1
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Boone C, Lewis SC. Bridging lipid metabolism and mitochondrial genome maintenance. J Biol Chem 2024; 300:107498. [PMID: 38944117 PMCID: PMC11326895 DOI: 10.1016/j.jbc.2024.107498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 06/19/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
Mitochondria are the nexus of cellular energy metabolism and major signaling hubs that integrate information from within and without the cell to implement cell function. Mitochondria harbor a distinct polyploid genome, mitochondrial DNA (mtDNA), that encodes respiratory chain components required for energy production. MtDNA mutation and depletion have been linked to obesity and metabolic syndrome in humans. At the cellular and subcellular levels, mtDNA synthesis is coordinated by membrane contact sites implicated in lipid transfer from the endoplasmic reticulum, tying genome maintenance to lipid storage and homeostasis. Here, we examine the relationship between mtDNA and lipid trafficking, the influence of lipotoxicity on mtDNA integrity, and how lipid metabolism may be disrupted in primary mtDNA disease.
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Affiliation(s)
- Casadora Boone
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California, USA
| | - Samantha C Lewis
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California, USA; Department of Molecular and Cell Biology, University of California, Berkeley, California, USA.
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2
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Cabané P, Correa C, Bode I, Aguilar R, Elorza AA. Biomarkers in Thyroid Cancer: Emerging Opportunities from Non-Coding RNAs and Mitochondrial Space. Int J Mol Sci 2024; 25:6719. [PMID: 38928426 PMCID: PMC11204084 DOI: 10.3390/ijms25126719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 06/01/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Thyroid cancer diagnosis primarily relies on imaging techniques and cytological analyses. In cases where the diagnosis is uncertain, the quantification of molecular markers has been incorporated after cytological examination. This approach helps physicians to make surgical decisions, estimate cancer aggressiveness, and monitor the response to treatments. Despite the availability of commercial molecular tests, their widespread use has been hindered in our experience due to cost constraints and variability between them. Thus, numerous groups are currently evaluating new molecular markers that ultimately will lead to improved diagnostic certainty, as well as better classification of prognosis and recurrence. In this review, we start reviewing the current preoperative testing methodologies, followed by a comprehensive review of emerging molecular markers. We focus on micro RNAs, long non-coding RNAs, and mitochondrial (mt) signatures, including mtDNA genes and circulating cell-free mtDNA. We envision that a robust set of molecular markers will complement the national and international clinical guides for proper assessment of the disease.
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Affiliation(s)
- Patricio Cabané
- Department of Head and Neck Surgery, Clinica INDISA, Santiago 7520440, Chile; (P.C.); (C.C.)
- Faculty of Medicine, Universidad Andres Bello, Santiago 8370071, Chile
- Department of Basic and Clinical Oncology, Faculty of Medicine, University of Chile, Santiago 8380453, Chile
| | - Claudio Correa
- Department of Head and Neck Surgery, Clinica INDISA, Santiago 7520440, Chile; (P.C.); (C.C.)
- Faculty of Medicine, Universidad Andres Bello, Santiago 8370071, Chile
| | - Ignacio Bode
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370071, Chile;
| | - Rodrigo Aguilar
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370071, Chile;
| | - Alvaro A. Elorza
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370071, Chile;
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3
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Spinazzola A, Perez-Rodriguez D, Ježek J, Holt IJ. Mitochondrial DNA competition: starving out the mutant genome. Trends Pharmacol Sci 2024; 45:225-242. [PMID: 38402076 DOI: 10.1016/j.tips.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/26/2024]
Abstract
High levels of pathogenic mitochondrial DNA (mtDNA) variants lead to severe genetic diseases, and the accumulation of such mutants may also contribute to common disorders. Thus, selecting against these mutants is a major goal in mitochondrial medicine. Although mutant mtDNA can drift randomly, mounting evidence indicates that active forces play a role in the selection for and against mtDNA variants. The underlying mechanisms are beginning to be clarified, and recent studies suggest that metabolic cues, including fuel availability, contribute to shaping mtDNA heteroplasmy. In the context of pathological mtDNAs, remodeling of nutrient metabolism supports mitochondria with deleterious mtDNAs and enables them to outcompete functional variants owing to a replicative advantage. The elevated nutrient requirement represents a mutant Achilles' heel because small molecules that restrict nutrient consumption or interfere with nutrient sensing can purge cells of deleterious mtDNAs and restore mitochondrial respiration. These advances herald the dawn of a new era of small-molecule therapies to counteract pathological mtDNAs.
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Affiliation(s)
- Antonella Spinazzola
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK.
| | - Diego Perez-Rodriguez
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK
| | - Jan Ježek
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK
| | - Ian J Holt
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK; Biodonostia Health Research Institute, 20014 San Sebastián, Spain; IKERBASQUE (Basque Foundation for Science), 48013 Bilbao, Spain; CIBERNED (Center for Networked Biomedical Research on Neurodegenerative Diseases, Ministry of Economy and Competitiveness, Institute Carlos III), 28031 Madrid, Spain; Universidad de País Vasco, Barrio Sarriena s/n, 48940 Leioa, Bilbao, Spain.
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4
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Zhang B, Sun R, Bai R, Sun Z, Liu R, Li W, Yao L, Sun H, Tang Y. G-quadruplex in mitochondria as a possible biomarker for mitophagy detection. Int J Biol Macromol 2024; 259:129337. [PMID: 38218296 DOI: 10.1016/j.ijbiomac.2024.129337] [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: 09/26/2023] [Revised: 01/06/2024] [Accepted: 01/06/2024] [Indexed: 01/15/2024]
Abstract
Mitochondrial autophagy (mitophagy) is a key physiological process that maintains the homeostasis of mitochondrial quality and quantity. Monitoring mitophagy is of great significance for detecting cellular abnormalities and developing therapeutic drugs. However, there are still very few biomarkers specifically developed for monitoring mitophagy. Here, we propose for the first time that mitochondrial G-quadruplex may serve as a biomarker for mitophagy detection, and develope a fluorescent light-up probe AMTC to monitor mitophagy in live cells. During mitophagy, AMTC fluorescence is significantly enhanced, but once mitophagy is inhibited, its fluorescence immediately decreases. The fluorescence behavior of AMTC implicates an increase in the formation of mitochondrial G-quadruplex during mitophagy. This inference has also been supported by the other two G-quadruplex probes. Taken together, this work provides a new possible biomarker and detection tool for the study of mitophagy.
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Affiliation(s)
- Boyang Zhang
- Beijing Institute of Graphic Communication, Beijing 102600, PR China
| | - Ranran Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Ruiyang Bai
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China
| | - Zhicheng Sun
- Beijing Institute of Graphic Communication, Beijing 102600, PR China
| | - Ruping Liu
- Beijing Institute of Graphic Communication, Beijing 102600, PR China.
| | - Wenchao Li
- Senior Department of Pediatrics, The Seventh Medical Center of Chinese People's Liberation Army General Hospital, Beijing, PR China.
| | - Li Yao
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Hongxia Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
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5
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Ji H, Zhang Q, Ding L, Chen R, Liu F, Li P. Structural and metabolic cumulus cell alteration affects oocyte quality in underweight women. ZYGOTE 2024; 32:77-86. [PMID: 38130161 DOI: 10.1017/s0967199423000588] [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] [Indexed: 12/23/2023]
Abstract
This study aimed to investigate the structural and metabolic changes in cumulus cells of underweight women and their effects on oocyte maturation and fertilization. The cytoplasmic ultrastructure was analyzed by electron microscopy, mitochondrial membrane potential by immunofluorescence, and mitochondrial DNA copy number by relative quantitative polymerase chain reaction. The expression of various proteins including the oxidative stress-derived product 4-hydroxynonenal (4-HNE) and autophagy and apoptosis markers such as Vps34, Atg-5, Beclin 1, Lc3-I, II, Bax, and Bcl-2 was assessed and compared between groups. Oocyte maturation and fertilization rates were lower in underweight women (P < 0.05), who presented with cumulus cells showing abnormal mitochondrial morphology and increased cell autophagy. Compared with the mitochondrial DNA copies of the control group, those of the underweight group increased but not significantly. The mitochondrial membrane potential was similar between the groups (P = 0.8). Vps34, Atg-5, Lc3-II, Bax, and Bcl-2 expression and 4-HNE levels were higher in the underweight group compared with the control group (P < 0.01); however, the Bax/Bcl-2 ratio was lower in the underweight group compared with the control group (P = 0.031). Additionally, Beclin 1 protein levels were higher in the underweight group compared with the control group but without statistical significance. In conclusion, malnutrition and other conditions in underweight women may adversely affect ovulation, and the development, and fertilization of oocytes resulting from changes to the intracellular structure of cumulus cells and metabolic processes. These changes may lead to reduced fertility or unsatisfactory reproduction outcomes in women.
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Affiliation(s)
- Hong Ji
- Department of Reproductive Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Zhenhai Road 10, 361003 Xiamen, Fujian Province, People's Republic of China
- Xiamen Key Laboratory of Reproduction and Genetics, Zhenhai Road 10, 361003, Xiamen, Fujian Province, People's Republic of China
| | - Qing Zhang
- Department of Reproductive Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Zhenhai Road 10, 361003 Xiamen, Fujian Province, People's Republic of China
- Xiamen Key Laboratory of Reproduction and Genetics, Zhenhai Road 10, 361003, Xiamen, Fujian Province, People's Republic of China
| | - Lu Ding
- Department of Reproductive Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Zhenhai Road 10, 361003 Xiamen, Fujian Province, People's Republic of China
- Xiamen Key Laboratory of Reproduction and Genetics, Zhenhai Road 10, 361003, Xiamen, Fujian Province, People's Republic of China
| | - Rongjuan Chen
- Department of Reproductive Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Zhenhai Road 10, 361003 Xiamen, Fujian Province, People's Republic of China
- Xiamen Key Laboratory of Reproduction and Genetics, Zhenhai Road 10, 361003, Xiamen, Fujian Province, People's Republic of China
| | - Fu Liu
- Department of Human Anatomy and Histoembryology, Xiamen Medical College, Guankou Middle Road 1999, 361023, Xiamen, Fujian Province, People's Republic of China
| | - Ping Li
- Department of Reproductive Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Zhenhai Road 10, 361003 Xiamen, Fujian Province, People's Republic of China
- Xiamen Key Laboratory of Reproduction and Genetics, Zhenhai Road 10, 361003, Xiamen, Fujian Province, People's Republic of China
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6
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Gilea AI, Magistrati M, Notaroberto I, Tiso N, Dallabona C, Baruffini E. The Saccharomyces cerevisiae mitochondrial DNA polymerase and its contribution to the knowledge about human POLG-related disorders. IUBMB Life 2023; 75:983-1002. [PMID: 37470284 DOI: 10.1002/iub.2770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/05/2023] [Indexed: 07/21/2023]
Abstract
Most eukaryotes possess a mitochondrial genome, called mtDNA. In animals and fungi, the replication of mtDNA is entrusted by the DNA polymerase γ, or Pol γ. The yeast Pol γ is composed only of a catalytic subunit encoded by MIP1. In humans, Pol γ is a heterotrimer composed of a catalytic subunit homolog to Mip1, encoded by POLG, and two accessory subunits. In the last 25 years, more than 300 pathological mutations in POLG have been identified as the cause of several mitochondrial diseases, called POLG-related disorders, which are characterized by multiple mtDNA deletions and/or depletion in affected tissues. In this review, at first, we summarize the biochemical properties of yeast Mip1, and how mutations, especially those introduced recently in the N-terminal and C-terminal regions of the enzyme, affect the in vitro activity of the enzyme and the in vivo phenotype connected to the mtDNA stability and to the mtDNA extended and point mutability. Then, we focus on the use of yeast harboring Mip1 mutations equivalent to the human ones to confirm their pathogenicity, identify the phenotypic defects caused by these mutations, and find both mechanisms and molecular compounds able to rescue the detrimental phenotype. A closing chapter will be dedicated to other polymerases found in yeast mitochondria, namely Pol ζ, Rev1 and Pol η, and to their genetic interactions with Mip1 necessary to maintain mtDNA stability and to avoid the accumulation of spontaneous or induced point mutations.
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Affiliation(s)
- Alexandru Ionut Gilea
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Martina Magistrati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Ilenia Notaroberto
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Natascia Tiso
- Department of Biology, University of Padova, Padova, Italy
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
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7
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Knorre DA. Mitochondrial heteroplasmy as a cause of cell-to-cell phenotypic heterogeneity in clonal populations. Front Cell Dev Biol 2023; 11:1276629. [PMID: 37886395 PMCID: PMC10598549 DOI: 10.3389/fcell.2023.1276629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Affiliation(s)
- Dmitry A. Knorre
- Department of Molecular Energetics of Microorganisms, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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8
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Lee Y, Kim B, Jang HS, Huh WK. Atg1-dependent phosphorylation of Vps34 is required for dynamic regulation of the phagophore assembly site and autophagy in Saccharomyces cerevisiae. Autophagy 2023; 19:2428-2442. [PMID: 36803233 PMCID: PMC10392759 DOI: 10.1080/15548627.2023.2182478] [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: 07/28/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Macroautophagy/autophagy is a key catabolic pathway in which double-membrane autophagosomes sequester various substrates destined for degradation, enabling cells to maintain homeostasis and survive under stressful conditions. Several autophagy-related (Atg) proteins are recruited to the phagophore assembly site (PAS) and cooperatively function to generate autophagosomes. Vps34 is a class III phosphatidylinositol 3-kinase, and Atg14-containing Vps34 complex I plays essential roles in autophagosome formation. However, the regulatory mechanisms of yeast Vps34 complex I are still poorly understood. Here, we demonstrate that Atg1-dependent phosphorylation of Vps34 is required for robust autophagy activity in Saccharomyces cerevisiae. Following nitrogen starvation, Vps34 in complex I is selectively phosphorylated on multiple serine/threonine residues in its helical domain. This phosphorylation is important for full autophagy activation and cell survival. The absence of Atg1 or its kinase activity leads to complete loss of Vps34 phosphorylation in vivo, and Atg1 directly phosphorylates Vps34 in vitro, regardless of its complex association type. We also demonstrate that the localization of Vps34 complex I to the PAS provides a molecular basis for the complex I-specific phosphorylation of Vps34. This phosphorylation is required for the normal dynamics of Atg18 and Atg8 at the PAS. Together, our results reveal a novel regulatory mechanism of yeast Vps34 complex I and provide new insights into the Atg1-dependent dynamic regulation of the PAS.Abbreviations: ATG: autophagy-related; BARA: the repeated, autophagy-specific Co-IP: co-immunoprecipitation; GFP: green fluorescent protein; IP-MS: immunoprecipitation followed by tandem mass spectrometry; NTD: the N-terminal domain; PAS: phagophore assembly site; PtdIns3P: phosphatidylinositol-3-phosphate; PtdIns3K: phosphatidylinositol 3-kinase; SUR: structurally uncharacterized region; Vps34[KD]: Vps34D731N.
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Affiliation(s)
- Yongook Lee
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Bongkeun Kim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hae-Soo Jang
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Won-Ki Huh
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
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9
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Neuroprotective effects of curculigoside against Alzheimer’s disease via regulation oxidative stress mediated mitochondrial dysfunction in L-Glu-exposed HT22 cells and APP/PS1 mice. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2022.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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10
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Trombly G, Said AM, Kudin AP, Peeva V, Altmüller J, Becker K, Köhrer K, Zsurka G, Kunz WS. The Fate of Oxidative Strand Breaks in Mitochondrial DNA. Antioxidants (Basel) 2023; 12:antiox12051087. [PMID: 37237953 DOI: 10.3390/antiox12051087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/27/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is particularly vulnerable to somatic mutagenesis. Potential mechanisms include DNA polymerase γ (POLG) errors and the effects of mutagens, such as reactive oxygen species. Here, we studied the effects of transient hydrogen peroxide (H2O2 pulse) on mtDNA integrity in cultured HEK 293 cells, applying Southern blotting, ultra-deep short-read and long-read sequencing. In wild-type cells, 30 min after the H2O2 pulse, linear mtDNA fragments appear, representing double-strand breaks (DSB) with ends characterized by short GC stretches. Intact supercoiled mtDNA species reappear within 2-6 h after treatment and are almost completely recovered after 24 h. BrdU incorporation is lower in H2O2-treated cells compared to non-treated cells, suggesting that fast recovery is not associated with mtDNA replication, but is driven by rapid repair of single-strand breaks (SSBs) and degradation of DSB-generated linear fragments. Genetic inactivation of mtDNA degradation in exonuclease deficient POLG p.D274A mutant cells results in the persistence of linear mtDNA fragments with no impact on the repair of SSBs. In conclusion, our data highlight the interplay between the rapid processes of SSB repair and DSB degradation and the much slower mtDNA re-synthesis after oxidative damage, which has important implications for mtDNA quality control and the potential generation of somatic mtDNA deletions.
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Affiliation(s)
- Genevieve Trombly
- Institute of Experimental Epileptology and Cognition Research, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Afaf Milad Said
- Institute of Experimental Epileptology and Cognition Research, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Alexei P Kudin
- Institute of Experimental Epileptology and Cognition Research, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Viktoriya Peeva
- Institute of Experimental Epileptology and Cognition Research, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Janine Altmüller
- Cologne Center for Genomics and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, 50923 Köln, Germany
- Institute of Human Genetics, University of Cologne, 50923 Köln, Germany
| | - Kerstin Becker
- Cologne Center for Genomics and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, 50923 Köln, Germany
- Biological and Medical Research Centre (BMFZ), Genomics & Transcriptomics Laboratory, Heinrich-Heine-University Duesseldorf, 40225 Düsseldorf, Germany
| | - Karl Köhrer
- Biological and Medical Research Centre (BMFZ), Genomics & Transcriptomics Laboratory, Heinrich-Heine-University Duesseldorf, 40225 Düsseldorf, Germany
| | - Gábor Zsurka
- Institute of Experimental Epileptology and Cognition Research, Medical Faculty, University of Bonn, 53127 Bonn, Germany
- Department of Epileptology, University Hospital Bonn, 53127 Bonn, Germany
| | - Wolfram S Kunz
- Institute of Experimental Epileptology and Cognition Research, Medical Faculty, University of Bonn, 53127 Bonn, Germany
- Department of Epileptology, University Hospital Bonn, 53127 Bonn, Germany
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11
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Dua N, Seshadri A, Badrinarayanan A. DarT-mediated mtDNA damage induces dynamic reorganization and selective segregation of mitochondria. J Cell Biol 2022; 221:213451. [PMID: 36074064 PMCID: PMC9463037 DOI: 10.1083/jcb.202205104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/23/2022] [Accepted: 08/08/2022] [Indexed: 11/22/2022] Open
Abstract
Mitochondria are dynamic organelles that play essential roles in cell growth and survival. Processes of fission and fusion are critical for the distribution, segregation, and maintenance of mitochondria and their genomes (mtDNA). While recent work has revealed the significance of mitochondrial organization for mtDNA maintenance, the impact of mtDNA perturbations on mitochondrial dynamics remains less understood. Here, we develop a tool to induce mitochondria-specific DNA damage using a mitochondrial-targeted base modifying bacterial toxin, DarT. Following damage, we observe dynamic reorganization of mitochondrial networks, likely driven by mitochondrial dysfunction. Changes in the organization are associated with the loss of mtDNA, independent of mitophagy. Unexpectedly, perturbation to exonuclease function of mtDNA replicative polymerase, Mip1, results in rapid loss of mtDNA. Our data suggest that, under damage, partitioning of defective mtDNA and organelle are de-coupled, with emphasis on mitochondrial segregation independent of its DNA. Together, our work underscores the importance of genome maintenance on mitochondrial function, which can act as a modulator of organelle organization and segregation.
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Affiliation(s)
- Nitish Dua
- National Centre for Biological Sciences - Tata Institute of Fundamental Research, Bangalore, Karnataka, India
| | - Akshaya Seshadri
- National Centre for Biological Sciences - Tata Institute of Fundamental Research, Bangalore, Karnataka, India.,SASTRA University, Thanjavur, Tamil Nadu, India
| | - Anjana Badrinarayanan
- National Centre for Biological Sciences - Tata Institute of Fundamental Research, Bangalore, Karnataka, India
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12
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Galeota-Sprung B, Fernandez A, Sniegowski P. Changes to the mtDNA copy number during yeast culture growth. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211842. [PMID: 35814911 PMCID: PMC9257595 DOI: 10.1098/rsos.211842] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
We show that the mitochondrial DNA (mtDNA) copy number in growing cultures of the yeast Saccharomyces cerevisiae increases by a factor of up to 4, being lowest (approx. 10 per haploid genome) and stable during rapid fermentative growth, and highest at the end of the respiratory phase. When yeast are grown on glucose, the onset of the mtDNA copy number increase coincides with the early stages of the diauxic shift, and the increase continues through respiration. A lesser yet still substantial copy number increase occurs when yeast are grown on a nonfermentable carbon source, i.e. when there is no diauxic shift. The mtDNA copy number increase during and for some time after the diauxic shift is not driven by an increase in cell size. The copy number increase occurs in both haploid and diploid strains but is markedly attenuated in a diploid wild isolate that is a ready sporulator. Strain-to-strain differences in mtDNA copy number are least apparent in fermentation and most apparent in late respiration or stationary phase. While changes in mitochondrial morphology and function were previously known to accompany changes in physiological state, it had not been previously shown that the mtDNA copy number changes substantially over time in a clonal growing culture. The mtDNA copy number in yeast is therefore a highly dynamic phenotype.
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Affiliation(s)
- Ben Galeota-Sprung
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Amy Fernandez
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Paul Sniegowski
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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13
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Milenkovic D, Sanz-Moreno A, Calzada-Wack J, Rathkolb B, Veronica Amarie O, Gerlini R, Aguilar-Pimentel A, Misic J, Simard ML, Wolf E, Fuchs H, Gailus-Durner V, de Angelis MH, Larsson NG. Mice lacking the mitochondrial exonuclease MGME1 develop inflammatory kidney disease with glomerular dysfunction. PLoS Genet 2022; 18:e1010190. [PMID: 35533204 PMCID: PMC9119528 DOI: 10.1371/journal.pgen.1010190] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/19/2022] [Accepted: 04/05/2022] [Indexed: 12/27/2022] Open
Abstract
Mitochondrial DNA (mtDNA) maintenance disorders are caused by mutations in ubiquitously expressed nuclear genes and lead to syndromes with variable disease severity and tissue-specific phenotypes. Loss of function mutations in the gene encoding the mitochondrial genome and maintenance exonuclease 1 (MGME1) result in deletions and depletion of mtDNA leading to adult-onset multisystem mitochondrial disease in humans. To better understand the in vivo function of MGME1 and the associated disease pathophysiology, we characterized a Mgme1 mouse knockout model by extensive phenotyping of ageing knockout animals. We show that loss of MGME1 leads to de novo formation of linear deleted mtDNA fragments that are constantly made and degraded. These findings contradict previous proposal that MGME1 is essential for degradation of linear mtDNA fragments and instead support a model where MGME1 has a critical role in completion of mtDNA replication. We report that Mgme1 knockout mice develop a dramatic phenotype as they age and display progressive weight loss, cataract and retinopathy. Surprisingly, aged animals also develop kidney inflammation, glomerular changes and severe chronic progressive nephropathy, consistent with nephrotic syndrome. These findings link the faulty mtDNA synthesis to severe inflammatory disease and thus show that defective mtDNA replication can trigger an immune response that causes age-associated progressive pathology in the kidney. We have addressed the controversy of the role of the mitochondrial genome and maintenance exonuclease 1 (MGME1) in mtDNA metabolism by characterization of knockout mice. Our findings show that loss of MGME1 leads to increased de novo formation of linear deleted mtDNA, thus contradicting previous report that MGME1 degrades long linear mtDNA molecules. In addition, we report that loss of MGME1 leads to age-associated pathology manifested as progressive weight loss, cataract and retinopathy. Aged knockout mice also develop kidney inflammation leading to glomerular changes, fibrosis and nephrotic syndrome. Defective mtDNA replication causing the formation of linear deleted mtDNA can thus trigger an immune response that leads to the development of progressive kidney disease in ageing animals.
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Affiliation(s)
| | - Adrián Sanz-Moreno
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Julia Calzada-Wack
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Birgit Rathkolb
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-University Munich, Munich, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Oana Veronica Amarie
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Raffaele Gerlini
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Antonio Aguilar-Pimentel
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Jelena Misic
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Eckhard Wolf
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Valerie Gailus-Durner
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Freising, Germany
- * E-mail: (NGL); (MH)
| | - Nils-Göran Larsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (NGL); (MH)
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14
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Wang P, Wu B, You S, Lu S, Xiong S, Zou Y, Jia P, Guo X, Zhang Y, Cao L, Sun Y, Zhang N. DNA Polymerase Gamma Recovers Mitochondrial Function and Inhibits Vascular Calcification by Interacted with p53. Int J Biol Sci 2022; 18:409-425. [PMID: 34975341 PMCID: PMC8692132 DOI: 10.7150/ijbs.65030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
DNA polymerase gamma (PolG) is the major polymerase of mitochondrial DNA (mtDNA) and essential for stabilizing mitochondrial function. Vascular calcification (VC) is common senescence related degenerative pathology phenomenon in the end-stage of multiple chronic diseases. Mitochondrial dysfunction was often observed in calcified vessels, but the function and mechanism of PolG in the calcification process was still unknown. The present study found PolGD257A/D257A mice presented more severe calcification of aortas than wild type (WT) mice with vitamin D3 (Vit D3) treatment, and this phenomenon was also confirmed in vitro. Mechanistically, PolG could enhance the recruitment and interaction of p53 in calcification condition to recover mitochondrial function and eventually to resist calcification. Meanwhile, we found the mutant PolG (D257A) failed to achieve the same rescue effects, suggesting the 3'-5' exonuclease activity guarantee the enhanced interaction of p53 and PolG in response to calcification stimulation. Thus, we believed that it was PolG, not mutant PolG, could maintain mitochondrial function and attenuate calcification in vitro and in vivo. And PolG could be a novel potential therapeutic target against calcification, providing a novel insight to clinical treatment.
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Affiliation(s)
- Pengbo Wang
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
| | - Boquan Wu
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
| | - Shilong You
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
| | - Saien Lu
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
| | - Shengjun Xiong
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
| | - Yuanming Zou
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
| | - Pengyu Jia
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
| | - Xiaofan Guo
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
| | - Ying Zhang
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
| | - Liu Cao
- College of Basic Medical Science, Institute of Translational Medicine, Key Laboratory of Medical Cell Biology, Ministry of Education, Key Laboratory of Liaoning Province, China Medical University, Shenyang, 110122, Liaoning Province, People Republic of China
| | - Yingxian Sun
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
| | - Naijin Zhang
- Department of Cardiology, The First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People Republic of China
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15
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Barilani M, Lovejoy C, Piras R, Abramov AY, Lazzari L, Angelova PR. Age-related changes in the energy of human mesenchymal stem cells. J Cell Physiol 2021; 237:1753-1767. [PMID: 34791648 DOI: 10.1002/jcp.30638] [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: 07/15/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 01/06/2023]
Abstract
Aging is a physiological process that leads to a higher risk for the most devastating diseases. There are a number of theories of human aging proposed, and many of them are directly or indirectly linked to mitochondria. Here, we used mesenchymal stem cells (MSCs) from young and older donors to study age-related changes in mitochondrial metabolism. We have found that aging in MSCs is associated with a decrease in mitochondrial membrane potential and lower NADH levels in mitochondria. Mitochondrial DNA content is higher in aged MSCs, but the overall mitochondrial mass is decreased due to increased rates of mitophagy. Despite the higher level of ATP in aged cells, a higher rate of ATP consumption renders them more vulnerable to energy deprivation compared to younger cells. Changes in mitochondrial metabolism in aged MSCs activate the overproduction of reactive oxygen species in mitochondria which is compensated by a higher level of the endogenous antioxidant glutathione. Thus, energy metabolism and redox state are the drivers for the aging of MSCs/mesenchymal stromal cells.
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Affiliation(s)
- Mario Barilani
- Department of Transfusion Medicine and Hematology, Laboratory of Regenerative Medicine - Cell Factory, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Christopher Lovejoy
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Roberta Piras
- Department of Transfusion Medicine and Hematology, Laboratory of Regenerative Medicine - Cell Factory, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Andrey Y Abramov
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Lorenza Lazzari
- Department of Transfusion Medicine and Hematology, Laboratory of Regenerative Medicine - Cell Factory, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Plamena R Angelova
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
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16
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Emerging methods for and novel insights gained by absolute quantification of mitochondrial DNA copy number and its clinical applications. Pharmacol Ther 2021; 232:107995. [PMID: 34592204 DOI: 10.1016/j.pharmthera.2021.107995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 02/07/2023]
Abstract
The past thirty years have seen a surge in interest in pathophysiological roles of mitochondria, and the accurate quantification of mitochondrial DNA copy number (mCN) in cells and tissue samples is a fundamental aspect of assessing changes in mitochondrial health and biogenesis. Quantification of mCN between studies is surprisingly variable due to a combination of physiological variability and diverse protocols being used to measure this endpoint. The advent of novel methods to quantify nucleic acids like digital polymerase chain reaction (dPCR) and high throughput sequencing offer the ability to measure absolute values of mCN. We conducted an in-depth survey of articles published between 1969 -- 2020 to create an overview of mCN values, to assess consensus values of tissue-specific mCN, and to evaluate consistency between methods of assessing mCN. We identify best practices for methods used to assess mCN, and we address the impact of using specific loci on the mitochondrial genome to determine mCN. Current data suggest that clinical measurement of mCN can provide diagnostic and prognostic value in a range of diseases and health conditions, with emphasis on cancer and cardiovascular disease, and the advent of means to measure absolute mCN should improve future clinical applications of mCN measurements.
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17
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Alikhani M, Touati E, Karimipoor M, Vosough M, Mohammadi M. Mitochondrial DNA Copy Number Variations in Gastrointestinal Tract Cancers: Potential Players. J Gastrointest Cancer 2021; 53:770-781. [PMID: 34486088 DOI: 10.1007/s12029-021-00707-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2021] [Indexed: 10/20/2022]
Abstract
Alterations of mitochondria have been linked to several cancers. Also, the mitochondrial DNA copy number (mtDNA-CN) is altered in various cancers, including gastrointestinal tract (GIT) cancers, and several research groups have investigated its potential as a cancer biomarker. However, the exact causes of mtDNA-CN variations are not yet revealed. This review discussed the conceivable players in this scheme, including reactive oxygen species (ROS), mtDNA genetic variations, DNA methylation, telomere length, autophagy, immune system activation, aging, and infections, and discussed their possible impact in the initiation and progression of cancer. By further exploring such mechanisms, mtDNA-CN variations may be effectively utilized as cancer biomarkers and provide grounds for developing novel cancer therapeutic agents.
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Affiliation(s)
- Mehdi Alikhani
- Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Eliette Touati
- Unit of Helicobacter Pathogenesis, Department of Microbiology, CNRS UMR2001, Institut Pasteur, 25-28 Rue du Dr Roux cedex 15, 75724, Paris, France
| | - Morteza Karimipoor
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Marjan Mohammadi
- Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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18
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Jakubke C, Roussou R, Maiser A, Schug C, Thoma F, Bunk D, Hörl D, Leonhardt H, Walter P, Klecker T, Osman C. Cristae-dependent quality control of the mitochondrial genome. SCIENCE ADVANCES 2021; 7:eabi8886. [PMID: 34516914 PMCID: PMC8442932 DOI: 10.1126/sciadv.abi8886] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/08/2021] [Indexed: 06/10/2023]
Abstract
Mitochondrial genomes (mtDNA) encode essential subunits of the mitochondrial respiratory chain. Mutations in mtDNA can cause a shortage in cellular energy supply, which can lead to numerous mitochondrial diseases. How cells secure mtDNA integrity over generations has remained unanswered. Here, we show that the single-celled yeast Saccharomyces cerevisiae can intracellularly distinguish between functional and defective mtDNA and promote generation of daughter cells with increasingly healthy mtDNA content. Purifying selection for functional mtDNA occurs in a continuous mitochondrial network and does not require mitochondrial fission but necessitates stable mitochondrial subdomains that depend on intact cristae morphology. Our findings support a model in which cristae-dependent proximity between mtDNA and the proteins it encodes creates a spatial “sphere of influence,” which links a lack of functional fitness to clearance of defective mtDNA.
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Affiliation(s)
- Christopher Jakubke
- Faculty of Biology, Ludwig-Maximilian-Universität München, 82152 Planegg-Martinsried, Germany
- Graduate School Life Science Munich, Planegg, Germany
| | - Rodaria Roussou
- Faculty of Biology, Ludwig-Maximilian-Universität München, 82152 Planegg-Martinsried, Germany
- Graduate School Life Science Munich, Planegg, Germany
| | - Andreas Maiser
- Faculty of Biology, Ludwig-Maximilian-Universität München, 82152 Planegg-Martinsried, Germany
| | | | - Felix Thoma
- Faculty of Biology, Ludwig-Maximilian-Universität München, 82152 Planegg-Martinsried, Germany
- Graduate School Life Science Munich, Planegg, Germany
| | - David Bunk
- Faculty of Biology, Ludwig-Maximilian-Universität München, 82152 Planegg-Martinsried, Germany
| | - David Hörl
- Faculty of Biology, Ludwig-Maximilian-Universität München, 82152 Planegg-Martinsried, Germany
| | - Heinrich Leonhardt
- Faculty of Biology, Ludwig-Maximilian-Universität München, 82152 Planegg-Martinsried, Germany
| | - Peter Walter
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Till Klecker
- Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
| | - Christof Osman
- Faculty of Biology, Ludwig-Maximilian-Universität München, 82152 Planegg-Martinsried, Germany
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19
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Giovarelli M, Zecchini S, Catarinella G, Moscheni C, Sartori P, Barbieri C, Roux-Biejat P, Napoli A, Vantaggiato C, Cervia D, Perrotta C, Clementi E, Latella L, De Palma C. Givinostat as metabolic enhancer reverting mitochondrial biogenesis deficit in Duchenne Muscular Dystrophy. Pharmacol Res 2021; 170:105751. [PMID: 34197911 DOI: 10.1016/j.phrs.2021.105751] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/11/2021] [Accepted: 06/27/2021] [Indexed: 12/13/2022]
Abstract
Duchenne Muscular Dystrophy (DMD) is a rare disorder characterized by progressive muscle wasting, weakness, and premature death. Remarkable progress has been made in genetic approaches, restoring dystrophin, or its function. However, the targeting of secondary pathological mechanisms, such as increasing muscle blood flow or stopping fibrosis, remains important to improve the therapeutic benefits, that depend on tackling both the genetic disease and the downstream consequences. Mitochondrial dysfunctions are one of the earliest deficits in DMD, arise from multiple cellular stressors and result in less than 50% of ATP content in dystrophic muscles. Here we establish that there are two temporally distinct phases of mitochondrial damage with depletion of mitochondrial mass at early stages and an accumulation of dysfunctional mitochondria at later stages, leading to a different oxidative fibers pattern, in young and adult mdx mice. We also observe a progressive mitochondrial biogenesis impairment associated with increased deacetylation of peroxisome proliferator-activated receptor-gamma coactivator 1 α (PGC-1α) promoter. Such histone deacetylation is inhibited by givinostat that positively modifies the epigenetic profile of PGC-1α promoter, sustaining mitochondrial biogenesis and oxidative fiber type switch. We, therefore, demonstrate that givinostat exerts relevant effects at mitochondrial level, acting as a metabolic remodeling agent capable of efficiently promoting mitochondrial biogenesis in dystrophic muscle.
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MESH Headings
- Acetylation
- Animals
- Carbamates/pharmacology
- Disease Models, Animal
- Energy Metabolism/drug effects
- Epigenesis, Genetic
- Histone Deacetylase Inhibitors/pharmacology
- Mice, Inbred mdx
- Mitochondria, Muscle/drug effects
- Mitochondria, Muscle/metabolism
- Mitochondria, Muscle/pathology
- Muscle, Skeletal/drug effects
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/pathology
- Muscular Dystrophy, Duchenne/drug therapy
- Muscular Dystrophy, Duchenne/genetics
- Muscular Dystrophy, Duchenne/metabolism
- Muscular Dystrophy, Duchenne/pathology
- Organelle Biogenesis
- Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/genetics
- Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism
- Promoter Regions, Genetic
- Mice
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Affiliation(s)
- Matteo Giovarelli
- Department of Biomedical and Clinical Sciences "Luigi Sacco" (DIBIC), Università degli Studi di Milano, via G.B. Grassi 74, 20157 Milan, Italy
| | - Silvia Zecchini
- Department of Biomedical and Clinical Sciences "Luigi Sacco" (DIBIC), Università degli Studi di Milano, via G.B. Grassi 74, 20157 Milan, Italy
| | - Giorgia Catarinella
- IRCCS, Fondazione Santa Lucia, Rome 00142, Italy; DAHFMO, Unit of Histology and Medical Embryology, Sapienza, University of Rome, Rome, Italy
| | - Claudia Moscheni
- Department of Biomedical and Clinical Sciences "Luigi Sacco" (DIBIC), Università degli Studi di Milano, via G.B. Grassi 74, 20157 Milan, Italy
| | - Patrizia Sartori
- Department of Biomedical Sciences for Health, Università degli Studi di Milano, via Mangiagalli 31, 20133 Milan, Italy
| | - Cecilia Barbieri
- Department of Biomedical and Clinical Sciences "Luigi Sacco" (DIBIC), Università degli Studi di Milano, via G.B. Grassi 74, 20157 Milan, Italy
| | - Paulina Roux-Biejat
- Department of Biomedical and Clinical Sciences "Luigi Sacco" (DIBIC), Università degli Studi di Milano, via G.B. Grassi 74, 20157 Milan, Italy
| | - Alessandra Napoli
- Department of Biomedical and Clinical Sciences "Luigi Sacco" (DIBIC), Università degli Studi di Milano, via G.B. Grassi 74, 20157 Milan, Italy
| | - Chiara Vantaggiato
- Scientific Institute, IRCCS Eugenio Medea, Laboratory of Molecular Biology, via Don Luigi Monza 20, 23842 Bosisio Parini, Italy
| | - Davide Cervia
- Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), Università degli Studi della Tuscia, largo dell'Università snc, 01100 Viterbo, Italy
| | - Cristiana Perrotta
- Department of Biomedical and Clinical Sciences "Luigi Sacco" (DIBIC), Università degli Studi di Milano, via G.B. Grassi 74, 20157 Milan, Italy
| | - Emilio Clementi
- Department of Biomedical and Clinical Sciences "Luigi Sacco" (DIBIC), Università degli Studi di Milano, via G.B. Grassi 74, 20157 Milan, Italy; Scientific Institute, IRCCS Eugenio Medea, Laboratory of Molecular Biology, via Don Luigi Monza 20, 23842 Bosisio Parini, Italy
| | - Lucia Latella
- IRCCS, Fondazione Santa Lucia, Rome 00142, Italy; Institute of Translational Pharmacology, National Research Council of Italy, Via Fosso del Cavaliere 100, Rome 00133, Italy
| | - Clara De Palma
- Department of Medical Biotechnology and Translational Medicine (BioMeTra), Università degli Studi di Milano, via L. Vanvitelli 32, 20129 Milan, Italy.
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20
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He ZH, Li M, Fang QJ, Liao FL, Zou SY, Wu X, Sun HY, Zhao XY, Hu YJ, Xu XX, Chen S, Sun Y, Chai RJ, Kong WJ. FOXG1 promotes aging inner ear hair cell survival through activation of the autophagy pathway. Autophagy 2021; 17:4341-4362. [PMID: 34006186 PMCID: PMC8726647 DOI: 10.1080/15548627.2021.1916194] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Presbycusis is the cumulative effect of aging on hearing. Recent studies have shown that common mitochondrial gene deletions are closely related to deafness caused by degenerative changes in the auditory system, and some of these nuclear factors are proposed to participate in the regulation of mitochondrial function. However, the detailed mechanisms involved in age-related degeneration of the auditory systems have not yet been fully elucidated. In this study, we found that FOXG1 plays an important role in the auditory degeneration process through regulation of macroautophagy/autophagy. Inhibition of FOXG1 decreased the autophagy activity and led to the accumulation of reactive oxygen species and subsequent apoptosis of cochlear hair cells. Recent clinical studies have found that aspirin plays important roles in the prevention and treatment of various diseases by regulating autophagy and mitochondria function. In this study, we found that aspirin increased the expression of FOXG1, which further activated autophagy and reduced the production of reactive oxygen species and inhibited apoptosis, and thus promoted the survival of mimetic aging HCs and HC-like OC-1 cells. This study demonstrates the regulatory function of the FOXG1 transcription factor through the autophagy pathway during hair cell degeneration in presbycusis, and it provides a new molecular approach for the treatment of age-related hearing loss. Abbreviations: AHL: age-related hearing loss; baf: bafilomycin A1; CD: common deletion; D-gal: D-galactose; GO: glucose oxidase; HC: hair cells; mtDNA: mitochondrial DNA; RAP: rapamycin; ROS: reactive oxygen species; TMRE: tetramethylrhodamine, ethyl ester
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Affiliation(s)
- Zu-Hong He
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Department of Otorhinolaryngology, Xiangyang Central Hospital, Affiliated Hospital Of Hubei University Of Arts and Science, Xiangyang 441021, China
| | - Ming Li
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qiao-Jun Fang
- State Key Laboratory of Bioelectronics, School of Life Sciences and Technology, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing, China
| | - Fu-Ling Liao
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science
| | - Sheng-Yu Zou
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xia Wu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hai-Ying Sun
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xue-Yan Zhao
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu-Juan Hu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao-Xiang Xu
- Department of Otorhinolaryngology, Xiangyang Central Hospital, Affiliated Hospital Of Hubei University Of Arts and Science, Xiangyang 441021, China
| | - Sen Chen
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Sun
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ren-Jie Chai
- State Key Laboratory of Bioelectronics, School of Life Sciences and Technology, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing, China.,Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Science, Beijing, China.,Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing, China.,Beijing Key Laboratory of Neural Regeneration and Repair, Capital Medical University, Beijing, China
| | - Wei-Jia Kong
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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21
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Sprenger HG, MacVicar T, Bahat A, Fiedler KU, Hermans S, Ehrentraut D, Ried K, Milenkovic D, Bonekamp N, Larsson NG, Nolte H, Giavalisco P, Langer T. Cellular pyrimidine imbalance triggers mitochondrial DNA-dependent innate immunity. Nat Metab 2021; 3:636-650. [PMID: 33903774 PMCID: PMC8144018 DOI: 10.1038/s42255-021-00385-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 03/15/2021] [Indexed: 12/14/2022]
Abstract
Cytosolic mitochondrial DNA (mtDNA) elicits a type I interferon response, but signals triggering the release of mtDNA from mitochondria remain enigmatic. Here, we show that mtDNA-dependent immune signalling via the cyclic GMP-AMP synthase‒stimulator of interferon genes‒TANK-binding kinase 1 (cGAS-STING-TBK1) pathway is under metabolic control and is induced by cellular pyrimidine deficiency. The mitochondrial protease YME1L preserves pyrimidine pools by supporting de novo nucleotide synthesis and by proteolysis of the pyrimidine nucleotide carrier SLC25A33. Deficiency of YME1L causes inflammation in mouse retinas and in cultured cells. It drives the release of mtDNA and a cGAS-STING-TBK1-dependent inflammatory response, which requires SLC25A33 and is suppressed upon replenishment of cellular pyrimidine pools. Overexpression of SLC25A33 is sufficient to induce immune signalling by mtDNA. Similarly, depletion of cytosolic nucleotides upon inhibition of de novo pyrimidine synthesis triggers mtDNA-dependent immune responses in wild-type cells. Our results thus identify mtDNA release and innate immune signalling as a metabolic response to cellular pyrimidine deficiencies.
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Affiliation(s)
- Hans-Georg Sprenger
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Thomas MacVicar
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Amir Bahat
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Kai Uwe Fiedler
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Steffen Hermans
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Katharina Ried
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Nina Bonekamp
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Nils-Göran Larsson
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Hendrik Nolte
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Thomas Langer
- Max Planck Institute for Biology of Ageing, Cologne, Germany.
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
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22
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Li D, Vogel P, Li-Harms X, Wang B, Kundu M. ATG14 and RB1CC1 play essential roles in maintaining muscle homeostasis. Autophagy 2021; 17:2576-2585. [PMID: 33794726 DOI: 10.1080/15548627.2021.1911549] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Defects in macroautophagy/autophagy are implicated in the pathogenesis of neuromuscular and heart diseases. To precisely define the roles of autophagy-related genes in skeletal and cardiac muscles, we generated muscle-specific rb1cc1- and atg14-conditional knockout (cKO) mice by using Ckm/Ckmm2-Cre and compared their phenotypes to those of ulk1 ulk2-conditional double-knockout (cDKO) mice. atg14-cKO mice developed hypertrophic cardiomyopathy, which was associated with abnormal accumulation of autophagic cargoes in the heart and early mortality. Skeletal muscles of both atg14-cKO and rb1cc1-cKO mice showed features of autophagic vacuolar myopathy with ubiquitin+ SQSTM1+ deposits, but only those of rb1cc1-cKO mice showed TARDBP/TDP-43+ pathology and other features of the inclusion body myopathy-like disease we previously described in ulk1 ulk2-cDKO mice. Herein, we highlight tissue-specific differences between skeletal and cardiac muscles in their reliance on core autophagy proteins and unique roles for ULK1-ULK2 and RB1CC1 among these proteins in the development of TARDBP+ pathology.ABBREVIATIONS:AVM: autophagic vacuolar myopathy; cDKO: conditional double knockout; cKO: conditional knockout; H&E: hematoxylin and eosin; IBM: inclusion body myopathy; mtDNA: mitochondrial DNA; PFA: paraformaldehyde; RNP: ribonucleoprotein; TBST: Tris-buffered saline with 0.2% Triton X-100.
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Affiliation(s)
- Dongfang Li
- Departments of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter Vogel
- Departments of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Veterinary Pathology Core, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiujie Li-Harms
- Departments of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bo Wang
- Departments of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.,State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, Fujian Province, China
| | - Mondira Kundu
- Departments of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
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23
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Stewart JB. Current progress with mammalian models of mitochondrial DNA disease. J Inherit Metab Dis 2021; 44:325-342. [PMID: 33099782 DOI: 10.1002/jimd.12324] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 12/16/2022]
Abstract
Mitochondrial disorders make up a large class of heritable diseases that cause a broad array of different human pathologies. They can affect many different organ systems, or display very specific tissue presentation, and can lead to illness either in childhood or later in life. While the over 1200 genes encoded in the nuclear DNA play an important role in human mitochondrial disease, it has been known for over 30 years that mutations of the mitochondria's own small, multicopy DNA chromosome (mtDNA) can lead to heritable human diseases. Unfortunately, animal mtDNA has resisted transgenic and directed genome editing technologies until quite recently. As such, animal models to aid in our understanding of these diseases, and to explore preclinical therapeutic research have been quite rare. This review will discuss the unusual properties of animal mitochondria that have hindered the generation of animal models. It will also discuss the existing mammalian models of human mtDNA disease, describe the methods employed in their generation, and will discuss recent advances in the targeting of DNA-manipulating enzymes to the mitochondria and how these may be employed to generate new models.
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Affiliation(s)
- James Bruce Stewart
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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24
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Medala VK, Gollapelli B, Dewanjee S, Ogunmokun G, Kandimalla R, Vallamkondu J. Mitochondrial dysfunction, mitophagy, and role of dynamin-related protein 1 in Alzheimer's disease. J Neurosci Res 2021; 99:1120-1135. [PMID: 33465841 DOI: 10.1002/jnr.24781] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 12/10/2020] [Indexed: 12/12/2022]
Abstract
Alzheimer's disease (AD) is the most common type of dementia and progressive neurodegenerative disease. The presence of β-amyloid (Aβ) plaques and phosphorylated Tau tangles are considered to be the two main hallmarks of AD. Recent findings have shown that different changes in the structure and dynamics of mitochondria play an important role in AD pathology progression. Mitochondrial changes in AD are expressed as enhanced mitochondrial fragmentation, altered mitochondrial dynamics, and changes in the expression of mitochondrial biogenesis genes in vitro and in vivo models. Therefore, targeting mitochondria and associated mitochondrial proteins seems to be a promising alternative instead of targeting Aβ and Tau in the prevention of Alzheimer's disease. The dynamin-related protein (Drp1) is one such protein that plays an important role in the regulation of mitochondrial division and maintenance of mitochondrial structures. Few researchers have shown that inhibition of Drp1 GTPase activity in neuronal cells rescues excessive mitochondrial fragmentation. In addition, the growing evidence revealed that Drp1 can interact with both Aβ and Tau protein in human brain tissues and mouse models. In this review, we would like to update existing knowledge about various changes in and around mitochondria related to the pathogenesis of Alzheimer's disease, with particular emphasis on mitophagy and autophagy.
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Affiliation(s)
| | - Buchaiah Gollapelli
- Department of Physics, National Institute of Technology-Warangal, Warangal, India
| | - Saikat Dewanjee
- Advanced Pharmacognosy Research Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | | | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, India.,Department of Biochemistry, Kakatiya Medical College, Warangal, India
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25
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Autophagy sustains glutamate and aspartate synthesis in Saccharomyces cerevisiae during nitrogen starvation. Nat Commun 2021; 12:57. [PMID: 33397945 PMCID: PMC7782722 DOI: 10.1038/s41467-020-20253-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/20/2020] [Indexed: 01/29/2023] Open
Abstract
Autophagy catabolizes cellular constituents to promote survival during nutrient deprivation. Yet, a metabolic comprehension of this recycling operation, despite its crucial importance, remains incomplete. Here, we uncover a specific metabolic function of autophagy that exquisitely adjusts cellular metabolism according to nitrogen availability in the budding yeast Saccharomyces cerevisiae. Autophagy enables metabolic plasticity to promote glutamate and aspartate synthesis, which empowers nitrogen-starved cells to replenish their nitrogen currency and sustain macromolecule synthesis. Our findings provide critical insights into the metabolic basis by which autophagy recycles cellular components and may also have important implications in understanding the role of autophagy in diseases such as cancer.
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26
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Bahat A, MacVicar T, Langer T. Metabolism and Innate Immunity Meet at the Mitochondria. Front Cell Dev Biol 2021; 9:720490. [PMID: 34386501 PMCID: PMC8353256 DOI: 10.3389/fcell.2021.720490] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/05/2021] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are master regulators of metabolism and have emerged as key signalling organelles of the innate immune system. Each mitochondrion harbours potent agonists of inflammation, including mitochondrial DNA (mtDNA), which are normally shielded from the rest of the cell and extracellular environment and therefore do not elicit detrimental inflammatory cascades. Mitochondrial damage and dysfunction can lead to the cytosolic and extracellular exposure of mtDNA, which triggers inflammation in a number of diseases including autoimmune neurodegenerative disorders. However, recent research has revealed that the extra-mitochondrial exposure of mtDNA is not solely a negative consequence of mitochondrial damage and pointed to an active role of mitochondria in innate immunity. Metabolic cues including nucleotide imbalance can stimulate the release of mtDNA from mitochondria in order to drive a type I interferon response. Moreover, important effectors of the innate immune response to pathogen infection, such as the mitochondrial antiviral signalling protein (MAVS), are located at the mitochondrial surface and modulated by the cellular metabolic status and mitochondrial dynamics. In this review, we explore how and why metabolism and innate immunity converge at the mitochondria and describe how mitochondria orchestrate innate immune signalling pathways in different metabolic scenarios. Understanding how cellular metabolism and metabolic programming of mitochondria are translated into innate immune responses bears relevance to a broad range of human diseases including cancer.
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Affiliation(s)
- Amir Bahat
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Thomas MacVicar
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Thomas Langer
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- *Correspondence: Thomas Langer,
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27
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Wang X, Weidling I, Koppel S, Menta B, Perez Ortiz J, Kalani A, Wilkins HM, Swerdlow RH. Detection of mitochondria-pertinent components in exosomes. Mitochondrion 2020; 55:100-110. [PMID: 32980480 PMCID: PMC7669644 DOI: 10.1016/j.mito.2020.09.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/27/2020] [Accepted: 09/18/2020] [Indexed: 01/01/2023]
Abstract
We screened cell line and plasma-derived exosomes for molecules that localize to mitochondria or that reflect mitochondrial integrity. SH-SY5Y cell-derived exosomes contained humanin, citrate synthase, and fibroblast growth factor 21 protein, and plasma-derived exosomes contained humanin, voltage-dependent anion-selective channel 1, and transcription factor A protein. Nuclear mitochondrial (NUMT) DNA complicated analyses of mitochondrial DNA (mtDNA), which otherwise suggested exosomes contain at most very low amounts of extended mtDNA sequences but likely contain degraded pieces of mtDNA. Cell and plasma-derived exosomes contained several mtDNA-derived mRNA sequences, including those for ND2, CO2, and humanin. These results can guide exosome-focused, mitochondria-pertinent biomarker development.
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Affiliation(s)
- Xiaowan Wang
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Ian Weidling
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Scott Koppel
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Blaise Menta
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Judit Perez Ortiz
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Anuradha Kalani
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Heather M Wilkins
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA
| | - Russell H Swerdlow
- Department of Neurology, University of Kansas, Medical Center, Kansas City, KS, USA; University of Kansas Alzheimer's Disease Center, Kansas City, KS, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA.
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28
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Gioran A, Chondrogianni N. Mitochondria (cross)talk with proteostatic mechanisms: Focusing on ageing and neurodegenerative diseases. Mech Ageing Dev 2020; 190:111324. [DOI: 10.1016/j.mad.2020.111324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/15/2022]
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29
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Wu C, Yao W, Kai W, Liu W, Wang W, Li S, Chen Y, Wu X, Wang L, Li Y, Tong J, Qian J, Zhang L, Hong Z, Yi C. Mitochondrial Fusion Machinery Specifically Involved in Energy Deprivation-Induced Autophagy. Front Cell Dev Biol 2020; 8:221. [PMID: 32318571 PMCID: PMC7154291 DOI: 10.3389/fcell.2020.00221] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/16/2020] [Indexed: 01/03/2023] Open
Abstract
Mitochondria are highly dynamic organelles, which can form a network in cells through fusion, fission, and tubulation. Its morphology is closely related to the function of mitochondria. The damaged mitochondria can be removed by mitophagy. However, the relationship between mitochondrial morphology and non-selective autophagy is not fully understood. We found that mitochondrial fusion machinery, not fission or tubulation machinery, is essential for energy deprivation-induced autophagy. In response to glucose starvation, deletion of mitochondrial fusion proteins severely impaired the association of Atg1/ULK1 with Atg13, and then affected the recruitment of Atg1 and other autophagic proteins to PAS (phagophore assembly site). Furthermore, the deletion of fusion proteins blocks mitochondrial respiration, the binding of Snf1-Mec1, the phosphorylation of Mec1 by Snf1, and the dissociation of Mec1 from mitochondria under prolonged starvation. We propose that mitochondrial fusion machinery regulates energy deprivation-induced autophagy through maintaining mitochondrial respiration.
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Affiliation(s)
- Choufei Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, School of Life Sciences, Huzhou University, Huzhou, China
| | - Weijing Yao
- Department of Biochemistry, Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenwen Kai
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, School of Life Sciences, Huzhou University, Huzhou, China
| | - Weikang Liu
- Department of Biochemistry, Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenlve Wang
- Department of Biochemistry, Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shuzhen Li
- Department of Biochemistry, Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingcong Chen
- Department of Biochemistry, Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoyong Wu
- Department of Biochemistry, Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liefeng Wang
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou, China
| | - Ying Li
- School of Life Sciences, Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Jingjing Tong
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Jing Qian
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, School of Nursing and Medicine, Huzhou University, Huzhou, China
| | - Liqin Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, School of Life Sciences, Huzhou University, Huzhou, China
| | - Zhi Hong
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China.,ZJU-UoE Institute, Zhejiang University School of Medicine, International Campus, Zhejiang University, Haining, China
| | - Cong Yi
- Department of Biochemistry, Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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30
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Step-wise elimination of α-mitochondrial nucleoids and mitochondrial structure as a basis for the strict uniparental inheritance in Cryptococcus neoformans. Sci Rep 2020; 10:2468. [PMID: 32051468 PMCID: PMC7016115 DOI: 10.1038/s41598-020-59277-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 01/27/2020] [Indexed: 01/24/2023] Open
Abstract
In most sexual eukaryotes, mitochondrial (mt) DNA is uniparentally inherited, although the detailed mechanisms underlying this phenomenon remain controversial. The most widely accepted explanations include the autophagic elimination of paternal mitochondria in the fertilized eggs and the active degradation of paternal mitochondrial DNA. To decode the precise program for the uniparental inheritance, we focused on Cryptococcus neoformans as a model system, in which mtDNA is inherited only from the a-parent, although gametes of a- and α-cells are of equal size and contribute equal amounts of mtDNA to the zygote. In this research, the process of preferential elimination of the mitochondria contributed by the α-parent (α-mitochondria) was studied by fluorescence microscopy and single cell analysis using optical tweezers, which revealed that α-mitochondria are preferentially reduced by the following three steps: (1) preferential reduction of α-mitochondrial (mt) nucleoids and α-mtDNA, (2) degradation of the α-mitochondrial structure and (3) proliferation of remaining mt nucleoids during the zygote development. Furthermore, AUTOPHAGY RELATED GENE (ATG) 8 and the gene encoding mitochondrial endonuclease G (NUC1) were disrupted, and the effects of their disruption on the uniparental inheritance were scrutinized. Disruption of ATG8 (ATG7) and NUC1 did not have severe effects on the uniparental inheritance, but microscopic examination revealed that α-mitochondria lacking mt nucleoids persisted in Δatg8 zygotes, indicating that autophagy is not critical for the uniparental inheritance per se but is responsible for the clearance of mitochondrial structures after the reduction of α-mt nucleoids.
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31
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Cecconi F. Autophagy, replication stress and DNA synthesis, an intricate relationship. Cell Death Differ 2020; 27:829-830. [PMID: 31900426 DOI: 10.1038/s41418-019-0479-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 11/09/2022] Open
Affiliation(s)
- Francesco Cecconi
- Unit of Cell Stress and Survival, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Society Research Center, 2100, Copenhagen, Denmark. .,Department of Biology, University of Rome Tor Vergata and Department of Pediatric Hemato-Oncology and Cell and Gene therapy, IRCCS Bambino Gesù Children's Hospital, 00143, Rome, Italy.
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32
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Mechanisms of Autophagy in Metabolic Stress Response. J Mol Biol 2020; 432:28-52. [DOI: 10.1016/j.jmb.2019.09.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/06/2019] [Accepted: 09/06/2019] [Indexed: 01/17/2023]
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33
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Saxena S, Somyajit K, Nagaraju G. XRCC2 Regulates Replication Fork Progression during dNTP Alterations. Cell Rep 2019; 25:3273-3282.e6. [PMID: 30566856 DOI: 10.1016/j.celrep.2018.11.085] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/08/2018] [Accepted: 11/21/2018] [Indexed: 02/07/2023] Open
Abstract
RAD51 paralogs are essential for maintenance of genomic integrity through protection of stalled replication forks and homology-directed repair (HDR) of double-strand breaks. Here, we find that a subset of RAD51 paralogs, XRCC2 (FANCU) and its binding partner RAD51D, restrain active DNA synthesis during dinucleotide triphosphate (dNTP) alterations in a manner independent of HDR. The absence of XRCC2 is associated with increased levels of RRM2, the regulatory subunit of ribonucleotide reductase (RNR), and concomitantly high nucleotide pools, leading to unrestrained fork progression and accumulation of DNA damage during dNTP alterations. Mechanistically, this function is independent of redox signaling and RAD51-mediated fork reversal and is regulated by ataxia-telangiectasia and Rad3-related (ATR) signaling through phosphorylation of XRCC2 (Ser247). Together, these findings identify roles of RAD51 paralogs in the control of replication fork progression and maintenance of genome stability during nucleotide pool alterations.
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Affiliation(s)
- Sneha Saxena
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Kumar Somyajit
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
| | - Ganesh Nagaraju
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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34
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Anderson CM, Macleod KF. Autophagy and cancer cell metabolism. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2019; 347:145-190. [PMID: 31451213 PMCID: PMC8211395 DOI: 10.1016/bs.ircmb.2019.06.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Autophagy is an ancient catabolic process used by cells to clear excess or dysfunctional organelles and large subcellular structures and thus performs an important housekeeping role for the cell. Autophagy is acutely sensitive to nutrient availability and is upregulated at a transcriptional and posttranslational level in response to nutrient deprivation. This serves to promote turnover of cellular content and recycling of nutrients for continued growth and survival. While important for most normal tissues, tumor cells appear to be particularly dependent on autophagy for survival under ischemic or therapeutic stress, and in response to loss of matrix attachment; autophagy is upregulated markedly in cancers as they progress to malignancy. Ras-driven tumors appear to be particularly dependent on autophagy and thus inhibition of autophagy is being pursued as a productive clinical approach for such cancers. However, this enthusiasm needs to be offset against possible negative effects of autophagy inhibition on normal tissue function and on limiting antitumor immune responses. In addressing all of these topics, we focus in on understanding how autophagy is induced by nutrient stress, its role in recycling metabolites for growing tumors, how selective forms of autophagy, such as mitophagy and ribophagy contribute specifically to tumorigenesis, how autophagy in the tumor microenvironment and throughout the animal affects access of the tumor to nutrients, and finally how different oncogenic pathways may determine which tumors respond to autophagy inhibition and which ones will not.
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Affiliation(s)
- Cara M Anderson
- The Ben May Department for Cancer Research, The Gordon Center for Integrative Sciences, The University of Chicago, Chicago, IL, United States; The Committee on Molecular Metabolism & Nutrition, The University of Chicago, Chicago, IL, United States
| | - Kay F Macleod
- The Ben May Department for Cancer Research, The Gordon Center for Integrative Sciences, The University of Chicago, Chicago, IL, United States; The Committee on Molecular Metabolism & Nutrition, The University of Chicago, Chicago, IL, United States; The Committee on Cancer Biology, University of Chicago, Chicago, IL, United States.
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35
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Cui R, Medeiros T, Willemsen D, Iasi LN, Collier GE, Graef M, Reichard M, Valenzano DR. Relaxed Selection Limits Lifespan by Increasing Mutation Load. Cell 2019; 178:385-399.e20. [DOI: 10.1016/j.cell.2019.06.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 03/18/2019] [Accepted: 06/03/2019] [Indexed: 02/07/2023]
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36
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Role of Mitochondrial DNA Damage in ROS-Mediated Pathogenesis of Age-Related Macular Degeneration (AMD). Int J Mol Sci 2019; 20:ijms20102374. [PMID: 31091656 PMCID: PMC6566654 DOI: 10.3390/ijms20102374] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/17/2019] [Accepted: 04/28/2019] [Indexed: 12/19/2022] Open
Abstract
Age-related macular degeneration (AMD) is a complex eye disease that affects millions of people worldwide and is the main reason for legal blindness and vision loss in the elderly in developed countries. Although the cause of AMD pathogenesis is not known, oxidative stress-related damage to retinal pigment epithelium (RPE) is considered an early event in AMD induction. However, the precise cause of such damage and of the induction of oxidative stress, including related oxidative effects occurring in RPE and the onset and progression of AMD, are not well understood. Many results point to mitochondria as a source of elevated levels of reactive oxygen species (ROS) in AMD. This ROS increase can be associated with aging and effects induced by other AMD risk factors and is correlated with damage to mitochondrial DNA. Therefore, mitochondrial DNA (mtDNA) damage can be an essential element of AMD pathogenesis. This is supported by many studies that show a greater susceptibility of mtDNA than nuclear DNA to DNA-damaging agents in AMD. Therefore, the mitochondrial DNA damage reaction (mtDDR) is important in AMD prevention and in slowing down its progression as is ROS-targeting AMD therapy. However, we know far less about mtDNA than its nuclear counterparts. Further research should measure DNA damage in order to compare it in mitochondria and the nucleus, as current methods have serious disadvantages.
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Nissanka N, Minczuk M, Moraes CT. Mechanisms of Mitochondrial DNA Deletion Formation. Trends Genet 2019; 35:235-244. [PMID: 30691869 DOI: 10.1016/j.tig.2019.01.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 02/02/2023]
Abstract
Mitochondrial DNA (mtDNA) encodes a subset of genes which are essential for oxidative phosphorylation. Deletions in the mtDNA can ablate a number of these genes and result in mitochondrial dysfunction, which is associated with bona fide mitochondrial disorders. Although mtDNA deletions are thought to occur as a result of replication errors or following double-strand breaks, the exact mechanism(s) behind deletion formation have yet to be determined. In this review we discuss the current knowledge about the fate of mtDNA following double-strand breaks, including the molecular players which mediate the degradation of linear mtDNA fragments and possible mechanisms of recircularization. We propose that mtDNA deletions formed from replication errors versus following double-strand breaks can be mediated by separate pathways.
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Affiliation(s)
- Nadee Nissanka
- Department of Neurology, University of Miami, Miller School of Medicine, FL 33136, USA
| | - Michal Minczuk
- Medical Research Council (MRC) Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Carlos T Moraes
- Department of Neurology, University of Miami, Miller School of Medicine, FL 33136, USA.
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Doxorubicin-induced cardiomyopathy associated with inhibition of autophagic degradation process and defects in mitochondrial respiration. Sci Rep 2019; 9:2002. [PMID: 30765730 PMCID: PMC6376057 DOI: 10.1038/s41598-018-37862-3] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 12/15/2018] [Indexed: 12/21/2022] Open
Abstract
Doxorubicin (Dox) is a highly effective anticancer drug but cause acute ventricular dysfunction, and also induce late-onset cardiomyopathy and heart failure. Despite extensive studies, the pathogenic sequelae leading to the progression of Dox-associated cardiomyopathy remains unknown. We assessed temporal changes in autophagy, mitochondrial dynamics, and bioenergetics in mouse models of acute and chronic Dox-cardiomyopathy. Time course study of acute Dox-treatment showed accumulation of LC3B II in heart lysates. Autophagy flux assays confirmed that the Dox-induced accumulation of autophagosomes occurs due to blockage of the lysosomal degradation process. Dox-induced autophagosomes and autolysosome accumulation were confirmed in vivo by using GFP-LC3 and mRFP-GFP-LC3 transgenic (Tg) mice. Mitochondria isolated from acute Dox-treated hearts showed significant suppression of oxygen consumption rate (OCR). Chronic Dox-cardiotoxicity also exhibited time-dependent accumulation of LC3B II levels and increased accumulation of green puncta in GFP-LC3 Tg hearts. Mitochondria isolated from chronic Dox-treated hearts also showed significant suppression of mitochondrial OCR. The in vivo impairment of autophagic degradation process and mitochondrial dysfunction data were confirmed in vitro using cultured neonatal cardiomyocytes. Both acute and chronic Dox-associated cardiomyopathy involves a multifocal disease process resulting from autophagosomes and autolysosomes accumulation, altered expression of mitochondrial dynamics and oxidative phosphorylation regulatory proteins, and mitochondrial respiratory dysfunction.
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Iwama R, Ohsumi Y. Analysis of autophagy activated during changes in carbon source availability in yeast cells. J Biol Chem 2019; 294:5590-5603. [PMID: 30755486 DOI: 10.1074/jbc.ra118.005698] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 02/05/2019] [Indexed: 11/06/2022] Open
Abstract
Autophagy is a conserved intracellular degradation system in eukaryotes. Recent studies have revealed that autophagy can be induced not only by nitrogen starvation but also by many other stimuli. However, questions persist regarding the types of conditions that induce autophagy, as well as the particular kinds of autophagy that are induced under these specific conditions. In experimental studies, abrupt nutrient changes are often used to induce autophagy. In this study, we investigated autophagy induction in batch culture on low-glucose medium, in which growth of yeast (Saccharomyces cerevisiae) cells is clearly reflected exclusively by carbon source state. In this medium, cells pass sequentially through three stages: glucose-utilizing, ethanol-utilizing, and ethanol-depleted phases. Using GFP cleavage assay by immunoblotting methods, fluorescence microscopy, and transmission electron microscopy ultrastructural analysis, we found that bulk autophagy and endoplasmic reticulum-phagy are induced starting at the ethanol-utilizing phase, and bulk autophagy is activated to a greater extent in the ethanol-depleted phase. Furthermore, we found that mitophagy is induced by ethanol depletion. Microautophagy occurred after glucose depletion and involved incorporation of cytosolic components and lipid droplets into the vacuolar lumen. Moreover, we observed that autophagy-deficient cells grow more slowly in the ethanol-utilizing phase and exhibit a delay in growth resumption when they are shifted to fresh medium from the ethanol-depleted phase. Our findings suggest that distinct types of autophagy are induced in yeast cells undergoing gradual changes in carbon source availability.
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Affiliation(s)
- Ryo Iwama
- From the Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259-S2-12 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Yoshinori Ohsumi
- From the Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259-S2-12 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
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40
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Zhao L. Mitochondrial DNA degradation: A quality control measure for mitochondrial genome maintenance and stress response. Enzymes 2019; 45:311-341. [PMID: 31627882 DOI: 10.1016/bs.enz.2019.08.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mitochondria play a central role in bioenergetics, and fulfill a plethora of functions in cell signaling, programmed cell death, and biosynthesis of key protein cofactors. Mitochondria harbor their own genomic DNA, which encodes protein subunits of the electron transport chain and a full set of transfer and ribosomal RNAs. Mitochondrial DNA (mtDNA) is essential for cellular and organismal functions, and defects in mitochondrial genome maintenance have been implicated in common human diseases and mitochondrial disorders. mtDNA repair and degradation are known pathways to cope with mtDNA damage; however, molecular factors involved in this process have remained unclear. Such knowledge is fundamental to the understanding of mitochondrial genomic maintenance and pathology, because mtDNA degradation may contribute to the etiology of mtDNA depletion syndromes and to the activation of the innate immune response by fragmented mtDNA. This article reviews the current literature regarding the importance of mitochondrial DNA degradation in mtDNA maintenance and stress response, and the recent progress in uncovering molecular factors involved in mtDNA degradation. These factors include key components of the mtDNA replication machinery, such as DNA polymerase γ, helicase Twinkle, and exonuclease MGME1, as well as a major DNA-packaging protein, mitochondrial transcription factor A (TFAM).
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Affiliation(s)
- Linlin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States.
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Abstract
Derived from bacterial ancestors, mitochondria have maintained their own albeit strongly reduced genome, mitochondrial DNA (mtDNA), which encodes for a small and highly specialized set of genes. MtDNA exists in tens to thousands of copies packaged in numerous nucleoprotein complexes, termed nucleoids, distributed throughout the dynamic mitochondrial network. Our understanding of the mechanisms of how cells regulate the copy number of mitochondrial genomes has been limited. Here, we summarize and discuss our recent findings that Mip1/POLG (mitochondrial DNA polymerase gamma) critically controls mtDNA copy number by operating in 2 opposing modes, synthesis and, unexpectedly, degradation of mtDNA, when yeast cells face nutrient starvation. The balance of the 2 modes of Mip1/POLG and thus mtDNA copy number dynamics depends on the integrity of macroautophagy/autophagy, which sustains continuous synthesis and maintenance of mtDNA. In autophagy-deficient cells, a combination of nucleotide insufficiency and elevated mitochondrial ROS production impairs mtDNA synthesis and drives mtDNA degradation by the 3'-5'-exonuclease activity of Mip1/POLG resulting in mitochondrial genome depletion and irreversible respiratory deficiency. Abbrivations: mtDNA: mitochondrial DNA; mtDCN: mitochondrial DNA copy number.
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Affiliation(s)
| | - Martin Graef
- a MPRG Graef, Max Planck Institute for Biology of Ageing , Cologne , Germany.,b Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) , University of Cologne , Cologne , Germany
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Medler T, Patel JM, Alice A, Baird JR, Hu HM, Gough MJ. Activating the Nucleic Acid-Sensing Machinery for Anticancer Immunity. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 344:173-214. [PMID: 30798988 PMCID: PMC6754183 DOI: 10.1016/bs.ircmb.2018.08.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleic acid sensing pathways have likely evolved as part of a broad pathogen sensing strategy intended to discriminate infectious agents and initiate appropriate innate and adaptive controls. However, in the absence of infectious agents, nucleic acid sensing pathways have been shown to play positive and negative roles in regulating tumorigenesis, tumor progression and metastatic spread. Understanding the normal biology behind these pathways and how they are regulated in malignant cells and in the tumor immune environment can help us devise strategies to exploit nucleic acid sensing to manipulate anti-cancer immunity.
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Affiliation(s)
- Terry Medler
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, Portland, OR, United States
| | - Jaina M Patel
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, Portland, OR, United States
| | - Alejandro Alice
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, Portland, OR, United States
| | - Jason R Baird
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, Portland, OR, United States
| | - Hong-Ming Hu
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, Portland, OR, United States
| | - Michael J Gough
- Earle A. Chiles Research Institute, Robert W. Franz Cancer Center, Providence Portland Medical Center, Portland, OR, United States.
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Nissanka N, Bacman SR, Plastini MJ, Moraes CT. The mitochondrial DNA polymerase gamma degrades linear DNA fragments precluding the formation of deletions. Nat Commun 2018; 9:2491. [PMID: 29950568 PMCID: PMC6021392 DOI: 10.1038/s41467-018-04895-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 05/25/2018] [Indexed: 02/03/2023] Open
Abstract
Double-strand breaks in the mitochondrial DNA (mtDNA) result in the formation of linear fragments that are rapidly degraded. However, the identity of the nuclease(s) performing this function is not known. We found that the exonuclease function of the mtDNA polymerase gamma (POLG) is required for this rapid degradation of mtDNA fragments. POLG is recruited to linearized DNA fragments in an origin of replication-independent manner. Moreover, in the absence of POLG exonuclease activity, the prolonged existence of mtDNA linear fragments leads to increased levels of mtDNA deletions, which have been previously identified in the mutator mouse, patients with POLG mutations and normal aging. Mitochondrial DNA fragments are rapidly degraded when double strand breaks occur. Here the authors reveal that the exonuclease activity of polymerase gamma is important for efficient degradation of these fragments and to avoid formation of large deletions.
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Affiliation(s)
- Nadee Nissanka
- Neuroscience Graduate Program, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Sandra R Bacman
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Melanie J Plastini
- Neuroscience Graduate Program, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Carlos T Moraes
- Neuroscience Graduate Program, University of Miami Miller School of Medicine, Miami, FL, 33136, USA. .,Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
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