1
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Kumari N, Antil H, Kumari S, Raghavan SC. Deficiency of ligase IV leads to reduced NHEJ, accumulation of DNA damage, and can sensitize cells to cancer therapeutics. Genomics 2023; 115:110731. [PMID: 37871849 DOI: 10.1016/j.ygeno.2023.110731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/14/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023]
Abstract
Ligase IV is a key enzyme involved during DNA double-strand breaks (DSBs) repair through nonhomologous end joining (NHEJ). However, in contrast to Ligase IV deficient mouse cells, which are embryonic lethal, Ligase IV deficient human cells, including pre-B cells, are viable. Using CRISPR-Cas9 mediated genome editing, we have generated six different LIG4 mutants in cervical cancer and normal kidney epithelial cell lines. While the LIG4 mutant cells showed a significant reduction in NHEJ, joining mediated through microhomology-mediated end joining (MMEJ) and homologous recombination (HR) were significantly high. The reduced NHEJ joining activity was restored by adding purified Ligase IV/XRCC4. Accumulation of DSBs and reduced cell viability were observed in LIG4 mutant cells. LIG4 mutant cells exhibited enhanced sensitivity towards DSB-inducing agents such as ionizing radiation (IR) and etoposide. More importantly, the LIG4 mutant of cervical cancer cells showed increased sensitivity towards FDA approved drugs such as Carboplatin, Cisplatin, Paclitaxel, Doxorubicin, and Bleomycin used for cervical cancer treatment. These drugs, in combination with IR showed enhanced cancer cell death in the background of LIG4 gene mutation. Thus, our study reveals that mutation in LIG4 results in compromised NHEJ, leading to sensitization of cervical cancer cells towards currently used cancer therapeutics.
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Affiliation(s)
- Nitu Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Himanshu Antil
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Susmita Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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2
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Alexeyev M. TFAM in mtDNA Homeostasis: Open Questions. DNA 2023; 3:134-136. [PMID: 37771599 PMCID: PMC10538575 DOI: 10.3390/dna3030011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Transcription factor A, mitochondrial (TFAM) is a key player in mitochondrial DNA (mtDNA) transcription and replication [...]
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Affiliation(s)
- Mikhail Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
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3
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Kozhukhar N, Alexeyev MF. The C-Terminal Tail of Mitochondrial Transcription Factor A Is Dispensable for Mitochondrial DNA Replication and Transcription In Situ. Int J Mol Sci 2023; 24:9430. [PMID: 37298383 PMCID: PMC10253692 DOI: 10.3390/ijms24119430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/04/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Mitochondrial transcription factor A (TFAM) is one of the widely studied but still incompletely understood mitochondrial protein, which plays a crucial role in the maintenance and transcription of mitochondrial DNA (mtDNA). The available experimental evidence is often contradictory in assigning the same function to various TFAM domains, partly owing to the limitations of those experimental systems. Recently, we developed the GeneSwap approach, which enables in situ reverse genetic analysis of mtDNA replication and transcription and is devoid of many of the limitations of the previously used techniques. Here, we utilized this approach to analyze the contributions of the TFAM C-terminal (tail) domain to mtDNA transcription and replication. We determined, at a single amino acid (aa) resolution, the TFAM tail requirements for in situ mtDNA replication in murine cells and established that tail-less TFAM supports both mtDNA replication and transcription. Unexpectedly, in cells expressing either C-terminally truncated murine TFAM or DNA-bending human TFAM mutant L6, HSP1 transcription was impaired to a greater extent than LSP transcription. Our findings are incompatible with the prevailing model of mtDNA transcription and thus suggest the need for further refinement.
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Affiliation(s)
| | - Mikhail F. Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
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4
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Khozhukhar N, Spadafora D, Rodriguez Rodriguez YA, Fayzulin R, Alexeyev M. Generation of Mammalian Cells Devoid of Mitochondrial DNA (ρ 0 cells). Curr Protoc 2023; 3:e679. [PMID: 36809687 PMCID: PMC10151036 DOI: 10.1002/cpz1.679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
To cope with DNA damage, mitochondria have developed a pathway whereby severely damaged or unrepairable mitochondrial DNA (mtDNA) molecules can be discarded and degraded, after which new molecules are synthesized using intact templates. In this unit, we describe a method that harnesses this pathway to eliminate mtDNA from mammalian cells by transiently overexpressing the Y147A mutant of human uracil-N-glycosylase (mUNG1) in mitochondria. We also provide alternate protocols for mtDNA elimination using either combined treatment with ethidium bromide (EtBr) and dideoxycytidine (ddC) or clustered regulatory interspersed short palindromic repeat (CRISPR)-Cas9-mediated knockout of TFAM or other genes essential for mtDNA replication. Support protocols detail approaches for several processes: (1) genotyping ρ0 cells of human, mouse, and rat origin by polymerase chain reaction (PCR); (2) quantification of mtDNA by quantitative PCR (qPCR); (3) preparation of calibrator plasmids for mtDNA quantification; and (4) quantification of mtDNA by direct droplet digital PCR (dddPCR). © 2023 Wiley Periodicals LLC. Basic Protocol: Inducing mtDNA loss with mUNG1 Alternate Protocol 1: Generation of ρ0 cells by mtDNA depletion with EtBr and ddC Alternate Protocol 2: Generation of ρ0 cells by knocking out genes critical for mtDNA replication Support Protocol 1: Genotyping ρ0 cells by DirectPCR Support Protocol 2: Determination of mtDNA copy number by qPCR Support Protocol 3: Preparation of calibrator plasmid for qPCR Support Protocol 4: Determination of mtCN by direct droplet digital PCR (dddPCR).
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Affiliation(s)
| | | | | | - Rafik Fayzulin
- University of South Alabama, Department of Physiology and Cell Biology
| | - Mikhail Alexeyev
- University of South Alabama, Department of Physiology and Cell Biology
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5
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TFAM's Contributions to mtDNA Replication and OXPHOS Biogenesis Are Genetically Separable. Cells 2022; 11:cells11233754. [PMID: 36497015 PMCID: PMC9739059 DOI: 10.3390/cells11233754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
The ability of animal orthologs of human mitochondrial transcription factor A (hTFAM) to support the replication of human mitochondrial DNA (hmtDNA) does not follow a simple pattern of phylogenetic closeness or sequence similarity. In particular, TFAM from chickens (Gallus gallus, chTFAM), unlike TFAM from the "living fossil" fish coelacanth (Latimeria chalumnae), cannot support hmtDNA replication. Here, we implemented the recently developed GeneSwap approach for reverse genetic analysis of chTFAM to obtain insights into this apparent contradiction. By implementing limited "humanization" of chTFAM focused either on amino acid residues that make DNA contacts, or the ones with significant variances in side chains, we isolated two variants, Ch13 and Ch22. The former has a low mtDNA copy number (mtCN) but robust respiration. The converse is true of Ch22. Ch13 and Ch22 complement each other's deficiencies. Opposite directionalities of changes in mtCN and respiration were also observed in cells expressing frog TFAM. This led us to conclude that TFAM's contributions to mtDNA replication and respiratory chain biogenesis are genetically separable. We also present evidence that TFAM residues that make DNA contacts play the leading role in mtDNA replication. Finally, we present evidence for a novel mode of regulation of the respiratory chain biogenesis by regulating the supply of rRNA subunits.
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6
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Kozhukhar N, Spadafora D, Rodriguez YAR, Alexeyev MF. A Method for In Situ Reverse Genetic Analysis of Proteins Involved mtDNA Replication. Cells 2022; 11:2168. [PMID: 35883613 PMCID: PMC9316749 DOI: 10.3390/cells11142168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/29/2022] [Accepted: 07/10/2022] [Indexed: 02/01/2023] Open
Abstract
The unavailability of tractable reverse genetic analysis approaches represents an obstacle to a better understanding of mitochondrial DNA replication. Here, we used CRISPR-Cas9 mediated gene editing to establish the conditional viability of knockouts in the key proteins involved in mtDNA replication. This observation prompted us to develop a set of tools for reverse genetic analysis in situ, which we called the GeneSwap approach. The technique was validated by identifying 730 amino acid (aa) substitutions in the mature human TFAM that are conditionally permissive for mtDNA replication. We established that HMG domains of TFAM are functionally independent, which opens opportunities for engineering chimeric TFAMs with customized properties for studies on mtDNA replication, mitochondrial transcription, and respiratory chain function. Finally, we present evidence that the HMG2 domain plays the leading role in TFAM species-specificity, thus indicating a potential pathway for TFAM-mtDNA evolutionary co-adaptations.
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Affiliation(s)
| | | | | | - Mikhail F. Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA; (N.K.); (D.S.); (Y.A.R.R.)
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7
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Abstract
In the course of its short history, mitochondrial DNA (mtDNA) has made a long journey from obscurity to the forefront of research on major biological processes. mtDNA alterations have been found in all major disease groups, and their significance remains the subject of intense research. Despite remarkable progress, our understanding of the major aspects of mtDNA biology, such as its replication, damage, repair, transcription, maintenance, etc., is frustratingly limited. The path to better understanding mtDNA and its role in cells, however, remains torturous and not without errors, which sometimes leave a long trail of controversy behind them. This review aims to provide a brief summary of our current knowledge of mtDNA and highlight some of the controversies that require attention from the mitochondrial research community.
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Affiliation(s)
- Inna Shokolenko
- Department of Biomedical Sciences, Pat Capps Covey College of Allied Health Professions, University of South Alabama, Mobile, AL 36688, USA
| | - Mikhail Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
- Correspondence:
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8
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Mitochondrial Neurodegeneration. Cells 2022; 11:cells11040637. [PMID: 35203288 PMCID: PMC8870525 DOI: 10.3390/cells11040637] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/28/2022] [Accepted: 02/06/2022] [Indexed: 01/27/2023] Open
Abstract
Mitochondria are cytoplasmic organelles, which generate energy as heat and ATP, the universal energy currency of the cell. This process is carried out by coupling electron stripping through oxidation of nutrient substrates with the formation of a proton-based electrochemical gradient across the inner mitochondrial membrane. Controlled dissipation of the gradient can lead to production of heat as well as ATP, via ADP phosphorylation. This process is known as oxidative phosphorylation, and is carried out by four multiheteromeric complexes (from I to IV) of the mitochondrial respiratory chain, carrying out the electron flow whose energy is stored as a proton-based electrochemical gradient. This gradient sustains a second reaction, operated by the mitochondrial ATP synthase, or complex V, which condensates ADP and Pi into ATP. Four complexes (CI, CIII, CIV, and CV) are composed of proteins encoded by genes present in two separate compartments: the nuclear genome and a small circular DNA found in mitochondria themselves, and are termed mitochondrial DNA (mtDNA). Mutations striking either genome can lead to mitochondrial impairment, determining infantile, childhood or adult neurodegeneration. Mitochondrial disorders are complex neurological syndromes, and are often part of a multisystem disorder. In this paper, we divide the diseases into those caused by mtDNA defects and those that are due to mutations involving nuclear genes; from a clinical point of view, we discuss pediatric disorders in comparison to juvenile or adult-onset conditions. The complementary genetic contributions controlling organellar function and the complexity of the biochemical pathways present in the mitochondria justify the extreme genetic and phenotypic heterogeneity of this new area of inborn errors of metabolism known as ‘mitochondrial medicine’.
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9
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Invernizzi F, Legati A, Nasca A, Lamantea E, Garavaglia B, Gusic M, Kopajtich R, Prokisch H, Zeviani M, Lamperti C, Ghezzi D. Myopathic mitochondrial DNA depletion syndrome associated with biallelic variants in LIG3. Brain 2021; 144:e74. [PMID: 34165507 PMCID: PMC8536928 DOI: 10.1093/brain/awab238] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Federica Invernizzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, 20126 Milan, Italy
| | - Andrea Legati
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, 20126 Milan, Italy
| | - Alessia Nasca
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, 20126 Milan, Italy
| | - Eleonora Lamantea
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, 20126 Milan, Italy
| | - Barbara Garavaglia
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, 20126 Milan, Italy
| | - Mirjana Gusic
- Institute of Human Genetics, School of Medicine, Technische Universität
München, 81675 Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, 85764
Neuherberg, Germany
| | - Robert Kopajtich
- Institute of Human Genetics, School of Medicine, Technische Universität
München, 81675 Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, 85764
Neuherberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technische Universität
München, 81675 Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, 85764
Neuherberg, Germany
| | - Massimo Zeviani
- Department of Neurosciences, University of Padova, 35128 Padova,
Italy
- Venetian Institute of Molecular Medicine, 35128 Padova, Italy
| | - Costanza Lamperti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, 20126 Milan, Italy
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, 20126 Milan, Italy
- Department of Pathophysiology and Transplantation, University of
Milan, 20122 Milan, Italy
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10
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Bonora E, Chakrabarty S, Kellaris G, Tsutsumi M, Bianco F, Bergamini C, Ullah F, Isidori F, Liparulo I, Diquigiovanni C, Masin L, Rizzardi N, Cratere MG, Boschetti E, Papa V, Maresca A, Cenacchi G, Casadio R, Martelli P, Matera I, Ceccherini I, Fato R, Raiola G, Arrigo S, Signa S, Sementa AR, Severino M, Striano P, Fiorillo C, Goto T, Uchino S, Oyazato Y, Nakamura H, Mishra SK, Yeh YS, Kato T, Nozu K, Tanboon J, Morioka I, Nishino I, Toda T, Goto YI, Ohtake A, Kosaki K, Yamaguchi Y, Nonaka I, Iijima K, Mimaki M, Kurahashi H, Raams A, MacInnes A, Alders M, Engelen M, Linthorst G, de Koning T, den Dunnen W, Dijkstra G, van Spaendonck K, van Gent DC, Aronica EM, Picco P, Carelli V, Seri M, Katsanis N, Duijkers FAM, Taniguchi-Ikeda M, De Giorgio R. Biallelic variants in LIG3 cause a novel mitochondrial neurogastrointestinal encephalomyopathy. Brain 2021; 144:1451-1466. [PMID: 33855352 DOI: 10.1093/brain/awab056] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 11/13/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022] Open
Abstract
Abnormal gut motility is a feature of several mitochondrial encephalomyopathies, and mutations in genes such as TYMP and POLG, have been linked to these rare diseases. The human genome encodes three DNA ligases, of which only one, ligase III (LIG3), has a mitochondrial splice variant and is crucial for mitochondrial health. We investigated the effect of reduced LIG3 activity and resulting mitochondrial dysfunction in seven patients from three independent families, who showed the common occurrence of gut dysmotility and neurological manifestations reminiscent of mitochondrial neurogastrointestinal encephalomyopathy. DNA from these patients was subjected to whole exome sequencing. In all patients, compound heterozygous variants in a new disease gene, LIG3, were identified. All variants were predicted to have a damaging effect on the protein. The LIG3 gene encodes the only mitochondrial DNA (mtDNA) ligase and therefore plays a pivotal role in mtDNA repair and replication. In vitro assays in patient-derived cells showed a decrease in LIG3 protein levels and ligase activity. We demonstrated that the LIG3 gene defects affect mtDNA maintenance, leading to mtDNA depletion without the accumulation of multiple deletions as observed in other mitochondrial disorders. This mitochondrial dysfunction is likely to cause the phenotypes observed in these patients. The most prominent and consistent clinical signs were severe gut dysmotility and neurological abnormalities, including leukoencephalopathy, epilepsy, migraine, stroke-like episodes, and neurogenic bladder. A decrease in the number of myenteric neurons, and increased fibrosis and elastin levels were the most prominent changes in the gut. Cytochrome c oxidase (COX) deficient fibres in skeletal muscle were also observed. Disruption of lig3 in zebrafish reproduced the brain alterations and impaired gut transit in vivo. In conclusion, we identified variants in the LIG3 gene that result in a mitochondrial disease characterized by predominant gut dysmotility, encephalopathy, and neuromuscular abnormalities.
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Affiliation(s)
- Elena Bonora
- Department of Medical and Surgical Sciences, St. Orsola-Malpighi Hospital, University of Bologna, Bologna, 40138, Italy
| | - Sanjiban Chakrabarty
- Department of Molecular Genetics, Erasmus MC, Rotterdam, 3000 CA, The Netherlands
| | - Georgios Kellaris
- Center for Human Disease Modeling, Duke University, Durham, NC 27710, USA
| | - Makiko Tsutsumi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi, 470-1192, Japan
| | - Francesca Bianco
- Department of Medical and Surgical Sciences, St. Orsola-Malpighi Hospital, University of Bologna, Bologna, 40138, Italy
| | - Christian Bergamini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Farid Ullah
- Center for Human Disease Modeling, Duke University, Durham, NC 27710, USA
| | - Federica Isidori
- Department of Medical and Surgical Sciences, St. Orsola-Malpighi Hospital, University of Bologna, Bologna, 40138, Italy
| | - Irene Liparulo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Chiara Diquigiovanni
- Department of Medical and Surgical Sciences, St. Orsola-Malpighi Hospital, University of Bologna, Bologna, 40138, Italy
| | - Luca Masin
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Nicola Rizzardi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Mariapia Giuditta Cratere
- Department of Medical and Surgical Sciences, St. Orsola-Malpighi Hospital, University of Bologna, Bologna, 40138, Italy.,Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Elisa Boschetti
- Department of Medical and Surgical Sciences, St. Orsola-Malpighi Hospital, University of Bologna, Bologna, 40138, Italy
| | - Valentina Papa
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, 40123, Italy
| | - Alessandra Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, 40139, Italy
| | - Giovanna Cenacchi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, 40123, Italy
| | - Rita Casadio
- Biocomputing Group, Department of Biological, Geological, Environmental Sciences, University of Bologna, Bologna, 40126, Italy
| | - Pierluigi Martelli
- Biocomputing Group, Department of Biological, Geological, Environmental Sciences, University of Bologna, Bologna, 40126, Italy
| | - Ivana Matera
- IRCCS Istituto Giannina Gaslini, Genova, 16128, Italy
| | | | - Romana Fato
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Giuseppe Raiola
- Department of Paediatrics, Pugliese-Ciaccio Hospital, Catanzaro, 88100, Italy
| | - Serena Arrigo
- IRCCS Istituto Giannina Gaslini, Genova, 16128, Italy
| | - Sara Signa
- IRCCS Istituto Giannina Gaslini, Genova, 16128, Italy
| | | | | | | | | | - Tsuyoshi Goto
- Laboratory of Molecular Function of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, 611-0011, Japan
| | - Shumpei Uchino
- Department of Pediatrics, Teikyo University School of Medicine, Tokyo, 173-8605, Japan.,Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yoshinobu Oyazato
- Department of Pediatrics, Kakogawa Central City Hospital, Kakogawa, Hyogo, 675-8611, Japan
| | - Hisayoshi Nakamura
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan
| | - Sushil K Mishra
- Glycoscience Group, National University of Ireland, Galway, H91 CF50, Ireland
| | - Yu-Sheng Yeh
- Laboratory of Molecular Function of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, 611-0011, Japan
| | - Takema Kato
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi, 470-1192, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Hyogo, 650-0017, Japan
| | - Jantima Tanboon
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan
| | - Ichiro Morioka
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan
| | - Tatsushi Toda
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yu-Ichi Goto
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan
| | - Akira Ohtake
- Department of Pediatrics & Clinical Genomics, Faculty of Medicine, Saitama Medical University, Saitama, 350-0495, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Yoshiki Yamaguchi
- Laboratory of Pharmaceutical Physical Chemistry, Tohoku Medical and Pharmaceutical University, Miyagi, 981-8558, Japan
| | - Ikuya Nonaka
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Hyogo, 650-0017, Japan
| | - Masakazu Mimaki
- Department of Pediatrics, Teikyo University School of Medicine, Tokyo, 173-8605, Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi, 470-1192, Japan
| | - Anja Raams
- Department of Molecular Genetics, Erasmus MC, Rotterdam, 3000 CA, The Netherlands
| | - Alyson MacInnes
- Department of Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam, 1100 DD, The Netherlands
| | - Mariel Alders
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, 1100 DD, The Netherlands
| | - Marc Engelen
- Department of Neurology, Amsterdam UMC, University of Amsterdam, Amsterdam, 1100 DD, The Netherlands
| | - Gabor Linthorst
- Department of Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam, 1100 DD, The Netherlands
| | - Tom de Koning
- Department of Metabolic Diseases, UMCG, Groningen, 9700 RB, The Netherlands
| | | | - Gerard Dijkstra
- Department of Gastroenterology, UMCG, Groningen, 9700 RB, The Netherlands
| | - Karin van Spaendonck
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, 1100 DD, The Netherlands
| | - Dik C van Gent
- Department of Molecular Genetics, Erasmus MC, Rotterdam, 3000 CA, The Netherlands
| | - Eleonora M Aronica
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, 1100 DD, The Netherlands
| | - Paolo Picco
- IRCCS Istituto Giannina Gaslini, Genova, 16128, Italy
| | - Valerio Carelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, 40123, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, 40139, Italy
| | - Marco Seri
- Department of Medical and Surgical Sciences, St. Orsola-Malpighi Hospital, University of Bologna, Bologna, 40138, Italy
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, NC 27710, USA
| | - Floor A M Duijkers
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, 1100 DD, The Netherlands
| | - Mariko Taniguchi-Ikeda
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi, 470-1192, Japan.,Department of Pediatrics, Kobe University Graduate School of Medicine, Hyogo, 650-0017, Japan.,Department of Clinical Genetics, Fujita Health University Hospital, Aichi, 470-1192, Japan
| | - Roberto De Giorgio
- Department of Morphology, Surgery and Experimental Medicine, St. Anna Hospital, University of Ferrara, Ferrara, 44124, Italy
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11
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Kozhukhar N, Alexeyev MF. Limited predictive value of TFAM in mitochondrial biogenesis. Mitochondrion 2019; 49:156-165. [PMID: 31419493 PMCID: PMC6885536 DOI: 10.1016/j.mito.2019.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/23/2019] [Accepted: 08/12/2019] [Indexed: 12/16/2022]
Abstract
Mitochondrial transcription factor A (TFAM) plays an important role in mitochondrial DNA (mtDNA) transcription and replication. In some experimental settings, TFAM expression parallels parameters of mitochondrial biogenesis, which led to a widespread acceptance of TFAM as marker of mitochondrial biogenesis. We modulated TFAM expression in several experimental systems and observed that it fails to consistently parallel mtDNA copy number and expression of mtDNA-encoded polypeptides. We suggest that the use of TFAM as a marker of mitochondrial biogenesis should be avoided outside of systems in which its performance has been carefully validated.
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Affiliation(s)
- Natalya Kozhukhar
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA.
| | - Mikhail F Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA.
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12
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Caracciolo D, Di Martino MT, Amodio N, Morelli E, Montesano M, Botta C, Scionti F, Talarico D, Altomare E, Gallo Cantafio ME, Zuccalà V, Maltese L, Todoerti K, Rossi M, Arbitrio M, Neri A, Tagliaferri P, Tassone P. miR-22 suppresses DNA ligase III addiction in multiple myeloma. Leukemia 2019; 33:487-498. [PMID: 30120376 PMCID: PMC6365379 DOI: 10.1038/s41375-018-0238-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 07/04/2018] [Accepted: 07/13/2018] [Indexed: 12/15/2022]
Abstract
Multiple myeloma (MM) is a hematologic malignancy characterized by high genomic instability. Here we provide evidence that hyper-activation of DNA ligase III (LIG3) is crucial for genomic instability and survival of MM cells. LIG3 mRNA expression in MM patients correlates with shorter survival and even increases with more advanced stage of disease. Knockdown of LIG3 impairs MM cells viability in vitro and in vivo, suggesting that neoplastic plasmacells are dependent on LIG3-driven repair. To investigate the mechanisms involved in LIG3 expression, we investigated the post-transcriptional regulation. We identified miR-22-3p as effective negative regulator of LIG3 in MM. Enforced expression of miR-22 in MM cells downregulated LIG3 protein, which in turn increased DNA damage inhibiting in vitro and in vivo cell growth. Taken together, our findings demonstrate that myeloma cells are addicted to LIG3, which can be effectively inhibited by miR-22, promoting a novel axis of genome stability regulation.
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Affiliation(s)
- Daniele Caracciolo
- Department of Experimental and Clinical Medicine, Magna Græcia University, Campus Salvatore Venuta, Catanzaro, Italy
| | - Maria Teresa Di Martino
- Department of Experimental and Clinical Medicine, Magna Græcia University, Campus Salvatore Venuta, Catanzaro, Italy
| | - Nicola Amodio
- Department of Experimental and Clinical Medicine, Magna Græcia University, Campus Salvatore Venuta, Catanzaro, Italy
| | - Eugenio Morelli
- Department of Experimental and Clinical Medicine, Magna Græcia University, Campus Salvatore Venuta, Catanzaro, Italy
| | - Martina Montesano
- Department of Experimental and Clinical Medicine, Magna Græcia University, Campus Salvatore Venuta, Catanzaro, Italy
| | - Cirino Botta
- Department of Experimental and Clinical Medicine, Magna Græcia University, Campus Salvatore Venuta, Catanzaro, Italy
| | - Francesca Scionti
- Department of Experimental and Clinical Medicine, Magna Græcia University, Campus Salvatore Venuta, Catanzaro, Italy
| | | | - Emanuela Altomare
- Department of Experimental and Clinical Medicine, Magna Græcia University, Campus Salvatore Venuta, Catanzaro, Italy
| | - Maria Eugenia Gallo Cantafio
- Department of Experimental and Clinical Medicine, Magna Græcia University, Campus Salvatore Venuta, Catanzaro, Italy
| | | | | | - Katia Todoerti
- Department of Oncology and Hemato-oncology, University of Milan, and Hematology, Fondazione Cà Granda IRCCS Policlinico, Milan, Italy
| | - Marco Rossi
- Department of Experimental and Clinical Medicine, Magna Græcia University, Campus Salvatore Venuta, Catanzaro, Italy
| | - Mariamena Arbitrio
- Department of Experimental and Clinical Medicine, Magna Græcia University, Campus Salvatore Venuta, Catanzaro, Italy
| | - Antonino Neri
- Department of Oncology and Hemato-oncology, University of Milan, and Hematology, Fondazione Cà Granda IRCCS Policlinico, Milan, Italy
| | - Pierosandro Tagliaferri
- Department of Experimental and Clinical Medicine, Magna Græcia University, Campus Salvatore Venuta, Catanzaro, Italy
| | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Magna Græcia University, Campus Salvatore Venuta, Catanzaro, Italy.
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA.
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13
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Nagai S, Ikeda K, Horie-Inoue K, Takeda S, Inoue S. Estrogen signaling increases nuclear receptor subfamily 4 group A member 1 expression and energy production in skeletal muscle cells. Endocr J 2018; 65:1209-1218. [PMID: 30333364 DOI: 10.1507/endocrj.ej17-0548] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Estrogen deficiency has been known to associate with musculoskeletal diseases in women, based on the clinical observations of frequent susceptibility to osteoporosis and sarcopenia among postmenopausal women. In skeletal muscles, estrogen has been assumed to play physiological roles in maintaining muscle mass and strength, although its precise molecular mechanism remains to be elucidated. We have previously shown that estrogen regulates energy metabolism through the downregulation of mitochondrial uncoupling protein 3 (UCP3) in skeletal muscles, which may contribute to the prolonged exercise endurance in female mice. In the present study, we investigated the effects of estrogen on the expression levels of all members of the nuclear receptor superfamily. Microarray analysis showed that the mRNA level of nuclear receptor subfamily 4 group A member 1 (Nr4a1) was upregulated by the transduction of a recombinant adenovirus expressing constitutively active estrogen receptor α (caERα) in differentiated myoblastic C2C12 cells. Thus we assumed that NR4A1 may be an estrogen-inducible gene in myoblastic cells. We also demonstrated that caERα increases the cellular ATP content along with an increase in mitochondrial DNA content in differentiated myoblastic C2C12 cells. In contrast, the knockdown of Nr4a1 using siRNA exhibited reduced ATP generation as well as a decrease in mitochondrial DNA content. Overall, the present study indicates a crosstalk between estrogen signaling and NR4A1 in skeletal muscle cells. We consider that estrogen-dependent NR4A1 upregulation could increase efficient ATP generation in skeletal muscle cells partly through enhancing mitochondrial functions.
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Affiliation(s)
- Saki Nagai
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama 350-1241, Japan
- Department of Obstetrics and Gynecology, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Kazuhiro Ikeda
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama 350-1241, Japan
| | - Kuniko Horie-Inoue
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama 350-1241, Japan
| | - Satoru Takeda
- Department of Obstetrics and Gynecology, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Satoshi Inoue
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama 350-1241, Japan
- Department of Functional Biogerontology, Tokyo Metropolitan Institute of Gerontology, Tokyo 173-0015, Japan
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14
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Khozhukhar N, Spadafora D, Rodriguez Y, Alexeyev M. Elimination of Mitochondrial DNA from Mammalian Cells. ACTA ACUST UNITED AC 2018; 78:20.11.1-20.11.14. [PMID: 30040188 DOI: 10.1002/cpcb.39] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To cope with DNA damage, mitochondria developed a pathway by which severely damaged or unrepairable mitochondrial DNA (mtDNA) molecules are abandoned and degraded, and new molecules are resynthesized using intact templates, if available. In this unit, we describe a method that harnesses this pathway to completely eliminate mtDNA from mammalian cells by transiently overexpressing the Y147A mutant of human uracil-N-glycosylase (mUNG1). We also provide an alternate protocol for mtDNA depletion using combined treatment with ethidium bromide (EtBr) and dideoxycytidine (ddC). Support protocols detail approaches for (1) genotyping ρ° cells of human, mouse, and rat origin by PCR; (2) quantitation of mtDNA by quantitative PCR (qPCR); and (3) preparation of calibrator plasmids for mtDNA quantitation. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Natalya Khozhukhar
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, Alabama
| | | | - Yelitza Rodriguez
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, Alabama
| | - Mikhail Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, Alabama
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15
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Shimada E, Ahsan FM, Nili M, Huang D, Atamdede S, TeSlaa T, Case D, Yu X, Gregory BD, Perrin BJ, Koehler CM, Teitell MA. PNPase knockout results in mtDNA loss and an altered metabolic gene expression program. PLoS One 2018; 13:e0200925. [PMID: 30024931 PMCID: PMC6053217 DOI: 10.1371/journal.pone.0200925] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 07/05/2018] [Indexed: 01/10/2023] Open
Abstract
Polynucleotide phosphorylase (PNPase) is an essential mitochondria-localized exoribonuclease implicated in multiple biological processes and human disorders. To reveal role(s) for PNPase in mitochondria, we established PNPase knockout (PKO) systems by first shifting culture conditions to enable cell growth with defective respiration. Interestingly, PKO established in mouse embryonic fibroblasts (MEFs) resulted in the loss of mitochondrial DNA (mtDNA). The transcriptional profile of PKO cells was similar to rho0 mtDNA deleted cells, with perturbations in cholesterol (FDR = 6.35 x 10-13), lipid (FDR = 3.21 x 10-11), and secondary alcohol (FDR = 1.04x10-12) metabolic pathway gene expression compared to wild type parental (TM6) MEFs. Transcriptome analysis indicates processes related to axonogenesis (FDR = 4.49 x 10-3), axon development (FDR = 4.74 x 10-3), and axonal guidance (FDR = 4.74 x 10-3) were overrepresented in PKO cells, consistent with previous studies detailing causative PNPase mutations in delayed myelination, hearing loss, encephalomyopathy, and chorioretinal defects in humans. Overrepresentation analysis revealed alterations in metabolic pathways in both PKO and rho0 cells. Therefore, we assessed the correlation of genes implicated in cell cycle progression and total metabolism and observed a strong positive correlation between PKO cells and rho0 MEFs compared to TM6 MEFs. We quantified the normalized biomass accumulation rate of PKO clones at 1.7% (SD ± 2.0%) and 2.4% (SD ± 1.6%) per hour, which was lower than TM6 cells at 3.3% (SD ± 3.5%) per hour. Furthermore, PKO in mouse inner ear hair cells caused progressive hearing loss that parallels human familial hearing loss previously linked to mutations in PNPase. Combined, our study reports that knockout of a mitochondrial nuclease results in mtDNA loss and suggests that mtDNA maintenance could provide a unifying connection for the large number of biological activities reported for PNPase.
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Affiliation(s)
- Eriko Shimada
- Molecular Biology Institute Interdepartmental Program, University of California Los Angeles, Los Angeles, California, United States of America
| | - Fasih M. Ahsan
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Mahta Nili
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Dian Huang
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California, United States of America
| | - Sean Atamdede
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Tara TeSlaa
- Molecular Biology Institute Interdepartmental Program, University of California Los Angeles, Los Angeles, California, United States of America
| | - Dana Case
- Molecular Biology Institute Interdepartmental Program, University of California Los Angeles, Los Angeles, California, United States of America
| | - Xiang Yu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Brian D. Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Benjamin J. Perrin
- Department of Biology, Indiana University–Purdue University Indianapolis, Indianapolis, Indiana, United States of America
| | - Carla M. Koehler
- Molecular Biology Institute Interdepartmental Program, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California, United States of America
| | - Michael A. Teitell
- Molecular Biology Institute Interdepartmental Program, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California, United States of America
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California, United States of America
- Broad Center for Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Pediatrics, University of California Los Angeles, Los Angeles, California, United States of America
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, United States of America
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16
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Structures of DNA-bound human ligase IV catalytic core reveal insights into substrate binding and catalysis. Nat Commun 2018; 9:2642. [PMID: 29980672 PMCID: PMC6035275 DOI: 10.1038/s41467-018-05024-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/16/2018] [Indexed: 11/26/2022] Open
Abstract
DNA ligase IV (LigIV) performs the final DNA nick-sealing step of classical nonhomologous end-joining, which is critical for immunoglobulin gene maturation and efficient repair of genotoxic DNA double-strand breaks. Hypomorphic LigIV mutations cause extreme radiation sensitivity and immunodeficiency in humans. To better understand the unique features of LigIV function, here we report the crystal structure of the catalytic core of human LigIV in complex with a nicked nucleic acid substrate in two distinct states—an open lysyl-AMP intermediate, and a closed DNA–adenylate form. Results from structural and mutagenesis experiments unveil a dynamic LigIV DNA encirclement mechanism characterized by extensive interdomain interactions and active site phosphoanhydride coordination, all of which are required for efficient DNA nick sealing. These studies provide a scaffold for defining impacts of LigIV catalytic core mutations and deficiencies in human LIG4 syndrome. DNA Ligase IV (LigIV) catalyzes nick sealing of DNA double-strand break substrates during non-homologous end-joining. Here the authors present the crystal structures of two human LigIV DNA-bound catalytic states, which provide insights into its catalytic mechanism and the molecular basis of LIG4 syndrome causing disease mutations.
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17
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Van Houten B, Santa-Gonzalez GA, Camargo M. DNA repair after oxidative stress: current challenges. CURRENT OPINION IN TOXICOLOGY 2018; 7:9-16. [PMID: 29159324 PMCID: PMC5693256 DOI: 10.1016/j.cotox.2017.10.009] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Reactive oxygen and nitrogen species damage cellular macromolecules including DNA. Cells have a robust base excision repair pathway to deal with this damage in both nuclear and mitochondrial genomes. However, mitochondria lack nucleotide excision repair. Evidence suggests that chronic oxidative stress can induce protective pathways lowering genotoxicity. Understanding oxidant injury to DNA and its repair is critical for our understanding the pathophysiology of a wide range of human disorders.
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Affiliation(s)
- Bennett Van Houten
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
- The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Gloria A Santa-Gonzalez
- University Research Center and Biology Institute, Genetics, Regeneration and Cancer Laboratory, SIU Lab 432, Universidad de Antioquia, Medellin, Colombia
| | - Mauricio Camargo
- University Research Center and Biology Institute, Genetics, Regeneration and Cancer Laboratory, SIU Lab 432, Universidad de Antioquia, Medellin, Colombia
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18
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Sallmyr A, Matsumoto Y, Roginskaya V, Van Houten B, Tomkinson AE. Inhibiting Mitochondrial DNA Ligase IIIα Activates Caspase 1-Dependent Apoptosis in Cancer Cells. Cancer Res 2016; 76:5431-41. [PMID: 27503931 PMCID: PMC5036517 DOI: 10.1158/0008-5472.can-15-3243] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 06/30/2016] [Indexed: 01/09/2023]
Abstract
Elevated levels of DNA ligase IIIα (LigIIIα) have been identified as a biomarker of an alteration in DNA repair in cancer cells that confers hypersensitivity to a LigIIIα inhibitor, L67, in combination with a poly (ADP-ribose) polymerase inhibitor. Because LigIIIα functions in the nucleus and mitochondria, we examined the effect of L67 on these organelles. Here, we show that, although the DNA ligase inhibitor selectively targets mitochondria, cancer and nonmalignant cells respond differently to disruption of mitochondrial DNA metabolism. Inhibition of mitochondrial LigIIIα in cancer cells resulted in abnormal mitochondrial morphology, reduced levels of mitochondrial DNA, and increased levels of mitochondrially generated reactive oxygen species that caused nuclear DNA damage. In contrast, these effects did not occur in nonmalignant cells. Furthermore, inhibition of mitochondrial LigIIIα activated a caspase 1-dependent apoptotic pathway, which is known to be part of inflammatory responses induced by pathogenic microorganisms in cancer, but not nonmalignant cells. These results demonstrate that the disruption of mitochondrial DNA metabolism elicits different responses in nonmalignant and cancer cells and suggests that the abnormal response in cancer cells may be exploited in the development of novel therapeutic strategies that selectively target cancer cells. Cancer Res; 76(18); 5431-41. ©2016 AACR.
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Affiliation(s)
- Annahita Sallmyr
- Departments of Internal Medicine and Molecular Genetics and Microbiology, and University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico
| | - Yoshihiro Matsumoto
- Departments of Internal Medicine and Molecular Genetics and Microbiology, and University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico
| | - Vera Roginskaya
- Department of Pharmacology and Cell Biology, University of Pittsburgh School of Medicine and The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Bennett Van Houten
- Department of Pharmacology and Cell Biology, University of Pittsburgh School of Medicine and The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Alan E Tomkinson
- Departments of Internal Medicine and Molecular Genetics and Microbiology, and University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico.
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19
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Spadafora D, Kozhukhar N, Chouljenko VN, Kousoulas KG, Alexeyev MF. Methods for Efficient Elimination of Mitochondrial DNA from Cultured Cells. PLoS One 2016; 11:e0154684. [PMID: 27136098 PMCID: PMC4852919 DOI: 10.1371/journal.pone.0154684] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 04/18/2016] [Indexed: 12/17/2022] Open
Abstract
Here, we document that persistent mitochondria DNA (mtDNA) damage due to mitochondrial overexpression of the Y147A mutant uracil-N-glycosylase as well as mitochondrial overexpression of bacterial Exonuclease III or Herpes Simplex Virus protein UL12.5M185 can induce a complete loss of mtDNA (ρ0 phenotype) without compromising the viability of cells cultured in media supplemented with uridine and pyruvate. Furthermore, we use these observations to develop rapid, sequence-independent methods for the elimination of mtDNA, and demonstrate utility of these methods for generating ρ0 cells of human, mouse and rat origin. We also demonstrate that ρ0 cells generated by each of these three methods can serve as recipients of mtDNA in fusions with enucleated cells.
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Affiliation(s)
- Domenico Spadafora
- Department of Pharmacology, University of South Alabama, Mobile, Alabama, United States of America
| | - Nataliya Kozhukhar
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, Alabama, United States of America
| | - Vladimir N. Chouljenko
- Division of Biotechnology & Molecular Medicine and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Konstantin G. Kousoulas
- Division of Biotechnology & Molecular Medicine and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Mikhail F. Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, Alabama, United States of America
- Center for Lung Biology, University of South Alabama, Mobile, Alabama, United States of America
- * E-mail:
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20
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Spadafora D, Kozhukhar N, Alexeyev MF. Presequence-Independent Mitochondrial Import of DNA Ligase Facilitates Establishment of Cell Lines with Reduced mtDNA Copy Number. PLoS One 2016; 11:e0152705. [PMID: 27031233 PMCID: PMC4816344 DOI: 10.1371/journal.pone.0152705] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 03/17/2016] [Indexed: 01/10/2023] Open
Abstract
Due to the essential role played by mitochondrial DNA (mtDNA) in cellular physiology and bioenergetics, methods for establishing cell lines with altered mtDNA content are of considerable interest. Here, we report evidence for the existence in mammalian cells of a novel, low- efficiency, presequence-independent pathway for mitochondrial protein import, which facilitates mitochondrial uptake of such proteins as Chlorella virus ligase (ChVlig) and Escherichia coli LigA. Mouse cells engineered to depend on this pathway for mitochondrial import of the LigA protein for mtDNA maintenance had severely (up to >90%) reduced mtDNA content. These observations were used to establish a method for the generation of mouse cell lines with reduced mtDNA copy number by, first, transducing them with a retrovirus encoding LigA, and then inactivating in these transductants endogenous Lig3 with CRISPR-Cas9. Interestingly, mtDNA depletion to an average level of one copy per cell proceeds faster in cells engineered to maintain mtDNA at low copy number. This makes a low-mtDNA copy number phenotype resulting from dependence on mitochondrial import of DNA ligase through presequence-independent pathway potentially useful for rapidly shifting mtDNA heteroplasmy through partial mtDNA depletion.
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Affiliation(s)
- Domenico Spadafora
- Department of Pharmacology, University of South Alabama, 307 University Blvd, Mobile, Alabama, 36688, United States of America
| | - Natalia Kozhukhar
- Department of Physiology and Cell Biology, 307 University Blvd, University of South Alabama, Mobile, Alabama, 36688, United States of America
| | - Mikhail F. Alexeyev
- Department of Physiology and Cell Biology, 307 University Blvd, University of South Alabama, Mobile, Alabama, 36688, United States of America
- Center for Lung Biology, University of South Alabama, 307 University Blvd, Mobile, Alabama, 36688, United States of America
- * E-mail:
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21
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Van Houten B, Hunter SE, Meyer JN. Mitochondrial DNA damage induced autophagy, cell death, and disease. Front Biosci (Landmark Ed) 2016; 21:42-54. [PMID: 26709760 DOI: 10.2741/4375] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Mammalian mitochondria contain multiple small genomes. While these organelles have efficient base excision removal of oxidative DNA lesions and alkylation damage, many DNA repair systems that work on nuclear DNA damage are not active in mitochondria. What is the fate of DNA damage in the mitochondria that cannot be repaired or that overwhelms the repair system? Some forms of mitochondrial DNA damage can apparently trigger mitochondrial DNA destruction, either via direct degradation or through specific forms of autophagy, such as mitophagy. However, accumulation of certain types of mitochondrial damage, in the absence of DNA ligase III (Lig3) or exonuclease G (EXOG), can directly trigger cell death. This review examines the cellular effects of persistent damage to mitochondrial genomes and discusses the very different cell fates that occur in response to different kinds of damage.
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Affiliation(s)
- Bennett Van Houten
- Department of Pharmacology Chemical Biology, University of Pittsburgh, 15213-1863,
| | - Senyene E Hunter
- School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516
| | - Joel N Meyer
- Nicholas School of the Environment, Duke University, Durham, NC 27708-0328
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22
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Marriott AS, Copeland NA, Cunningham R, Wilkinson MC, McLennan AG, Jones NJ. Diadenosine 5', 5'''-P(1),P(4)-tetraphosphate (Ap4A) is synthesized in response to DNA damage and inhibits the initiation of DNA replication. DNA Repair (Amst) 2015. [PMID: 26204256 DOI: 10.1016/j.dnarep.2015.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The level of intracellular diadenosine 5', 5'''-P(1),P(4)-tetraphosphate (Ap4A) increases several fold in mammalian cells treated with non-cytotoxic doses of interstrand DNA-crosslinking agents such as mitomycin C. It is also increased in cells lacking DNA repair proteins including XRCC1, PARP1, APTX and FANCG, while >50-fold increases (up to around 25 μM) are achieved in repair mutants exposed to mitomycin C. Part of this induced Ap4A is converted into novel derivatives, identified as mono- and di-ADP-ribosylated Ap4A. Gene knockout experiments suggest that DNA ligase III is primarily responsible for the synthesis of damage-induced Ap4A and that PARP1 and PARP2 can both catalyze its ADP-ribosylation. Degradative proteins such as aprataxin may also contribute to the increase. Using a cell-free replication system, Ap4A was found to cause a marked inhibition of the initiation of DNA replicons, while elongation was unaffected. Maximum inhibition of 70-80% was achieved with 20 μM Ap4A. Ap3A, Ap5A, Gp4G and ADP-ribosylated Ap4A were without effect. It is proposed that Ap4A acts as an important inducible ligand in the DNA damage response to prevent the replication of damaged DNA.
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Affiliation(s)
- Andrew S Marriott
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Nikki A Copeland
- Division of Biomedical and Life Sciences, University of Lancaster, Lancaster LA1 4YG, UK
| | - Ryan Cunningham
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Mark C Wilkinson
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Alexander G McLennan
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Nigel J Jones
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
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23
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Kukshal V, Kim IK, Hura GL, Tomkinson AE, Tainer JA, Ellenberger T. Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining. Nucleic Acids Res 2015; 43:7021-31. [PMID: 26130724 PMCID: PMC4538836 DOI: 10.1093/nar/gkv652] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/15/2015] [Indexed: 12/14/2022] Open
Abstract
Mammalian DNA ligase III (LigIII) functions in both nuclear and mitochondrial DNA metabolism. In the nucleus, LigIII has functional redundancy with DNA ligase I whereas LigIII is the only mitochondrial DNA ligase and is essential for the survival of cells dependent upon oxidative respiration. The unique LigIII zinc finger (ZnF) domain is not required for catalytic activity but senses DNA strand breaks and stimulates intermolecular ligation of two DNAs by an unknown mechanism. Consistent with this activity, LigIII acts in an alternative pathway of DNA double strand break repair that buttresses canonical non-homologous end joining (NHEJ) and is manifest in NHEJ-defective cancer cells, but how LigIII acts in joining intermolecular DNA ends versus nick ligation is unclear. To investigate how LigIII efficiently joins two DNAs, we developed a real-time, fluorescence-based assay of DNA bridging suitable for high-throughput screening. On a nicked duplex DNA substrate, the results reveal binding competition between the ZnF and the oligonucleotide/oligosaccharide-binding domain, one of three domains constituting the LigIII catalytic core. In contrast, these domains collaborate and are essential for formation of a DNA-bridging intermediate by adenylated LigIII that positions a pair of blunt-ended duplex DNAs for efficient and specific intermolecular ligation.
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Affiliation(s)
- Vandna Kukshal
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - In-Kwon Kim
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Gregory L Hura
- Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alan E Tomkinson
- Department of Internal Medicine and University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA
| | - John A Tainer
- Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tom Ellenberger
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
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24
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Mitochondrial DNA: A disposable genome? Biochim Biophys Acta Mol Basis Dis 2015; 1852:1805-9. [PMID: 26071375 DOI: 10.1016/j.bbadis.2015.05.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/10/2015] [Accepted: 05/14/2015] [Indexed: 01/21/2023]
Abstract
In mammalian cells, mitochondria are the only organelles besides the nucleus that house genomic DNA. The mammalian mitochondrial genome is represented by prokaryotic-type, circular, highly compacted DNA molecules. Today, more than a half-century after their discovery, the biology of these small and redundant molecules remains much less understood than that of their nuclear counterparts. One peculiarity of the mitochondrial genome that emerged in recent years is its disposable nature, as evidenced by cells abandoning a fraction of their mitochondrial DNA (mtDNA) in response to various stimuli with little or no physiological consequence. Here, we review some recent developments in the field of mtDNA biology and discuss emerging questions on the disposability and indispensability of mtDNA.
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25
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Szczepanowska K, Trifunovic A. Different faces of mitochondrial DNA mutators. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1362-72. [PMID: 26014346 DOI: 10.1016/j.bbabio.2015.05.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 05/15/2015] [Accepted: 05/17/2015] [Indexed: 10/23/2022]
Abstract
A number of studies have shown that ageing is associated with increased amounts of mtDNA deletions and/or point mutations in a variety of species as diverse as Caenorhabditis elegans, Drosophila melanogaster, mice, rats, dogs, primates and humans. This detected vulnerability of mtDNA has led to the suggestion that the accumulation of somatic mtDNA mutations might arise from increased oxidative damage and could play an important role in the ageing process by producing cells with a decreased oxidative capacity. However, the vast majority of DNA polymorphisms and disease-causing base-substitution mutations and age-associated mutations that have been detected in human mtDNA are transition mutations. They are likely arising from the slight infidelity of the mitochondrial DNA polymerase. Indeed, transition mutations are also the predominant type of mutation found in mtDNA mutator mice, a model for premature ageing caused by increased mutation load due to the error prone mitochondrial DNA synthesis. These particular misincorporation events could also be exacerbated by dNTP pool imbalances. The role of different repair, replication and maintenance mechanisms that contribute to mtDNA integrity and mutagenesis will be discussed in details in this article. This article is part of a Special Issue entitled: Mitochondrial Dysfunction in Aging.
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Affiliation(s)
- Karolina Szczepanowska
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD) and Institute for Mitochondrial Diseases and Ageing, Medical Faculty, University of Cologne, D-50931 Cologne, Germany
| | - Aleksandra Trifunovic
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD) and Institute for Mitochondrial Diseases and Ageing, Medical Faculty, University of Cologne, D-50931 Cologne, Germany.
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26
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Fayzulin RZ, Perez M, Kozhukhar N, Spadafora D, Wilson GL, Alexeyev MF. A method for mutagenesis of mouse mtDNA and a resource of mouse mtDNA mutations for modeling human pathological conditions. Nucleic Acids Res 2015; 43:e62. [PMID: 25820427 PMCID: PMC4482060 DOI: 10.1093/nar/gkv140] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 02/10/2015] [Indexed: 12/23/2022] Open
Abstract
Mutations in human mitochondrial DNA (mtDNA) can cause mitochondrial disease and have been associated with neurodegenerative disorders, cancer, diabetes and aging. Yet our progress toward delineating the precise contributions of mtDNA mutations to these conditions is impeded by the limited availability of faithful transmitochondrial animal models. Here, we report a method for the isolation of mutations in mouse mtDNA and its implementation for the generation of a collection of over 150 cell lines suitable for the production of transmitochondrial mice. This method is based on the limited mutagenesis of mtDNA by proofreading-deficient DNA-polymerase γ followed by segregation of the resulting highly heteroplasmic mtDNA population by means of intracellular cloning. Among generated cell lines, we identify nine which carry mutations affecting the same amino acid or nucleotide positions as in human disease, including a mutation in the ND4 gene responsible for 70% of Leber Hereditary Optic Neuropathies (LHON). Similar to their human counterparts, cybrids carrying the homoplasmic mouse LHON mutation demonstrated reduced respiration, reduced ATP content and elevated production of mitochondrial reactive oxygen species (ROS). The generated resource of mouse mtDNA mutants will be useful both in modeling human mitochondrial disease and in understanding the mechanisms of ROS production mediated by mutations in mtDNA.
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Affiliation(s)
- Rafik Z Fayzulin
- Department of Cell Biology and Neuroscience, University of South Alabama, Mobile, AL 36688, USA
| | - Michael Perez
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Natalia Kozhukhar
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Domenico Spadafora
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Glenn L Wilson
- Department of Cell Biology and Neuroscience, University of South Alabama, Mobile, AL 36688, USA
| | - Mikhail F Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
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27
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Szklarczyk R, Nooteboom M, Osiewacz HD. Control of mitochondrial integrity in ageing and disease. Philos Trans R Soc Lond B Biol Sci 2015; 369:20130439. [PMID: 24864310 DOI: 10.1098/rstb.2013.0439] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Various molecular and cellular pathways are active in eukaryotes to control the quality and integrity of mitochondria. These pathways are involved in keeping a 'healthy' population of this essential organelle during the lifetime of the organism. Quality control (QC) systems counteract processes that lead to organellar dysfunction manifesting as degenerative diseases and ageing. We discuss disease- and ageing-related pathways involved in mitochondrial QC: mtDNA repair and reorganization, regeneration of oxidized amino acids, refolding and degradation of severely damaged proteins, degradation of whole mitochondria by mitophagy and finally programmed cell death. The control of the integrity of mtDNA and regulation of its expression is essential to remodel single proteins as well as mitochondrial complexes that determine mitochondrial functions. The redundancy of components, such as proteases, and the hierarchies of the QC raise questions about crosstalk between systems and their precise regulation. The understanding of the underlying mechanisms on the genomic, proteomic, organellar and cellular levels holds the key for the development of interventions for mitochondrial dysfunctions, degenerative processes, ageing and age-related diseases resulting from impairments of mitochondria.
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Affiliation(s)
- Radek Szklarczyk
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands Department of Clinical Genetics, Unit Clinical Genomics, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
| | - Marco Nooteboom
- Department of Biochemistry (286), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands
| | - Heinz D Osiewacz
- Faculty for Biosciences and Cluster of Excellence 'Macromolecular Complexes', Goethe University, Molecular Developmental Biology, 60438 Frankfurt am Main, Germany
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28
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Shokolenko IN, Wilson GL, Alexeyev MF. The "fast" and the "slow" modes of mitochondrial DNA degradation. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:490-8. [PMID: 24724936 DOI: 10.3109/19401736.2014.905829] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In a living cell, oxidative stress resulting from an external or internal insult can result in mitochondrial DNA (mtDNA) damage and degradation. Here, we show that in HeLa cells, mtDNA can withstand relatively high levels of extracellular oxidant H2O2 before it is damaged to a point of degradation, and that mtDNA levels in these cells quickly recover after removal of the stressor. In contrast, mtDNA degradation in mouse fibroblast cells is induced at eight-fold lower concentrations of H2O2, and restoration of the lost mtDNA proceeds much slower. Importantly, mtDNA levels in HeLa cells continue to decline even after withdrawal of the stressor thus marking the "slow" mode of mtDNA degradation. Conversely, in mouse fibroblasts maximal loss of mtDNA is achieved during treatment, and is already detectable at 5 min after exposure, indicating the "fast" mode. These differences may modulate susceptibility to oxidative stress of those organs, which consist of multiple cell types.
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Affiliation(s)
- Inna N Shokolenko
- a Department of Cell Biology and Neuroscience , University of South Alabama , Mobile , AL , USA
| | - Glenn L Wilson
- a Department of Cell Biology and Neuroscience , University of South Alabama , Mobile , AL , USA
| | - Mikhail F Alexeyev
- a Department of Cell Biology and Neuroscience , University of South Alabama , Mobile , AL , USA
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29
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Overexpression of DNA ligase III in mitochondria protects cells against oxidative stress and improves mitochondrial DNA base excision repair. DNA Repair (Amst) 2014; 16:44-53. [PMID: 24674627 DOI: 10.1016/j.dnarep.2014.01.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 01/21/2014] [Accepted: 01/27/2014] [Indexed: 01/06/2023]
Abstract
Base excision repair (BER) is the most prominent DNA repair pathway in human mitochondria. BER also results in a temporary generation of AP-sites, single-strand breaks and nucleotide gaps. Thus, incomplete BER can result in the generation of DNA repair intermediates that can disrupt mitochondrial DNA replication and transcription and generate mutations. We carried out BER analysis in highly purified mitochondrial extracts from human cell lines U2OS and HeLa, and mouse brain using a circular DNA substrate containing a lesion at a specific position. We found that DNA ligation is significantly slower than the preceding mitochondrial BER steps. Overexpression of DNA ligase III in mitochondria improved the rate of overall BER, increased cell survival after menadione induced oxidative stress and reduced autophagy following the inhibition of the mitochondrial electron transport chain complex I by rotenone. Our results suggest that the amount of DNA ligase III in mitochondria may be critical for cell survival following prolonged oxidative stress, and demonstrate a functional link between mitochondrial DNA damage and repair, cell survival upon oxidative stress, and removal of dysfunctional mitochondria by autophagy.
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30
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Sharma NK, Lebedeva M, Thomas T, Kovalenko OA, Stumpf JD, Shadel GS, Santos JH. Intrinsic mitochondrial DNA repair defects in Ataxia Telangiectasia. DNA Repair (Amst) 2014; 13:22-31. [PMID: 24342190 PMCID: PMC6211587 DOI: 10.1016/j.dnarep.2013.11.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 11/12/2013] [Accepted: 11/26/2013] [Indexed: 12/28/2022]
Abstract
Ataxia Telangiectasia (A-T) is a progressive childhood disorder characterized most notably by cerebellar degeneration and predisposition to cancer. A-T is caused by mutations in the kinase ATM, a master regulator of the DNA double-strand break response. In addition to DNA-damage signaling defects, A-T cells display mitochondrial dysfunction that is thought to contribute to A-T pathogenesis. However, the molecular mechanism leading to mitochondrial dysfunction in A-T remains unclear. Here, we show that lack of ATM leads to reduced mitochondrial DNA (mtDNA) integrity and mitochondrial dysfunction, which are associated to defective mtDNA repair. While protein levels of mtDNA repair proteins are essentially normal, in the absence of ATM levels specifically of DNA ligase III (Lig3), the only DNA ligase working in mitochondria is reduced. The reduction of Lig3 is observed in different A-T patient cells, in brain and pre-B cells derived from ATM knockout mice as well as upon transient or stable knockdown of ATM. Furthermore, pharmacological inhibition of Lig3 in wild type cells phenocopies the mtDNA repair defects observed in A-T patient cells. As targeted deletion of LIG3 in the central nervous system causes debilitating ataxia in mice, reduced Lig3 protein levels and the consequent mtDNA repair defect may contribute to A-T neurodegeneration. A-T is thus the first disease characterized by diminished Lig3.
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Affiliation(s)
- Nilesh K Sharma
- Department of Pharmacology and Physiology, New Jersey Medical School of UMDNJ, 185 South Orange Avenue, Medical Sciences Building, Newark, NJ 07103, United States
| | - Maria Lebedeva
- Department of Genetics, Yale School of Medicine, 310 Cedar Street, BML 371, New Haven, CT 06520, United States
| | - Terace Thomas
- Department of Pharmacology and Physiology, New Jersey Medical School of UMDNJ, 185 South Orange Avenue, Medical Sciences Building, Newark, NJ 07103, United States
| | - Olga A Kovalenko
- Department of Pharmacology and Physiology, New Jersey Medical School of UMDNJ, 185 South Orange Avenue, Medical Sciences Building, Newark, NJ 07103, United States
| | - Jeffrey D Stumpf
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences (NIEHS), 111 TW Alexander Drive, Building 101, Durham, NC 27709, United States
| | - Gerald S Shadel
- Department of Genetics, Yale School of Medicine, 310 Cedar Street, BML 371, New Haven, CT 06520, United States; Department of Pathology, Yale School of Medicine, 310 Cedar Street, BML 371, New Haven, CT 06520, United States
| | - Janine H Santos
- Department of Pharmacology and Physiology, New Jersey Medical School of UMDNJ, 185 South Orange Avenue, Medical Sciences Building, Newark, NJ 07103, United States.
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