52
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Shvetsova AN, Mennerich D, Kerätär JM, Hiltunen JK, Kietzmann T. Non-electron transfer chain mitochondrial defects differently regulate HIF-1α degradation and transcription. Redox Biol 2017; 12:1052-1061. [PMID: 28531964 PMCID: PMC5440747 DOI: 10.1016/j.redox.2017.05.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/19/2017] [Accepted: 05/05/2017] [Indexed: 12/23/2022] Open
Abstract
Mitochondria are the main consumers of molecular O2 in a cell as well as an abundant source of reactive oxygen species (ROS). Both, molecular oxygen and ROS are powerful regulators of the hypoxia-inducible factor-1α-subunit (HIF-α). While a number of mechanisms in the oxygen-dependent HIF-α regulation are quite well known, the view with respect to mitochondria is less clear. Several approaches using pharmacological or genetic tools targeting the mitochondrial electron transport chain (ETC) indicated that ROS, mainly formed at the Rieske cluster of complex III of the ETC, are drivers of HIF-1α activation. However, studies investigating non-ETC located mitochondrial defects and their effects on HIF-1α regulation are scarce, if at all existing. Thus, in the present study we examined three cell lines with non-ETC mitochondrial defects and focused on HIF-1α degradation and transcription, target gene expression, as well as ROS levels. We found that cells lacking the key enzyme 2-enoyl thioester reductase/mitochondrial enoyl-CoA reductase (MECR), and cells lacking manganese superoxide dismutase (MnSOD) showed a reduced induction of HIF-1α under long-term (20h) hypoxia. By contrast, cells lacking the mitochondrial DNA depletion syndrome channel protein Mpv17 displayed enhanced levels of HIF-1α already under normoxic conditions. Further, we show that ROS do not exert a uniform pattern when mediating their effects on HIF-1α, although all mitochondrial defects in the used cell types increased ROS formation. Moreover, all defects caused a different HIF-1α regulation via promoting HIF-1α degradation as well as via changes in HIF-1α transcription. Thereby, MECR- and MnSOD-deficient cells showed a reduction in HIF-1α mRNA levels whereas the Mpv17 lacking cells displayed enhanced HIF-1α mRNA levels under normoxia and hypoxia. Altogether, our study shows for the first time that mitochondrial defects which are not related to the ETC and Krebs cycle contribute differently to HIF-1α regulation by affecting HIF-1α degradation and HIF-1α transcription where ROS play not a major role.
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Affiliation(s)
- Antonina N Shvetsova
- Faculty of Biochemistry and Molecular Medicine, and Biocenter Oulu, University of Oulu, FI-90014 Oulu, Finland
| | - Daniela Mennerich
- Faculty of Biochemistry and Molecular Medicine, and Biocenter Oulu, University of Oulu, FI-90014 Oulu, Finland
| | - Juha M Kerätär
- Faculty of Biochemistry and Molecular Medicine, and Biocenter Oulu, University of Oulu, FI-90014 Oulu, Finland
| | - J Kalervo Hiltunen
- Faculty of Biochemistry and Molecular Medicine, and Biocenter Oulu, University of Oulu, FI-90014 Oulu, Finland
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine, and Biocenter Oulu, University of Oulu, FI-90014 Oulu, Finland.
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53
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Desai R, Frazier AE, Durigon R, Patel H, Jones AW, Dalla Rosa I, Lake NJ, Compton AG, Mountford HS, Tucker EJ, Mitchell ALR, Jackson D, Sesay A, Di Re M, van den Heuvel LP, Burke D, Francis D, Lunke S, McGillivray G, Mandelstam S, Mochel F, Keren B, Jardel C, Turner AM, Ian Andrews P, Smeitink J, Spelbrink JN, Heales SJ, Kohda M, Ohtake A, Murayama K, Okazaki Y, Lombès A, Holt IJ, Thorburn DR, Spinazzola A. ATAD3 gene cluster deletions cause cerebellar dysfunction associated with altered mitochondrial DNA and cholesterol metabolism. Brain 2017; 140:1595-1610. [PMID: 28549128 PMCID: PMC5445257 DOI: 10.1093/brain/awx094] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 03/09/2017] [Indexed: 12/03/2022] Open
Abstract
Although mitochondrial disorders are clinically heterogeneous, they frequently involve the central nervous system and are among the most common neurogenetic disorders. Identifying the causal genes has benefited enormously from advances in high-throughput sequencing technologies; however, once the defect is known, researchers face the challenge of deciphering the underlying disease mechanism. Here we characterize large biallelic deletions in the region encoding the ATAD3C, ATAD3B and ATAD3A genes. Although high homology complicates genomic analysis of the ATAD3 defects, they can be identified by targeted analysis of standard single nucleotide polymorphism array and whole exome sequencing data. We report deletions that generate chimeric ATAD3B/ATAD3A fusion genes in individuals from four unrelated families with fatal congenital pontocerebellar hypoplasia, whereas a case with genomic rearrangements affecting the ATAD3C/ATAD3B genes on one allele and ATAD3B/ATAD3A genes on the other displays later-onset encephalopathy with cerebellar atrophy, ataxia and dystonia. Fibroblasts from affected individuals display mitochondrial DNA abnormalities, associated with multiple indicators of altered cholesterol metabolism. Moreover, drug-induced perturbations of cholesterol homeostasis cause mitochondrial DNA disorganization in control cells, while mitochondrial DNA aggregation in the genetic cholesterol trafficking disorder Niemann-Pick type C disease further corroborates the interdependence of mitochondrial DNA organization and cholesterol. These data demonstrate the integration of mitochondria in cellular cholesterol homeostasis, in which ATAD3 plays a critical role. The dual problem of perturbed cholesterol metabolism and mitochondrial dysfunction could be widespread in neurological and neurodegenerative diseases.
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Affiliation(s)
- Radha Desai
- MRC Laboratory, Mill Hill, London NW71AA, UK
| | - Ann E Frazier
- Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Melbourne VIC 3052, Australia
| | - Romina Durigon
- Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London, NW3 2PF, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Aleck W Jones
- Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London, NW3 2PF, UK
| | - Ilaria Dalla Rosa
- Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London, NW3 2PF, UK
| | - Nicole J Lake
- Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Melbourne VIC 3052, Australia
| | - Alison G Compton
- Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Melbourne VIC 3052, Australia
| | - Hayley S Mountford
- Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Melbourne VIC 3052, Australia
| | - Elena J Tucker
- Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Melbourne VIC 3052, Australia
| | - Alice L R Mitchell
- Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London, NW3 2PF, UK
| | - Deborah Jackson
- Bioinformatics and Biostatistics, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Abdul Sesay
- Bioinformatics and Biostatistics, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Miriam Di Re
- Mitochondrial Biology Unit, Hills Road, Cambridge, CB2 0XY, UK
| | - Lambert P van den Heuvel
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Derek Burke
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, UK and Laboratory Medicine, Great Ormond Street Hospital, London, UK
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne VIC 3052, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne VIC 3052, Australia.,Department of Pathology, University of Melbourne, Melbourne 3052, Australia
| | - George McGillivray
- MRC Laboratory, Mill Hill, London NW71AA, UK.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne VIC 3052, Australia
| | - Simone Mandelstam
- Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Melbourne VIC 3052, Australia.,The Florey Institute of Neuroscience and Mental Health Melbourne, Australia.,Departments of Radiology and Paediatrics, University of Melbourne, Melbourne, Australia
| | - Fanny Mochel
- AP-HP, Department of Genetics, GHU Pitié-Salpêtrière, Paris, F-75651 France.,Inserm U975; CNRS UMR 7225, ICM; F-75013, Paris, France
| | - Boris Keren
- Inserm U975; CNRS UMR 7225, ICM; F-75013, Paris, France.,AP-HP, Service de Biochimie Métabolique et Centre de Génétique moléculaire et chromosomique, GHU Pitié-Salpêtrière, Paris, F-75651 France
| | - Claude Jardel
- AP-HP, Service de Biochimie Métabolique et Centre de Génétique moléculaire et chromosomique, GHU Pitié-Salpêtrière, Paris, F-75651 France.,Inserm U1016; CNRS UMR 8104; Université Paris-Descartes-Paris 5; Institut Cochin, 75014 Paris, France
| | - Anne M Turner
- Department of Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia.,School of Women's and Children's Health, University of New South Wales, Kensington, NSW, Australia
| | - P Ian Andrews
- School of Women's and Children's Health, University of New South Wales, Kensington, NSW, Australia.,Department of Paediatric Neurology, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Jan Smeitink
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Johannes N Spelbrink
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Simon J Heales
- Department of Genetics and Genomic Medicine, Institute of Child Health, University College London, London, UK and Laboratory Medicine, Great Ormond Street Hospital, London, UK.,Department of Molecular Neuroscience, Institute of Neurology, University College London, Queen Square, London, UK
| | - Masakazu Kohda
- Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
| | - Akira Ohtake
- Department of Pediatrics, Saitama Medical University, Moroyama-machi, Iruma-gun, Saitama, Japan
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
| | - Yasushi Okazaki
- Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan.,Division of Functional Genomics and Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
| | - Anne Lombès
- MRC Laboratory, Mill Hill, London NW71AA, UK.,Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ian J Holt
- MRC Laboratory, Mill Hill, London NW71AA, UK.,Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London, NW3 2PF, UK.,Biodonostia Health Research Institute, 20014 San Sebastián, Spain. IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - David R Thorburn
- Murdoch Childrens Research Institute, Royal Children's Hospital and Department of Paediatrics, University of Melbourne, Melbourne VIC 3052, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne VIC 3052, Australia
| | - Antonella Spinazzola
- Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London, NW3 2PF, UK.,MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
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55
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Berglund AK, Navarrete C, Engqvist MKM, Hoberg E, Szilagyi Z, Taylor RW, Gustafsson CM, Falkenberg M, Clausen AR. Nucleotide pools dictate the identity and frequency of ribonucleotide incorporation in mitochondrial DNA. PLoS Genet 2017; 13:e1006628. [PMID: 28207748 PMCID: PMC5336301 DOI: 10.1371/journal.pgen.1006628] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/03/2017] [Accepted: 02/09/2017] [Indexed: 01/22/2023] Open
Abstract
Previous work has demonstrated the presence of ribonucleotides in human mitochondrial DNA (mtDNA) and in the present study we use a genome-wide approach to precisely map the location of these. We find that ribonucleotides are distributed evenly between the heavy- and light-strand of mtDNA. The relative levels of incorporated ribonucleotides reflect that DNA polymerase γ discriminates the four ribonucleotides differentially during DNA synthesis. The observed pattern is also dependent on the mitochondrial deoxyribonucleotide (dNTP) pools and disease-causing mutations that change these pools alter both the absolute and relative levels of incorporated ribonucleotides. Our analyses strongly suggest that DNA polymerase γ-dependent incorporation is the main source of ribonucleotides in mtDNA and argues against the existence of a mitochondrial ribonucleotide excision repair pathway in human cells. Furthermore, we clearly demonstrate that when dNTP pools are limiting, ribonucleotides serve as a source of building blocks to maintain DNA replication. Increased levels of embedded ribonucleotides in patient cells with disturbed nucleotide pools may contribute to a pathogenic mechanism that affects mtDNA stability and impair new rounds of mtDNA replication. Human mitochondria contain a small double-stranded DNA genome (mtDNA) of only 16,569 base pairs (bp) that encodes 13 essential subunits of the oxidative phosphorylation system. Depletion of mtDNA and different types of mtDNA mutations cause mitochondrial disease, and are also implicated in biological ageing. For almost half a century it has been known that mtDNA contains ribonucleotides, but their identity and precise location are not known. The source of these ribonucleotides and their relevance for mitochondrial genome stability in healthy individuals and in patients with mitochondrial defects has not been addressed. We have used a combination of next-generation sequencing, and in vivo and in vitro biochemistry to address some of these questions. Our findings demonstrate that DNA polymerase γ-dependent incorporation is the main source of ribonucleotides in mtDNA and argues against the existence of ribonucleotide excision repair pathways in human mitochondria. Our data also reveal that when dNTP pools are limiting, ribonucleotides serves as a second line of building blocks for DNA synthesis. We also demonstrate increased levels of embedded ribonucleotides in patient cells with disturbed nucleotide pools, which may constitute a new pathogenic mechanism that affects mtDNA stability and impairs later rounds of mtDNA replication.
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Affiliation(s)
| | - Clara Navarrete
- Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | | | - Emily Hoberg
- Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Zsolt Szilagyi
- Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Robert W. Taylor
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Maria Falkenberg
- Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- * E-mail: (MF); (ARC)
| | - Anders R. Clausen
- Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- * E-mail: (MF); (ARC)
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56
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El-Hattab AW, Craigen WJ, Scaglia F. Mitochondrial DNA maintenance defects. Biochim Biophys Acta Mol Basis Dis 2017; 1863:1539-1555. [PMID: 28215579 DOI: 10.1016/j.bbadis.2017.02.017] [Citation(s) in RCA: 180] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/31/2017] [Accepted: 02/14/2017] [Indexed: 01/12/2023]
Abstract
The maintenance of mitochondrial DNA (mtDNA) depends on a number of nuclear gene-encoded proteins including a battery of enzymes forming the replisome needed to synthesize mtDNA. These enzymes need to be in balanced quantities to function properly that is in part achieved by exchanging intramitochondrial contents through mitochondrial fusion. In addition, mtDNA synthesis requires a balanced supply of nucleotides that is achieved by nucleotide recycling inside the mitochondria and import from the cytosol. Mitochondrial DNA maintenance defects (MDMDs) are a group of diseases caused by pathogenic variants in the nuclear genes involved in mtDNA maintenance resulting in impaired mtDNA synthesis leading to quantitative (mtDNA depletion) and qualitative (multiple mtDNA deletions) defects in mtDNA. Defective mtDNA leads to organ dysfunction due to insufficient mtDNA-encoded protein synthesis, resulting in an inadequate energy production to meet the needs of affected organs. MDMDs are inherited as autosomal recessive or dominant traits, and are associated with a broad phenotypic spectrum ranging from mild adult-onset ophthalmoplegia to severe infantile fatal hepatic failure. To date, pathogenic variants in 20 nuclear genes known to be crucial for mtDNA maintenance have been linked to MDMDs, including genes encoding enzymes of mtDNA replication machinery (POLG, POLG2, TWNK, TFAM, RNASEH1, MGME1, and DNA2), genes encoding proteins that function in maintaining a balanced mitochondrial nucleotide pool (TK2, DGUOK, SUCLG1, SUCLA2, ABAT, RRM2B, TYMP, SLC25A4, AGK, and MPV17), and genes encoding proteins involved in mitochondrial fusion (OPA1, MFN2, and FBXL4).
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Affiliation(s)
- Ayman W El-Hattab
- Division of Clinical Genetics and Metabolic Disorders, Pediatrics Department, Tawam Hospital, Al-Ain, United Arab Emirates
| | - William J Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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