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Stiban J, So M, Kaguni LS. Iron-Sulfur Clusters in Mitochondrial Metabolism: Multifaceted Roles of a Simple Cofactor. BIOCHEMISTRY (MOSCOW) 2017; 81:1066-1080. [PMID: 27908232 DOI: 10.1134/s0006297916100059] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Iron-sulfur metabolism is essential for cellular function and is a key process in mitochondria. In this review, we focus on the structure and assembly of mitochondrial iron-sulfur clusters and their roles in various metabolic processes that occur in mitochondria. Iron-sulfur clusters are crucial in mitochondrial respiration, in which they are required for the assembly, stability, and function of respiratory complexes I, II, and III. They also serve important functions in the citric acid cycle, DNA metabolism, and apoptosis. Whereas the identification of iron-sulfur containing proteins and their roles in numerous aspects of cellular function has been a long-standing research area, that in mitochondria is comparatively recent, and it is likely that their roles within mitochondria have been only partially revealed. We review the status of the field and provide examples of other cellular iron-sulfur proteins to highlight their multifarious roles.
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Affiliation(s)
- Johnny Stiban
- Birzeit University, Department of Biology and Biochemistry, West Bank Birzeit, 627, Palestine.
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52
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O'Driscoll M. The pathological consequences of impaired genome integrity in humans; disorders of the DNA replication machinery. J Pathol 2017; 241:192-207. [PMID: 27757957 DOI: 10.1002/path.4828] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/12/2016] [Accepted: 10/13/2016] [Indexed: 12/13/2022]
Abstract
Accurate and efficient replication of the human genome occurs in the context of an array of constitutional barriers, including regional topological constraints imposed by chromatin architecture and processes such as transcription, catenation of the helical polymer and spontaneously generated DNA lesions, including base modifications and strand breaks. DNA replication is fundamentally important for tissue development and homeostasis; differentiation programmes are intimately linked with stem cell division. Unsurprisingly, impairments of the DNA replication machinery can have catastrophic consequences for genome stability and cell division. Functional impacts on DNA replication and genome stability have long been known to play roles in malignant transformation through a variety of complex mechanisms, and significant further insights have been gained from studying model organisms in this context. Congenital hypomorphic defects in components of the DNA replication machinery have been and continue to be identified in humans. These disorders present with a wide range of clinical features. Indeed, in some instances, different mutations in the same gene underlie different clinical presentations. Understanding the origin and molecular basis of these features opens a window onto the range of developmental impacts of suboptimal DNA replication and genome instability in humans. Here, I will briefly overview the basic steps involved in DNA replication and the key concepts that have emerged from this area of research, before switching emphasis to the pathological consequences of defects within the DNA replication network; the human disorders. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Mark O'Driscoll
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
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53
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Ponce I, Aldunate C, Valenzuela L, Sepúlveda S, Garrido G, Kemmerling U, Cabrera G, Galanti N. A Flap Endonuclease (TcFEN1) Is Involved in Trypanosoma cruzi
Cell Proliferation, DNA Repair, and Parasite Survival. J Cell Biochem 2016; 118:1722-1732. [DOI: 10.1002/jcb.25830] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 12/07/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Ivan Ponce
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina; Universidad de Chile; Santiago 8380453 Chile
| | - Carmen Aldunate
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina; Universidad de Chile; Santiago 8380453 Chile
| | - Lucia Valenzuela
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina; Universidad de Chile; Santiago 8380453 Chile
| | - Sofia Sepúlveda
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina; Universidad de Chile; Santiago 8380453 Chile
| | - Gilda Garrido
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina; Universidad de Chile; Santiago 8380453 Chile
| | - Ulrike Kemmerling
- Programa de Anatomía y Biología del Desarrollo, Instituto de Ciencias Biomédicas, Facultad de Medicina; Universidad de Chile; Santiago 8380453 Chile
| | - Gonzalo Cabrera
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina; Universidad de Chile; Santiago 8380453 Chile
| | - Norbel Galanti
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina; Universidad de Chile; Santiago 8380453 Chile
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Replication intermediates that escape Dna2 activity are processed by Holliday junction resolvase Yen1. Nat Commun 2016; 7:13157. [PMID: 27779184 PMCID: PMC5093310 DOI: 10.1038/ncomms13157] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 09/08/2016] [Indexed: 12/29/2022] Open
Abstract
Cells have evolved mechanisms to protect, restart and repair perturbed replication forks, allowing full genome duplication, even under replication stress. Interrogating the interplay between nuclease-helicase Dna2 and Holliday junction (HJ) resolvase Yen1, we find the Dna2 helicase activity acts parallel to homologous recombination (HR) in promoting DNA replication and chromosome detachment at mitosis after replication fork stalling. Yen1, but not the HJ resolvases Slx1-Slx4 and Mus81-Mms4, safeguards chromosome segregation by removing replication intermediates that escape Dna2. Post-replicative DNA damage checkpoint activation in Dna2 helicase-defective cells causes terminal G2/M arrest by precluding Yen1-dependent repair, whose activation requires progression into anaphase. These findings explain the exquisite replication stress sensitivity of Dna2 helicase-defective cells, and identify a non-canonical role for Yen1 in the processing of replication intermediates that is distinct from HJ resolution. The involvement of Dna2 helicase activity in completing replication may have implications for DNA2-associated pathologies, including cancer and Seckel syndrome.
DNA replication stress drives genome instability and cancer. Here, Ölmezer and colleagues show that the helicase activity of multifunctional enzyme Dna2 suppresses dead-end replication structures that impair chromosome segregation if not removed by Holliday junction resolvase Yen1 in yeast.
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Pinto C, Kasaciunaite K, Seidel R, Cejka P. Human DNA2 possesses a cryptic DNA unwinding activity that functionally integrates with BLM or WRN helicases. eLife 2016; 5. [PMID: 27612385 PMCID: PMC5030094 DOI: 10.7554/elife.18574] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/08/2016] [Indexed: 12/13/2022] Open
Abstract
Human DNA2 (hDNA2) contains both a helicase and a nuclease domain within the same polypeptide. The nuclease of hDNA2 is involved in a variety of DNA metabolic processes. Little is known about the role of the hDNA2 helicase. Using bulk and single-molecule approaches, we show that hDNA2 is a processive helicase capable of unwinding kilobases of dsDNA in length. The nuclease activity prevents the engagement of the helicase by competing for the same substrate, hence prominent DNA unwinding by hDNA2 alone can only be observed using the nuclease-deficient variant. We show that the helicase of hDNA2 functionally integrates with BLM or WRN helicases to promote dsDNA degradation by forming a heterodimeric molecular machine. This collectively suggests that the hDNA2 motor promotes the enzyme's capacity to degrade dsDNA in conjunction with BLM or WRN and thus promote the repair of broken DNA. DOI:http://dx.doi.org/10.7554/eLife.18574.001
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Affiliation(s)
- Cosimo Pinto
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | | | - Ralf Seidel
- Institute of Experimental Physics I, University of Leipzig, Leipzig, Germany
| | - Petr Cejka
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
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56
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Sen A, Cox RT. Fly Models of Human Diseases: Drosophila as a Model for Understanding Human Mitochondrial Mutations and Disease. Curr Top Dev Biol 2016; 121:1-27. [PMID: 28057297 DOI: 10.1016/bs.ctdb.2016.07.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondrial diseases are a prevalent, heterogeneous class of diseases caused by defects in oxidative phosphorylation, whose severity depends upon particular genetic mutations. These diseases can be difficult to diagnose, and current therapeutics have limited efficacy, primarily treating only symptoms. Because mitochondria play a pivotal role in numerous cellular functions, especially ATP production, their diminished activity has dramatic physiological consequences. While this in and of itself makes treating mitochondrial disease complex, these organelles contain their own DNA, mtDNA, whose products are required for ATP production, in addition to the hundreds of nucleus-encoded proteins. Drosophila offers a tractable whole-animal model to understand the mechanisms underlying loss of mitochondrial function, the subsequent cellular and tissue damage that results, and how these organelles are inherited. Human and Drosophila mtDNAs encode the same set of products, and the homologous nucleus-encoded genes required for mitochondrial function are conserved. In addition, Drosophila contain sufficiently complex organ systems to effectively recapitulate many basic symptoms of mitochondrial diseases, yet are relatively easy and fast to genetically manipulate. There are several Drosophila models for specific mitochondrial diseases, which have been recently reviewed (Foriel, Willems, Smeitink, Schenck, & Beyrath, 2015). In this review, we highlight the conservation between human and Drosophila mtDNA, the present and future techniques for creating mtDNA mutations for further study, and how Drosophila has contributed to our current understanding of mitochondrial inheritance.
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Affiliation(s)
- A Sen
- Uniformed Services University, Bethesda, MD, United States
| | - R T Cox
- Uniformed Services University, Bethesda, MD, United States.
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57
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Deshmukh AL, Kumar C, Singh DK, Maurya P, Banerjee D. Dynamics of replication proteins during lagging strand synthesis: A crossroads for genomic instability and cancer. DNA Repair (Amst) 2016; 42:72-81. [DOI: 10.1016/j.dnarep.2016.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/22/2016] [Accepted: 04/22/2016] [Indexed: 01/18/2023]
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Jia N, Liu X, Gao H. A DNA2 Homolog Is Required for DNA Damage Repair, Cell Cycle Regulation, and Meristem Maintenance in Plants. PLANT PHYSIOLOGY 2016; 171:318-33. [PMID: 26951435 PMCID: PMC4854720 DOI: 10.1104/pp.16.00312] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 03/04/2016] [Indexed: 05/18/2023]
Abstract
Plant meristem cells divide and differentiate in a spatially and temporally regulated manner, ultimately giving rise to organs. In this study, we isolated the Arabidopsis jing he sheng 1 (jhs1) mutant, which exhibited retarded growth, an abnormal pattern of meristem cell division and differentiation, and morphological defects such as fasciation, an irregular arrangement of siliques, and short roots. We identified JHS1 as a homolog of human and yeast DNA Replication Helicase/Nuclease2, which is known to be involved in DNA replication and damage repair. JHS1 is strongly expressed in the meristem of Arabidopsis. The jhs1 mutant was sensitive to DNA damage stress and had an increased DNA damage response, including increased expression of genes involved in DNA damage repair and cell cycle regulation, and a higher frequency of homologous recombination. In the meristem of the mutant plants, cell cycle progression was delayed at the G2 or late S phase and genes essential for meristem maintenance were misregulated. These results suggest that JHS1 plays an important role in DNA replication and damage repair, meristem maintenance, and development in plants.
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Affiliation(s)
- Ning Jia
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China (N.J., X.L., H.G.)
| | - Xiaomin Liu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China (N.J., X.L., H.G.)
| | - Hongbo Gao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China (N.J., X.L., H.G.)
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59
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Young MJ, Copeland WC. Human mitochondrial DNA replication machinery and disease. Curr Opin Genet Dev 2016; 38:52-62. [PMID: 27065468 DOI: 10.1016/j.gde.2016.03.005] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/03/2016] [Accepted: 03/08/2016] [Indexed: 12/21/2022]
Abstract
The human mitochondrial genome is replicated by DNA polymerase γ in concert with key components of the mitochondrial DNA (mtDNA) replication machinery. Defects in mtDNA replication or nucleotide metabolism cause deletions, point mutations, or depletion of mtDNA. The resulting loss of cellular respiration ultimately induces mitochondrial genetic diseases, including mtDNA depletion syndromes (MDS) such as Alpers or early infantile hepatocerebral syndromes, and mtDNA deletion disorders such as progressive external ophthalmoplegia, ataxia-neuropathy, or mitochondrial neurogastrointestinal encephalomyopathy. Here we review the current literature regarding human mtDNA replication and heritable disorders caused by genetic changes of the POLG, POLG2, Twinkle, RNASEH1, DNA2, and MGME1 genes.
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Affiliation(s)
- Matthew J Young
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, P.O. Box 12233, Research Triangle Park, NC 27709, United States
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, P.O. Box 12233, Research Triangle Park, NC 27709, United States.
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60
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Liu W, Zhou M, Li Z, Li H, Polaczek P, Dai H, Wu Q, Liu C, Karanja KK, Popuri V, Shan SO, Schlacher K, Zheng L, Campbell JL, Shen B. A Selective Small Molecule DNA2 Inhibitor for Sensitization of Human Cancer Cells to Chemotherapy. EBioMedicine 2016; 6:73-86. [PMID: 27211550 PMCID: PMC4856754 DOI: 10.1016/j.ebiom.2016.02.043] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 02/29/2016] [Accepted: 02/29/2016] [Indexed: 12/31/2022] Open
Abstract
Cancer cells frequently up-regulate DNA replication and repair proteins such as the multifunctional DNA2 nuclease/helicase, counteracting DNA damage due to replication stress and promoting survival. Therefore, we hypothesized that blocking both DNA replication and repair by inhibiting the bifunctional DNA2 could be a potent strategy to sensitize cancer cells to stresses from radiation or chemotherapeutic agents. We show that homozygous deletion of DNA2 sensitizes cells to ionizing radiation and camptothecin (CPT). Using a virtual high throughput screen, we identify 4-hydroxy-8-nitroquinoline-3-carboxylic acid (C5) as an effective and selective inhibitor of DNA2. Mutagenesis and biochemical analysis define the C5 binding pocket at a DNA-binding motif that is shared by the nuclease and helicase activities, consistent with structural studies that suggest that DNA binding to the helicase domain is necessary for nuclease activity. C5 targets the known functions of DNA2 in vivo: C5 inhibits resection at stalled forks as well as reducing recombination. C5 is an even more potent inhibitor of restart of stalled DNA replication forks and over-resection of nascent DNA in cells defective in replication fork protection, including BRCA2 and BOD1L. C5 sensitizes cells to CPT and synergizes with PARP inhibitors.
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Affiliation(s)
- Wenpeng Liu
- Colleges of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China; Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA; Division of Chemistry and Chemical Engineering, Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mian Zhou
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
| | - Zhengke Li
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
| | - Hongzhi Li
- Molecular Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Piotr Polaczek
- Division of Chemistry and Chemical Engineering, Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Huifang Dai
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
| | - Qiong Wu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
| | - Changwei Liu
- Colleges of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China; Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
| | - Kenneth K Karanja
- Division of Chemistry and Chemical Engineering, Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Vencat Popuri
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Katharina Schlacher
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA.
| | - Judith L Campbell
- Division of Chemistry and Chemical Engineering, Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA.
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61
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Bannwarth S, Berg-Alonso L, Augé G, Fragaki K, Kolesar JE, Lespinasse F, Lacas-Gervais S, Burel-Vandenbos F, Villa E, Belmonte F, Michiels JF, Ricci JE, Gherardi R, Harrington L, Kaufman BA, Paquis-Flucklinger V. Inactivation of Pif1 helicase causes a mitochondrial myopathy in mice. Mitochondrion 2016; 30:126-37. [PMID: 26923168 DOI: 10.1016/j.mito.2016.02.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 02/19/2016] [Accepted: 02/19/2016] [Indexed: 12/13/2022]
Abstract
Mutations in genes coding for mitochondrial helicases such as TWINKLE and DNA2 are involved in mitochondrial myopathies with mtDNA instability in both human and mouse. We show that inactivation of Pif1, a third member of the mitochondrial helicase family, causes a similar phenotype in mouse. pif1-/- animals develop a mitochondrial myopathy with respiratory chain deficiency. Pif1 inactivation is responsible for a deficiency to repair oxidative stress-induced mtDNA damage in mouse embryonic fibroblasts that is improved by complementation with mitochondrial isoform mPif1(67). These results open new perspectives for the exploration of patients with mtDNA instability disorders.
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Affiliation(s)
- Sylvie Bannwarth
- IRCAN, CNRS UMR 7284/INSERM U1081/UNS, Faculté de Médecine, Nice, France; Service de Génétique Médicale, Hôpital Archet 2, CHU de Nice, Nice, France
| | | | - Gaëlle Augé
- IRCAN, CNRS UMR 7284/INSERM U1081/UNS, Faculté de Médecine, Nice, France; Service de Génétique Médicale, Hôpital Archet 2, CHU de Nice, Nice, France
| | - Konstantina Fragaki
- IRCAN, CNRS UMR 7284/INSERM U1081/UNS, Faculté de Médecine, Nice, France; Service de Génétique Médicale, Hôpital Archet 2, CHU de Nice, Nice, France
| | - Jill E Kolesar
- Department of Medicine, Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, USA
| | | | - Sandra Lacas-Gervais
- Centre Commun de Microscopie Electronique Appliquée, Faculté des Sciences, Université de Nice Sophia Antipolis, Nice, France
| | | | - Elodie Villa
- INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), équipe "contrôle métabolique des morts cellulaires", Nice Sophia-Antipolis University, France
| | - Frances Belmonte
- Department of Medicine, Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, USA
| | | | - Jean-Ehrland Ricci
- INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), équipe "contrôle métabolique des morts cellulaires", Nice Sophia-Antipolis University, France
| | | | - Lea Harrington
- Université de Montréal, Institut de Recherche en Immunologie et en Cancérologie, 2950 chemin de Polytechnique, Montréal, Québec H3T 1J4, Canada
| | - Brett A Kaufman
- Department of Medicine, Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Véronique Paquis-Flucklinger
- IRCAN, CNRS UMR 7284/INSERM U1081/UNS, Faculté de Médecine, Nice, France; Service de Génétique Médicale, Hôpital Archet 2, CHU de Nice, Nice, France.
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Samadder P, Aithal R, Belan O, Krejci L. Cancer TARGETases: DSB repair as a pharmacological target. Pharmacol Ther 2016; 161:111-131. [PMID: 26899499 DOI: 10.1016/j.pharmthera.2016.02.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cancer is a disease attributed to the accumulation of DNA damages due to incapacitation of DNA repair pathways resulting in genomic instability and a mutator phenotype. Among the DNA lesions, double stranded breaks (DSBs) are the most toxic forms of DNA damage which may arise as a result of extrinsic DNA damaging agents or intrinsic replication stress in fast proliferating cancer cells. Accurate repair of DSBs is therefore paramount to the cell survival, and several classes of proteins such as kinases, nucleases, helicases or core recombinational proteins have pre-defined jobs in precise execution of DSB repair pathways. On one hand, the proper functioning of these proteins ensures maintenance of genomic stability in normal cells, and on the other hand results in resistance to various drugs employed in cancer therapy and therefore presents a suitable opportunity for therapeutic targeting. Higher relapse and resistance in cancer patients due to non-specific, cytotoxic therapies is an alarming situation and it is becoming more evident to employ personalized treatment based on the genetic landscape of the cancer cells. For the success of personalized treatment, it is of immense importance to identify more suitable targetable proteins in DSB repair pathways and also to explore new synthetic lethal interactions with these pathways. Here we review the various alternative approaches to target the various protein classes termed as cancer TARGETases in DSB repair pathway to obtain more beneficial and selective therapy.
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Affiliation(s)
- Pounami Samadder
- National Centre for Biomolecular Research, Masaryk University, 62500 Brno, Czech Republic; International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, 60200 Brno, Czech Republic
| | - Rakesh Aithal
- National Centre for Biomolecular Research, Masaryk University, 62500 Brno, Czech Republic; Department of Biology, Masaryk University, 62500 Brno, Czech Republic
| | - Ondrej Belan
- Department of Biology, Masaryk University, 62500 Brno, Czech Republic
| | - Lumir Krejci
- National Centre for Biomolecular Research, Masaryk University, 62500 Brno, Czech Republic; International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, 60200 Brno, Czech Republic; Department of Biology, Masaryk University, 62500 Brno, Czech Republic.
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63
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Uittenbogaard M, Chiaramello A. Novel subcellular localization of the DNA helicase Twinkle at the kinetochore complex during mitosis in neuronal-like progenitor cells. Histochem Cell Biol 2015; 145:275-86. [PMID: 26678504 DOI: 10.1007/s00418-015-1388-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2015] [Indexed: 11/28/2022]
Abstract
During mitosis, the kinetochore, a multi-protein structure located on the centromeric DNA, is responsible for proper segregation of the replicated genome. More specifically, the outer kinetochore complex component Ndc80/Hec1 plays a critical role in regulating microtubule attachment to the spindle for accurate sister chromatid segregation. In addition, DNA helicases play a key contribution for precise and complete disjunction of sister chromatids held together through double-stranded DNA catenations until anaphase. In this study, we focused our attention on the nuclear-encoded DNA helicase Twinkle, which functions as an essential helicase for replication of mitochondrial DNA. It regulates the copy number of the mitochondrial genome, while maintaining its integrity, two processes essential for mitochondrial biogenesis and bioenergetic functions. Although the majority of the Twinkle protein is imported into mitochondria, a small fraction remains cytosolic with an unknown function. In this study, we report a novel expression pattern of Twinkle during chromosomal segregation at distinct mitotic phases. By immunofluorescence microscopy, we found that Twinkle protein colocalizes with the outer kinetochore protein HEC1 as early as prophase until late anaphase in neuronal-like progenitor cells. Thus, our collective results have revealed an unexpected cell cycle-regulated expression pattern of the DNA helicase Twinkle, known for its role in mtDNA replication. Therefore, its recruitment to the kinetochore suggests an evolutionary conserved function for both mitochondrial and nuclear genomic inheritance.
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Affiliation(s)
- Martine Uittenbogaard
- Department of Anatomy and Regenerative Biology, George Washington University Medical Center, 2300 I Street N.W., Washington, DC, 20037, USA
| | - Anne Chiaramello
- Department of Anatomy and Regenerative Biology, George Washington University Medical Center, 2300 I Street N.W., Washington, DC, 20037, USA.
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64
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Patil S, Moeys S, von Dassow P, Huysman MJJ, Mapleson D, De Veylder L, Sanges R, Vyverman W, Montresor M, Ferrante MI. Identification of the meiotic toolkit in diatoms and exploration of meiosis-specific SPO11 and RAD51 homologs in the sexual species Pseudo-nitzschia multistriata and Seminavis robusta. BMC Genomics 2015; 16:930. [PMID: 26572248 PMCID: PMC4647503 DOI: 10.1186/s12864-015-1983-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 10/04/2015] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Sexual reproduction is an obligate phase in the life cycle of most eukaryotes. Meiosis varies among organisms, which is reflected by the variability of the gene set associated to the process. Diatoms are unicellular organisms that belong to the stramenopile clade and have unique life cycles that can include a sexual phase. RESULTS The exploration of five diatom genomes and one diatom transcriptome led to the identification of 42 genes potentially involved in meiosis. While these include the majority of known meiosis-related genes, several meiosis-specific genes, including DMC1, could not be identified. Furthermore, phylogenetic analyses supported gene identification and revealed ancestral loss and recent expansion in the RAD51 family in diatoms. The two sexual species Pseudo-nitzschia multistriata and Seminavis robusta were used to explore the expression of meiosis-related genes: RAD21, SPO11-2, RAD51-A, RAD51-B and RAD51-C were upregulated during meiosis, whereas other paralogs in these families showed no differential expression patterns, suggesting that they may play a role during vegetative divisions. An almost identical toolkit is shared among Pseudo-nitzschia multiseries and Fragilariopsis cylindrus, as well as two species for which sex has not been observed, Phaeodactylum tricornutum and Thalassiosira pseudonana, suggesting that these two may retain a facultative sexual phase. CONCLUSIONS Our results reveal the conserved meiotic toolkit in six diatom species and indicate that Stramenopiles share major modifications of canonical meiosis processes ancestral to eukaryotes, with important divergences in each Kingdom.
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Affiliation(s)
- Shrikant Patil
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121, Naples, Italy.
| | - Sara Moeys
- Department of Biology, Protistology and Aquatic Ecology, Ghent University, 9000, Ghent, Belgium. .,Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), 9052, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
| | - Peter von Dassow
- Facultad de Ciencias Biológicas, Instituto Milenio de Oceanografía, Pontificia Universidad Católica de Chile, Santiago, Chile. .,UMI 3614, Evolutionary Biology and Ecology of Algae, CNRS-UPMC Sorbonne Universités, PUCCh, UACH, Station Biologique de Roscoff, Roscoff, France.
| | - Marie J J Huysman
- Department of Biology, Protistology and Aquatic Ecology, Ghent University, 9000, Ghent, Belgium. .,Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), 9052, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
| | - Daniel Mapleson
- The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Lieven De Veylder
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), 9052, Ghent, Belgium. .,Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
| | - Remo Sanges
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121, Naples, Italy.
| | - Wim Vyverman
- Department of Biology, Protistology and Aquatic Ecology, Ghent University, 9000, Ghent, Belgium.
| | - Marina Montresor
- Stazione Zoologica Anton Dohrn, Villa Comunale 1, 80121, Naples, Italy.
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65
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Iida R, Ueki M, Yasuda T. Identification of interacting partners of Human Mpv17-like protein with a mitigating effect of mitochondrial dysfunction through mtDNA damage. Free Radic Biol Med 2015; 87:336-45. [PMID: 26165189 DOI: 10.1016/j.freeradbiomed.2015.07.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 07/07/2015] [Accepted: 07/07/2015] [Indexed: 11/16/2022]
Abstract
Human Mpv17-like protein (M-LPH) has been suggested to participate in mitochondrial function. In this study, we investigated the proteins that interact with M-LPH, and identified four: H2A histone family, member X (H2AX), ribosomal protein S14 (RPS14), ribosomal protein S3 (RPS3) and B-cell receptor-associated protein 31 (Bap31). Immunofluorescence and subcellular fractionation studies revealed that M-LPH is localized predominantly in the nucleus, to some extent in a subset of mitochondria, and marginally in the cytosol. Mitochondrial M-LPH appeared as punctate foci, and these were co-localized with a subset of mitochondrial transcription factor A (TFAM) and mtDNA, indicating that M-LPH is localized in or in close proximity to mitochondrial nucleoids. RNAi-mediated knockdown of M-LPH resulted in an increase of mtDNA damage and reduced the expression of mtDNA-encoded genes. A ROS inducer, antimycin A, caused an increase in both the number and size of the mitochondrial M-LPH foci, and these foci were co-localized with two enzymes, DNA polymerase γ (POLG) and DNA ligase III (LIG3), both involved in mtDNA repair. Furthermore, knockdown of M-LPH hampered mitochondrial localization of these enzymes. Taken together, these observations suggest that M-LPH is involved in the maintenance of mtDNA and protects cells from mitochondrial dysfunction.
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Affiliation(s)
- Reiko Iida
- Division of Life Science, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan; Organization for Life Science Advancement Programs, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan.
| | - Misuzu Ueki
- Division of Medical Genetics and Biochemistry, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Toshihiro Yasuda
- Organization for Life Science Advancement Programs, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan; Division of Medical Genetics and Biochemistry, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
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66
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Tammaro M, Liao S, Beeharry N, Yan H. DNA double-strand breaks with 5' adducts are efficiently channeled to the DNA2-mediated resection pathway. Nucleic Acids Res 2015; 44:221-31. [PMID: 26420828 PMCID: PMC4705695 DOI: 10.1093/nar/gkv969] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/15/2015] [Indexed: 11/14/2022] Open
Abstract
DNA double-strand breaks (DSBs) with 5′ adducts are frequently formed from many nucleic acid processing enzymes, in particular DNA topoisomerase 2 (TOP2). The key intermediate of TOP2 catalysis is the covalent complex (TOP2cc), consisting of two TOP2 subunits covalently linked to the 5′ ends of the nicked DNA. In cells, TOP2ccs can be trapped by cancer drugs such as etoposide and then converted into DNA double-strand breaks (DSBs) that carry adducts at the 5′ end. The repair of such DSBs is critical to the survival of cells, but the underlying mechanism is still not well understood. We found that etoposide-induced DSBs are efficiently resected into 3′ single-stranded DNA in cells and the major nuclease for resection is the DNA2 protein. DNA substrates carrying model 5′ adducts were efficiently resected in Xenopus egg extracts and immunodepletion of Xenopus DNA2 also strongly inhibited resection. These results suggest that DNA2-mediated resection is a major mechanism for the repair of DSBs with 5′ adducts.
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Affiliation(s)
- Margaret Tammaro
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Shuren Liao
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Neil Beeharry
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | - Hong Yan
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
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67
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Akhmedov AT, Marín-García J. Mitochondrial DNA maintenance: an appraisal. Mol Cell Biochem 2015; 409:283-305. [DOI: 10.1007/s11010-015-2532-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/06/2015] [Indexed: 12/13/2022]
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68
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Primer removal during mammalian mitochondrial DNA replication. DNA Repair (Amst) 2015; 34:28-38. [PMID: 26303841 DOI: 10.1016/j.dnarep.2015.07.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 07/02/2015] [Indexed: 12/17/2022]
Abstract
The small circular mitochondrial genome in mammalian cells is replicated by a dedicated replisome, defects in which can cause mitochondrial disease in humans. A fundamental step in mitochondrial DNA (mtDNA) replication and maintenance is the removal of the RNA primers needed for replication initiation. The nucleases RNase H1, FEN1, DNA2, and MGME1 have been implicated in this process. Here we review the role of these nucleases in the light of primer removal pathways in mitochondria, highlight associations with disease, as well as consider the implications for mtDNA replication initiation.
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69
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Ahmed N, Ronchi D, Comi GP. Genes and Pathways Involved in Adult Onset Disorders Featuring Muscle Mitochondrial DNA Instability. Int J Mol Sci 2015; 16:18054-76. [PMID: 26251896 PMCID: PMC4581235 DOI: 10.3390/ijms160818054] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/27/2015] [Accepted: 07/28/2015] [Indexed: 12/31/2022] Open
Abstract
Replication and maintenance of mtDNA entirely relies on a set of proteins encoded by the nuclear genome, which include members of the core replicative machinery, proteins involved in the homeostasis of mitochondrial dNTPs pools or deputed to the control of mitochondrial dynamics and morphology. Mutations in their coding genes have been observed in familial and sporadic forms of pediatric and adult-onset clinical phenotypes featuring mtDNA instability. The list of defects involved in these disorders has recently expanded, including mutations in the exo-/endo-nuclease flap-processing proteins MGME1 and DNA2, supporting the notion that an enzymatic DNA repair system actively takes place in mitochondria. The results obtained in the last few years acknowledge the contribution of next-generation sequencing methods in the identification of new disease loci in small groups of patients and even single probands. Although heterogeneous, these genes can be conveniently classified according to the pathway to which they belong. The definition of the molecular and biochemical features of these pathways might be helpful for fundamental knowledge of these disorders, to accelerate genetic diagnosis of patients and the development of rational therapies. In this review, we discuss the molecular findings disclosed in adult patients with muscle pathology hallmarked by mtDNA instability.
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Affiliation(s)
- Naghia Ahmed
- Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Dino Ferrari Centre, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, via Francesco Sforza 35, Milan 20122, Italy.
| | - Dario Ronchi
- Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Dino Ferrari Centre, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, via Francesco Sforza 35, Milan 20122, Italy.
| | - Giacomo Pietro Comi
- Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Dino Ferrari Centre, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, via Francesco Sforza 35, Milan 20122, Italy.
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70
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Strauss C, Kornowski M, Benvenisty A, Shahar A, Masury H, Ben-Porath I, Ravid T, Arbel-Eden A, Goldberg M. The DNA2 nuclease/helicase is an estrogen-dependent gene mutated in breast and ovarian cancers. Oncotarget 2015; 5:9396-409. [PMID: 25238049 PMCID: PMC4253442 DOI: 10.18632/oncotarget.2414] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Genomic instability, a hallmark of cancer, is commonly caused by failures in the DNA damage response. Here we conducted a bioinformatical screen to reveal DNA damage response genes that are upregulated by estrogen and highly mutated in breast and ovarian cancers. This screen identified 53 estrogen-dependent cancer genes, some of which are novel. Notably, the screen retrieved 9 DNA helicases as well as 5 nucleases. DNA2, which functions as both a helicase and a nuclease and plays a role in DNA repair and replication, was retrieved in the screen. Mutations in DNA2, found in estrogen-dependent cancers, are clustered in the helicase and nuclease domains, suggesting activity impairment. Indeed, we show that mutations found in ovarian cancers impair DNA2 activity. Depletion of DNA2 in cells reduces their tumorogenicity in mice. In human, high expression of DNA2 correlates with poor survival of estrogen receptor-positive patients but not of estrogen receptor-negative patients. We also demonstrate that depletion of DNA2 in cells reduces proliferation, while addition of estrogen restores proliferation. These findings suggest that cells responding to estrogen will proliferate despite being impaired in DNA2 activity, potentially promoting genomic instability and triggering cancer development.
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Affiliation(s)
- Carmit Strauss
- Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Maya Kornowski
- Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Avraham Benvenisty
- Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Amit Shahar
- Department of Developmental Biology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel
| | - Hadas Masury
- Department of Developmental Biology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel
| | - Ittai Ben-Porath
- Department of Developmental Biology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel
| | - Tommer Ravid
- Department of Biochemistry, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Ayelet Arbel-Eden
- Department of Medical Laboratory Sciences, Hadassah Academic College, Jerusalem, 91010, Israel
| | - Michal Goldberg
- Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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71
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Levikova M, Cejka P. The Saccharomyces cerevisiae Dna2 can function as a sole nuclease in the processing of Okazaki fragments in DNA replication. Nucleic Acids Res 2015; 43:7888-97. [PMID: 26175049 PMCID: PMC4652754 DOI: 10.1093/nar/gkv710] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Accepted: 07/01/2015] [Indexed: 01/30/2023] Open
Abstract
During DNA replication, synthesis of the lagging strand occurs in stretches termed Okazaki fragments. Before adjacent fragments are ligated, any flaps resulting from the displacement of the 5' DNA end of the Okazaki fragment must be cleaved. Previously, Dna2 was implicated to function upstream of flap endonuclease 1 (Fen1 or Rad27) in the processing of long flaps bound by the replication protein A (RPA). Here we show that Dna2 efficiently cleaves long DNA flaps exactly at or directly adjacent to the base. A fraction of the flaps cleaved by Dna2 can be immediately ligated. When coupled with DNA replication, the flap processing activity of Dna2 leads to a nearly complete Okazaki fragment maturation at sub-nanomolar Dna2 concentrations. Our results indicate that a subsequent nucleolytic activity of Fen1 is not required in most cases. In contrast Dna2 is completely incapable to cleave short flaps. We show that also Dna2, like Fen1, interacts with proliferating cell nuclear antigen (PCNA). We propose a model where Dna2 alone is responsible for cleaving of RPA-bound long flaps, while Fen1 or exonuclease 1 (Exo1) cleave short flaps. Our results argue that Dna2 can function in a separate, rather than in a Fen1-dependent pathway.
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Affiliation(s)
- Maryna Levikova
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Petr Cejka
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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72
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Primer retention owing to the absence of RNase H1 is catastrophic for mitochondrial DNA replication. Proc Natl Acad Sci U S A 2015; 112:9334-9. [PMID: 26162680 DOI: 10.1073/pnas.1503653112] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Encoding ribonuclease H1 (RNase H1) degrades RNA hybridized to DNA, and its function is essential for mitochondrial DNA maintenance in the developing mouse. Here we define the role of RNase H1 in mitochondrial DNA replication. Analysis of replicating mitochondrial DNA in embryonic fibroblasts lacking RNase H1 reveals retention of three primers in the major noncoding region (NCR) and one at the prominent lagging-strand initiation site termed Ori-L. Primer retention does not lead immediately to depletion, as the persistent RNA is fully incorporated in mitochondrial DNA. However, the retained primers present an obstacle to the mitochondrial DNA polymerase γ in subsequent rounds of replication and lead to the catastrophic generation of a double-strand break at the origin when the resulting gapped molecules are copied. Hence, the essential role of RNase H1 in mitochondrial DNA replication is the removal of primers at the origin of replication.
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73
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Abstract
DNA damage response pathways are crucial for protecting genome stability in all eukaryotes. Saccharomyces cerevisiaeDna2 has both helicase and nuclease activities that are essential for Okazaki fragment maturation, and Dna2 is involved in long-range DNA end resection at double-strand breaks. Dna2 forms nuclear foci in response to DNA replication stress and to double-strand breaks. We find that Dna2-GFP focus formation occurs mainly during S phase in unperturbed cells. Dna2 colocalizes in nuclear foci with 25 DNA repair proteins that define recombination repair centers in response to phleomycin-induced DNA damage. To systematically identify genes that affect Dna2 focus formation, we crossed Dna2-GFP into 4293 nonessential gene deletion mutants and assessed Dna2-GFP nuclear focus formation after phleomycin treatment. We identified 37 gene deletions that affect Dna2-GFP focus formation, 12 with fewer foci and 25 with increased foci. Together these data comprise a useful resource for understanding Dna2 regulation in response to DNA damage.
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74
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Skoneczna A, Kaniak A, Skoneczny M. Genetic instability in budding and fission yeast-sources and mechanisms. FEMS Microbiol Rev 2015; 39:917-67. [PMID: 26109598 PMCID: PMC4608483 DOI: 10.1093/femsre/fuv028] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2015] [Indexed: 12/17/2022] Open
Abstract
Cells are constantly confronted with endogenous and exogenous factors that affect their genomes. Eons of evolution have allowed the cellular mechanisms responsible for preserving the genome to adjust for achieving contradictory objectives: to maintain the genome unchanged and to acquire mutations that allow adaptation to environmental changes. One evolutionary mechanism that has been refined for survival is genetic variation. In this review, we describe the mechanisms responsible for two biological processes: genome maintenance and mutation tolerance involved in generations of genetic variations in mitotic cells of both Saccharomyces cerevisiae and Schizosaccharomyces pombe. These processes encompass mechanisms that ensure the fidelity of replication, DNA lesion sensing and DNA damage response pathways, as well as mechanisms that ensure precision in chromosome segregation during cell division. We discuss various factors that may influence genome stability, such as cellular ploidy, the phase of the cell cycle, transcriptional activity of a particular region of DNA, the proficiency of DNA quality control systems, the metabolic stage of the cell and its respiratory potential, and finally potential exposure to endogenous or environmental stress. The stability of budding and fission yeast genomes is influenced by two contradictory factors: (1) the need to be fully functional, which is ensured through the replication fidelity pathways of nuclear and mitochondrial genomes through sensing and repairing DNA damage, through precise chromosome segregation during cell division; and (2) the need to acquire changes for adaptation to environmental challenges.
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Affiliation(s)
- Adrianna Skoneczna
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
| | - Aneta Kaniak
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
| | - Marek Skoneczny
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
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75
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The exonuclease activity of DNA polymerase γ is required for ligation during mitochondrial DNA replication. Nat Commun 2015; 6:7303. [PMID: 26095671 PMCID: PMC4557304 DOI: 10.1038/ncomms8303] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 04/27/2015] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial DNA (mtDNA) polymerase γ (POLγ) harbours a 3′–5′ exonuclease proofreading activity. Here we demonstrate that this activity is required for the creation of ligatable ends during mtDNA replication. Exonuclease-deficient POLγ fails to pause on reaching a downstream 5′-end. Instead, the enzyme continues to polymerize into double-stranded DNA, creating an unligatable 5′-flap. Disease-associated mutations can both increase and decrease exonuclease activity and consequently impair DNA ligation. In mice, inactivation of the exonuclease activity causes an increase in mtDNA mutations and premature ageing phenotypes. These mutator mice also contain high levels of truncated, linear fragments of mtDNA. We demonstrate that the formation of these fragments is due to impaired ligation, causing nicks near the origin of heavy-strand DNA replication. In the subsequent round of replication, the nicks lead to double-strand breaks and linear fragment formation. Mitochondrial DNA (mtDNA) polymerase γ has a 3′–5′ exonuclease proofreading activity. Here, the authors show it is required for creating ligatable ends during mtDNA replication, and inactivation of the activity in mice causes strand-specific nicks in DNA and the formation of linear mtDNA fragments.
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76
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Ding L, Liu Y. Borrowing nuclear DNA helicases to protect mitochondrial DNA. Int J Mol Sci 2015; 16:10870-87. [PMID: 25984607 PMCID: PMC4463680 DOI: 10.3390/ijms160510870] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/09/2015] [Accepted: 05/11/2015] [Indexed: 01/20/2023] Open
Abstract
In normal cells, mitochondria are the primary organelles that generate energy, which is critical for cellular metabolism. Mitochondrial dysfunction, caused by mitochondrial DNA (mtDNA) mutations or an abnormal mtDNA copy number, is linked to a range of human diseases, including Alzheimer's disease, premature aging and cancer. mtDNA resides in the mitochondrial lumen, and its duplication requires the mtDNA replicative helicase, Twinkle. In addition to Twinkle, many DNA helicases, which are encoded by the nuclear genome and are crucial for nuclear genome integrity, are transported into the mitochondrion to also function in mtDNA replication and repair. To date, these helicases include RecQ-like helicase 4 (RECQ4), petite integration frequency 1 (PIF1), DNA replication helicase/nuclease 2 (DNA2) and suppressor of var1 3-like protein 1 (SUV3). Although the nuclear functions of some of these DNA helicases have been extensively studied, the regulation of their mitochondrial transport and the mechanisms by which they contribute to mtDNA synthesis and maintenance remain largely unknown. In this review, we attempt to summarize recent research progress on the role of mammalian DNA helicases in mitochondrial genome maintenance and the effects on mitochondria-associated diseases.
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Affiliation(s)
- Lin Ding
- Department of Radiation Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010-3000, USA.
| | - Yilun Liu
- Department of Radiation Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010-3000, USA.
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77
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Kaniak-Golik A, Skoneczna A. Mitochondria-nucleus network for genome stability. Free Radic Biol Med 2015; 82:73-104. [PMID: 25640729 DOI: 10.1016/j.freeradbiomed.2015.01.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 11/25/2014] [Accepted: 01/13/2015] [Indexed: 12/21/2022]
Abstract
The proper functioning of the cell depends on preserving the cellular genome. In yeast cells, a limited number of genes are located on mitochondrial DNA. Although the mechanisms underlying nuclear genome maintenance are well understood, much less is known about the mechanisms that ensure mitochondrial genome stability. Mitochondria influence the stability of the nuclear genome and vice versa. Little is known about the two-way communication and mutual influence of the nuclear and mitochondrial genomes. Although the mitochondrial genome replicates independent of the nuclear genome and is organized by a distinct set of mitochondrial nucleoid proteins, nearly all genome stability mechanisms responsible for maintaining the nuclear genome, such as mismatch repair, base excision repair, and double-strand break repair via homologous recombination or the nonhomologous end-joining pathway, also act to protect mitochondrial DNA. In addition to mitochondria-specific DNA polymerase γ, the polymerases α, η, ζ, and Rev1 have been found in this organelle. A nuclear genome instability phenotype results from a failure of various mitochondrial functions, such as an electron transport chain activity breakdown leading to a decrease in ATP production, a reduction in the mitochondrial membrane potential (ΔΨ), and a block in nucleotide and amino acid biosynthesis. The loss of ΔΨ inhibits the production of iron-sulfur prosthetic groups, which impairs the assembly of Fe-S proteins, including those that mediate DNA transactions; disturbs iron homeostasis; leads to oxidative stress; and perturbs wobble tRNA modification and ribosome assembly, thereby affecting translation and leading to proteotoxic stress. In this review, we present the current knowledge of the mechanisms that govern mitochondrial genome maintenance and demonstrate ways in which the impairment of mitochondrial function can affect nuclear genome stability.
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Affiliation(s)
- Aneta Kaniak-Golik
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
| | - Adrianna Skoneczna
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland.
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78
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Abstract
Mec1 (ATR in humans) is the principal kinase responsible for checkpoint activation in response to replication stress and DNA damage in Saccharomyces cerevisiae. Checkpoint initiation requires stimulation of Mec1 kinase activity by specific activators. The complexity of checkpoint initiation in yeast increases with the complexity of chromosomal states during the different phases of the cell cycle. In G1 phase, the checkpoint clamp 9-1-1 is both necessary and sufficient for full activation of Mec1 kinase whereas in G2/M, robust checkpoint function requires both 9-1-1 and the replisome assembly protein Dpb11 (human TopBP1). A third activator, Dna2, is employed specifically during S phase to stimulate Mec1 kinase and to initiate the replication checkpoint. Dna2 is an essential nuclease-helicase that is required for proper Okazaki fragment maturation, for double-strand break repair, and for protecting stalled replication forks. Remarkably, all three Mec1 activators use an unstructured region of the protein, containing two critically important aromatic residues, in order to activate Mec1. A role for these checkpoint activators in channeling aberrant replication structures into checkpoint complexes is discussed.
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Affiliation(s)
- Paulina H Wanrooij
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Peter M Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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79
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Teasley DC, Parajuli S, Nguyen M, Moore HR, Alspach E, Lock YJ, Honaker Y, Saharia A, Piwnica-Worms H, Stewart SA. Flap Endonuclease 1 Limits Telomere Fragility on the Leading Strand. J Biol Chem 2015; 290:15133-45. [PMID: 25922071 DOI: 10.1074/jbc.m115.647388] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Indexed: 01/01/2023] Open
Abstract
The existence of redundant replication and repair systems that ensure genome stability underscores the importance of faithful DNA replication. Nowhere is this complexity more evident than in challenging DNA templates, including highly repetitive or transcribed sequences. Here, we demonstrate that flap endonuclease 1 (FEN1), a canonical lagging strand DNA replication protein, is required for normal, complete leading strand replication at telomeres. We find that the loss of FEN1 nuclease activity, but not DNA repair activities, results in leading strand-specific telomere fragility. Furthermore, we show that FEN1 depletion-induced telomere fragility is increased by RNA polymerase II inhibition and is rescued by ectopic RNase H1 expression. These data suggest that FEN1 limits leading strand-specific telomere fragility by processing RNA:DNA hybrid/flap intermediates that arise from co-directional collisions occurring between the replisome and RNA polymerase. Our data reveal the first molecular mechanism for leading strand-specific telomere fragility and the first known role for FEN1 in leading strand DNA replication. Because FEN1 mutations have been identified in human cancers, our findings raise the possibility that unresolved RNA:DNA hybrid structures contribute to the genomic instability associated with cancer.
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Affiliation(s)
- Daniel C Teasley
- From the Departments of Cell Biology and Physiology and Integrating Communications within the Cancer Environment Institute, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Shankar Parajuli
- From the Departments of Cell Biology and Physiology and Integrating Communications within the Cancer Environment Institute, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Mai Nguyen
- From the Departments of Cell Biology and Physiology and Integrating Communications within the Cancer Environment Institute, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Hayley R Moore
- From the Departments of Cell Biology and Physiology and Integrating Communications within the Cancer Environment Institute, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Elise Alspach
- From the Departments of Cell Biology and Physiology and Integrating Communications within the Cancer Environment Institute, Washington University School of Medicine, Saint Louis, Missouri 63110
| | - Ying Jie Lock
- From the Departments of Cell Biology and Physiology and
| | - Yuchi Honaker
- From the Departments of Cell Biology and Physiology and
| | | | | | - Sheila A Stewart
- From the Departments of Cell Biology and Physiology and Integrating Communications within the Cancer Environment Institute, Washington University School of Medicine, Saint Louis, Missouri 63110 Medicine,
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80
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Welch AJ, Bedoya-Reina OC, Carretero-Paulet L, Miller W, Rode KD, Lindqvist C. Polar bears exhibit genome-wide signatures of bioenergetic adaptation to life in the arctic environment. Genome Biol Evol 2015; 6:433-50. [PMID: 24504087 PMCID: PMC3942037 DOI: 10.1093/gbe/evu025] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Polar bears (Ursus maritimus) face extremely cold temperatures and periods of fasting, which might result in more severe energetic challenges than those experienced by their sister species, the brown bear (U. arctos). We have examined the mitochondrial and nuclear genomes of polar and brown bears to investigate whether polar bears demonstrate lineage-specific signals of molecular adaptation in genes associated with cellular respiration/energy production. We observed increased evolutionary rates in the mitochondrial cytochrome c oxidase I gene in polar but not brown bears. An amino acid substitution occurred near the interaction site with a nuclear-encoded subunit of the cytochrome c oxidase complex and was predicted to lead to a functional change, although the significance of this remains unclear. The nuclear genomes of brown and polar bears demonstrate different adaptations related to cellular respiration. Analyses of the genomes of brown bears exhibited substitutions that may alter the function of proteins that regulate glucose uptake, which could be beneficial when feeding on carbohydrate-dominated diets during hyperphagia, followed by fasting during hibernation. In polar bears, genes demonstrating signatures of functional divergence and those potentially under positive selection were enriched in functions related to production of nitric oxide (NO), which can regulate energy production in several different ways. This suggests that polar bears may be able to fine-tune intracellular levels of NO as an adaptive response to control trade-offs between energy production in the form of adenosine triphosphate versus generation of heat (thermogenesis).
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Affiliation(s)
- Andreanna J Welch
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo
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81
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Levin L, Blumberg A, Barshad G, Mishmar D. Mito-nuclear co-evolution: the positive and negative sides of functional ancient mutations. Front Genet 2014; 5:448. [PMID: 25566330 PMCID: PMC4274989 DOI: 10.3389/fgene.2014.00448] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/08/2014] [Indexed: 12/31/2022] Open
Abstract
Most cell functions are carried out by interacting factors, thus underlying the functional importance of genetic interactions between genes, termed epistasis. Epistasis could be under strong selective pressures especially in conditions where the mutation rate of one of the interacting partners notably differs from the other. Accordingly, the order of magnitude higher mitochondrial DNA (mtDNA) mutation rate as compared to the nuclear DNA (nDNA) of all tested animals, should influence systems involving mitochondrial-nuclear (mito-nuclear) interactions. Such is the case of the energy producing oxidative phosphorylation (OXPHOS) and mitochondrial translational machineries which are comprised of factors encoded by both the mtDNA and the nDNA. Additionally, the mitochondrial RNA transcription and mtDNA replication systems are operated by nDNA-encoded proteins that bind mtDNA regulatory elements. As these systems are central to cell life there is strong selection toward mito-nuclear co-evolution to maintain their function. However, it is unclear whether (A) mito-nuclear co-evolution befalls only to retain mitochondrial functions during evolution or, also, (B) serves as an adaptive tool to adjust for the evolving energetic demands as species' complexity increases. As the first step to answer these questions we discuss evidence of both negative and adaptive (positive) selection acting on the mtDNA and nDNA-encoded genes and the effect of both types of selection on mito-nuclear interacting factors. Emphasis is given to the crucial role of recurrent ancient (nodal) mutations in such selective events. We apply this point-of-view to the three available types of mito-nuclear co-evolution: protein-protein (within the OXPHOS system), protein-RNA (mainly within the mitochondrial ribosome), and protein-DNA (at the mitochondrial replication and transcription machineries).
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Affiliation(s)
- Liron Levin
- Department of Life Sciences, Ben-Gurion University of the Negev Beersheba, Israel
| | - Amit Blumberg
- Department of Life Sciences, Ben-Gurion University of the Negev Beersheba, Israel
| | - Gilad Barshad
- Department of Life Sciences, Ben-Gurion University of the Negev Beersheba, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev Beersheba, Israel
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82
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Quantitative PCR-based measurement of nuclear and mitochondrial DNA damage and repair in mammalian cells. Methods Mol Biol 2014; 1105:419-37. [PMID: 24623245 DOI: 10.1007/978-1-62703-739-6_31] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In this chapter, we describe a gene-specific quantitative PCR (QPCR)-based assay for the measurement of DNA damage, using amplification of long DNA targets. This assay has been used extensively to measure the integrity of both nuclear and mitochondrial genomes exposed to different genotoxins and has proven to be particularly valuable in identifying reactive oxygen species-mediated mitochondrial DNA damage. QPCR can be used to quantify both the formation of DNA damage as well as the kinetics of damage removal. One of the main strengths of the assay is that it permits monitoring the integrity of mtDNA directly from total cellular DNA without the need for isolating mitochondria or a separate step of mitochondrial DNA purification. Here we discuss advantages and limitations of using QPCR to assay DNA damage in mammalian cells. In addition, we give a detailed protocol of the QPCR assay that helps facilitate its successful deployment in any molecular biology laboratory.
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83
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Cupp JD, Nielsen BL. Minireview: DNA replication in plant mitochondria. Mitochondrion 2014; 19 Pt B:231-7. [PMID: 24681310 PMCID: PMC4177014 DOI: 10.1016/j.mito.2014.03.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 02/28/2014] [Accepted: 03/19/2014] [Indexed: 10/25/2022]
Abstract
Higher plant mitochondrial genomes exhibit much greater structural complexity compared to most other organisms. Unlike well-characterized metazoan mitochondrial DNA (mtDNA) replication, an understanding of the mechanism(s) and proteins involved in plant mtDNA replication remains unclear. Several plant mtDNA replication proteins, including DNA polymerases, DNA primase/helicase, and accessory proteins have been identified. Mitochondrial dynamics, genome structure, and the complexity of dual-targeted and dual-function proteins that provide at least partial redundancy suggest that plants have a unique model for maintaining and replicating mtDNA when compared to the replication mechanism utilized by most metazoan organisms.
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Affiliation(s)
- John D Cupp
- Department of Microbiology & Molecular Biology, Brigham Young University, Provo, UT 84602, United States.
| | - Brent L Nielsen
- Department of Microbiology & Molecular Biology, Brigham Young University, Provo, UT 84602, United States.
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84
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DNA and RNA quadruplex-binding proteins. Int J Mol Sci 2014; 15:17493-517. [PMID: 25268620 PMCID: PMC4227175 DOI: 10.3390/ijms151017493] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 09/15/2014] [Accepted: 09/22/2014] [Indexed: 02/01/2023] Open
Abstract
Four-stranded DNA structures were structurally characterized in vitro by NMR, X-ray and Circular Dichroism spectroscopy in detail. Among the different types of quadruplexes (i-Motifs, minor groove quadruplexes, G-quadruplexes, etc.), the best described are G-quadruplexes which are featured by Hoogsteen base-paring. Sequences with the potential to form quadruplexes are widely present in genome of all organisms. They are found often in repetitive sequences such as telomeric ones, and also in promoter regions and 5' non-coding sequences. Recently, many proteins with binding affinity to G-quadruplexes have been identified. One of the initially portrayed G-rich regions, the human telomeric sequence (TTAGGG)n, is recognized by many proteins which can modulate telomerase activity. Sequences with the potential to form G-quadruplexes are often located in promoter regions of various oncogenes. The NHE III1 region of the c-MYC promoter has been shown to interact with nucleolin protein as well as other G-quadruplex-binding proteins. A number of G-rich sequences are also present in promoter region of estrogen receptor alpha. In addition to DNA quadruplexes, RNA quadruplexes, which are critical in translational regulation, have also been predicted and observed. For example, the RNA quadruplex formation in telomere-repeat-containing RNA is involved in interaction with TRF2 (telomere repeat binding factor 2) and plays key role in telomere regulation. All these fundamental examples suggest the importance of quadruplex structures in cell processes and their understanding may provide better insight into aging and disease development.
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85
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Holt IJ, Jacobs HT. Unique features of DNA replication in mitochondria: a functional and evolutionary perspective. Bioessays 2014; 36:1024-31. [PMID: 25220172 DOI: 10.1002/bies.201400052] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Last year, we reported a new mechanism of DNA replication in mammals. It occurs inside mitochondria and entails the use of processed transcripts, termed bootlaces, which hybridize with the displaced parental strand as the replication fork advances. Here we discuss possible reasons why such an unusual mechanism of DNA replication might have evolved. The bootlace mechanism can minimize the occurrence and impact of single-strand breaks that would otherwise threaten genome stability. Furthermore, by providing an implicit mismatch recognition system, it should limit the occurrence of replication-dependent deletions and insertions, and defend against invading elements. Such a mechanism may also limit attempts to manipulate the mammalian mitochondrial genome.
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Affiliation(s)
- Ian J Holt
- MRC National Institute for Medical Research, London, UK
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86
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Bharti SK, Sommers JA, Zhou J, Kaplan DL, Spelbrink JN, Mergny JL, Brosh RM. DNA sequences proximal to human mitochondrial DNA deletion breakpoints prevalent in human disease form G-quadruplexes, a class of DNA structures inefficiently unwound by the mitochondrial replicative Twinkle helicase. J Biol Chem 2014; 289:29975-93. [PMID: 25193669 DOI: 10.1074/jbc.m114.567073] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Mitochondrial DNA deletions are prominent in human genetic disorders, cancer, and aging. It is thought that stalling of the mitochondrial replication machinery during DNA synthesis is a prominent source of mitochondrial genome instability; however, the precise molecular determinants of defective mitochondrial replication are not well understood. In this work, we performed a computational analysis of the human mitochondrial genome using the "Pattern Finder" G-quadruplex (G4) predictor algorithm to assess whether G4-forming sequences reside in close proximity (within 20 base pairs) to known mitochondrial DNA deletion breakpoints. We then used this information to map G4P sequences with deletions characteristic of representative mitochondrial genetic disorders and also those identified in various cancers and aging. Circular dichroism and UV spectral analysis demonstrated that mitochondrial G-rich sequences near deletion breakpoints prevalent in human disease form G-quadruplex DNA structures. A biochemical analysis of purified recombinant human Twinkle protein (gene product of c10orf2) showed that the mitochondrial replicative helicase inefficiently unwinds well characterized intermolecular and intramolecular G-quadruplex DNA substrates, as well as a unimolecular G4 substrate derived from a mitochondrial sequence that nests a deletion breakpoint described in human renal cell carcinoma. Although G4 has been implicated in the initiation of mitochondrial DNA replication, our current findings suggest that mitochondrial G-quadruplexes are also likely to be a source of instability for the mitochondrial genome by perturbing the normal progression of the mitochondrial replication machinery, including DNA unwinding by Twinkle helicase.
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Affiliation(s)
- Sanjay Kumar Bharti
- From the Laboratory of Molecular Gerontology, NIA, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224
| | - Joshua A Sommers
- From the Laboratory of Molecular Gerontology, NIA, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224
| | - Jun Zhou
- the ARNA Laboratory, University of Bordeaux, F-33000 Bordeaux, France, INSERM U869, Institut Européen de Chimie et Biologie (IECB), F-33600 Pessac, France
| | - Daniel L Kaplan
- the Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida 32312
| | - Johannes N Spelbrink
- the FinMIT Centre of Excellence, BioMediTech and Tampere University Hospital, Pirkanmaa Hospital District, University of Tampere, FI-33014 Tampere, Finland, and the Department of Pediatrics, Nijmegan Centre for Mitochondrial Disorders, Radboud University Medical Centre, Geert Grooteplein 10, P. O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Jean-Louis Mergny
- the ARNA Laboratory, University of Bordeaux, F-33000 Bordeaux, France, INSERM U869, Institut Européen de Chimie et Biologie (IECB), F-33600 Pessac, France
| | - Robert M Brosh
- From the Laboratory of Molecular Gerontology, NIA, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224,
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87
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Wanschers BF, Szklarczyk R, van den Brand MA, Jonckheere A, Suijskens J, Smeets R, Rodenburg RJ, Stephan K, Helland IB, Elkamil A, Rootwelt T, Ott M, van den Heuvel L, Nijtmans LG, Huynen MA. A mutation in the human CBP4 ortholog UQCC3 impairs complex III assembly, activity and cytochrome b stability. Hum Mol Genet 2014; 23:6356-65. [DOI: 10.1093/hmg/ddu357] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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88
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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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89
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Hensen F, Cansiz S, Gerhold JM, Spelbrink JN. To be or not to be a nucleoid protein: A comparison of mass-spectrometry based approaches in the identification of potential mtDNA-nucleoid associated proteins. Biochimie 2014; 100:219-26. [DOI: 10.1016/j.biochi.2013.09.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/17/2013] [Indexed: 01/09/2023]
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90
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Muftuoglu M, Mori MP, de Souza-Pinto NC. Formation and repair of oxidative damage in the mitochondrial DNA. Mitochondrion 2014; 17:164-81. [PMID: 24704805 DOI: 10.1016/j.mito.2014.03.007] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 03/18/2014] [Accepted: 03/18/2014] [Indexed: 12/13/2022]
Abstract
The mitochondrial DNA (mtDNA) encodes for only 13 polypeptides, components of 4 of the 5 oxidative phosphorylation complexes. But despite this apparently small numeric contribution, all 13 subunits are essential for the proper functioning of the oxidative phosphorylation circuit. Thus, accumulation of lesions, mutations and deletions/insertions in the mtDNA could have severe functional consequences, including mitochondrial diseases, aging and age-related diseases. The DNA is a chemically unstable molecule, which can be easily oxidized, alkylated, deaminated and suffer other types of chemical modifications, throughout evolution the organisms that survived were those who developed efficient DNA repair processes. In the last two decades, it has become clear that mitochondria have DNA repair pathways, which operate, at least for some types of lesions, as efficiently as the nuclear DNA repair pathways. The mtDNA is localized in a particularly oxidizing environment, making it prone to accumulate oxidatively generated DNA modifications (ODMs). In this article, we: i) review the major types of ODMs formed in mtDNA and the known repair pathways that remove them; ii) discuss the possible involvement of other repair pathways, just recently characterized in mitochondria, in the repair of these modifications; and iii) address the role of DNA repair in mitochondrial function and a possible cross-talk with other pathways that may potentially participate in mitochondrial genomic stability, such as mitochondrial dynamics and nuclear-mitochondrial signaling. Oxidative stress and ODMs have been increasingly implicated in disease and aging, and thus we discuss how variations in DNA repair efficiency may contribute to the etiology of such conditions or even modulate their clinical outcomes.
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Affiliation(s)
- Meltem Muftuoglu
- Department of Molecular Biology and Genetics, Acibadem University, Atasehir, 34752 Istanbul, Turkey
| | - Mateus P Mori
- Depto. de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000 Brazil
| | - Nadja C de Souza-Pinto
- Depto. de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000 Brazil.
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91
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Karanja KK, Lee EH, Hendrickson EA, Campbell JL. Preventing over-resection by DNA2 helicase/nuclease suppresses repair defects in Fanconi anemia cells. Cell Cycle 2014; 13:1540-50. [PMID: 24626199 DOI: 10.4161/cc.28476] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
FANCD2 is required for the repair of DNA damage by the FA (Fanconi anemia) pathway, and, consequently, FANCD2-deficient cells are sensitive to compounds such as cisplatin and formaldehyde that induce DNA:DNA and DNA:protein crosslinks, respectively. The DNA2 helicase/nuclease is required for RNA/DNA flap removal from Okazaki fragments during DNA replication and for the resection of DSBs (double-strand breaks) during HDR (homology-directed repair) of replication stress-induced damage. A knockdown of DNA2 renders normal cells as sensitive to cisplatin (in the absence of EXO1) and to formaldehyde (even in the presence of EXO1) as FANCD2(-/-) cells. Surprisingly, however, the depletion of DNA2 in FANCD2-deficient cells rescues the sensitivity of FANCD2(-/-) cells to cisplatin and formaldehyde. We previously showed that the resection activity of DNA2 acts downstream of FANCD2 to insure HDR of the DSBs arising when replication forks encounter ICL (interstrand crosslink) damage. The suppression of FANCD2(-/-) by DNA2 knockdowns suggests that DNA2 and FANCD2 also have antagonistic roles: in the absence of FANCD2, DNA2 somehow corrupts repair. To demonstrate that DNA2 is deleterious to crosslink repair, we used psoralen-induced ICL damage to trigger the repair of a site-specific crosslink in a GFP reporter and observed that "over-resection" can account for reduced repair. Our work demonstrates that excessive resection can lead to genome instability and shows that strict regulatory processes have evolved to inhibit resection nucleases. The suppression of FANCD2(-/-) phenotypes by DNA2 depletion may have implications for FA therapies and for the use of ICL-inducing agents in chemotherapy.
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Affiliation(s)
- Kenneth K Karanja
- Braun Laboratories; California Institute of Technology; Pasadena, CA USA
| | - Eu Han Lee
- Department of Biochemistry, Molecular Biology, and Biophysics; University of Minnesota; Minneapolis, MN USA
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics; University of Minnesota; Minneapolis, MN USA
| | - Judith L Campbell
- Braun Laboratories; California Institute of Technology; Pasadena, CA USA
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92
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Tucker EJ, Wanschers BFJ, Szklarczyk R, Mountford HS, Wijeyeratne XW, van den Brand MAM, Leenders AM, Rodenburg RJ, Reljić B, Compton AG, Frazier AE, Bruno DL, Christodoulou J, Endo H, Ryan MT, Nijtmans LG, Huynen MA, Thorburn DR. Mutations in the UQCC1-interacting protein, UQCC2, cause human complex III deficiency associated with perturbed cytochrome b protein expression. PLoS Genet 2013; 9:e1004034. [PMID: 24385928 PMCID: PMC3873243 DOI: 10.1371/journal.pgen.1004034] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 10/29/2013] [Indexed: 12/01/2022] Open
Abstract
Mitochondrial oxidative phosphorylation (OXPHOS) is responsible for generating the majority of cellular ATP. Complex III (ubiquinol-cytochrome c oxidoreductase) is the third of five OXPHOS complexes. Complex III assembly relies on the coordinated expression of the mitochondrial and nuclear genomes, with 10 subunits encoded by nuclear DNA and one by mitochondrial DNA (mtDNA). Complex III deficiency is a debilitating and often fatal disorder that can arise from mutations in complex III subunit genes or one of three known complex III assembly factors. The molecular cause for complex III deficiency in about half of cases, however, is unknown and there are likely many complex III assembly factors yet to be identified. Here, we used Massively Parallel Sequencing to identify a homozygous splicing mutation in the gene encoding Ubiquinol-Cytochrome c Reductase Complex Assembly Factor 2 (UQCC2) in a consanguineous Lebanese patient displaying complex III deficiency, severe intrauterine growth retardation, neonatal lactic acidosis and renal tubular dysfunction. We prove causality of the mutation via lentiviral correction studies in patient fibroblasts. Sequence-profile based orthology prediction shows UQCC2 is an ortholog of the Saccharomyces cerevisiae complex III assembly factor, Cbp6p, although its sequence has diverged substantially. Co-purification studies show that UQCC2 interacts with UQCC1, the predicted ortholog of the Cbp6p binding partner, Cbp3p. Fibroblasts from the patient with UQCC2 mutations have deficiency of UQCC1, while UQCC1-depleted cells have reduced levels of UQCC2 and complex III. We show that UQCC1 binds the newly synthesized mtDNA-encoded cytochrome b subunit of complex III and that UQCC2 patient fibroblasts have specific defects in the synthesis or stability of cytochrome b. This work reveals a new cause for complex III deficiency that can assist future patient diagnosis, and provides insight into human complex III assembly by establishing that UQCC1 and UQCC2 are complex III assembly factors participating in cytochrome b biogenesis. Mitochondrial complex III deficiency is a devastating disorder that impairs energy generation, and leads to variable symptoms such as developmental regression, seizures, kidney dysfunction and frequently death. The genetic basis of complex III deficiency is not fully understood, with around half of cases having no known cause. This lack of genetic diagnosis is partly due to an incomplete understanding of the genes required for complex III assembly and function. We have identified two key proteins required for complex III, UQCC1 and UQCC2, and have elucidated the role of these inter-dependent proteins in the biogenesis of cytochrome b, the only complex III subunit that is encoded by mitochondrial DNA. We have shown that mutations in UQCC2 cause human complex III deficiency in a patient with neonatal lactic acidosis and renal tubulopathy. This work contributes to an improved understanding of complex III biogenesis, and will aid future molecular diagnoses of complex III deficiency.
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Affiliation(s)
- Elena J. Tucker
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Bas F. J. Wanschers
- Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Radek Szklarczyk
- Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Hayley S. Mountford
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Xiaonan W. Wijeyeratne
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Mariël A. M. van den Brand
- Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Anne M. Leenders
- Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Richard J. Rodenburg
- Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Boris Reljić
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Alison G. Compton
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Ann E. Frazier
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Damien L. Bruno
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - John Christodoulou
- Genetic Metabolic Disorders Research Unit, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Disciplines of Paediatrics & Child Health and Genetic Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Hitoshi Endo
- Department of Biochemistry, Jichi Medical University, Tochigi, Japan
| | - Michael T. Ryan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
- ARC Centre of Excellence for Coherent X-ray Science, La Trobe University, Melbourne, Australia
| | - Leo G. Nijtmans
- Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Martijn A. Huynen
- Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
- * E-mail: (MAH); (DRT)
| | - David R. Thorburn
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Victoria, Australia
- * E-mail: (MAH); (DRT)
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93
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A short review on the implications of base excision repair pathway for neurons: relevance to neurodegenerative diseases. Mitochondrion 2013; 16:38-49. [PMID: 24220222 DOI: 10.1016/j.mito.2013.10.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 10/31/2013] [Accepted: 10/31/2013] [Indexed: 12/13/2022]
Abstract
Oxidative DNA damage results from the attack by reactive oxygen and nitrogen species (ROS/RNS) on human genome. This includes base modifications such as oxidized bases, abasic (AP) sites, and single-strand breaks (SSBs), all of which are repaired by the base excision repair (BER) pathway, one among the six known repair pathways. BER-pathway in mammalian cells involves several evolutionarily conserved proteins and is also linked to genome replication and transcription. The BER-pathway enzymes, namely, DNA glycosylases (DGs) and the end-processing proteins such as abasic endonuclease (APE1), form complexes with downstream repair enzymes via protein-protein and DNA-protein interactions. An emerging concept for BER proteins is their involvement in non-canonical functions associated to RNA metabolism, which is opening new interesting perspectives. Various mechanisms that are underlined in maintaining neuronal cell genome integrity are identified, but are inconclusive in providing protection against oxidative damage in neurodegenerative disorders, main emphasis is given towards the role played by the proteins of BER-pathway that is discussed. In addition, mechanisms of action of BER-pathway in nuclear vs. mitochondria as well as the non-canonical functions are discussed in connection to human neurodegenerative diseases.
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94
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Rajala N, Gerhold JM, Martinsson P, Klymov A, Spelbrink JN. Replication factors transiently associate with mtDNA at the mitochondrial inner membrane to facilitate replication. Nucleic Acids Res 2013; 42:952-67. [PMID: 24163258 PMCID: PMC3902951 DOI: 10.1093/nar/gkt988] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mitochondrial DNA (mtDNA) is organized in discrete protein-DNA complexes, nucleoids, that are usually considered to be mitochondrial-inner-membrane associated. Here we addressed the association of replication factors with nucleoids and show that endogenous mtDNA helicase Twinkle and single-stranded DNA-binding protein, mtSSB, co-localize only with a subset of nucleoids. Using nucleotide analogs to identify replicating mtDNA in situ, the fraction of label-positive nucleoids that is Twinkle/mtSSB positive, is highest with the shortest labeling-pulse. In addition, the recruitment of mtSSB is shown to be Twinkle dependent. These proteins thus transiently associate with mtDNA in an ordered manner to facilitate replication. To understand the nature of mtDNA replication complexes, we examined nucleoid protein membrane association and show that endogenous Twinkle is firmly membrane associated even in the absence of mtDNA, whereas mtSSB and other nucleoid-associated proteins are found in both membrane-bound and soluble fractions. Likewise, a substantial amount of mtDNA is found as soluble or loosely membrane bound. We show that, by manipulation of Twinkle levels, mtDNA membrane association is partially dependent on Twinkle. Our results thus show that Twinkle recruits or is assembled with mtDNA at the inner membrane to form a replication platform and amount to the first clear demonstration that nucleoids are dynamic both in composition and concurrent activity.
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Affiliation(s)
- Nina Rajala
- FinMIT Centre of Excellence, Institute of Biomedical Technology & Tampere University Hospital, Pirkanmaa Hospital District, FI-33014 University of Tampere, Finland and Department of Pediatrics, Institute for Genetic and Metabolic Disease, Radboud University Medical Centre, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
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95
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Budd ME, Campbell JL. Dna2 is involved in CA strand resection and nascent lagging strand completion at native yeast telomeres. J Biol Chem 2013; 288:29414-29. [PMID: 23963457 DOI: 10.1074/jbc.m113.472456] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Post-replicational telomere end processing involves both extension by telomerase and resection to produce 3'-GT-overhangs that extend beyond the complementary 5'-CA-rich strand. Resection must be carefully controlled to maintain telomere length. At short de novo telomeres generated artificially by HO endonuclease in the G2 phase, we show that dna2-defective strains are impaired in both telomere elongation and sequential 5'-CA resection. At native telomeres in dna2 mutants, GT-overhangs do clearly elongate during late S phase but are shorter than in wild type, suggesting a role for Dna2 in 5'-CA resection but also indicating significant redundancy with other nucleases. Surprisingly, elimination of Mre11 nuclease or Exo1, which are complementary to Dna2 in resection of internal double strand breaks, does not lead to further shortening of GT-overhangs in dna2 mutants. A second step in end processing involves filling in of the CA-strand to maintain appropriate telomere length. We show that Dna2 is required for normal telomeric CA-strand fill-in. Yeast dna2 mutants, like mutants in DNA ligase 1 (cdc9), accumulate low molecular weight, nascent lagging strand DNA replication intermediates at telomeres. Based on this and other results, we propose that FEN1 is not sufficient and that either Dna2 or Exo1 is required to supplement FEN1 in maturing lagging strands at telomeres. Telomeres may be among the subset of genomic locations where Dna2 helicase/nuclease is essential for the two-nuclease pathway of primer processing on lagging strands.
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Affiliation(s)
- Martin E Budd
- From Braun Laboratories, California Institute of Technology, Pasadena, California 91125
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96
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Abstract
Helicases have major roles in genome maintenance by unwinding structured nucleic acids. Their prominence is marked by various cancers and genetic disorders that are linked to helicase defects. Although considerable effort has been made to understand the functions of DNA helicases that are important for genomic stability and cellular homeostasis, the complexity of the DNA damage response leaves us with unanswered questions regarding how helicase-dependent DNA repair pathways are regulated and coordinated with cell cycle checkpoints. Further studies may open the door to targeting helicases in order to improve cancer treatments based on DNA-damaging chemotherapy or radiation.
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Affiliation(s)
- Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Boulevard, Baltimore, Maryland 21224, USA.
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97
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Alexeyev M, Shokolenko I, Wilson G, LeDoux S. The maintenance of mitochondrial DNA integrity--critical analysis and update. Cold Spring Harb Perspect Biol 2013; 5:a012641. [PMID: 23637283 DOI: 10.1101/cshperspect.a012641] [Citation(s) in RCA: 286] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA molecules in mitochondria, just like those in the nucleus of eukaryotic cells, are constantly damaged by noxious agents. Eukaryotic cells have developed efficient mechanisms to deal with this assault. The process of DNA repair in mitochondria, initially believed nonexistent, has now evolved into a mature area of research. In recent years, it has become increasingly appreciated that mitochondria possess many of the same DNA repair pathways that the nucleus does. Moreover, a unique pathway that is enabled by high redundancy of the mitochondrial DNA and allows for the disposal of damaged DNA molecules operates in this organelle. In this review, we attempt to present a unified view of our current understanding of the process of DNA repair in mitochondria with an emphasis on issues that appear controversial.
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Affiliation(s)
- Mikhail Alexeyev
- Department of Cell Biology and Neuroscience, University of South Alabama, Mobile, AL 36688, USA
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98
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Lin W, Sampathi S, Dai H, Liu C, Zhou M, Hu J, Huang Q, Campbell J, Shin-Ya K, Zheng L, Chai W, Shen B. Mammalian DNA2 helicase/nuclease cleaves G-quadruplex DNA and is required for telomere integrity. EMBO J 2013; 32:1425-39. [PMID: 23604072 DOI: 10.1038/emboj.2013.88] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 03/26/2013] [Indexed: 01/23/2023] Open
Abstract
Efficient and faithful replication of telomeric DNA is critical for maintaining genome integrity. The G-quadruplex (G4) structure arising in the repetitive TTAGGG sequence is thought to stall replication forks, impairing efficient telomere replication and leading to telomere instabilities. However, pathways modulating telomeric G4 are poorly understood, and it is unclear whether defects in these pathways contribute to genome instabilities in vivo. Here, we report that mammalian DNA2 helicase/nuclease recognizes and cleaves telomeric G4 in vitro. Consistent with DNA2's role in removing G4, DNA2 deficiency in mouse cells leads to telomere replication defects, elevating the levels of fragile telomeres (FTs) and sister telomere associations (STAs). Such telomere defects are enhanced by stabilizers of G4. Moreover, DNA2 deficiency induces telomere DNA damage and chromosome segregation errors, resulting in tetraploidy and aneuploidy. Consequently, DNA2-deficient mice develop aneuploidy-associated cancers containing dysfunctional telomeres. Collectively, our genetic, cytological, and biochemical results suggest that mammalian DNA2 reduces replication stress at telomeres, thereby preserving genome stability and suppressing cancer development, and that this may involve, at least in part, nucleolytic processing of telomeric G4.
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Affiliation(s)
- Weiqiang Lin
- Department of Radiation Biology, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA 91010, USA
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99
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van Bon BWM, Oortveld MAW, Nijtmans LG, Fenckova M, Nijhof B, Besseling J, Vos M, Kramer JM, de Leeuw N, Castells-Nobau A, Asztalos L, Viragh E, Ruiter M, Hofmann F, Eshuis L, Collavin L, Huynen MA, Asztalos Z, Verstreken P, Rodenburg RJ, Smeitink JA, de Vries BBA, Schenck A. CEP89 is required for mitochondrial metabolism and neuronal function in man and fly. Hum Mol Genet 2013; 22:3138-51. [PMID: 23575228 DOI: 10.1093/hmg/ddt170] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It is estimated that the human mitochondrial proteome consists of 1000-1500 distinct proteins. The majority of these support the various biochemical pathways that are active in these organelles. Individuals with an oxidative phosphorylation disorder of unknown cause provide a unique opportunity to identify novel genes implicated in mitochondrial biology. We identified a homozygous deletion of CEP89 in a patient with isolated complex IV deficiency, intellectual disability and multisystemic problems. CEP89 is a ubiquitously expressed and highly conserved gene of unknown function. Immunocytochemistry and cellular fractionation experiments showed that CEP89 is present both in the cytosol and in the mitochondrial intermembrane space. Furthermore, we ascertained in vitro that downregulation of CEP89 resulted in a severe decrease in complex IV in-gel activity and altered mobility, suggesting that the complex is aberrantly formed. Two-dimensional BN-SDS gel analysis revealed that CEP89 associates with a high-molecular weight complex. Together, these data confirm a role for CEP89 in mitochondrial metabolism. In addition, we modeled CEP89 loss of function in Drosophila. Ubiquitous knockdown of fly Cep89 decreased complex IV activity and resulted in complete lethality. Furthermore, Cep89 is required for mitochondrial integrity, membrane depolarization and synaptic transmission of photoreceptor neurons, and for (sub)synaptic organization of the larval neuromuscular junction. Finally, we tested neuronal Cep89 knockdown flies in the light-off jump reflex habituation assay, which revealed its role in learning. We conclude that CEP89 proteins play an important role in mitochondrial metabolism, especially complex IV activity, and are required for neuronal and cognitive function across evolution.
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Affiliation(s)
- Bregje W M van Bon
- Department of Human Genetics, Radboud University Medical Centre, 6500 HB, Nijmegen, The Netherlands
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100
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Ronchi D, Di Fonzo A, Lin W, Bordoni A, Liu C, Fassone E, Pagliarani S, Rizzuti M, Zheng L, Filosto M, Ferrò M, Ranieri M, Magri F, Peverelli L, Li H, Yuan YC, Corti S, Sciacco M, Moggio M, Bresolin N, Shen B, Comi G. Mutations in DNA2 link progressive myopathy to mitochondrial DNA instability. Am J Hum Genet 2013; 92:293-300. [PMID: 23352259 DOI: 10.1016/j.ajhg.2012.12.014] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Revised: 11/05/2012] [Accepted: 12/27/2012] [Indexed: 11/24/2022] Open
Abstract
Syndromes associated with multiple mtDNA deletions are due to different molecular defects that can result in a wide spectrum of predominantly adult-onset clinical presentations, ranging from progressive external ophthalmoplegia (PEO) to multisystemic disorders of variable severity. The autosomal-dominant form of PEO is genetically heterogeneous. Recently, causative mutations have been reported in several nuclear genes that encode proteins of the mtDNA replisome machinery (POLG, POLG2, and C10orf2) or that are involved in pathways for the synthesis of deoxyribonuclotides (ANT1 and RRM2B). Despite these findings, putative mutations remain unknown in half of the subjects with PEO. We report the identification, by exome sequencing, of mutations in DNA2 in adult-onset individuals with a form of mitochondrial myopathy featuring instability of muscle mtDNA. DNA2 encodes a helicase/nuclease family member that is most likely involved in mtDNA replication, as well as in the long-patch base-excision repair (LP-BER) pathway. In vitro biochemical analysis of purified mutant proteins revealed a severe impairment of nuclease, helicase, and ATPase activities. These results implicate human DNA2 and the LP-BER pathway in the pathogenesis of adult-onset disorders of mtDNA maintenance.
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