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Mitochondrial genome stability in human: understanding the role of DNA repair pathways. Biochem J 2021; 478:1179-1197. [DOI: 10.1042/bcj20200920] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 11/17/2022]
Abstract
Mitochondria are semiautonomous organelles in eukaryotic cells and possess their own genome that replicates independently. Mitochondria play a major role in oxidative phosphorylation due to which its genome is frequently exposed to oxidative stress. Factors including ionizing radiation, radiomimetic drugs and replication fork stalling can also result in different types of mutations in mitochondrial DNA (mtDNA) leading to genome fragility. Mitochondria from myopathies, dystonia, cancer patient samples show frequent mtDNA mutations such as point mutations, insertions and large-scale deletions that could account for mitochondria-associated disease pathogenesis. The mechanism by which such mutations arise following exposure to various DNA-damaging agents is not well understood. One of the well-studied repair pathways in mitochondria is base excision repair. Other repair pathways such as mismatch repair, homologous recombination and microhomology-mediated end joining have also been reported. Interestingly, nucleotide excision repair and classical nonhomologous DNA end joining are not detected in mitochondria. In this review, we summarize the potential causes of mitochondrial genome fragility, their implications as well as various DNA repair pathways that operate in mitochondria.
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2
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UCP2 ameliorates mitochondrial dysfunction, inflammation, and oxidative stress in lipopolysaccharide-induced acute kidney injury. Int Immunopharmacol 2019; 71:336-349. [DOI: 10.1016/j.intimp.2019.03.043] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 03/21/2019] [Indexed: 12/19/2022]
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3
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Melatonin Balance the Autophagy and Apoptosis by Regulating UCP2 in the LPS-Induced Cardiomyopathy. Molecules 2018; 23:molecules23030675. [PMID: 29547569 PMCID: PMC6017117 DOI: 10.3390/molecules23030675] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 02/28/2018] [Accepted: 03/01/2018] [Indexed: 12/30/2022] Open
Abstract
To explore the mechanism of mitochondrial uncoupling protein 2 (UCP2) mediating the protective of melatonin when septic cardiomyopathy. UCP2 knocked out mice and cardiomyocytes were used to study the effect of melatonin in response to LPS. Indicators of myocardial and mitochondria injury including mitochondrial membrane potential, mitochondrial permeability transition pore, calcium loading, ROS, and ATP detection were assessed. In addition cell viability and apoptosis as well as autophagy-associated proteins were evaluated. Melatonin was able to protect heart function from LPS, which weakened in the UCP2-knockout mice. Consistently, genipin, a pharmacologic inhibitor of UCP2, augmented LPS-induced damage of AC16 cells. In contrast, melatonin upregulated UCP2 expression and protected the cells from the changes in morphology, mitochondrial membrane potential loss, mitochondrial Ca2+ overload, the opening of mitochondrial permeability transition pore, and subsequent increased ROS generation as well as ATP reduction. Mitophagy proteins (Beclin-1 and LC-3β) were increased while apoptosis-associated proteins (cytochrome C and caspase-3) were decreased when UCP2 was up-regulated. In conclusion, UCP2 may play a protecting role against LPS by regulating the balance between autophagy and apoptosis of cardiomyocytes, and by which mechanisms, it may contribute to homeostasis of cardiac function and cardiomyocytes activity. Melatonin may protect cardiomyocytes through modulating UCP2.
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VenkatRao V, Chaitanya RK, Naresh Kumar D, Bramhaiah M, Dutta-Gupta A. Developmental and hormone-induced changes of mitochondrial electron transport chain enzyme activities during the last instar larval development of maize stem borer, Chilo partellus (Lepidoptera: Crambidae). Gen Comp Endocrinol 2016; 239:32-39. [PMID: 26709029 DOI: 10.1016/j.ygcen.2015.12.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 12/07/2015] [Accepted: 12/15/2015] [Indexed: 12/28/2022]
Abstract
The energy demand for structural remodelling in holometabolous insects is met by cellular mitochondria. Developmental and hormone-induced changes in the mitochondrial respiratory activity during insect metamorphosis are not well documented. The present study investigates activities of enzymes of mitochondrial electron transport chain (ETC) namely, NADH:ubiquinone oxidoreductase or complex I, Succinate: ubiquinone oxidoreductase or complex II, Ubiquinol:ferricytochrome c oxidoreductase or complex III, cytochrome c oxidase or complex IV and F1F0ATPase (ATPase), during Chilo partellus development. Further, the effect of juvenile hormone (JH) analog, methoprene, and brain and corpora-allata-corpora-cardiaca (CC-CA) homogenates that represent neurohormones, on the ETC enzyme activities was monitored. The enzymatic activities increased from penultimate to last larval stage and thereafter declined during pupal development with an exception of ATPase which showed high enzyme activity during last larval and pupal stages compared to the penultimate stage. JH analog, methoprene differentially modulated ETC enzyme activities. It stimulated complex I and IV enzyme activities, but did not alter the activities of complex II, III and ATPase. On the other hand, brain homogenate declined the ATPase activity while the injected CC-CA homogenate stimulated complex I and IV enzyme activities. Cumulatively, the present study is the first to show that mitochondrial ETC enzyme system is under hormone control, particularly of JH and neurohormones during insect development.
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Affiliation(s)
- V VenkatRao
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - R K Chaitanya
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - D Naresh Kumar
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - M Bramhaiah
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - A Dutta-Gupta
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
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5
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Abstract
Recent advances in the field of mitochondrial DNA (mtDNA) replication highlight the diversity of both the mechanisms utilized and the structural and functional organization of the proteins at mtDNA replication fork, despite the relative simplicity of the animal mtDNA genome. DNA polymerase γ, mtDNA helicase and mitochondrial single-stranded DNA-binding protein-the key replisome proteins, have evolved distinct structural features and biochemical properties. These appear to be correlated with mtDNA genomic features in different metazoan taxa and with their modes of DNA replication, although substantial integrative research is warranted to establish firmly these links. To date, several modes of mtDNA replication have been described for animals: rolling circle, theta, strand-displacement, and RITOLS/bootlace. Resolution of a continuing controversy relevant to mtDNA replication in mammals/vertebrates will have a direct impact on the mechanistic interpretation of mtDNA-related human diseases. Here we review these subjects, integrating earlier and recent data to provide a perspective on the major challenges for future research.
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Affiliation(s)
- G L Ciesielski
- Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland; Michigan State University, East Lansing, MI, United States
| | - M T Oliveira
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
| | - L S Kaguni
- Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland; Michigan State University, East Lansing, MI, United States.
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6
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Clemente P, Pajak A, Laine I, Wibom R, Wedell A, Freyer C, Wredenberg A. SUV3 helicase is required for correct processing of mitochondrial transcripts. Nucleic Acids Res 2015; 43:7398-413. [PMID: 26152302 PMCID: PMC4551930 DOI: 10.1093/nar/gkv692] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/25/2015] [Indexed: 12/05/2022] Open
Abstract
Mitochondrial gene expression is largely regulated by post-transcriptional mechanisms that control the amount and translation of each mitochondrial mRNA. Despite its importance for mitochondrial function, the mechanisms and proteins involved in mRNA turnover are still not fully characterized. Studies in yeast and human cell lines have indicated that the mitochondrial helicase SUV3, together with the polynucleotide phosphorylase, PNPase, composes the mitochondrial degradosome. To further investigate the in vivo function of SUV3 we disrupted the homolog of SUV3 in Drosophila melanogaster (Dm). Loss of dmsuv3 led to the accumulation of mitochondrial mRNAs, without increasing rRNA levels, de novo transcription or decay intermediates. Furthermore, we observed a severe decrease in mitochondrial tRNAs accompanied by an accumulation of unprocessed precursor transcripts. These processing defects lead to reduced mitochondrial translation and a severe respiratory chain complex deficiency, resulting in a pupal lethal phenotype. In summary, our results propose that SUV3 is predominantly required for the processing of mitochondrial polycistronic transcripts in metazoan and that this function is independent of PNPase.
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Affiliation(s)
- Paula Clemente
- Division of Metabolic Diseases, Department of Laboratory Medicine; Karolinska Institutet, Stockholm 17177, Sweden
| | - Aleksandra Pajak
- Division of Metabolic Diseases, Department of Laboratory Medicine; Karolinska Institutet, Stockholm 17177, Sweden
| | - Isabelle Laine
- Division of Metabolic Diseases, Department of Laboratory Medicine; Karolinska Institutet, Stockholm 17177, Sweden
| | - Rolf Wibom
- Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Anna Wedell
- Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm 17176, Sweden Department of Molecular Medicine and Surgery, Science for Life Laboratory, Karolinska Institutet, Stockholm 17176, Sweden
| | - Christoph Freyer
- Division of Metabolic Diseases, Department of Laboratory Medicine; Karolinska Institutet, Stockholm 17177, Sweden Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Anna Wredenberg
- Division of Metabolic Diseases, Department of Laboratory Medicine; Karolinska Institutet, Stockholm 17177, Sweden Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm 17176, Sweden
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7
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Phillips WS, Coleman-Hulbert AL, Weiss ES, Howe DK, Ping S, Wernick RI, Estes S, Denver DR. Selfish Mitochondrial DNA Proliferates and Diversifies in Small, but not Large, Experimental Populations of Caenorhabditis briggsae. Genome Biol Evol 2015; 7:2023-37. [PMID: 26108490 PMCID: PMC4524483 DOI: 10.1093/gbe/evv116] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Evolutionary interactions across levels of biological organization contribute to a variety of fundamental processes including genome evolution, reproductive mode transitions, species diversification, and extinction. Evolutionary theory predicts that so-called “selfish” genetic elements will proliferate when the host effective population size (Ne) is small, but direct tests of this prediction remain few. We analyzed the evolutionary dynamics of deletion-containing mitochondrial DNA (ΔmtDNA) molecules, previously characterized as selfish elements, in six different natural strains of the nematode Caenorhabditis briggsae allowed to undergo experimental evolution in a range of population sizes (N = 1, 10, 100, and 1,000) for a maximum of 50 generations. Mitochondrial DNA (mtDNA) was analyzed for replicate lineages at each five-generation time point. Ten different ΔmtDNA molecule types were observed and characterized across generations in the experimental populations. Consistent with predictions from evolutionary theory, lab lines evolved in small-population sizes (e.g., nematode N = 1) were more susceptible to accumulation of high levels of preexisting ΔmtDNA compared with those evolved in larger populations. New ΔmtDNA elements were observed to increase in frequency and persist across time points, but almost exclusively at small population sizes. In some cases, ΔmtDNA levels decreased across generations when population size was large (nematode N = 1,000). Different natural strains of C. briggsae varied in their susceptibilities to ΔmtDNA accumulation, owing in part to preexisting compensatory mtDNA alleles in some strains that prevent deletion formation. This analysis directly demonstrates that the evolutionary trajectories of ΔmtDNA elements depend upon the population-genetic environments and molecular-genetic features of their hosts.
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Affiliation(s)
| | | | - Emily S Weiss
- Department of Integrative Biology, Oregon State University
| | - Dana K Howe
- Department of Integrative Biology, Oregon State University
| | - Sita Ping
- Department of Integrative Biology, Oregon State University
| | | | | | - Dee R Denver
- Department of Integrative Biology, Oregon State University
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8
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Oliveira MT, Haukka J, Kaguni LS. Evolution of the metazoan mitochondrial replicase. Genome Biol Evol 2015; 7:943-59. [PMID: 25740821 PMCID: PMC4419789 DOI: 10.1093/gbe/evv042] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2015] [Indexed: 01/10/2023] Open
Abstract
The large number of complete mitochondrial DNA (mtDNA) sequences available for metazoan species makes it a good system for studying genome diversity, although little is known about the mechanisms that promote and/or are correlated with the evolution of this organellar genome. By investigating the molecular evolutionary history of the catalytic and accessory subunits of the mtDNA polymerase, pol γ, we sought to develop mechanistic insight into its function that might impact genome structure by exploring the relationships between DNA replication and animal mitochondrial genome diversity. We identified three evolutionary patterns among metazoan pol γs. First, a trend toward stabilization of both sequence and structure occurred in vertebrates, with both subunits evolving distinctly from those of other animal groups, and acquiring at least four novel structural elements, the most important of which is the HLH-3β (helix-loop-helix, 3 β-sheets) domain that allows the accessory subunit to homodimerize. Second, both subunits of arthropods and tunicates have become shorter and evolved approximately twice as rapidly as their vertebrate homologs. And third, nematodes have lost the gene for the accessory subunit, which was accompanied by the loss of its interacting domain in the catalytic subunit of pol γ, and they show the highest rate of molecular evolution among all animal taxa. These findings correlate well with the mtDNA genomic features of each group described above, and with their modes of DNA replication, although a substantive amount of biochemical work is needed to draw conclusive links regarding the latter. Describing the parallels between evolution of pol γ and metazoan mtDNA architecture may also help in understanding the processes that lead to mitochondrial dysfunction and to human disease-related phenotypes.
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Affiliation(s)
- Marcos T Oliveira
- Institute of Biosciences and Medical Technology, University of Tampere, Finland Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho," Jaboticabal, SP, Brazil
| | - Jani Haukka
- Institute of Biosciences and Medical Technology, University of Tampere, Finland
| | - Laurie S Kaguni
- Institute of Biosciences and Medical Technology, University of Tampere, Finland Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University
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Chen Z, Qi Y, French S, Zhang G, Covian Garcia R, Balaban R, Xu H. Genetic mosaic analysis of a deleterious mitochondrial DNA mutation in Drosophila reveals novel aspects of mitochondrial regulation and function. Mol Biol Cell 2014; 26:674-84. [PMID: 25501370 PMCID: PMC4325838 DOI: 10.1091/mbc.e14-11-1513] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A lethal mtDNA mutation affecting COX is fully rescued by AOX. The mutant genome level remains constant in the somatic tissues along the aging process in heteroplasmic flies. A genetic scheme creates tissue-specific heteroplasmy in otherwise heteroplasmic background and reveals that Ca2+ mishandling contributes to the neurodegeneration. Various human diseases are associated with mitochondrial DNA (mtDNA) mutations, but heteroplasmy—the coexistence of mutant and wild-type mtDNA—complicates their study. We previously isolated a temperature-lethal mtDNA mutation in Drosophila, mt:CoIT300I, which affects the cytochrome c oxidase subunit I (CoI) locus. In the present study, we found that the decrease in cytochrome c oxidase (COX) activity was ascribable to a temperature-dependent destabilization of cytochrome a heme. Consistently, the viability of homoplasmic flies at 29°C was fully restored by expressing an alternative oxidase, which specifically bypasses the cytochrome chains. Heteroplasmic flies are fully viable and were used to explore the age-related and tissue-specific phenotypes of mt:CoIT300I. The proportion of mt:CoIT300I genome remained constant in somatic tissues along the aging process, suggesting a lack of quality control mechanism to remove defective mitochondria containing a deleterious mtDNA mutation. Using a genetic scheme that expresses a mitochondrially targeted restriction enzyme to induce tissue-specific homoplasmy in heteroplasmic flies, we found that mt:CoIT300I homoplasmy in the eye caused severe neurodegeneration at 29°C. Degeneration was suppressed by improving mitochondrial Ca2+ uptake, suggesting that Ca2+ mishandling contributed to mt:CoIT300I pathogenesis. Our results demonstrate a novel approach for Drosophila mtDNA genetics and its application in modeling mtDNA diseases.
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Affiliation(s)
- Zhe Chen
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20892
| | - Yun Qi
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20892
| | - Stephanie French
- Laboratory of Cardiac Energetics, National Heart, Lung, and Blood Institute, Bethesda, MD 20892
| | - Guofeng Zhang
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
| | - Raúl Covian Garcia
- Laboratory of Cardiac Energetics, National Heart, Lung, and Blood Institute, Bethesda, MD 20892
| | - Robert Balaban
- Laboratory of Cardiac Energetics, National Heart, Lung, and Blood Institute, Bethesda, MD 20892
| | - Hong Xu
- Laboratory of Molecular Genetics, National Institutes of Health, Bethesda, MD 20892
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10
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Baggio F, Bratic A, Mourier A, Kauppila TES, Tain LS, Kukat C, Habermann B, Partridge L, Larsson NG. Drosophila melanogaster LRPPRC2 is involved in coordination of mitochondrial translation. Nucleic Acids Res 2014; 42:13920-38. [PMID: 25428350 PMCID: PMC4267620 DOI: 10.1093/nar/gku1132] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Members of the pentatricopeptide repeat domain (PPR) protein family bind RNA and are important for post-transcriptional control of organelle gene expression in unicellular eukaryotes, metazoans and plants. They also have a role in human pathology, as mutations in the leucine-rich PPR-containing (LRPPRC) gene cause severe neurodegeneration. We have previously shown that the mammalian LRPPRC protein and its Drosophila melanogaster homolog DmLRPPRC1 (also known as bicoid stability factor) are necessary for mitochondrial translation by controlling stability and polyadenylation of mRNAs. We here report characterization of DmLRPPRC2, a second fruit fly homolog of LRPPRC, and show that it has a predominant mitochondrial localization and interacts with a stem-loop interacting RNA binding protein (DmSLIRP2). Ubiquitous downregulation of DmLrpprc2 expression causes respiratory chain dysfunction, developmental delay and shortened lifespan. Unexpectedly, decreased DmLRPPRC2 expression does not globally affect steady-state levels or polyadenylation of mitochondrial transcripts. However, some mitochondrial transcripts abnormally associate with the mitochondrial ribosomes and some products are dramatically overproduced and other ones decreased, which, in turn, results in severe deficiency of respiratory chain complexes. The function of DmLRPPRC2 thus seems to be to ensure that mitochondrial transcripts are presented to the mitochondrial ribosomes in an orderly fashion to avoid poorly coordinated translation.
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Affiliation(s)
- Francesca Baggio
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Ana Bratic
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Arnaud Mourier
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Timo E S Kauppila
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Luke S Tain
- Department of the Biological Mechanisms of Ageing, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Christian Kukat
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Bianca Habermann
- Department of Computational Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Linda Partridge
- Department of the Biological Mechanisms of Ageing, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany Department of Laboratory Medicine, Karolinska Institutet, Stockholm 17177, Sweden
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11
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Fernández-Ayala DJM, Jiménez-Gancedo S, Guerra I, Navas P. Invertebrate models for coenzyme q10 deficiency. Mol Syndromol 2014; 5:170-9. [PMID: 25126050 DOI: 10.1159/000362751] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The human syndrome of coenzyme Q (CoQ) deficiency is a heterogeneous mitochondrial disease characterized by a diminution of CoQ content in cells and tissues that affects all the electron transport processes CoQ is responsible for, like the electron transference in mitochondria for respiration and ATP production and the antioxidant capacity that it exerts in membranes and lipoproteins. Supplementation with external CoQ is the main attempt to address these pathologies, but quite variable results have been obtained ranging from little response to a dramatic recovery. Here, we present the importance of modeling human CoQ deficiencies in animal models to understand the genetics and the pathology of this disease, although the election of an organism is crucial and can sometimes be controversial. Bacteria and yeast harboring mutations that lead to CoQ deficiency are unable to grow if they have to respire but develop without any problems on media with fermentable carbon sources. The complete lack of CoQ in mammals causes embryonic lethality, whereas other mutations produce tissue-specific diseases as in humans. However, working with transgenic mammals is time and cost intensive, with no assurance of obtaining results. Caenorhabditis elegans and Drosophila melanogaster have been used for years as organisms to study embryonic development, biogenesis, degenerative pathologies, and aging because of the genetic facilities and the speed of working with these animal models. In this review, we summarize several attempts to model reliable human CoQ deficiencies in invertebrates, focusing on mutant phenotypes pretty similar to those observed in human patients.
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Affiliation(s)
- Daniel J M Fernández-Ayala
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo Olavide - CSIC, and CIBERER Instituto de Salud Carlos III, Seville, Spain
| | - Sandra Jiménez-Gancedo
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo Olavide - CSIC, and CIBERER Instituto de Salud Carlos III, Seville, Spain
| | - Ignacio Guerra
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo Olavide - CSIC, and CIBERER Instituto de Salud Carlos III, Seville, Spain
| | - Plácido Navas
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo Olavide - CSIC, and CIBERER Instituto de Salud Carlos III, Seville, Spain
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12
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Fukuoh A, Cannino G, Gerards M, Buckley S, Kazancioglu S, Scialo F, Lihavainen E, Ribeiro A, Dufour E, Jacobs HT. Screen for mitochondrial DNA copy number maintenance genes reveals essential role for ATP synthase. Mol Syst Biol 2014; 10:734. [PMID: 24952591 PMCID: PMC4265055 DOI: 10.15252/msb.20145117] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The machinery of mitochondrial DNA (mtDNA) maintenance is only partially characterized and is of wide interest due to its involvement in disease. To identify novel components of this machinery, plus other cellular pathways required for mtDNA viability, we implemented a genome-wide RNAi screen in Drosophila S2 cells, assaying for loss of fluorescence of mtDNA nucleoids stained with the DNA-intercalating agent PicoGreen. In addition to previously characterized components of the mtDNA replication and transcription machineries, positives included many proteins of the cytosolic proteasome and ribosome (but not the mitoribosome), three proteins involved in vesicle transport, some other factors involved in mitochondrial biogenesis or nuclear gene expression, > 30 mainly uncharacterized proteins and most subunits of ATP synthase (but no other OXPHOS complex). ATP synthase knockdown precipitated a burst of mitochondrial ROS production, followed by copy number depletion involving increased mitochondrial turnover, not dependent on the canonical autophagy machinery. Our findings will inform future studies of the apparatus and regulation of mtDNA maintenance, and the role of mitochondrial bioenergetics and signaling in modulating mtDNA copy number.
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Affiliation(s)
- Atsushi Fukuoh
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate school of Medical Sciences, Fukuoka, Japan Department of Medical Laboratory Science, Junshin Gakuen University, Fukuoka, Japan
| | - Giuseppe Cannino
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
| | - Mike Gerards
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
| | - Suzanne Buckley
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
| | - Selena Kazancioglu
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
| | - Filippo Scialo
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
| | - Eero Lihavainen
- Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Andre Ribeiro
- Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Eric Dufour
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
| | - Howard T Jacobs
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland Research Program of Molecular Neurology, University of Helsinki, Helsinki, Finland
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13
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A comprehensive approach to determining BER capacities and their change with aging inDrosophila melanogastermitochondria by oligonucleotide microarray. FEBS Lett 2014; 588:1673-9. [DOI: 10.1016/j.febslet.2014.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/24/2014] [Accepted: 03/06/2014] [Indexed: 11/22/2022]
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14
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Wilding M. Can we define maternal age as a genetic disease? Facts Views Vis Obgyn 2014; 6:105-8. [PMID: 25009733 PMCID: PMC4086015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
>Maternal age is strongly associated with a decrease in the probability of achieving pregnancy and the birth of a healthy child. Among current theories of the mechanism of this decrease is the hypothesis that a progressive degeneration of the respiratory capacity of mitochondria in eggs of women of advanced age leads to an energy deficit and consequent secondary effects on the oocyte and developing embryo. Mitochondria are uniquely inherited through the female germ line and these organelles contain DNA sequences that are independent from the genome. It is therefore possible that offspring born to females of advanced age inherit suboptimal mitochondria and that these persist throughout the life of the new being. This could in turn lead to long-term consequences for the offspring of females of advanced age such as a reduced potential lifespan in relation to the age of the mother at conception. In this review and hypothesis, we discuss the evidence relating to this theory and suggest that on this basis the maternal age effect could be classified as an inheritable genetic disease.
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Affiliation(s)
- M. Wilding
- CREATE Fertility, 3-5 Pepys Road, London SW20 8NJ, United Kingdom
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15
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McKinney EA, Oliveira MT. Replicating animal mitochondrial DNA. Genet Mol Biol 2013; 36:308-15. [PMID: 24130435 PMCID: PMC3795181 DOI: 10.1590/s1415-47572013000300002] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Accepted: 07/11/2013] [Indexed: 11/22/2022] Open
Abstract
The field of mitochondrial DNA (mtDNA) replication has been experiencing incredible progress in recent years, and yet little is certain about the mechanism(s) used by animal cells to replicate this plasmid-like genome. The long-standing strand-displacement model of mammalian mtDNA replication (for which single-stranded DNA intermediates are a hallmark) has been intensively challenged by a new set of data, which suggests that replication proceeds via coupled leading- and lagging-strand synthesis (resembling bacterial genome replication) and/or via long stretches of RNA intermediates laid on the mtDNA lagging-strand (the so called RITOLS). The set of proteins required for mtDNA replication is small and includes the catalytic and accessory subunits of DNA polymerase γ, the mtDNA helicase Twinkle, the mitochondrial single-stranded DNA-binding protein, and the mitochondrial RNA polymerase (which most likely functions as the mtDNA primase). Mutations in the genes coding for the first three proteins are associated with human diseases and premature aging, justifying the research interest in the genetic, biochemical and structural properties of the mtDNA replication machinery. Here we summarize these properties and discuss the current models of mtDNA replication in animal cells.
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Affiliation(s)
- Emily A McKinney
- Institute of Biomedical Technology, University of Tampere, Tampere, Finland
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Martínez-Azorín F, Calleja M, Hernández-Sierra R, Farr CL, Kaguni LS, Garesse R. Muscle-specific overexpression of the catalytic subunit of DNA polymerase γ induces pupal lethality in Drosophila melanogaster. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2013; 83:127-137. [PMID: 23729397 PMCID: PMC4703106 DOI: 10.1002/arch.21101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We show the physiological effects and molecular characterization of overexpression of the catalytic core of mitochondrial DNA (mtDNA) polymerase (pol γ-α) in muscle of Drosophila melanogaster. Muscle-specific overexpression of pol γ-α using the UAS/GAL4 (where UAS is upstream activation sequence) system produced more than 90% of lethality at the end of pupal stage at 25°C, and the survivor adult flies showed a significant reduction in life span. The survivor flies displayed a decreased mtDNA level that is accompanied by a corresponding decrease in the levels of the nucleoid-binding protein mitochondrial transcription factor A (mtTFA). Furthermore, an increase in apoptosis is detected in larvae and adults overexpressing pol γ-α. We suggest that the pupal lethality and reduced life span of survivor adult flies are both caused mainly by massive apoptosis of muscle cells induced by mtDNA depletion.
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Affiliation(s)
- Francisco Martínez-Azorín
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas Alberto Sols CSIC-UAM, Facultad de Medicina CIBERER ISCIII, Universidad Autónoma de Madrid, Madrid, Spain.
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Selfish little circles: transmission bias and evolution of large deletion-bearing mitochondrial DNA in Caenorhabditis briggsae nematodes. PLoS One 2012; 7:e41433. [PMID: 22859984 PMCID: PMC3409194 DOI: 10.1371/journal.pone.0041433] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 06/25/2012] [Indexed: 01/19/2023] Open
Abstract
Selfish DNA poses a significant challenge to genome stability and organismal fitness in diverse eukaryotic lineages. Although selfish mitochondrial DNA (mtDNA) has known associations with cytoplasmic male sterility in numerous gynodioecious plant species and is manifested as petite mutants in experimental yeast lab populations, examples of selfish mtDNA in animals are less common. We analyzed the inheritance and evolution of mitochondrial DNA bearing large heteroplasmic deletions including nad5 gene sequences (nad5Δ mtDNA), in the nematode Caenorhabditis briggsae. The deletion is widespread in C. briggsae natural populations and is associated with deleterious organismal effects. We studied the inheritance patterns of nad5Δ mtDNA using eight sets of C. briggsae mutation-accumulation (MA) lines, each initiated from a different natural strain progenitor and bottlenecked as single hermaphrodites across generations. We observed a consistent and strong drive toward higher levels of deletion-bearing molecules in the heteroplasmic pool of mtDNA after ten generations of bottlenecking. Our results demonstrate a uniform transmission bias whereby nad5Δ mtDNA accumulates to higher levels relative to intact mtDNA in multiple genetically diverse natural strains of C. briggsae. We calculated an average 1% per-generation transmission bias for deletion-bearing mtDNA relative to intact genomes. Our study, coupled with known deleterious phenotypes associated with high deletion levels, shows that nad5Δ mtDNA are selfish genetic elements that have evolved in natural populations of C. briggsae, offering a powerful new system to study selfish mtDNA dynamics in metazoans.
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Molecular mechanisms for age-associated mitochondrial deficiency in skeletal muscle. J Aging Res 2012; 2012:768304. [PMID: 22548174 PMCID: PMC3324903 DOI: 10.1155/2012/768304] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 01/23/2012] [Indexed: 01/01/2023] Open
Abstract
The abundance, morphology, and functional properties of mitochondria decay in skeletal muscle during the process of ageing. Although the precise mechanisms remain to be elucidated, these mechanisms include decreased mitochondrial DNA (mtDNA) repair and mitochondrial biogenesis. Mitochondria possess their own protection system to repair mtDNA damage, which leads to defects of mtDNA-encoded gene expression and respiratory chain complex enzymes. However, mtDNA mutations have shown to be accumulated with age in skeletal muscle. When damaged mitochondria are eliminated by autophagy, mitochondrial biogenesis plays an important role in sustaining energy production and physiological homeostasis. The capacity for mitochondrial biogenesis has shown to decrease with age in skeletal muscle, contributing to progressive mitochondrial deficiency. Understanding how these endogenous systems adapt to altered physiological conditions during the process of ageing will provide a valuable insight into the underlying mechanisms that regulate cellular homeostasis. Here we will summarize the current knowledge about the molecular mechanisms responsible for age-associated mitochondrial deficiency in skeletal muscle. In particular, recent findings on the role of mtDNA repair and mitochondrial biogenesis in maintaining mitochondrial functionality in aged skeletal muscle will be highlighted.
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Kalifa L, Quintana DF, Schiraldi LK, Phadnis N, Coles GL, Sia RA, Sia EA. Mitochondrial genome maintenance: roles for nuclear nonhomologous end-joining proteins in Saccharomyces cerevisiae. Genetics 2012; 190:951-64. [PMID: 22214610 PMCID: PMC3296257 DOI: 10.1534/genetics.111.138214] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 12/31/2011] [Indexed: 12/27/2022] Open
Abstract
Mitochondrial DNA (mtDNA) deletions are associated with sporadic and inherited diseases and age-associated neurodegenerative disorders. Approximately 85% of mtDNA deletions identified in humans are flanked by short directly repeated sequences; however, mechanisms by which these deletions arise are unknown. A limitation in deciphering these mechanisms is the essential nature of the mitochondrial genome in most living cells. One exception is budding yeast, which are facultative anaerobes and one of the few organisms for which directed mtDNA manipulation is possible. Using this model system, we have developed a system to simultaneously monitor spontaneous direct-repeat-mediated deletions (DRMDs) in the nuclear and mitochondrial genomes. In addition, the mitochondrial DRMD reporter contains a unique KpnI restriction endonuclease recognition site that is not present in otherwise wild-type (WT) mtDNA. We have expressed KpnI fused to a mitochondrial localization signal to induce a specific mitochondrial double-strand break (mtDSB). Here we report that loss of the MRX (Mre11p, Rad50p, Xrs2p) and Ku70/80 (Ku70p, Ku80p) complexes significantly impacts the rate of spontaneous deletion events in mtDNA, and these proteins contribute to the repair of induced mtDSBs. Furthermore, our data support homologous recombination (HR) as the predominant pathway by which mtDNA deletions arise in yeast, and suggest that the MRX and Ku70/80 complexes are partially redundant in mitochondria.
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Affiliation(s)
- Lidza Kalifa
- Department of Biology, University of Rochester, Rochester, New York 14627
| | - Daniel F. Quintana
- Department of Biology, University of Rochester, Rochester, New York 14627
| | - Laura K. Schiraldi
- Department of Biology, University of Rochester, Rochester, New York 14627
- Department of Biology, The College at Brockport, State University of New York, Brockport, New York 14420
| | - Naina Phadnis
- Department of Biology, University of Rochester, Rochester, New York 14627
| | - Garry L. Coles
- Department of Biology, The College at Brockport, State University of New York, Brockport, New York 14420
| | - Rey A. Sia
- Department of Biology, The College at Brockport, State University of New York, Brockport, New York 14420
| | - Elaine A. Sia
- Department of Biology, University of Rochester, Rochester, New York 14627
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Mechanism of transcription initiation by the yeast mitochondrial RNA polymerase. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:930-8. [PMID: 22353467 DOI: 10.1016/j.bbagrm.2012.02.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 02/03/2012] [Accepted: 02/04/2012] [Indexed: 02/03/2023]
Abstract
Mitochondria are the major supplier of cellular energy in the form of ATP. Defects in normal ATP production due to dysfunctions in mitochondrial gene expression are responsible for many mitochondrial and aging related disorders. Mitochondria carry their own DNA genome which is transcribed by relatively simple transcriptional machinery consisting of the mitochondrial RNAP (mtRNAP) and one or more transcription factors. The mtRNAPs are remarkably similar in sequence and structure to single-subunit bacteriophage T7 RNAP but they require accessory transcription factors for promoter-specific initiation. Comparison of the mechanisms of T7 RNAP and mtRNAP provides a framework to better understand how mtRNAP and the transcription factors work together to facilitate promoter selection, DNA melting, initiating nucleotide binding, and promoter clearance. This review focuses primarily on the mechanistic characterization of transcription initiation by the yeast Saccharomyces cerevisiae mtRNAP (Rpo41) and its transcription factor (Mtf1) drawing insights from the homologous T7 and the human mitochondrial transcription systems. We discuss regulatory mechanisms of mitochondrial transcription and the idea that the mtRNAP acts as the in vivo ATP "sensor" to regulate gene expression. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
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Roestenberg P, Manjeri GR, Valsecchi F, Smeitink JAM, Willems PHGM, Koopman WJH. Pharmacological targeting of mitochondrial complex I deficiency: the cellular level and beyond. Mitochondrion 2011; 12:57-65. [PMID: 21757032 DOI: 10.1016/j.mito.2011.06.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 01/20/2011] [Accepted: 06/25/2011] [Indexed: 12/20/2022]
Abstract
Complex I (CI) represents a major entry point of electrons in the mitochondrial electron transport chain (ETC). It consists of 45 different subunits, encoded by the mitochondrial (mtDNA) and nuclear DNA (nDNA). In humans, mutations in nDNA-encoded subunits cause severe neurodegenerative disorders like Leigh Syndrome with onset in early childhood. The pathophysiological mechanism of these disorders is still poorly understood. Here we summarize the current knowledge concerning the consequences of nDNA-encoded CI mutations in patient-derived cells, present mouse models for human CI deficiency, and discuss potential treatment strategies for CI deficiency.
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Affiliation(s)
- Peggy Roestenberg
- Department of Biochemistry, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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Huang W, Yu M, Jiao Y, Ma J, Ma M, Wang Z, Wu H, Tan D. Mitochondrial transcription termination factor 2 binds to entire mitochondrial DNA and negatively regulates mitochondrial gene expression. Acta Biochim Biophys Sin (Shanghai) 2011; 43:472-9. [PMID: 21558281 DOI: 10.1093/abbs/gmr035] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial transcription termination factor 2 (mTERF2) is a mitochondrial matrix protein that binds to the mitochondrial DNA. Previous studies have shown that overexpression of mTERF2 can inhibit cell proliferation, but the mechanism has not been well defined so far. This study aimed to present the binding pattern of mTERF2 to the mitochondrial DNA (mtDNA) in vivo, and investigated the biological function of mTERF2 on the replication of mtDNA, mRNA transcription, and protein translation. The mTERF2 binding to entire mtDNA was identified via the chromatin immunoprecipitation analysis. The mtDNA replication efficiency and expression levels of mitochondria genes were significantly inhibited when the mTERF2 was overexpressed in HeLa cells. The inhibition level of mtDNA content was the same with the decreased levels of mRNA and mitochondrial protein expression. Overall, the mTERF2 might be a cell growth inhibitor based on its negative effect on mtDNA replication, which eventually down-regulated all of the oxidative phosphorylation components in the mitochondria that were essential for the cell's energy metabolism.
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Affiliation(s)
- Weiwei Huang
- Laboratory of Biochemistry and Molecular Biology, School of Life Sciences, Yunnan University, Kunming, China
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23
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Modeling mitochondrial encephalomyopathy in Drosophila. Neurobiol Dis 2010; 40:40-5. [PMID: 20472065 DOI: 10.1016/j.nbd.2010.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 05/04/2010] [Accepted: 05/06/2010] [Indexed: 11/21/2022] Open
Abstract
Mitochondrial encephalomyopathies are disturbingly complex and devastating diseases, reflecting the underlying importance of the affected organelle. Therapeutic approaches for these diseases remain limited due to a poor understanding of disease pathogenesis resulting largely from a lack of tractable model systems in which to study these diseases. This is especially so for disease conditions resulting from mutations directly affecting the mitochondrial genome. Recent studies using Drosophila to develop genetic models with endogenous mitochondrial mutations suggest the fruit fly will contribute significantly to our understanding of mitochondrial disease pathogenesis and the development of novel therapeutic avenues.
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