pietro Montaldo
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- *Correspondence: Nicola Pietro Montaldo,
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2
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de Sousa MML, Ye J, Luna L, Hildrestrand G, Bjørås K, Scheffler K, Bjørås M. Impact of Oxidative DNA Damage and the Role of DNA Glycosylases in Neurological Dysfunction. Int J Mol Sci 2021; 22:12924. [PMID: 34884729 PMCID: PMC8657561 DOI: 10.3390/ijms222312924] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 11/16/2022] Open
Abstract
The human brain requires a high rate of oxygen consumption to perform intense metabolic activities, accounting for 20% of total body oxygen consumption. This high oxygen uptake results in the generation of free radicals, including reactive oxygen species (ROS), which, at physiological levels, are beneficial to the proper functioning of fundamental cellular processes. At supraphysiological levels, however, ROS and associated lesions cause detrimental effects in brain cells, commonly observed in several neurodegenerative disorders. In this review, we focus on the impact of oxidative DNA base lesions and the role of DNA glycosylase enzymes repairing these lesions on brain function and disease. Furthermore, we discuss the role of DNA base oxidation as an epigenetic mechanism involved in brain diseases, as well as potential roles of DNA glycosylases in different epigenetic contexts. We provide a detailed overview of the impact of DNA glycosylases on brain metabolism, cognition, inflammation, tissue loss and regeneration, and age-related neurodegenerative diseases based on evidence collected from animal and human models lacking these enzymes, as well as post-mortem studies on patients with neurological disorders.
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Affiliation(s)
- Mirta Mittelstedt Leal de Sousa
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7028 Trondheim, Norway; (J.Y.); (K.B.)
| | - Jing Ye
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7028 Trondheim, Norway; (J.Y.); (K.B.)
| | - Luisa Luna
- Department of Microbiology, Oslo University Hospital, University of Oslo, Rikshospitalet, 0424 Oslo, Norway; (L.L.); (G.H.)
| | - Gunn Hildrestrand
- Department of Microbiology, Oslo University Hospital, University of Oslo, Rikshospitalet, 0424 Oslo, Norway; (L.L.); (G.H.)
| | - Karine Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7028 Trondheim, Norway; (J.Y.); (K.B.)
| | - Katja Scheffler
- Department of Neurology, St. Olavs Hospital, 7006 Trondheim, Norway;
- Department of Laboratory Medicine, St. Olavs Hospital, 7006 Trondheim, Norway
- Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7028 Trondheim, Norway; (J.Y.); (K.B.)
- Department of Microbiology, Oslo University Hospital, University of Oslo, Rikshospitalet, 0424 Oslo, Norway; (L.L.); (G.H.)
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3
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Waneka G, Svendsen JM, Havird JC, Sloan DB. Mitochondrial mutations in Caenorhabditis elegans show signatures of oxidative damage and an AT-bias. Genetics 2021; 219:6346985. [PMID: 34849888 DOI: 10.1093/genetics/iyab116] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/09/2021] [Indexed: 01/25/2023] Open
Abstract
Rapid mutation rates are typical of mitochondrial genomes (mtDNAs) in animals, but it is not clear why. The difficulty of obtaining measurements of mtDNA mutation that are not biased by natural selection has stymied efforts to distinguish between competing hypotheses about the causes of high mtDNA mutation rates. Several studies which have measured mtDNA mutations in nematodes have yielded small datasets with conflicting conclusions about the relative abundance of different substitution classes (i.e., the mutation spectrum). We therefore leveraged Duplex Sequencing, a high-fidelity DNA sequencing technique, to characterize de novo mtDNA mutations in Caenorhabditis elegans. This approach detected nearly an order of magnitude more mtDNA mutations than documented in any previous nematode mutation study. Despite an existing extreme AT bias in the C. elegans mtDNA (75.6% AT), we found that a significant majority of mutations increase genomic AT content. Compared to some prior studies in nematodes and other animals, the mutation spectrum reported here contains an abundance of CG→AT transversions, supporting the hypothesis that oxidative damage may be a driver of mtDNA mutations in nematodes. Furthermore, we found an excess of G→T and C→T changes on the coding DNA strand relative to the template strand, consistent with increased exposure to oxidative damage. Analysis of the distribution of mutations across the mtDNA revealed significant variation among protein-coding genes and as well as among neighboring nucleotides. This high-resolution view of mitochondrial mutations in C. elegans highlights the value of this system for understanding relationships among oxidative damage, replication error, and mtDNA mutation.
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Affiliation(s)
- Gus Waneka
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA and
| | - Joshua M Svendsen
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA and
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA and
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4
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Suzuki T, Masuda H, Mori M, Ito R, Kamiya H. Action-at-a-distance mutations at 5'-GpA-3' sites induced by oxidized guanine in WRN-knockdown cells. Mutagenesis 2021; 36:349-357. [PMID: 34272950 DOI: 10.1093/mutage/geab027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/16/2021] [Indexed: 12/14/2022] Open
Abstract
G:C sites distant from 8-oxo-7,8-dihydroguanine (G O, 8-hydroxyguanine) are frequently mutated when the lesion-bearing plasmid DNA is replicated in human cells with reduced Werner syndrome (WRN) protein. To detect the untargeted mutations preferentially, the oxidized guanine base was placed downstream of the reporter supF gene and the plasmid DNA was introduced into WRN-knockdown cells. The total mutant frequency seemed higher in the WRN-knockdown cells as compared to the control cells. Mutation analyses revealed that substitution mutations occurred at the G:C pairs of 5'-GpA-3'/5'-TpC-3' sites, the preferred sequence for the apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3 (APOBEC3)-family cytosine deaminases, in the supF gene in both control and knockdown cells. These mutations were observed more frequently at G sites than C sites on the DNA strand where the G O base was originally located. This tendency was promoted by the knockdown of the WRN protein. The present results imply the possible involvement of APOBEC3-family cytosine deaminases in the action-at-a-distance (untargeted) mutations at G:C (or G) sites induced by G O and in cancer initiation by oxidative stress.
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Affiliation(s)
- Tetsuya Suzuki
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi, Minami-ku, Hiroshima, Japan
| | - Hiroshi Masuda
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi, Minami-ku, Hiroshima, Japan
| | - Madoka Mori
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi, Minami-ku, Hiroshima, Japan
| | - Rikako Ito
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi, Minami-ku, Hiroshima, Japan
| | - Hiroyuki Kamiya
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Kasumi, Minami-ku, Hiroshima, Japan
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Scheffler K, Jalland CMO, Benestad SL, Moldal T, Ersdal C, Gunnes G, Suganthan R, Bjørås M, Tranulis MA. DNA glycosylase Neil2 contributes to genomic responses in the spleen during clinical prion disease. Free Radic Biol Med 2020; 152:348-354. [PMID: 32259578 DOI: 10.1016/j.freeradbiomed.2020.03.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/19/2020] [Accepted: 03/29/2020] [Indexed: 02/02/2023]
Abstract
The DNA glycosylase Neil2 is a member of the base excision repair (BER) family of enzymes, which are important for repair of oxidative DNA damage. Specifically, Neil2 participates in repair of oxidized bases in single-stranded DNA of transcriptionally active genes. Mice with genetic ablation of Neil2 (Neil2-/-) display no overt phenotypes, but an age-dependent accumulation of oxidative DNA damage and increased inflammatory responsiveness. In young mice intra-cerebrally inoculated with prions, vigorous prion propagation starts rapidly in the germinal follicles of the spleen due to inoculum spillover. Here, we compare experimental prion disease in Neil2-/- mice with that in wild-type mice at disease onset and end-stage. Specifically, we investigated disease progression, accumulation of DNA damage, and mitochondrial respiratory complex activity in brain and spleen. We used genome-wide RNA sequencing of the spleen to compare the immune responses to prion propagation between the two groups of mice, at both onset and end-stage prion disease. The Neil2-/- mice deteriorated more rapidly than wild-type mice after onset of clinical signs. Levels of DNA damage in brain increased in both mouse groups, slightly more in the Neil2-/- mice. Transcriptome data from spleen at disease onset were similar between the mouse groups with moderate genomic responses. However, at end-stage a substantial response was evident in the wild-type mice but not in Neil2-/- mice. Our data show that Neil2 counteracts toxic signaling in clinical prion disease, and this is separate from gross pathological manifestations and PrPSc accumulation.
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Affiliation(s)
- Katja Scheffler
- Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology, Trondheim, Norway; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway; Department of Neurology, St. Olavs Hospital, Trondheim, Norway; Department of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway.
| | - Clara M O Jalland
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Campus Adamstuen, Oslo, Norway
| | | | | | - Cecilie Ersdal
- Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Campus Sandnes, Norway
| | - Gjermund Gunnes
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Campus Adamstuen, Oslo, Norway
| | - Rajikala Suganthan
- Department of Microbiology, Oslo University Hospital and University of Oslo, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway; Department of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway; Department of Microbiology, Oslo University Hospital and University of Oslo, Norway
| | - Michael A Tranulis
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Campus Adamstuen, Oslo, Norway
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Chiaratti MR, Macabelli CH, Augusto Neto JD, Grejo MP, Pandey AK, Perecin F, Collado MD. Maternal transmission of mitochondrial diseases. Genet Mol Biol 2020; 43:e20190095. [PMID: 32141474 PMCID: PMC7197987 DOI: 10.1590/1678-4685-gmb-2019-0095] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 11/01/2019] [Indexed: 12/19/2022] Open
Abstract
Given the major role of the mitochondrion in cellular homeostasis, dysfunctions of this organelle may lead to several common diseases in humans. Among these, maternal diseases linked to mitochondrial DNA (mtDNA) mutations are of special interest due to the unclear pattern of mitochondrial inheritance. Multiple copies of mtDNA are present in a cell, each encoding for 37 genes essential for mitochondrial function. In cases of mtDNA mutations, mitochondrial malfunctioning relies on mutation load, as mutant and wild-type molecules may co-exist within the cell. Since the mutation load associated with disease manifestation varies for different mutations and tissues, it is hard to predict the progeny phenotype based on mutation load in the progenitor. In addition, poorly understood mechanisms act in the female germline to prevent the accumulation of deleterious mtDNA in the following generations. In this review, we outline basic aspects of mitochondrial inheritance in mammals and how they may lead to maternally-inherited diseases. Furthermore, we discuss potential therapeutic strategies for these diseases, which may be used in the future to prevent their transmission.
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Affiliation(s)
- Marcos R Chiaratti
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Laboratório de Genética e Biotecnologia, São Carlos, SP, Brazil
| | - Carolina H Macabelli
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Laboratório de Genética e Biotecnologia, São Carlos, SP, Brazil
| | - José Djaci Augusto Neto
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Laboratório de Genética e Biotecnologia, São Carlos, SP, Brazil
| | - Mateus Priolo Grejo
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Laboratório de Genética e Biotecnologia, São Carlos, SP, Brazil
| | - Anand Kumar Pandey
- Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana, India
| | - Felipe Perecin
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Laboratório de Morfofisiologia Molecular e Desenvolvimento, Pirassununga, SP, Brazil
| | - Maite Del Collado
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Laboratório de Morfofisiologia Molecular e Desenvolvimento, Pirassununga, SP, Brazil
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7
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Anderson AP, Luo X, Russell W, Yin YW. Oxidative damage diminishes mitochondrial DNA polymerase replication fidelity. Nucleic Acids Res 2020; 48:817-829. [PMID: 31799610 PMCID: PMC6954441 DOI: 10.1093/nar/gkz1018] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/12/2019] [Accepted: 11/22/2019] [Indexed: 12/20/2022] Open
Abstract
Mitochondrial DNA (mtDNA) resides in a high ROS environment and suffers more mutations than its nuclear counterpart. Increasing evidence suggests that mtDNA mutations are not the results of direct oxidative damage, rather are caused, at least in part, by DNA replication errors. To understand how the mtDNA replicase, Pol γ, can give rise to elevated mutations, we studied the effect of oxidation of Pol γ on replication errors. Pol γ is a high fidelity polymerase with polymerase (pol) and proofreading exonuclease (exo) activities. We show that Pol γ exo domain is far more sensitive to oxidation than pol; under oxidative conditions, exonuclease activity therefore declines more rapidly than polymerase. The oxidized Pol γ becomes editing-deficient, displaying a 20-fold elevated mutations than the unoxidized enzyme. Mass spectrometry analysis reveals that Pol γ exo domain is a hotspot for oxidation. The oxidized exo residues increase the net negative charge around the active site that should reduce the affinity to mismatched primer/template DNA. Our results suggest that the oxidative stress induced high mutation frequency on mtDNA can be indirectly caused by oxidation of the mitochondrial replicase.
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Affiliation(s)
- Andrew P Anderson
- Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Xuemei Luo
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - William Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Y Whitney Yin
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77550, USA
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8
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Matkarimov BT, Saparbaev MK. DNA Repair and Mutagenesis in Vertebrate Mitochondria: Evidence for Asymmetric DNA Strand Inheritance. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1241:77-100. [DOI: 10.1007/978-3-030-41283-8_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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9
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Billard P, Poncet DA. Replication Stress at Telomeric and Mitochondrial DNA: Common Origins and Consequences on Ageing. Int J Mol Sci 2019; 20:ijms20194959. [PMID: 31597307 PMCID: PMC6801922 DOI: 10.3390/ijms20194959] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/04/2019] [Accepted: 10/05/2019] [Indexed: 12/12/2022] Open
Abstract
Senescence is defined as a stress-induced durable cell cycle arrest. We herein revisit the origin of two of these stresses, namely mitochondrial metabolic compromise, associated with reactive oxygen species (ROS) production, and replicative senescence, activated by extreme telomere shortening. We discuss how replication stress-induced DNA damage of telomeric DNA (telDNA) and mitochondrial DNA (mtDNA) can be considered a common origin of senescence in vitro, with consequences on ageing in vivo. Unexpectedly, mtDNA and telDNA share common features indicative of a high degree of replicative stress, such as G-quadruplexes, D-loops, RNA:DNA heteroduplexes, epigenetic marks, or supercoiling. To avoid these stresses, both compartments use similar enzymatic strategies involving, for instance, endonucleases, topoisomerases, helicases, or primases. Surprisingly, many of these replication helpers are active at both telDNA and mtDNA (e.g., RNAse H1, FEN1, DNA2, RecQ helicases, Top2α, Top2β, TOP3A, DNMT1/3a/3b, SIRT1). In addition, specialized telomeric proteins, such as TERT (telomerase reverse transcriptase) and TERC (telomerase RNA component), or TIN2 (shelterin complex), shuttle from telomeres to mitochondria, and, by doing so, modulate mitochondrial metabolism and the production of ROS, in a feedback manner. Hence, mitochondria and telomeres use common weapons and cooperate to resist/prevent replication stresses, otherwise producing common consequences, namely senescence and ageing.
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Affiliation(s)
- Pauline Billard
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, 69008 Lyon, France.
- Institut de Biopathologie moléculaire, Centre de Bio-Pathologie Est, Groupement hospitalier Est, Hospices Civils de Lyon, 69500 Bron, France.
| | - Delphine A Poncet
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, 69008 Lyon, France.
- Institut de Biopathologie moléculaire, Centre de Bio-Pathologie Est, Groupement hospitalier Est, Hospices Civils de Lyon, 69500 Bron, France.
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Zuo L, Prather ER, Stetskiv M, Garrison DE, Meade JR, Peace TI, Zhou T. Inflammaging and Oxidative Stress in Human Diseases: From Molecular Mechanisms to Novel Treatments. Int J Mol Sci 2019; 20:E4472. [PMID: 31510091 PMCID: PMC6769561 DOI: 10.3390/ijms20184472] [Citation(s) in RCA: 256] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 09/04/2019] [Indexed: 02/06/2023] Open
Abstract
It has been proposed that a chronic state of inflammation correlated with aging known as inflammaging, is implicated in multiple disease states commonly observed in the elderly population. Inflammaging is associated with over-abundance of reactive oxygen species in the cell, which can lead to oxidation and damage of cellular components, increased inflammation, and activation of cell death pathways. This review focuses on inflammaging and its contribution to various age-related diseases such as cardiovascular disease, cancer, neurodegenerative diseases, chronic obstructive pulmonary disease, diabetes, and rheumatoid arthritis. Recently published mechanistic details of the roles of reactive oxygen species in inflammaging and various diseases will also be discussed. Advancements in potential treatments to ameliorate inflammaging, oxidative stress, and consequently, reduce the morbidity of multiple disease states will be explored.
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Affiliation(s)
- Li Zuo
- College of Arts and Sciences, University of Maine Presque Isle Campus, Presque Isle, ME 04769, USA.
- Radiologic Sciences and Respiratory Therapy Division, School of Health and Rehabilitation Sciences, The Ohio State University College of Medicine, Columbus, OH 43210, USA.
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA.
| | - Evan R Prather
- Radiologic Sciences and Respiratory Therapy Division, School of Health and Rehabilitation Sciences, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Mykola Stetskiv
- Radiologic Sciences and Respiratory Therapy Division, School of Health and Rehabilitation Sciences, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Davis E Garrison
- Radiologic Sciences and Respiratory Therapy Division, School of Health and Rehabilitation Sciences, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - James R Meade
- Radiologic Sciences and Respiratory Therapy Division, School of Health and Rehabilitation Sciences, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Timotheus I Peace
- College of Arts and Sciences, University of Maine Presque Isle Campus, Presque Isle, ME 04769, USA
| | - Tingyang Zhou
- Radiologic Sciences and Respiratory Therapy Division, School of Health and Rehabilitation Sciences, The Ohio State University College of Medicine, Columbus, OH 43210, USA
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
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11
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Mitochondria in the signaling pathways that control longevity and health span. Ageing Res Rev 2019; 54:100940. [PMID: 31415807 PMCID: PMC7479635 DOI: 10.1016/j.arr.2019.100940] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/09/2019] [Accepted: 08/06/2019] [Indexed: 12/26/2022]
Abstract
Genetic and pharmacological intervention studies have identified evolutionarily conserved and functionally interconnected networks of cellular energy homeostasis, nutrient-sensing, and genome damage response signaling pathways, as prominent regulators of longevity and health span in various species. Mitochondria are the primary sites of ATP production and are key players in several other important cellular processes. Mitochondrial dysfunction diminishes tissue and organ functional performance and is a commonly considered feature of the aging process. Here we review the evidence that through reciprocal and multilevel functional interactions, mitochondria are implicated in the lifespan modulation function of these pathways, which altogether constitute a highly dynamic and complex system that controls the aging process. An important characteristic of these pathways is their extensive crosstalk and apparent malleability to modification by non-invasive pharmacological, dietary, and lifestyle interventions, with promising effects on lifespan and health span in animal models and potentially also in humans.
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12
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Kauppila JHK, Bonekamp NA, Mourier A, Isokallio MA, Just A, Kauppila TES, Stewart JB, Larsson NG. Base-excision repair deficiency alone or combined with increased oxidative stress does not increase mtDNA point mutations in mice. Nucleic Acids Res 2019; 46:6642-6669. [PMID: 29860357 PMCID: PMC6061787 DOI: 10.1093/nar/gky456] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 05/11/2018] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial DNA (mtDNA) mutations become more prevalent with age and are postulated to contribute to the ageing process. Point mutations of mtDNA have been suggested to originate from two main sources, i.e. replicative errors and oxidative damage, but the contribution of each of these processes is much discussed. To elucidate the origin of mtDNA mutations, we measured point mutation load in mice with deficient mitochondrial base-excision repair (BER) caused by knockout alleles preventing mitochondrial import of the DNA repair glycosylases OGG1 and MUTYH (Ogg1 dMTS, Mutyh dMTS). Surprisingly, we detected no increase in the mtDNA mutation load in old Ogg1 dMTS mice. As DNA repair is especially important in the germ line, we bred the BER deficient mice for five consecutive generations but found no increase in the mtDNA mutation load in these maternal lineages. To increase reactive oxygen species (ROS) levels and oxidative damage, we bred the Ogg1 dMTS mice with tissue specific Sod2 knockout mice. Although increased superoxide levels caused a plethora of changes in mitochondrial function, we did not detect any changes in the mutation load of mtDNA or mtRNA. Our results show that the importance of oxidative damage as a contributor of mtDNA mutations should be re-evaluated.
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Affiliation(s)
- Johanna H K Kauppila
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Nina A Bonekamp
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Arnaud Mourier
- Université de Bordeaux and the Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires UMR 5095, Saint-Saëns, Bordeaux, France
| | - Marita A Isokallio
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Alexandra Just
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Timo E S Kauppila
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - James B Stewart
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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13
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Lia D, Reyes A, de Melo Campos JTA, Piolot T, Baijer J, Radicella JP, Campalans A. Mitochondrial maintenance under oxidative stress depends on mitochondrially localised α-OGG1. J Cell Sci 2018; 131:jcs.213538. [PMID: 29848661 DOI: 10.1242/jcs.213538] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/21/2018] [Indexed: 12/18/2022] Open
Abstract
Accumulation of 8-oxoguanine (8-oxoG) in mitochondrial DNA and mitochondrial dysfunction have been observed in cells deficient for the DNA glycosylase OGG1 when exposed to oxidative stress. In human cells, up to eight mRNAs for OGG1 can be generated by alternative splicing and it is still unclear which of them codes for the protein that ensures the repair of 8-oxoG in mitochondria. Here, we show that the α-OGG1 isoform, considered up to now to be exclusively nuclear, has a functional mitochondrial-targeting sequence and is imported into mitochondria. We analyse the sub-mitochondrial localisation of α-OGG1 with unprecedented resolution and show that this DNA glycosylase is associated with DNA in mitochondrial nucleoids. We show that the presence of α-OGG1 inside mitochondria and its enzymatic activity are required to preserve the mitochondrial network in cells exposed to oxidative stress. Altogether, these results unveil a new role of α-OGG1 in the mitochondria and indicate that the same isoform ensures the repair of 8-oxoG in both nuclear and mitochondrial genomes. The activity of α-OGG1 in mitochondria is sufficient for the recovery of organelle function after oxidative stress.
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Affiliation(s)
- Debora Lia
- Institut de Biologie François Jacob (IBFJ), Institute of Cellular and Molecular Radiobiology, CEA, UMR967 INSERM, 96265 Fontenay aux Roses, France.,Université Paris Diderot/Université Paris-Sud, 96265 Fontenay aux Roses, France
| | - Aurelio Reyes
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Julliane Tamara Araújo de Melo Campos
- Institut de Biologie François Jacob (IBFJ), Institute of Cellular and Molecular Radiobiology, CEA, UMR967 INSERM, 96265 Fontenay aux Roses, France.,Laboratório de Biologia Molecular e Genômica, Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN 59072-970, Brazil
| | - Tristan Piolot
- Institut Curie, CNRS UMR3215, INSERM U934, 75248 Paris, France
| | - Jan Baijer
- Institut de Biologie François Jacob (IBFJ), Institute of Cellular and Molecular Radiobiology, CEA, UMR967 INSERM, 96265 Fontenay aux Roses, France.,Université Paris Diderot/Université Paris-Sud, 96265 Fontenay aux Roses, France
| | - J Pablo Radicella
- Institut de Biologie François Jacob (IBFJ), Institute of Cellular and Molecular Radiobiology, CEA, UMR967 INSERM, 96265 Fontenay aux Roses, France.,Université Paris Diderot/Université Paris-Sud, 96265 Fontenay aux Roses, France
| | - Anna Campalans
- Institut de Biologie François Jacob (IBFJ), Institute of Cellular and Molecular Radiobiology, CEA, UMR967 INSERM, 96265 Fontenay aux Roses, France .,Université Paris Diderot/Université Paris-Sud, 96265 Fontenay aux Roses, France
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14
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Scheffler K, Rachek L, You P, Rowe AD, Wang W, Kuśnierczyk A, Kittelsen L, Bjørås M, Eide L. 8-oxoguanine DNA glycosylase (Ogg1) controls hepatic gluconeogenesis. DNA Repair (Amst) 2017; 61:56-62. [PMID: 29207315 DOI: 10.1016/j.dnarep.2017.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/25/2022]
Abstract
Mitochondrial DNA (mtDNA) resides in close proximity to metabolic reactions, and is maintained by the 8-oxoguanine DNA glycosylase (Ogg1) and other members of the base excision repair pathway. Here, we tested the hypothesis that changes in liver metabolism as under fasting/feeding conditions would be sensed by liver mtDNA, and that Ogg1 deficient mice might unravel a metabolic phenotype. Wild type (WT) and ogg1-/- mice were either fed ad libitum or subjected to fasting for 24h, and the corresponding effects on liver gene expression, DNA damage, as well as serum values were analyzed. Ogg1 deficient mice fed ad libitum exhibited hyperglycemia, elevated insulin levels and higher liver glycogen content as well as increased accumulation of 8oxoG in mtDNA compared to age- and gender matched WT mice. Interestingly, these phenotypes were absent in ogg1-/- mice during fasting. Gene expression and functional analyses suggest that the diabetogenic phenotype in the ogg1-/- mice is due to a failure to suppress gluconeogensis in the fed state. The ogg1-/- mice exhibited reduced mitochondrial electron transport chain (ETC) capacity and a combined low activity of the pyruvate dehydrogenase (PDH), alluding to inefficient channeling of glycolytic products into the citric acid cycle. Our data demonstrate a physiological role of base excision repair that goes beyond DNA maintenance, and implies that DNA repair is involved in regulating metabolism.
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Affiliation(s)
- Katja Scheffler
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway; Department of Microbiology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Lyudmila Rachek
- University of South Alabama, Mobile, AL, United States of America
| | - Panpan You
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway
| | - Alexander D Rowe
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway; Department of Newborn Screening, Oslo University Hospital, Norway
| | - Wei Wang
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway; Department of Microbiology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Anna Kuśnierczyk
- Proteomics and Metabolomics Core Facility, PROMEC, Department of Cancer research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Lene Kittelsen
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway
| | - Magnar Bjørås
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway; Department of Microbiology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Lars Eide
- Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, Norway.
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15
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Pawar T, Bjørås M, Klungland A, Eide L. Metabolism and DNA repair shape a specific modification pattern in mitochondrial DNA. Mitochondrion 2017; 40:16-28. [PMID: 28893634 DOI: 10.1016/j.mito.2017.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/29/2017] [Accepted: 09/05/2017] [Indexed: 11/28/2022]
Abstract
The mitochondrial DNA (mtDNA) resides in the vicinity of energy-rich reactions. Thus, chemical modifications of mtDNA might mirror mitochondrial processes and could serve as biomarkers of metabolic processes in the mitochondria. This hypothesis was tested by assessing modifications at 17 different sites in the mtDNA as a function of cell type, oxidative stress and mitochondrial activity. Two mouse mutants with a metabolic phenotype were compared to wild-type (WT) mice: the ogg1-/- mouse that lacks the 8-oxoguanine DNA glycosylase (OGG1), and the alkbh7-/- mouse missing the ALKBH7 protein that has been implicated in fatty acid oxidation. It was found that cell type, oxidative stress and mitochondrial complex activity shaped distinct modification patterns in mtDNA, and that OGG1 and ALKBH7 independently modulated these modification patterns. The modifications included ribonucleotides, which also accumulated in mtDNA with age. Interestingly, this age-dependent accumulation most likely involves DNA repair, as mtDNA from ogg1-/- mice did not accumulate modifications with age. On the other hand, alkbh7-/- mtDNA accumulated more modifications with age than WT mtDNA. Our results show that mtDNA is dynamically modified with metabolic activity and imply a novel synergy between metabolism and mtDNA repair proteins.
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Affiliation(s)
- Tina Pawar
- Department of Medical Biochemistry, University of Oslo, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, University of Oslo, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway; Department of clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Arne Klungland
- Department of Microbiology, University of Oslo, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway
| | - Lars Eide
- Department of Medical Biochemistry, University of Oslo, Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway.
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16
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D'Errico M, Parlanti E, Pascucci B, Fortini P, Baccarini S, Simonelli V, Dogliotti E. Single nucleotide polymorphisms in DNA glycosylases: From function to disease. Free Radic Biol Med 2017; 107:278-291. [PMID: 27932076 DOI: 10.1016/j.freeradbiomed.2016.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/25/2016] [Accepted: 12/02/2016] [Indexed: 02/08/2023]
Abstract
Oxidative stress is associated with a growing number of diseases that span from cancer to neurodegeneration. Most oxidatively induced DNA base lesions are repaired by the base excision repair (BER) pathway which involves the action of various DNA glycosylases. There are numerous genome wide studies attempting to associate single-nucleotide polymorphisms (SNPs) with predispositions to various types of disease; often, these common variants do not have significant alterations in their biochemical function and do not exhibit a convincing phenotype. Nevertheless several lines of evidence indicate that SNPs in DNA repair genes may modulate DNA repair capacity and contribute to risk of disease. This overview provides a convincing picture that SNPs of DNA glycosylases that remove oxidatively generated DNA lesions are susceptibility factors for a wide disease spectrum that includes besides cancer (particularly lung, breast and gastrointestinal tract), cochlear/ocular disorders, myocardial infarction and neurodegenerative disorders which can be all grouped under the umbrella of oxidative stress-related pathologies.
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Affiliation(s)
- Mariarosaria D'Errico
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
| | - Eleonora Parlanti
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Barbara Pascucci
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via Salaria, Km 29,300, 00016 Monterotondo Stazione, Rome, Italy
| | - Paola Fortini
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Sara Baccarini
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Valeria Simonelli
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Eugenia Dogliotti
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
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17
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Boiteux S, Coste F, Castaing B. Repair of 8-oxo-7,8-dihydroguanine in prokaryotic and eukaryotic cells: Properties and biological roles of the Fpg and OGG1 DNA N-glycosylases. Free Radic Biol Med 2017; 107:179-201. [PMID: 27903453 DOI: 10.1016/j.freeradbiomed.2016.11.042] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 11/22/2016] [Accepted: 11/25/2016] [Indexed: 01/23/2023]
Abstract
Oxidatively damaged DNA results from the attack of sugar and base moieties by reactive oxygen species (ROS), which are formed as byproducts of normal cell metabolism and during exposure to endogenous or exogenous chemical or physical agents. Guanine, having the lowest redox potential, is the DNA base the most susceptible to oxidation, yielding products such as 8-oxo-7,8-dihydroguanine (8-oxoG) and 2-6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG). In DNA, 8-oxoG was shown to be mutagenic yielding GC to TA transversions upon incorporation of dAMP opposite this lesion by replicative DNA polymerases. In prokaryotic and eukaryotic cells, 8-oxoG is primarily repaired by the base excision repair pathway (BER) initiated by a DNA N-glycosylase, Fpg and OGG1, respectively. In Escherichia coli, Fpg cooperates with MutY and MutT to prevent 8-oxoG-induced mutations, the "GO-repair system". In Saccharomyces cerevisiae, OGG1 cooperates with nucleotide excision repair (NER), mismatch repair (MMR), post-replication repair (PRR) and DNA polymerase η to prevent mutagenesis. Human and mouse cells mobilize all these pathways using OGG1, MUTYH (MutY-homolog also known as MYH), MTH1 (MutT-homolog also known as NUDT1), NER, MMR, NEILs and DNA polymerases η and λ, to prevent 8-oxoG-induced mutations. In fact, mice deficient in both OGG1 and MUTYH develop cancer in different organs at adult age, which points to the critical impact of 8-oxoG repair on genetic stability in mammals. In this review, we will focus on Fpg and OGG1 proteins, their biochemical and structural properties as well as their biological roles. Other DNA N-glycosylases able to release 8-oxoG from damaged DNA in various organisms will be discussed. Finally, we will report on the role of OGG1 in human disease and the possible use of 8-oxoG DNA N-glycosylases as therapeutic targets.
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Affiliation(s)
- Serge Boiteux
- Centre de Biophysique Moléculaire, CNRS, UPR4301, rue Charles Sadron, 45072 Orléans, France.
| | - Franck Coste
- Centre de Biophysique Moléculaire, CNRS, UPR4301, rue Charles Sadron, 45072 Orléans, France
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire, CNRS, UPR4301, rue Charles Sadron, 45072 Orléans, France.
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18
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Abstract
Mitochondria were first postulated to contribute to aging more than 40 years ago. During the following decades, multiple lines of evidence in model organisms and humans showed that impaired mitochondrial function can contribute to age-associated disease phenotypes and aging. However, in contrast to the original theory favoring oxidative damage as a cause for mtDNA mutations, there are now strong data arguing that most mammalian mtDNA mutations originate as replication errors made by the mtDNA polymerase. Currently, a substantial amount of mitochondrial research is focused on finding ways to either remove or counteract the effects of mtDNA mutations with the hope of extending the human health- and lifespan. This review summarizes the current knowledge regarding the formation of mtDNA mutations and their impact on mitochondrial function. We also critically discuss proposed pathways interlinked with mammalian mtDNA mutations and suggest future research strategies to elucidate the role of mtDNA mutations in aging.
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Affiliation(s)
- Timo E S Kauppila
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, D-50931 Cologne, Germany
| | - Johanna H K Kauppila
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, D-50931 Cologne, Germany
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, D-50931 Cologne, Germany; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden.
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19
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DeBalsi KL, Hoff KE, Copeland WC. Role of the mitochondrial DNA replication machinery in mitochondrial DNA mutagenesis, aging and age-related diseases. Ageing Res Rev 2017; 33:89-104. [PMID: 27143693 DOI: 10.1016/j.arr.2016.04.006] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/19/2016] [Accepted: 04/19/2016] [Indexed: 12/19/2022]
Abstract
As regulators of bioenergetics in the cell and the primary source of endogenous reactive oxygen species (ROS), dysfunctional mitochondria have been implicated for decades in the process of aging and age-related diseases. Mitochondrial DNA (mtDNA) is replicated and repaired by nuclear-encoded mtDNA polymerase γ (Pol γ) and several other associated proteins, which compose the mtDNA replication machinery. Here, we review evidence that errors caused by this replication machinery and failure to repair these mtDNA errors results in mtDNA mutations. Clonal expansion of mtDNA mutations results in mitochondrial dysfunction, such as decreased electron transport chain (ETC) enzyme activity and impaired cellular respiration. We address the literature that mitochondrial dysfunction, in conjunction with altered mitochondrial dynamics, is a major driving force behind aging and age-related diseases. Additionally, interventions to improve mitochondrial function and attenuate the symptoms of aging are examined.
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Affiliation(s)
- Karen L DeBalsi
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Kirsten E Hoff
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
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20
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Abstract
5-Methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are fingerprints of epigenetic modifications. These bases have been found in the mitochondrial DNA (mtDNA) and together with the discovery of mitochondrial localization of DNA methyltransferases, this implies that mtDNA is under epigenetic regulation. However, the indirect methods hitherto used to assess mitochondrial 5mC and 5hmC require attention as they readily generate artificial signals that may lead to erroneous conclusions. Here, we demonstrate how three independent, frequently used methods to identify epigenetic modification of DNA readily generate false mtDNA epigenetic signals. The three methods were selective 5mC/5hmC-mediated inhibition of restriction enzymes, bisulfite conversion and 5hmC glucosylation-dependent immunocapture. Adequate controls for all methods are suggested.
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Affiliation(s)
- Tina Pawar
- a Department of Medical Biochemistry , Institute of Clinical Medicine, University of Oslo , Oslo , Norway
| | - Lars Eide
- a Department of Medical Biochemistry , Institute of Clinical Medicine, University of Oslo , Oslo , Norway
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21
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Distante S, Eikeland J, Pawar T, Skinnes R, Høie K, You P, Mørkrid L, Eide L. Blood removal therapy in hereditary hemochromatosis induces a stress response resulting in improved genome integrity. Transfusion 2016; 56:1435-41. [PMID: 27045387 DOI: 10.1111/trf.13588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 02/05/2016] [Accepted: 02/05/2016] [Indexed: 01/12/2023]
Abstract
BACKGROUND Hereditary hemochromatosis (HH) is a common disease of iron metabolism, manifesting with iron overload and affecting up to 1% of individuals of northern European descent. Untreated HH can result in irreversible damage of the liver and pancreas, potentially leading to cancer and diabetes. Therapy consists of normalizing iron stores by repeated blood donations (phlebotomy). Treated HH patients have normal survival rates and report less tiredness after phlebotomy; however, it is not understood why musculoskeletal symptoms may persist in spite of iron removal. We hypothesize that phlebotomy therapy does not simply reverse iron accumulation but has additional effects at the subcellular level. In particular, the systemic impact of phlebotomy on mitochondria and genome integrity is largely unknown. STUDY DESIGN AND METHODS The effects of phlebotomy therapy on mitochondrial iron proteins and genome integrity were investigated in peripheral blood mononuclear blood cells from HH patients. RESULTS After the reduction of systemic iron load in these patients with phlebotomy, we observed increased expression of mitochondrial superoxide dismutase, reduced iron sulfur assembly protein (Iscu1/2), and improved genome integrity. CONCLUSION We conclude that phlebotomy therapy in HH does not merely restore systemic iron homeostasis, but induces an "oxidative stress" defense response that manifests as improved genome integrity. These findings provide novel insights into an ancient therapy.
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Affiliation(s)
- Sonia Distante
- Department of Medical Biochemistry, Oslo University Hospital
| | - Joakim Eikeland
- Department of Medical Biochemistry, Oslo University Hospital
| | - Tina Pawar
- Department of Medical Biochemistry, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ragnhild Skinnes
- Department of Medical Biochemistry, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kari Høie
- Department of Medical Biochemistry, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Panpan You
- Department of Medical Biochemistry, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Lars Mørkrid
- Department of Medical Biochemistry, Oslo University Hospital.,Department of Medical Biochemistry, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Lars Eide
- Department of Medical Biochemistry, Oslo University Hospital.,Department of Medical Biochemistry, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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22
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Guo W, Zheng B, Guo D, Cai Z, Wang Y. Association of AluYb8 insertion/deletion polymorphism in the MUTYH gene with mtDNA maintain in the type 2 diabetes mellitus patients. Mol Cell Endocrinol 2015; 409:33-40. [PMID: 25829257 DOI: 10.1016/j.mce.2015.03.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/16/2015] [Accepted: 03/23/2015] [Indexed: 12/15/2022]
Abstract
A common AluYb8-element insertion/deletion polymorphism of the MUTYH gene (AluYb8MUTYH) is a novel genetic risk factor for type 2 diabetes mellitus (T2DM). In the present study, mtDNA sequencing analysis indicated that the mtDNA sequence heteroplasmy was not associated with AluYb8MUTYH polymorphism. To better understand the genetic risk for T2DM, we investigated the association of this polymorphism with mtDNA content, mtDNA breakage and mtDNA transcription in the leukocytes of T2DM patients. The mtDNA content and unbroken mtDNA were significantly increased in the mutant patients than in the wild-type patients (P <0.05, respectively). However, no association between mtDNA transcription and AluYb8MUTYH variant was observed. The results suggested that the AluYb8MUTYH variant was associated with an altered mtDNA maintain in T2DM patients. The high level of mtDNA content observed in the mutant patients may have resulted from inefficient base excision repair of mitochondrial MUTYH and a compensatory mechanism that is triggered by elevated oxidative stress.
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Affiliation(s)
- Wenwen Guo
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, No.22 HanKou Road, Nanjing 210093, China; Department of Medical Genetics, Nanjing University School of Medicine, No.22 HanKou Road, Nanjing 210093, China; Clinical Molecular Diagnostic Center, Second Hospital, Nanjing Medical University, No.121 Jiangjiayuan Road, Nanjing 210011, China
| | - Bixia Zheng
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, No.22 HanKou Road, Nanjing 210093, China; Department of Medical Genetics, Nanjing University School of Medicine, No.22 HanKou Road, Nanjing 210093, China
| | - Dong Guo
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, No.22 HanKou Road, Nanjing 210093, China; Department of Medical Genetics, Nanjing University School of Medicine, No.22 HanKou Road, Nanjing 210093, China
| | - Zhenming Cai
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, No.22 HanKou Road, Nanjing 210093, China; Department of Medical Genetics, Nanjing University School of Medicine, No.22 HanKou Road, Nanjing 210093, China
| | - Yaping Wang
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, No.22 HanKou Road, Nanjing 210093, China; Department of Medical Genetics, Nanjing University School of Medicine, No.22 HanKou Road, Nanjing 210093, China.
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23
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Errichiello E, Balsamo A, Cerni M, Venesio T. Mitochondrial variants in MT-CO2 and D-loop instability are involved in MUTYH-associated polyposis. J Mol Med (Berl) 2015; 93:1271-81. [PMID: 26138249 DOI: 10.1007/s00109-015-1312-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 05/28/2015] [Accepted: 06/16/2015] [Indexed: 12/21/2022]
Abstract
UNLABELLED Mitochondrial DNA alterations have been widely reported in different human tumours, including colorectal carcinoma, but their mutational spectrum and pathogenic role in specific subsets of patients with polyposis syndromes have been poorly investigated. We compared the breadth of somatic variants across the mitochondrial genome of MUTYH-associated polyposis (MAP) patients with homogeneous groups of classical/attenuated familial adenomatous polyposis (FAP/AFAP) and sporadic cases. Overall, we screened 121 adenomas and seven adenocarcinomas and their corresponding germinal controls, for mitochondrial genes with a crucial role in oxidative phosphorylation and translation (MT-CO1, MT-CO2, MT-CO3, MT-TD, MT-TS1, MT-ATP6) as well as a hypervariable sequence (HV-II) within the control region displacement loop (D-loop), a marker of hypermutability and clonal expansion. The sequencing analysis revealed the presence of 17 variants, mostly causing non-synonymous changes in conserved amino acid residues, typically distributed in the MT-CO2 gene of MAP patients (P < 0.0001), who frequently carried the hot spot m.7763G>A variant. Accordingly, D-loop instability was also significantly associated with variants grouped inside the MT-CO2 gene (P = 0.0061). This is the first report showing a locus-specific distribution of mitochondrial DNA alterations in a subtype of colorectal tumourigenesis. In addition, our findings suggest that MT-CO2 variants, representing early molecular events in MAP tumorigenesis, might be a potential prognostic biomarker for the cancer-risk assessment of patients affected by this syndrome. KEY MESSAGES We compared the frequencies of mtDNA variants in MAP vs. FAP/AFAP/sporadic patients. We found a gene-specific (MT-CO2) distribution of mtDNA variants in MAP cases. Most mtDNA variants caused non-synonymous changes in conserved amino acid residues. D-loop instability was significantly associated with variants grouped inside MT-CO2. MT-CO2 variants might be a potential prognostic biomarker in MAP patients.
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Affiliation(s)
- Edoardo Errichiello
- Molecular Pathology Laboratory, Unit of Pathology, Institute for Cancer Research and Treatment, FPO-IRCCS, Strada Provinciale 142, 10060, Candiolo, Torino, Italy
| | - Antonella Balsamo
- Molecular Pathology Laboratory, Unit of Pathology, Institute for Cancer Research and Treatment, FPO-IRCCS, Strada Provinciale 142, 10060, Candiolo, Torino, Italy
| | - Marianna Cerni
- Molecular Pathology Laboratory, Unit of Pathology, Institute for Cancer Research and Treatment, FPO-IRCCS, Strada Provinciale 142, 10060, Candiolo, Torino, Italy
| | - Tiziana Venesio
- Molecular Pathology Laboratory, Unit of Pathology, Institute for Cancer Research and Treatment, FPO-IRCCS, Strada Provinciale 142, 10060, Candiolo, Torino, Italy.
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24
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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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25
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Abstract
This chapter describes the use of real-time qPCR to analyze the integrity of mitochondrial nucleic acids quantitatively. The method has low material requirement, is low cost, and can detect modifications with high resolution. The method is specifically designed for mitochondrial RNA and DNA, but can be easily transferred to other high-copy number cases. This procedure describes analyses of brain nucleic acids, but other tissues or cells can be analyzed similarly.
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Sampath H. Oxidative DNA damage in disease--insights gained from base excision repair glycosylase-deficient mouse models. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2014; 55:689-703. [PMID: 25044514 DOI: 10.1002/em.21886] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 06/24/2014] [Indexed: 05/10/2023]
Abstract
Cellular components, including nucleic acids, are subject to oxidative damage. If left unrepaired, this damage can lead to multiple adverse cellular outcomes, including increased mutagenesis and cell death. The major pathway for repair of oxidative base lesions is the base excision repair pathway, catalyzed by DNA glycosylases with overlapping but distinct substrate specificities. To understand the role of these glycosylases in the initiation and progression of disease, several transgenic mouse models have been generated to carry a targeted deletion or overexpression of one or more glycosylases. This review summarizes some of the major findings from transgenic animal models of altered DNA glycosylase expression, especially as they relate to pathologies ranging from metabolic disease and cancer to inflammation and neuronal health.
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Affiliation(s)
- Harini Sampath
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon
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Wanagat J, Ahmadieh N, Bielas JH, Ericson NG, Van Remmen H. Skeletal muscle mitochondrial DNA deletions are not increased in CuZn-superoxide dismutase deficient mice. Exp Gerontol 2014; 61:15-9. [PMID: 25449857 DOI: 10.1016/j.exger.2014.11.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 11/13/2014] [Accepted: 11/18/2014] [Indexed: 11/25/2022]
Abstract
Mitochondrial DNA (mtDNA) deletion mutations are proposed contributors to aging-related muscle fiber loss and atrophy, but evidence of a causal role for these mutations in muscle aging is lacking. Elucidating the etiology of in vivo mtDNA deletion mutations will help to better understand and test the possible roles of these mutations in aging. The implication of mtDNA mutations in aging is based on the susceptibility of mtDNA to oxidative damage by reactive oxygen species (ROS) due to residing in mitochondria, the primary source of endogenous ROS. Cells possess many pathways for neutralizing ROSs, including a variety of superoxide dismutases (SOD). Mice lacking CuZnSOD (Sod1(-/-) mice) have high levels of oxidative damage in many tissues including skeletal muscle and are a model for testing the role of oxidative damage in the formation of mtDNA deletion mutations. The increased DNA oxidative damage in Sod1(-/-) mice is associated with increased mtDNA deletion mutations in a variety of tissues, but skeletal muscle mtDNA mutations have not been reported. We hypothesized that a life-long absence of mouse muscle CuZnSOD would increase mtDNA deletion mutation frequency and focal accumulation of these mutations in aging mouse skeletal muscle. Focal accumulations of mtDNA deletion mutations were detected by histochemical staining for cytochrome c oxidase (cytOX) activity and detection of cytOX-negative fibers, a marker of focal mtDNA mutation accumulation, within approximately 20,000 muscle fibers through a distance of 1000μm. Total DNA was extracted from intervening unstained sections and mtDNA deletion mutation frequency was measured by a droplet digital PCR. Droplet digital PCR quantification of mtDNA deletion mutations showed no difference in mtDNA deletion mutation frequency in Sod1(-/-) mouse muscle compared to wild-type mice and we observed no significant increase in the number of cytOX-negative muscle fibers, in Sod1(-/-) mice compared to wild-type mice. These data demonstrate that not all changes in cellular oxidative stress are linked to mtDNA deletion mutations and shift the focus to other etiologies for these mutations that need to be clarified to better test their possible role in aging.
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Affiliation(s)
- Jonathan Wanagat
- Department of Medicine, Division of Geriatrics, UCLA, Los Angeles, CA 90095, United States.
| | - Nazanin Ahmadieh
- Department of Medicine, Division of Geriatrics, UCLA, Los Angeles, CA 90095, United States
| | - Jason H Bielas
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, United States
| | - Nolan G Ericson
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, United States
| | - Holly Van Remmen
- Oklahoma Medical Research Foundation, Oklahoma City, OK 73012, United States
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Bliksøen M, Baysa A, Eide L, Bjørås M, Suganthan R, Vaage J, Stensløkken KO, Valen G. Mitochondrial DNA damage and repair during ischemia-reperfusion injury of the heart. J Mol Cell Cardiol 2014; 78:9-22. [PMID: 25446179 DOI: 10.1016/j.yjmcc.2014.11.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/10/2014] [Accepted: 11/11/2014] [Indexed: 11/28/2022]
Abstract
Ischemia-reperfusion (IR) injury of the heart generates reactive oxygen species that oxidize macromolecules including mitochondrial DNA (mtDNA). The 8-oxoguanine DNA glycosylase (OGG1) works synergistically with MutY DNA glycosylase (MYH) to maintain mtDNA integrity. Our objective was to study the functional outcome of lacking the repair enzymes OGG1 and MYH after myocardial IR and we hypothesized that OGG1 and MYH are important enzymes to preserve mtDNA and heart function after IR. Ex vivo global ischemia for 30min followed by 10min of reperfusion induced mtDNA damage that was removed within 60min of reperfusion in wild-type mice. After 60min of reperfusion the ogg1(-/-) mice demonstrated increased mtDNA copy number and decreased mtDNA damage removal suggesting that OGG1 is responsible for removal of IR-induced mtDNA damage and copy number regulation. mtDNA damage was not detected in the ogg1(-/-)/myh(-/-), inferring that adenine opposite 8-oxoguanine is an abundant mtDNA lesion upon IR. The level and integrity of mtDNA were restored in all genotypes after 35min of regional ischemia and six week reperfusion with no change in cardiac function. No consistent upregulation of other mitochondrial base excision repair enzymes in any of our knockout models was found. Thus repair of mtDNA oxidative base lesions may not be important for maintenance of cardiac function during IR injury in vivo. This article is part of a Special Issue entitled "Mitochondria: From Basic Mitochondrial Biology to Cardiovascular Disease."
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Affiliation(s)
- M Bliksøen
- Department of Physiology, Institute of Basic Medical Sciences, Norway; Center for Heart Failure Research, University of Oslo, Norway
| | - A Baysa
- Department of Physiology, Institute of Basic Medical Sciences, Norway; Center for Heart Failure Research, University of Oslo, Norway
| | - L Eide
- Department of Medical Biochemistry, University of Oslo, Norway
| | - M Bjørås
- Department of Microbiology, University of Oslo and Oslo University Hospital Rikshospitalet, Norway
| | - R Suganthan
- Department of Microbiology, University of Oslo and Oslo University Hospital Rikshospitalet, Norway
| | - J Vaage
- Department of Emergency Medicine and Intensive Care, University of Oslo and Oslo University Hospital, Ullevål, Oslo, Norway
| | - K O Stensløkken
- Department of Physiology, Institute of Basic Medical Sciences, Norway; Center for Heart Failure Research, University of Oslo, Norway.
| | - G Valen
- Department of Physiology, Institute of Basic Medical Sciences, Norway; Center for Heart Failure Research, University of Oslo, Norway
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Wang W, Scheffler K, Esbensen Y, Strand JM, Stewart JB, Bjørås M, Eide L. Addressing RNA integrity to determine the impact of mitochondrial DNA mutations on brain mitochondrial function with age. PLoS One 2014; 9:e96940. [PMID: 24819950 PMCID: PMC4018447 DOI: 10.1371/journal.pone.0096940] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/12/2014] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial DNA (mtDNA) mutations can result in mitochondrial dysfunction, but emerging experimental data question the fundamental role of mtDNA mutagenesis in age-associated mitochondrial impairment. The multicopy nature of mtDNA renders the impact of a given mtDNA mutation unpredictable. In this study, we compared mtDNA stability and mtRNA integrity during normal aging. Seven distinct sites in mouse brain mtDNA and corresponding mtRNA were analyzed. Accumulation of mtDNA mutations during aging was highly site-specific. The variation in mutation frequencies overrode the age-mediated increase by more than 100-fold and aging generally did not influence mtDNA mutagenesis. Errors introduced by mtRNA polymerase were also site-dependent and up to two hundred-fold more frequent than mtDNA mutations, and independent of mtDNA mutation frequency. We therefore conclude that mitochondrial transcription fidelity limits the impact of mtDNA mutations.
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Affiliation(s)
- Wei Wang
- Department of Medical Biochemistry, Oslo University Hospital, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Katja Scheffler
- Department of Medical Biochemistry, Oslo University Hospital, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Ying Esbensen
- Department of Clinical Molecular Biology and Laboratory Sciences (EpiGen), Division of Medicine, Akershus University Hospital and University of Oslo, Lørenskog, Norway
| | - Janne M. Strand
- Department of Medical Biochemistry, Oslo University Hospital, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | | | - Magnar Bjørås
- Department of Medical Biochemistry, Oslo University Hospital, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Lars Eide
- Department of Medical Biochemistry, Oslo University Hospital, University of Oslo, Oslo, Norway
- * E-mail:
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Kennedy SR, Salk JJ, Schmitt MW, Loeb LA. Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage. PLoS Genet 2013; 9:e1003794. [PMID: 24086148 PMCID: PMC3784509 DOI: 10.1371/journal.pgen.1003794] [Citation(s) in RCA: 254] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 07/29/2013] [Indexed: 01/12/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is believed to be highly vulnerable to age-associated damage and mutagenesis by reactive oxygen species (ROS). However, somatic mtDNA mutations have historically been difficult to study because of technical limitations in accurately quantifying rare mtDNA mutations. We have applied the highly sensitive Duplex Sequencing methodology, which can detect a single mutation among >107 wild type molecules, to sequence mtDNA purified from human brain tissue from both young and old individuals with unprecedented accuracy. We find that the frequency of point mutations increases ∼5-fold over the course of 80 years of life. Overall, the mutation spectra of both groups are comprised predominantly of transition mutations, consistent with misincorporation by DNA polymerase γ or deamination of cytidine and adenosine as the primary mutagenic events in mtDNA. Surprisingly, G→T mutations, considered the hallmark of oxidative damage to DNA, do not significantly increase with age. We observe a non-uniform, age-independent distribution of mutations in mtDNA, with the D-loop exhibiting a significantly higher mutation frequency than the rest of the genome. The coding regions, but not the D-loop, exhibit a pronounced asymmetric accumulation of mutations between the two strands, with G→A and T→C mutations occurring more often on the light strand than the heavy strand. The patterns and biases we observe in our data closely mirror the mutational spectrum which has been reported in studies of human populations and closely related species. Overall our results argue against oxidative damage being a major driver of aging and suggest that replication errors by DNA polymerase γ and/or spontaneous base hydrolysis are responsible for the bulk of accumulating point mutations in mtDNA. Owing to their evolutionary history, mitochondria harbor independently replicating genomes. Failure to faithfully transmit the genetic information of mtDNA during replication can lead to the production of dysfunctional electron transport proteins and a subsequent decline in energy production. Cellularly-derived reactive oxygen species (ROS) and environmental agents preferentially damage mtDNA compared to nuclear DNA. However, little is known about the consequences of mtDNA damage for mutagenesis. This lack of knowledge stems, in part, from an absence of methods capable of accurately detecting these mutations throughout the mitochondrial genome. Using a new, highly sensitive DNA sequencing strategy, we find that the frequency of point mutations is 10–100-fold lower than what has been previously reported using less precise means. Moreover, the frequency increases 5-fold over an 80 year lifespan. We also find that it is predominantly transition mutations, rather than mutations commonly associated with oxidative damage to mtDNA, that increase with age. This finding is inconsistent with free radical theories of aging. Finally, the mutagenic patterns and biases we observe in our data are similar to what is seen in population studies of mitochondrial polymorphisms and suggest a common mechanism by which somatic and germline mtDNA mutations arise.
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Affiliation(s)
- Scott R. Kennedy
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Jesse J. Salk
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Michael W. Schmitt
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Lawrence A. Loeb
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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Khobta A, Epe B. Repair of oxidatively generated DNA damage in Cockayne syndrome. Mech Ageing Dev 2013; 134:253-60. [PMID: 23518175 DOI: 10.1016/j.mad.2013.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 02/12/2013] [Accepted: 03/01/2013] [Indexed: 11/16/2022]
Abstract
Defects in the repair of endogenously (especially oxidatively) generated DNA modifications and the resulting genetic instability can potentially explain the clinical symptoms of Cockayne syndrome (CS), a hereditary disease characterized by developmental defects and neurological degeneration. In this review, we describe the evidence for the involvement of CSA and CSB proteins, which are mutated in most of the CS patients, in the repair and processing of DNA damage induced by reactive oxygen species and the implications for the induction of cell death and mutations. Taken together, the data demonstrate that CSA and CSB, in addition to their established role in transcription-coupled nucleotide excision repair, can modulate the base excision repair (BER) of oxidized DNA bases both directly (by interaction with BER proteins) and indirectly (by modulating the expression of the DNA repair genes). Both nuclear and mitochondrial DNA repair is affected by mutations in CSA and CSB genes. However, the observed retardations of repair and the resulting accumulation of unrepaired endogenously generated DNA lesions are often mild, thus pointing to the relevance of additional roles of the CS proteins, e.g. in the mitochondrial response to oxidatively generated DNA damage and in the maintenance of gene transcription.
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Affiliation(s)
- Andriy Khobta
- Institute of Pharmacy and Biochemistry, University of Mainz, Staudingerweg 5, D-55099 Mainz, Germany.
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