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Kratz K, Artola-Borán M, Kobayashi-Era S, Koh G, Oliveira G, Kobayashi S, Oliveira A, Zou X, Richter J, Tsuda M, Sasanuma H, Takeda S, Loizou JI, Sartori AA, Nik-Zainal S, Jiricny J. FANCD2-Associated Nuclease 1 Partially Compensates for the Lack of Exonuclease 1 in Mismatch Repair. Mol Cell Biol 2021; 41:e0030321. [PMID: 34228493 PMCID: PMC8384067 DOI: 10.1128/mcb.00303-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 11/20/2022] Open
Abstract
Germline mutations in the mismatch repair (MMR) genes MSH2, MSH6, MLH1, and PMS2 are linked to cancer of the colon and other organs, characterized by microsatellite instability and a large increase in mutation frequency. Unexpectedly, mutations in EXO1, encoding the only exonuclease genetically implicated in MMR, are not linked to familial cancer and cause a substantially weaker mutator phenotype. This difference could be explained if eukaryotic cells possessed additional exonucleases redundant with EXO1. Analysis of the MLH1 interactome identified FANCD2-associated nuclease 1 (FAN1), a novel enzyme with biochemical properties resembling EXO1. We now show that FAN1 efficiently substitutes for EXO1 in MMR assays and that this functional complementation is modulated by its interaction with MLH1. FAN1 also contributes to MMR in vivo; cells lacking both EXO1 and FAN1 have an MMR defect and display resistance to N-methyl-N-nitrosourea (MNU) and 6-thioguanine (TG). Moreover, FAN1 loss amplifies the mutational profile of EXO1-deficient cells, suggesting that the two nucleases act redundantly in the same antimutagenic pathway. However, the increased drug resistance and mutator phenotype of FAN1/EXO1-deficient cells are less prominent than those seen in cells lacking MSH6 or MLH1. Eukaryotic cells thus apparently possess additional mechanisms that compensate for the loss of EXO1.
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Affiliation(s)
- Katja Kratz
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Mariela Artola-Borán
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Saho Kobayashi-Era
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- Institute of Biochemistry of the ETH Zurich, Zurich, Switzerland
| | - Gene Koh
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Academic Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, United Kingdom
- MRC Cancer Unit, The Clinical School, University of Cambridge, Cambridge, United Kingdom
| | - Goncalo Oliveira
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Centre, Medical University of Vienna, Vienna, Austria
| | - Shunsuke Kobayashi
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- Institute of Biochemistry of the ETH Zurich, Zurich, Switzerland
| | - Andreia Oliveira
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- Institute of Biochemistry of the ETH Zurich, Zurich, Switzerland
| | - Xueqing Zou
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Academic Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, United Kingdom
- MRC Cancer Unit, The Clinical School, University of Cambridge, Cambridge, United Kingdom
| | - Julia Richter
- Institute of Biochemistry of the ETH Zurich, Zurich, Switzerland
| | - Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Joanna I. Loizou
- Institute of Cancer Research, Department of Medicine I, Comprehensive Cancer Centre, Medical University of Vienna, Vienna, Austria
| | | | - Serena Nik-Zainal
- Academic Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, United Kingdom
- MRC Cancer Unit, The Clinical School, University of Cambridge, Cambridge, United Kingdom
| | - Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
- Institute of Biochemistry of the ETH Zurich, Zurich, Switzerland
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2
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DNA-damage tolerance through PCNA ubiquitination and sumoylation. Biochem J 2021; 477:2655-2677. [PMID: 32726436 DOI: 10.1042/bcj20190579] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022]
Abstract
DNA-damage tolerance (DDT) is employed by eukaryotic cells to bypass replication-blocking lesions induced by DNA-damaging agents. In budding yeast Saccharomyces cerevisiae, DDT is mediated by RAD6 epistatic group genes and the central event for DDT is sequential ubiquitination of proliferating cell nuclear antigen (PCNA), a DNA clamp required for replication and DNA repair. DDT consists of two parallel pathways: error-prone DDT is mediated by PCNA monoubiquitination, which recruits translesion synthesis DNA polymerases to bypass lesions with decreased fidelity; and error-free DDT is mediated by K63-linked polyubiquitination of PCNA at the same residue of monoubiquitination, which facilitates homologous recombination-mediated template switch. Interestingly, the same PCNA residue is also subjected to sumoylation, which leads to inhibition of unwanted recombination at replication forks. All three types of PCNA posttranslational modifications require dedicated conjugating and ligation enzymes, and these enzymes are highly conserved in eukaryotes, from yeast to human.
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3
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Lou J, Yang Y, Gu Q, Price BA, Qiu Y, Fedoriw Y, Desai S, Mose LE, Chen B, Tateishi S, Parker JS, Vaziri C, Wu D. Rad18 mediates specific mutational signatures and shapes the genomic landscape of carcinogen-induced tumors in vivo. NAR Cancer 2021; 3:zcaa037. [PMID: 33447826 PMCID: PMC7787264 DOI: 10.1093/narcan/zcaa037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/01/2020] [Accepted: 12/31/2020] [Indexed: 12/16/2022] Open
Abstract
The E3 ubiquitin ligase Rad18 promotes a damage-tolerant and error-prone mode of DNA replication termed trans-lesion synthesis that is pathologically activated in cancer. However, the impact of vertebrate Rad18 on cancer genomes is not known. To determine how Rad18 affects mutagenesis in vivo, we have developed and implemented a novel computational pipeline to analyze genomes of carcinogen (7, 12-Dimethylbenz[a]anthracene, DMBA)-induced skin tumors from Rad18+/+ and Rad18- / - mice. We show that Rad18 mediates specific mutational signatures characterized by high levels of A(T)>T(A) single nucleotide variations (SNVs). In Rad18- /- tumors, an alternative mutation pattern arises, which is characterized by increased numbers of deletions >4 bp. Comparison with annotated human mutational signatures shows that COSMIC signature 22 predominates in Rad18+/+ tumors whereas Rad18- / - tumors are characterized by increased contribution of COSMIC signature 3 (a hallmark of BRCA-mutant tumors). Analysis of The Cancer Genome Atlas shows that RAD18 expression is strongly associated with high SNV burdens, suggesting RAD18 also promotes mutagenesis in human cancers. Taken together, our results show Rad18 promotes mutagenesis in vivo, modulates DNA repair pathway choice in neoplastic cells, and mediates specific mutational signatures that are present in human tumors.
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Affiliation(s)
- Jitong Lou
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
| | - Yang Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
| | - Qisheng Gu
- Division of Oral and Craniofacial Health Sciences, Adam School of Dentistry, University of North Carolina at Chapel Hill, 385 S. Columbia Street, Chapel Hill, NC 27599, USA
| | - Brandon A Price
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, Chapel Hill, NC 27599, USA
| | - Yuheng Qiu
- Department of Statistics, Purdue University, 250 N. University St, West Lafayette, IN 47907, USA
| | - Yuri Fedoriw
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
| | - Siddhi Desai
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
| | - Lisle E Mose
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, Chapel Hill, NC 27599, USA
| | - Brian Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
| | - Satoshi Tateishi
- Department of Cell Maintenance, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo Chuoku, Kumamoto 860-0811, Japan
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, Chapel Hill, NC 27599, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina at Chapel Hill, 135 Dauer Drive, 3101 McGavran-Greenberg Hall, Chapel Hill, NC 27599, USA
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4
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Gadgil RY, Romer EJ, Goodman CC, Rider SD, Damewood FJ, Barthelemy JR, Shin-Ya K, Hanenberg H, Leffak M. Replication stress at microsatellites causes DNA double-strand breaks and break-induced replication. J Biol Chem 2020; 295:15378-15397. [PMID: 32873711 DOI: 10.1074/jbc.ra120.013495] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/23/2020] [Indexed: 12/12/2022] Open
Abstract
Short tandemly repeated DNA sequences, termed microsatellites, are abundant in the human genome. These microsatellites exhibit length instability and susceptibility to DNA double-strand breaks (DSBs) due to their tendency to form stable non-B DNA structures. Replication-dependent microsatellite DSBs are linked to genome instability signatures in human developmental diseases and cancers. To probe the causes and consequences of microsatellite DSBs, we designed a dual-fluorescence reporter system to detect DSBs at expanded (CTG/CAG) n and polypurine/polypyrimidine (Pu/Py) mirror repeat structures alongside the c-myc replication origin integrated at a single ectopic chromosomal site. Restriction cleavage near the (CTG/CAG)100 microsatellite leads to homology-directed single-strand annealing between flanking AluY elements and reporter gene deletion that can be detected by flow cytometry. However, in the absence of restriction cleavage, endogenous and exogenous replication stressors induce DSBs at the (CTG/CAG)100 and Pu/Py microsatellites. DSBs map to a narrow region at the downstream edge of the (CTG)100 lagging-strand template. (CTG/CAG) n chromosome fragility is repeat length-dependent, whereas instability at the (Pu/Py) microsatellites depends on replication polarity. Strikingly, restriction-generated DSBs and replication-dependent DSBs are not repaired by the same mechanism. Knockdown of DNA damage response proteins increases (Rad18, polymerase (Pol) η, Pol κ) or decreases (Mus81) the sensitivity of the (CTG/CAG)100 microsatellites to replication stress. Replication stress and DSBs at the ectopic (CTG/CAG)100 microsatellite lead to break-induced replication and high-frequency mutagenesis at a flanking thymidine kinase gene. Our results show that non-B structure-prone microsatellites are susceptible to replication-dependent DSBs that cause genome instability.
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Affiliation(s)
- Rujuta Yashodhan Gadgil
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Eric J Romer
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Caitlin C Goodman
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - S Dean Rider
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - French J Damewood
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Joanna R Barthelemy
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA
| | - Kazuo Shin-Ya
- Biomedical Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Helmut Hanenberg
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich Heine University, Düsseldorf, Germany; Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Michael Leffak
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio, USA.
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5
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Masuda Y, Masutani C. Spatiotemporal regulation of PCNA ubiquitination in damage tolerance pathways. Crit Rev Biochem Mol Biol 2019; 54:418-442. [PMID: 31736364 DOI: 10.1080/10409238.2019.1687420] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
DNA is constantly exposed to a wide variety of exogenous and endogenous agents, and most DNA lesions inhibit DNA synthesis. To cope with such problems during replication, cells have molecular mechanisms to resume DNA synthesis in the presence of DNA lesions, which are known as DNA damage tolerance (DDT) pathways. The concept of ubiquitination-mediated regulation of DDT pathways in eukaryotes was established via genetic studies in the yeast Saccharomyces cerevisiae, in which two branches of the DDT pathway are regulated via ubiquitination of proliferating cell nuclear antigen (PCNA): translesion DNA synthesis (TLS) and homology-dependent repair (HDR), which are stimulated by mono- and polyubiquitination of PCNA, respectively. Over the subsequent nearly two decades, significant progress has been made in understanding the mechanisms that regulate DDT pathways in other eukaryotes. Importantly, TLS is intrinsically error-prone because of the miscoding nature of most damaged nucleotides and inaccurate replication of undamaged templates by TLS polymerases (pols), whereas HDR is theoretically error-free because the DNA synthesis is thought to be predominantly performed by pol δ, an accurate replicative DNA pol, using the undamaged sister chromatid as its template. Thus, the regulation of the choice between the TLS and HDR pathways is critical to determine the appropriate biological outcomes caused by DNA damage. In this review, we summarize our current understanding of the species-specific regulatory mechanisms of PCNA ubiquitination and how cells choose between TLS and HDR. We then provide a hypothetical model for the spatiotemporal regulation of DDT pathways in human cells.
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Affiliation(s)
- Yuji Masuda
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan.,Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Chikahide Masutani
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan.,Graduate School of Medicine, Nagoya University, Nagoya, Japan
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6
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Liu H, Wu Y, He F, Cheng Z, Zhao Z, Xiang C, Feng X, Bai X, Takeda S, Wu X, Qing Y. Brca1 is involved in tolerance to adefovir dipivoxil‑induced DNA damage. Int J Mol Med 2019; 43:2491-2498. [PMID: 31017265 DOI: 10.3892/ijmm.2019.4164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 03/29/2019] [Indexed: 02/05/2023] Open
Abstract
Nucleos(t)ide analogues (NAs) are currently the most important anti‑viral treatment option for patients with chronic hepatitis B (CHB). Adefovir dipivoxil (ADV), a diester pro‑drug of adefovir, has been widely used for the clinical therapy of hepatitis B virus infection. It has been previously reported that adefovir induced chromosomal aberrations (CAs) in the in vitro human peripheral blood lymphocyte assay, while the genotoxic mechanism remains elusive. To evaluate the possible mechanisms, the genotoxic effects of ADV on the TK6 and DT40 cell lines, as well as DNA repair‑deficient variants of DT40 cells, were assessed in the present study. A karyotype assay revealed ADV‑induced CAs, particularly chromosomal breaks, in wild‑type DT40 and TK6 cells. A γ‑H2AX foci formation assay confirmed the presence of DNA damage following treatment with ADV. Furthermore, Brca1‑/‑ DT40 cells exhibited an increased sensitivity to ADV, while the knockdown of various other DNA damage‑associated genes did not markedly affect the sensitivity. These comprehensive genetic studies identified the genotoxic capacity of ADV and suggested that Brca1 may be involved in the tolerance of ADV‑induced DNA damage. These results may contribute to the development of novel drugs against CHB with higher therapeutic efficacy and less genotoxicity.
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Affiliation(s)
- Hao Liu
- Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yang Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Fang He
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Ziyuan Cheng
- Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Zilu Zhao
- Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Cuifang Xiang
- Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xiaoyu Feng
- Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xin Bai
- Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606‑8501, Japan
| | - Xiaohua Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yong Qing
- Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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7
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Robinson M, Shah P, Cui YH, He YY. The Role of Dynamic m 6 A RNA Methylation in Photobiology. Photochem Photobiol 2018; 95:95-104. [PMID: 29729018 DOI: 10.1111/php.12930] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 04/24/2018] [Indexed: 02/06/2023]
Abstract
N6 -methyladenosine (m6 A) is the most abundant internal RNA modification among numerous post-transcriptional modifications identified in eukaryotic mRNA. m6 A modification of RNA is catalyzed by the "writer" m6 A methyltransferase enzyme complex, consisting of METTL3, METTL14, WTAP and KIAA1429. The m6 A modification is reversible and can be removed by "eraser" m6 A demethylase enzymes, namely, FTO and ALKBH5. The biological function of m6 A modification on RNA is carried out by RNA-binding effector proteins called "readers." Varied functions of the reader proteins regulate mRNA metabolism by affecting stability, translation, splicing or nuclear export. The epitranscriptomic gene regulation by m6 A RNA methylation regulates various pathways, which contribute to basic cellular processes essential for cell maintenance, development and cell fate, and affect response to external stimuli and stressors. In this review, we summarize the recent advances in the regulation and function of m6 A RNA methylation, with a focus on UV-induced DNA damage response and the circadian clock machinery. Insights into the mechanisms of m6 A RNA regulation and post-transcriptional regulatory function in these biological processes may facilitate the development of new preventive and therapeutic strategies for various diseases related to dysregulation of UV damage response and circadian rhythm.
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Affiliation(s)
- Myles Robinson
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL.,Pritzker School of Medicine, University of Chicago, Chicago, IL
| | - Palak Shah
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL
| | - Yan-Hong Cui
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL
| | - Yu-Ying He
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL
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8
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Tsuda M, Terada K, Ooka M, Kobayashi K, Sasanuma H, Fujisawa R, Tsurimoto T, Yamamoto J, Iwai S, Kadoda K, Akagawa R, Huang SYN, Pommier Y, Sale JE, Takeda S, Hirota K. The dominant role of proofreading exonuclease activity of replicative polymerase ε in cellular tolerance to cytarabine (Ara-C). Oncotarget 2018; 8:33457-33474. [PMID: 28380422 PMCID: PMC5464882 DOI: 10.18632/oncotarget.16508] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/28/2017] [Indexed: 11/25/2022] Open
Abstract
Chemotherapeutic nucleoside analogs, such as Ara-C, 5-Fluorouracil (5-FU) and Trifluridine (FTD), are frequently incorporated into DNA by the replicative DNA polymerases. However, it remains unclear how this incorporation kills cycling cells. There are two possibilities: Nucleoside analog triphosphates inhibit the replicative DNA polymerases, and/or nucleotide analogs mis-incorporated into genomic DNA interfere with the next round of DNA synthesis as replicative DNA polymerases recognize them as template DNA lesions, arresting synthesis. To address the first possibility, we selectively disrupted the proofreading exonuclease activity of DNA polymerase ε (Polε), the leading-strand replicative polymerase in avian DT40 and human TK6 cell lines. To address the second, we disrupted RAD18, a gene involved in translesion DNA synthesis, a mechanism that relieves stalled replication. Strikingly, POLE1exo−/− cells, but not RAD18−/− cells, were hypersensitive to Ara-C, while RAD18−/− cells were hypersensitive to FTD. gH2AX focus formation following a pulse of Ara-C was immediate and did not progress into the next round of replication, while gH2AX focus formation following a pulse of 5-FU and FTD was delayed to the next round of replication. Biochemical studies indicate that human proofreading-deficient Polε-exo− holoenzyme incorporates Ara-CTP, but subsequently extend from this base several times less efficiently than from intact nucleotides. Together our results suggest that Ara-C acts by blocking extension of the nascent DNA strand and is counteracted by the proofreading activity of Polε, while 5-FU and FTD are efficiently incorporated but act as replication fork blocks in the subsequent S phase, which is counteracted by translesion synthesis.
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Affiliation(s)
- Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-Ku, Kyoto 606-8501, Japan
| | - Kazuhiro Terada
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-Ku, Kyoto 606-8501, Japan
| | - Masato Ooka
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-Shi, Tokyo 192-0397, Japan
| | - Koji Kobayashi
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-Shi, Tokyo 192-0397, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-Ku, Kyoto 606-8501, Japan
| | - Ryo Fujisawa
- Department of Biology, School of Sciences, Kyushu University, Nishi-Ku, Fukuoka 819-0395, Japan
| | - Toshiki Tsurimoto
- Department of Biology, School of Sciences, Kyushu University, Nishi-Ku, Fukuoka 819-0395, Japan
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kei Kadoda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-Ku, Kyoto 606-8501, Japan.,Division of Radiation Life Science, Research Reactor Institute, Kyoto University, Kumatori, Sennan, Osaka 590-0494, Japan
| | - Remi Akagawa
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-Ku, Kyoto 606-8501, Japan
| | - Shar-Yin Naomi Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julian E Sale
- Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-Ku, Kyoto 606-8501, Japan
| | - Kouji Hirota
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-Ku, Kyoto 606-8501, Japan.,Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-Shi, Tokyo 192-0397, Japan
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9
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The translesion DNA polymerases Pol ζ and Rev1 are activated independently of PCNA ubiquitination upon UV radiation in mutants of DNA polymerase δ. PLoS Genet 2017; 13:e1007119. [PMID: 29281621 PMCID: PMC5760103 DOI: 10.1371/journal.pgen.1007119] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 01/09/2018] [Accepted: 11/20/2017] [Indexed: 02/07/2023] Open
Abstract
Replicative DNA polymerases cannot insert efficiently nucleotides at sites of base lesions. This function is taken over by specialized translesion DNA synthesis (TLS) polymerases to allow DNA replication completion in the presence of DNA damage. In eukaryotes, Rad6- and Rad18-mediated PCNA ubiquitination at lysine 164 promotes recruitment of TLS polymerases, allowing cells to efficiently cope with DNA damage. However, several studies showed that TLS polymerases can be recruited also in the absence of PCNA ubiquitination. We hypothesized that the stability of the interactions between DNA polymerase δ (Pol δ) subunits and/or between Pol δ and PCNA at the primer/template junction is a crucial factor to determine the requirement of PCNA ubiquitination. To test this hypothesis, we used a structural mutant of Pol δ in which the interaction between Pol3 and Pol31 is inhibited. We found that in yeast, rad18Δ-associated UV hypersensitivity is suppressed by pol3-ct, a mutant allele of the POL3 gene that encodes the catalytic subunit of replicative Pol δ. pol3-ct suppressor effect was specifically dependent on the Rev1 and Pol ζ TLS polymerases. This result strongly suggests that TLS polymerases could rely much less on PCNA ubiquitination when Pol δ interaction with PCNA is partially compromised by mutations. In agreement with this model, we found that the pol3-FI allele suppressed rad18Δ-associated UV sensitivity as observed for pol3-ct. This POL3 allele carries mutations within a putative PCNA Interacting Peptide (PIP) motif. We then provided molecular and genetic evidence that this motif could contribute to Pol δ-PCNA interaction indirectly, although it is not a bona fide PIP. Overall, our results suggest that the primary role of PCNA ubiquitination is to allow TLS polymerases to outcompete Pol δ for PCNA access upon DNA damage. Replicative DNA polymerases have the essential role of replicating genomic DNA during the S phase of each cell cycle. DNA replication occurs smoothly and accurately if the DNA to be replicated is undamaged. Conversely, replicative DNA polymerases stall abruptly when they encounter a damaged base on their template. In this case, alternative specialized DNA polymerases are recruited to insert nucleotides at sites of base lesions. However, these translesion polymerases are not processive and they are poorly accurate. Therefore, they need to be tightly regulated. This is achieved by the covalent binding of the small ubiquitin peptide to the polymerase cofactor PCNA that subsequently triggers the recruitment of translesion polymerases at sites of DNA damage. Yet, recruitment of translesion polymerases independently of PCNA ubiquitination also has been documented, although the underlying mechanism is not known. Moreover, this observation makes more difficult to understand the exact role of PCNA ubiquitination. Here, we present strong genetic evidence in Saccharomyces cerevisiae implying that the replicative DNA polymerase δ (Pol δ) prevents the recruitment of the translesion polymerases Pol ζ and Rev1 following UV irradiation unless PCNA is ubiquitinated. Thus, the primary role of PCNA ubiquitination would be to allow translesion polymerases to outcompete Pol δ upon DNA damage. In addition, our results led us to propose that translesion polymerases could be recruited independently of PCNA ubiquitination when Pol δ association with PCNA is challenged, for instance at difficult-to-replicate loci.
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10
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Kadoda K, Moriwaki T, Tsuda M, Sasanuma H, Ishiai M, Takata M, Ide H, Masunaga SI, Takeda S, Tano K. Selective cytotoxicity of the anti-diabetic drug, metformin, in glucose-deprived chicken DT40 cells. PLoS One 2017; 12:e0185141. [PMID: 28926637 PMCID: PMC5605006 DOI: 10.1371/journal.pone.0185141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 09/05/2017] [Indexed: 12/14/2022] Open
Abstract
Metformin is a biguanide drug that is widely used in the treatment of diabetes. Epidemiological studies have indicated that metformin exhibits anti-cancer activity. However, the molecular mechanisms underlying this activity currently remain unclear. We hypothesized that metformin is cytotoxic in a tumor-specific environment such as glucose deprivation and/or low oxygen (O2) tension. We herein demonstrated that metformin was highly cytotoxic under glucose-depleted, but not hypoxic (2% O2) conditions. In order to elucidate the underlying mechanisms of this selective cytotoxicity, we treated exposed DNA repair-deficient chicken DT40 cells with metformin under glucose-depleted conditions and measured cellular sensitivity. Under glucose-depleted conditions, metformin specifically killed fancc and fancl cells that were deficient in FANCC and FANCL proteins, respectively, which are involved in DNA interstrand cross-link repair. An analysis of chromosomal aberrations in mitotic chromosome spreads revealed that a clinically relevant concentration of metformin induced DNA double-strand breaks (DSBs) in fancc and fancl cells under glucose-depleted conditions. In summary, metformin induced DNA damage under glucose-depleted conditions and selectively killed cells. This metformin-mediated selective toxicity may suppress the growth of malignant tumors that are intrinsically deprived of glucose.
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Affiliation(s)
- Kei Kadoda
- Division of Radiation Life Science, Research Reactor Institute, Kyoto University, Kumatori, Osaka, Japan
| | - Takahito Moriwaki
- Division of Radiation Life Science, Research Reactor Institute, Kyoto University, Kumatori, Osaka, Japan
| | - Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masamichi Ishiai
- Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan
| | - Minoru Takata
- Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan
| | - Hiroshi Ide
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Shin-ichiro Masunaga
- Division of Radiation Life Science, Research Reactor Institute, Kyoto University, Kumatori, Osaka, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keizo Tano
- Division of Radiation Life Science, Research Reactor Institute, Kyoto University, Kumatori, Osaka, Japan
- * E-mail:
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11
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Liu Y, Wu X, Hu X, Chen Z, Liu H, Takeda S, Qing Y. Multiple repair pathways mediate cellular tolerance to resveratrol-induced DNA damage. Toxicol In Vitro 2017; 42:130-138. [PMID: 28431926 DOI: 10.1016/j.tiv.2017.04.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/01/2017] [Accepted: 04/12/2017] [Indexed: 02/05/2023]
Abstract
Resveratrol (RSV) has been reported to exert health benefits for the prevention and treatment of many diseases, including cancer. The anticancer mechanisms of RSV seem to be complex and may be associated with genotoxic potential. To better understand the genotoxic mechanisms, we used wild-type (WT) and a panel of isogenic DNA-repair deficient DT40 cell lines to identify the DNA damage effects and molecular mechanisms of cellular tolerance to RSV. Our results showed that RSV induced significant formation of γ-H2AX foci and chromosome aberrations (CAs) in WT cells, suggesting direct DNA damage effects. Comparing the survival of WT with isogenic DNA-repair deficient DT40 cell lines demonstrated that single strand break repair (SSBR) deficient cell lines of Parp1-/-, base excision repair (BER) deficient cell lines of Polβ-/-, homologous recombination (HR) mutants of Brca1-/- and Brca2-/- and translesion DNA synthesis (TLS) mutants of Rev3-/- and Rad18-/- were more sensitive to RSV. The sensitivities of cells were associated with enhanced DNA damage comparing the accumulation of γ-H2AX foci and number of CAs of isogenic DNA-repair deficient DT40 cell lines with WT cells. These results clearly demonstrated that RSV-induced DNA damage in DT40 cells, and multiple repair pathways including BER, SSBR, HR and TLS, play critical roles in response to RSV- induced genotoxicity.
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Affiliation(s)
- Ying Liu
- Department of Pharmacology, Key Laboratory of Drug Targeting and Drug Delivery Systems of Education Ministry, West China School of Pharmacy, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiaohua Wu
- Department of Pharmacology, Key Laboratory of Drug Targeting and Drug Delivery Systems of Education Ministry, West China School of Pharmacy, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Xiaoqing Hu
- Department of Pharmacology, Key Laboratory of Drug Targeting and Drug Delivery Systems of Education Ministry, West China School of Pharmacy, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ziyuan Chen
- Department of Pharmacology, Key Laboratory of Drug Targeting and Drug Delivery Systems of Education Ministry, West China School of Pharmacy, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hao Liu
- Department of Pharmacology, Key Laboratory of Drug Targeting and Drug Delivery Systems of Education Ministry, West China School of Pharmacy, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yong Qing
- Department of Pharmacology, Key Laboratory of Drug Targeting and Drug Delivery Systems of Education Ministry, West China School of Pharmacy, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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12
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Translesion Synthesis DNA Polymerase Kappa Is Indispensable for DNA Repair Synthesis in Cisplatin Exposed Dorsal Root Ganglion Neurons. Mol Neurobiol 2017; 55:2506-2515. [PMID: 28391554 DOI: 10.1007/s12035-017-0507-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/21/2017] [Indexed: 10/19/2022]
Abstract
In the peripheral nervous system (PNS) in the absence of tight blood barrier, neurons are at increased risk of DNA damage, yet the question of how effectively PNS neurons manage DNA damage remains largely unanswered. Genotoxins in systemic circulation include chemotherapeutic drugs that reach peripheral neurons and damage their DNA. Because neurotoxicity of platinum-based class of chemotherapeutic drugs has been implicated in PNS neuropathies, we utilized an in vitro model of Dorsal Root Ganglia (DRGs) to investigate how peripheral neurons respond to cisplatin that forms intra- and interstrand crosslinks with their DNA. Our data revealed strong transcriptional upregulation of the translesion synthesis DNA polymerase kappa (Pol κ), while expression of other DNA polymerases remained unchanged. DNA Pol κ is involved in bypass synthesis of diverse DNA lesions and considered a vital player in cellular survival under injurious conditions. To assess the impact of Pol κ deficiency on cisplatin-exposed DRG neurons, Pol κ levels were reduced using siRNA. Pol κ targeting siRNA diminished the cisplatin-induced nuclear Pol κ immunoreactivity in DRG neurons and decreased the extent of cisplatin-induced DNA repair synthesis, as reflected in reduced incorporation of thymidine analog into nuclear DNA. Moreover, Pol κ depletion exacerbated global transcriptional suppression induced by cisplatin in DRG neurons. Collectively, these findings provide the first evidence for critical role of Pol κ in DNA damage response in the nervous system and call attention to implications of polymorphisms that modify Pol κ activity, on maintenance of genomic integrity and neuronal function in exogenously challenged PNS.
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13
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Xiang Y, Laurent B, Hsu CH, Nachtergaele S, Lu Z, Sheng W, Xu C, Chen H, Ouyang J, Wang S, Ling D, Hsu PH, Zou L, Jambhekar A, He C, Shi Y. RNA m 6A methylation regulates the ultraviolet-induced DNA damage response. Nature 2017; 543:573-576. [PMID: 28297716 PMCID: PMC5490984 DOI: 10.1038/nature21671] [Citation(s) in RCA: 612] [Impact Index Per Article: 87.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 01/27/2017] [Indexed: 12/17/2022]
Abstract
Cell proliferation and survival require the faithful maintenance and propagation of genetic information, which are threatened by the ubiquitous sources of DNA damage present intracellularly and in the external environment. A system of DNA repair, called the DNA damage response, detects and repairs damaged DNA and prevents cell division until the repair is complete. Here we report that methylation at the 6 position of adenosine (m6A) in RNA is rapidly (within 2 min) and transiently induced at DNA damage sites in response to ultraviolet irradiation. This modification occurs on numerous poly(A)+ transcripts and is regulated by the methyltransferase METTL3 (methyltransferase-like 3) and the demethylase FTO (fat mass and obesity-associated protein). In the absence of METTL3 catalytic activity, cells showed delayed repair of ultraviolet-induced cyclobutane pyrimidine adducts and elevated sensitivity to ultraviolet, demonstrating the importance of m6A in the ultraviolet-responsive DNA damage response. Multiple DNA polymerases are involved in the ultraviolet response, some of which resynthesize DNA after the lesion has been excised by the nucleotide excision repair pathway, while others participate in trans-lesion synthesis to allow replication past damaged lesions in S phase. DNA polymerase κ (Pol κ), which has been implicated in both nucleotide excision repair and trans-lesion synthesis, required the catalytic activity of METTL3 for immediate localization to ultraviolet-induced DNA damage sites. Importantly, Pol κ overexpression qualitatively suppressed the cyclobutane pyrimidine removal defect associated with METTL3 loss. Thus, we have uncovered a novel function for RNA m6A modification in the ultraviolet-induced DNA damage response, and our findings collectively support a model in which m6A RNA serves as a beacon for the selective, rapid recruitment of Pol κ to damage sites to facilitate repair and cell survival.
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Affiliation(s)
- Yang Xiang
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Benoit Laurent
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Chih-Hung Hsu
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Sigrid Nachtergaele
- Department of Chemistry, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.,Institute for Biophysical Dynamics, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.,Howard Hughes Medical Institute, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Zhike Lu
- Department of Chemistry, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.,Institute for Biophysical Dynamics, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.,Howard Hughes Medical Institute, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Wanqiang Sheng
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Chuanyun Xu
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hao Chen
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jian Ouyang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts 02109, USA.,Department of Pathology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts 02109, USA
| | - Siqing Wang
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dominic Ling
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Pang-Hung Hsu
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung City 202, Taiwan
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts 02109, USA.,Department of Pathology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts 02109, USA
| | - Ashwini Jambhekar
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Chuan He
- Department of Chemistry, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.,Institute for Biophysical Dynamics, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.,Howard Hughes Medical Institute, University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Yang Shi
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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14
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Toth A, Hegedus L, Juhasz S, Haracska L, Burkovics P. The DNA-binding box of human SPARTAN contributes to the targeting of Polη to DNA damage sites. DNA Repair (Amst) 2016; 49:33-42. [PMID: 27838458 DOI: 10.1016/j.dnarep.2016.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/25/2016] [Accepted: 10/25/2016] [Indexed: 11/16/2022]
Abstract
Inappropriate repair of UV-induced DNA damage results in human diseases such as Xeroderma pigmentosum (XP), which is associated with an extremely high risk of skin cancer. A variant form of XP is caused by the absence of Polη, which is normally able to bypass UV-induced DNA lesions in an error-free manner. However, Polη is highly error prone when replicating undamaged DNA and, thus, the regulation of the proper targeting of Polη is crucial for the prevention of mutagenesis and UV-induced cancer formation. Spartan is a novel regulator of the damage tolerance pathway, and its association with Ub-PCNA has a role in Polη targeting; however, our knowledge about its function is only rudimentary. Here, we describe a new biochemical property of purified human SPARTAN by showing that it is a DNA-binding protein. Using a DNA binding mutant, we provide in vivo evidence that DNA binding by SPARTAN regulates the targeting of Polη to damage sites after UV exposure, and this function contributes highly to its DNA-damage tolerance function.
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Affiliation(s)
- Agnes Toth
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Lili Hegedus
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Szilvia Juhasz
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Lajos Haracska
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Peter Burkovics
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary.
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15
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Kobayashi K, Guilliam TA, Tsuda M, Yamamoto J, Bailey LJ, Iwai S, Takeda S, Doherty AJ, Hirota K. Repriming by PrimPol is critical for DNA replication restart downstream of lesions and chain-terminating nucleosides. Cell Cycle 2016; 15:1997-2008. [PMID: 27230014 PMCID: PMC4968974 DOI: 10.1080/15384101.2016.1191711] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/12/2016] [Accepted: 05/14/2016] [Indexed: 01/28/2023] Open
Abstract
PrimPol is a DNA damage tolerance enzyme possessing both translesion synthesis (TLS) and primase activities. To uncover its potential role in TLS-mediated IgVλ hypermutation and define its interplay with other TLS polymerases, PrimPol(-/-) and PrimPol(-/-)/Polη(-/-)/Polζ (-/-) gene knockouts were generated in avian cells. Loss of PrimPol had no significant impact on the rate of hypermutation or the mutation spectrum of IgVλ. However, PrimPol(-/-) cells were sensitive to methylmethane sulfonate, suggesting that it may bypass abasic sites at the IgVλ segment by repriming DNA synthesis downstream of these sites. PrimPol(-/-) cells were also sensitive to cisplatin and hydroxyurea, indicating that it assists in maintaining / restarting replication at a variety of lesions. To accurately measure the relative contribution of the TLS and primase activities, we examined DNA damage sensitivity in PrimPol(-/-) cells complemented with polymerase or primase-deficient PrimPol. Polymerase-defective, but not primase-deficient, PrimPol suppresses the hypersensitivity of PrimPol(-/-) cells. This indicates that its primase, rather than TLS activity, is pivotal for DNA damage tolerance. Loss of TLS polymerases, Polη and Polζ has an additive effect on the sensitivity of PrimPol(-/-) cells. Moreover, we found that PrimPol and Polη-Polζ redundantly prevented cell death and facilitated unperturbed cell cycle progression. PrimPol(-/-) cells also exhibited increased sensitivity to a wide variety of chain-terminating nucleoside analogs (CTNAs). PrimPol could perform close-coupled repriming downstream of CTNAs and oxidative damage in vitro. Together, these results indicate that PrimPol's repriming activity plays a central role in reinitiating replication downstream from CTNAs and other specific DNA lesions.
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Affiliation(s)
- Kaori Kobayashi
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan
| | - Thomas A. Guilliam
- Genome Damage and Stability Center, School of Life Sciences, University of Sussex, Brighton, UK
| | - Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, Japan
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Laura J. Bailey
- Genome Damage and Stability Center, School of Life Sciences, University of Sussex, Brighton, UK
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto, Japan
| | - Aidan J. Doherty
- Genome Damage and Stability Center, School of Life Sciences, University of Sussex, Brighton, UK
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan
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16
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Jiang L, Wu X, He F, Liu Y, Hu X, Takeda S, Qing Y. Genetic Evidence for Genotoxic Effect of Entecavir, an Anti-Hepatitis B Virus Nucleotide Analog. PLoS One 2016; 11:e0147440. [PMID: 26800464 PMCID: PMC4723259 DOI: 10.1371/journal.pone.0147440] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/04/2016] [Indexed: 02/05/2023] Open
Abstract
Nucleoside analogues (NAs) have been the most frequently used treatment option for chronic hepatitis B patients. However, they may have genotoxic potentials due to their interference with nucleic acid metabolism. Entecavir, a deoxyguanosine analog, is one of the most widely used oral antiviral NAs against hepatitis B virus. It has reported that entecavir gave positive responses in both genotoxicity and carcinogenicity assays. However the genotoxic mechanism of entecavir remains elusive. To evaluate the genotoxic mechanisms, we analyzed the effect of entecavir on a panel of chicken DT40 B-lymphocyte isogenic mutant cell line deficient in DNA repair and damage tolerance pathways. Our results showed that Parp1-/- mutant cells defective in single-strand break (SSB) repair were the most sensitive to entecavir. Brca1-/-, Ubc13-/- and translesion-DNA-synthesis deficient cells including Rad18-/- and Rev3-/- were hypersensitive to entecavir. XPA-/- mutant deficient in nucleotide excision repair was also slightly sensitive to entecavir. γ-H2AX foci forming assay confirmed the existence of DNA damage by entecavir in Parp1-/-, Rad18-/- and Brca1-/- mutants. Karyotype assay further showed entecavir-induced chromosomal aberrations, especially the chromosome gaps in Parp1-/-, Brca1-/-, Rad18-/- and Rev3-/- cells when compared with wild-type cells. These genetic comprehensive studies clearly identified the genotoxic potentials of entecavir and suggested that SSB and postreplication repair pathways may suppress entecavir-induced genotoxicity.
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Affiliation(s)
- Lei Jiang
- Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiaohua Wu
- Regenerative Medicine Research Center, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Fang He
- Center of Infectious Diseases, Division of Molecular Biology of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ying Liu
- Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiaoqing Hu
- Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, 606–8501, Japan
| | - Yong Qing
- Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, 610041, China
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17
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Kanemaru Y, Suzuki T, Niimi N, Grúz P, Matsumoto K, Adachi N, Honma M, Nohmi T. Catalytic and non-catalytic roles of DNA polymerase κ in the protection of human cells against genotoxic stresses. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2015; 56:650-62. [PMID: 26031400 DOI: 10.1002/em.21961] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 05/13/2015] [Accepted: 05/26/2015] [Indexed: 05/07/2023]
Abstract
DNA polymerase κ (Pol κ) is a specialized DNA polymerase involved in translesion DNA synthesis. Although its bypass activities across lesions are well characterized in biochemistry, its cellular protective roles against genotoxic insults are still elusive. To better understand the in vivo protective roles, we have established a human cell line deficient in the expression of Pol κ (KO) and another expressing catalytically dead Pol κ (CD), to examine the cytotoxic sensitivity to 11 genotoxins including ultraviolet C light (UV). These cell lines were established in a genetic background of Nalm-6-MSH+, a human lymphoblastic cell line that has high efficiency for gene targeting, and functional p53 and mismatch repair activities. We classified the genotoxins into four groups. Group 1 includes benzo[a]pyrene diolepoxide, mitomycin C, and bleomycin, where the sensitivity was equally higher in KO and CD than in the cell line expressing wild-type Pol κ (WT). Group 2 includes hydrogen peroxide and menadione, where hypersensitivity was observed only in KO. Group 3 includes methyl methanesulfonate and ethyl methanesulfonate, where hypersensitivity was observed only in CD. Group 4 includes UV and three chemicals, where the chemicals exhibited similar cytotoxicity to all three cell lines. The results suggest that Pol κ not only protects cells from genotoxic DNA lesions via DNA polymerase activities, but also contributes to genome integrity by acting as a non-catalytic protein against oxidative damage caused by hydrogen peroxide and menadione. The non-catalytic roles of Pol κ in protection against oxidative damage by hydrogen peroxide are discussed.
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Affiliation(s)
- Yuki Kanemaru
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Setagaya-Ku, Tokyo, 158-8501, Japan
- Division of Toxicology, Department of Pharmacology Toxicology and Therapeutics, Showa University School of Pharmacy, Shinagawa-Ku, Tokyo, 142-0064, Japan
| | - Tetsuya Suzuki
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Setagaya-Ku, Tokyo, 158-8501, Japan
| | - Naoko Niimi
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Setagaya-Ku, Tokyo, 158-8501, Japan
| | - Petr Grúz
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Setagaya-Ku, Tokyo, 158-8501, Japan
| | - Kyomu Matsumoto
- Toxicology Division, The Institute of Environmental Toxicology, Joso-Shi, Ibaraki, 303-0043, Japan
| | - Noritaka Adachi
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, 236-0027, Japan
| | - Masamitsu Honma
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Setagaya-Ku, Tokyo, 158-8501, Japan
| | - Takehiko Nohmi
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Setagaya-Ku, Tokyo, 158-8501, Japan
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18
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Paul-Konietzko K, Thomale J, Arakawa H, Iliakis G. DNA Ligases I and III Support Nucleotide Excision Repair in DT40 Cells with Similar Efficiency. Photochem Photobiol 2015; 91:1173-80. [DOI: 10.1111/php.12487] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 06/15/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Katja Paul-Konietzko
- Institute of Medical Radiation Biology; University of Duisburg-Essen Medical School; Essen Germany
| | - Juergen Thomale
- Institute of Cell Biology; University of Duisburg-Essen Medical School; Essen Germany
| | - Hiroshi Arakawa
- Institute for Radiocytogenetics; Helmholtz Zentrum München; German Research Center for Environmental Health; Neuherberg Germany
| | - George Iliakis
- Institute of Medical Radiation Biology; University of Duisburg-Essen Medical School; Essen Germany
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19
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McIntyre J, Woodgate R. Regulation of translesion DNA synthesis: Posttranslational modification of lysine residues in key proteins. DNA Repair (Amst) 2015; 29:166-79. [PMID: 25743599 PMCID: PMC4426011 DOI: 10.1016/j.dnarep.2015.02.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 01/30/2023]
Abstract
Posttranslational modification of proteins often controls various aspects of their cellular function. Indeed, over the past decade or so, it has been discovered that posttranslational modification of lysine residues plays a major role in regulating translesion DNA synthesis (TLS) and perhaps the most appreciated lysine modification is that of ubiquitination. Much of the recent interest in ubiquitination stems from the fact that proliferating cell nuclear antigen (PCNA) was previously shown to be specifically ubiquitinated at K164 and that such ubiquitination plays a key role in regulating TLS. In addition, TLS polymerases themselves are now known to be ubiquitinated. In the case of human polymerase η, ubiquitination at four lysine residues in its C-terminus appears to regulate its ability to interact with PCNA and modulate TLS. Within the past few years, advances in global proteomic research have revealed that many proteins involved in TLS are, in fact, subject to a previously underappreciated number of lysine modifications. In this review, we will summarize the known lysine modifications of several key proteins involved in TLS; PCNA and Y-family polymerases η, ι, κ and Rev1 and we will discuss the potential regulatory effects of such modification in controlling TLS in vivo.
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Affiliation(s)
- Justyna McIntyre
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
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20
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Tada K, Kobayashi M, Takiuchi Y, Iwai F, Sakamoto T, Nagata K, Shinohara M, Io K, Shirakawa K, Hishizawa M, Shindo K, Kadowaki N, Hirota K, Yamamoto J, Iwai S, Sasanuma H, Takeda S, Takaori-Kondo A. Abacavir, an anti-HIV-1 drug, targets TDP1-deficient adult T cell leukemia. SCIENCE ADVANCES 2015; 1:e1400203. [PMID: 26601161 PMCID: PMC4640626 DOI: 10.1126/sciadv.1400203] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/29/2015] [Indexed: 05/07/2023]
Abstract
Adult T cell leukemia (ATL) is an aggressive T cell malignancy caused by human T cell leukemia virus type 1 (HTLV-1) and has a poor prognosis. We analyzed the cytotoxic effects of various nucleoside analog reverse transcriptase inhibitors (NRTIs) for HIV-1 on ATL cells and found that abacavir potently and selectively kills ATL cells. Although NRTIs have minimal genotoxicities on host cells, the therapeutic concentration of abacavir induced numerous DNA double-strand breaks (DSBs) in the chromosomal DNA of ATL cells. DSBs persisted over time in ATL cells but not in other cell lines, suggesting impaired DNA repair. We found that the reduced expression of tyrosyl-DNA phosphodiesterase 1 (TDP1), a repair enzyme, is attributable to the cytotoxic effect of abacavir on ATL cells. We also showed that TDP1 removes abacavir from DNA ends in vitro. These results suggest a model in which ATL cells with reduced TDP1 expression are unable to excise abacavir incorporated into genomic DNA, leading to irreparable DSBs. On the basis of the above mechanism, we propose abacavir as a promising chemotherapeutic agent for ATL.
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Affiliation(s)
- Kohei Tada
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawaracho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Masayuki Kobayashi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawaracho, Sakyo-ku, Kyoto 606-8507, Japan
- Corresponding author: E-mail: (M.K.); (A.T.-K.)
| | - Yoko Takiuchi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawaracho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Fumie Iwai
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawaracho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Takashi Sakamoto
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawaracho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kayoko Nagata
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawaracho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Masanobu Shinohara
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawaracho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Katsuhiro Io
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawaracho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawaracho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Masakatsu Hishizawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawaracho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Keisuke Shindo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawaracho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Norimitsu Kadowaki
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawaracho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji-shi, Tokyo 192-0397, Japan
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawaracho, Sakyo-ku, Kyoto 606-8507, Japan
- Corresponding author: E-mail: (M.K.); (A.T.-K.)
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21
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Hirota K, Yoshikiyo K, Guilbaud G, Tsurimoto T, Murai J, Tsuda M, Phillips LG, Narita T, Nishihara K, Kobayashi K, Yamada K, Nakamura J, Pommier Y, Lehmann A, Sale JE, Takeda S. The POLD3 subunit of DNA polymerase δ can promote translesion synthesis independently of DNA polymerase ζ. Nucleic Acids Res 2015; 43:1671-83. [PMID: 25628356 PMCID: PMC4330384 DOI: 10.1093/nar/gkv023] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The replicative DNA polymerase Polδ consists of a catalytic subunit POLD1/p125 and three regulatory subunits POLD2/p50, POLD3/p66 and POLD4/p12. The ortholog of POLD3 in Saccharomyces cerevisiae, Pol32, is required for a significant proportion of spontaneous and UV-induced mutagenesis through its additional role in translesion synthesis (TLS) as a subunit of DNA polymerase ζ. Remarkably, chicken DT40 B lymphocytes deficient in POLD3 are viable and able to replicate undamaged genomic DNA with normal kinetics. Like its counterpart in yeast, POLD3 is required for fully effective TLS, its loss resulting in hypersensitivity to a variety of DNA damaging agents, a diminished ability to maintain replication fork progression after UV irradiation and a significant decrease in abasic site-induced mutagenesis in the immunoglobulin loci. However, these defects appear to be largely independent of Polζ, suggesting that POLD3 makes a significant contribution to TLS independently of Polζ in DT40 cells. Indeed, combining polη, polζ and pold3 mutations results in synthetic lethality. Additionally, we show in vitro that POLD3 promotes extension beyond an abasic by the Polδ holoenzyme suggesting that while POLD3 is not required for normal replication, it may help Polδ to complete abasic site bypass independently of canonical TLS polymerases.
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Affiliation(s)
- Kouji Hirota
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan Department of Chemistry, GraduateSchool of Science and Engineering, Tokyo Metropolitan University, Minami-Osawa, Hachioji- shi, Tokyo 192-0397, Japan
| | - Kazunori Yoshikiyo
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Guillaume Guilbaud
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Toshiki Tsurimoto
- Department of Biology, School of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Junko Murai
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Lara G Phillips
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Takeo Narita
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kana Nishihara
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kaori Kobayashi
- Department of Chemistry, GraduateSchool of Science and Engineering, Tokyo Metropolitan University, Minami-Osawa, Hachioji- shi, Tokyo 192-0397, Japan
| | - Kouich Yamada
- Division of Genetic Biochemistry, National Institute of Health and Nutrition, Tokyo 162-8636, Japan
| | - Jun Nakamura
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yves Pommier
- Department of Biology, School of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Alan Lehmann
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Julian E Sale
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
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22
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Wit N, Buoninfante OA, van den Berk PCM, Jansen JG, Hogenbirk MA, de Wind N, Jacobs H. Roles of PCNA ubiquitination and TLS polymerases κ and η in the bypass of methyl methanesulfonate-induced DNA damage. Nucleic Acids Res 2014; 43:282-94. [PMID: 25505145 PMCID: PMC4288191 DOI: 10.1093/nar/gku1301] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Translesion synthesis (TLS) provides a highly conserved mechanism that enables DNA synthesis on a damaged template. TLS is performed by specialized DNA polymerases of which polymerase (Pol) κ is important for the cellular response to DNA damage induced by benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (BPDE), ultraviolet (UV) light and the alkylating agent methyl methanesulfonate (MMS). As TLS polymerases are intrinsically error-prone, tight regulation of their activity is required. One level of control is provided by ubiquitination of the homotrimeric DNA clamp PCNA at lysine residue 164 (PCNA-Ub). We here show that Polκ can function independently of PCNA modification and that Polη can function as a backup during TLS of MMS-induced lesions. Compared to cell lines deficient for PCNA modification (Pcna(K164R)) or Polκ, double mutant cell lines display hypersensitivity to MMS but not to BPDE or UV-C. Double mutant cells also displayed delayed post-replicative TLS, accumulate higher levels of replication stress and delayed S-phase progression. Furthermore, we show that Polη and Polκ are redundant in the DNA damage bypass of MMS-induced DNA damage. Taken together, we provide evidence for PCNA-Ub-independent activation of Polκ and establish Polη as an important backup polymerase in the absence of Polκ in response to MMS-induced DNA damage.
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Affiliation(s)
- Niek Wit
- Division of Biological Stress Responses, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Paul C M van den Berk
- Division of Biological Stress Responses, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jacob G Jansen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marc A Hogenbirk
- Division of Biological Stress Responses, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Niels de Wind
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Heinz Jacobs
- Division of Biological Stress Responses, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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23
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Impact of DNA repair pathways on the cytotoxicity of piperlongumine in chicken DT40 cell-lines. Genes Cancer 2014; 5:285-92. [PMID: 25221646 PMCID: PMC4162141 DOI: 10.18632/genesandcancer.26] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 08/08/2014] [Indexed: 12/23/2022] Open
Abstract
Piperlongumine is a naturally-occurring small molecule with various biological activities. Recent studies demonstrate that piperlongumine selectively kills various types of transformed cells with minimal toxicity to non-transformed cells by inducing a high level of reactive oxygen species (ROS). ROS generates various types of DNA lesions, including base modifications and single strand breaks. In order to examine the contribution of ROS-induced DNA damage to the cytotoxicity by piperlongumine, various DNA repair-deficient chicken DT40 cell-lines with a single DNA repair gene deletion were tested for cellular sensitivity to piperlongumine. The results showed that cell lines defective in homologous recombination (HR) display hyper-sensitivity to piperlongumine, while other cell lines with a deficiency in non-homologous end joining (NHEJ), base excision repair (BER), nucleotide excision repair (NER), Fanconi anemia (FA) pathway, or translesion DNA synthesis (TLS) polymerases, show no sensitivity to piperlongumine. The results strongly implicate that double strand breaks (DSBs) generated by piperlongumine are major cytotoxic DNA lesions. Furthermore, a deletion of 53BP1 or Ku70 in the BRCA1-deficient cell line restored cellular resistance to piperlongumine. This strongly supports the idea that piperlongumine induces DSB- mediated cell death. Interestingly, piperlongumine makes the wild type DT40 cell line hypersensitive to a PARP-inhibitor, Olaparib. The results implicate that piperlongumine inhibits HR. Further analysis with cell-based HR assay and the kinetic study of Rad51 foci formation confirmed that piperlongumine suppresses HR activity. Altogether, we revealed novel mechanisms of piperlongumine-induced cytotoxicity.
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24
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Thangavel C, Boopathi E, Ciment S, Liu Y, O'Neill R, Sharma A, McMahon SB, Mellert H, Addya S, Ertel A, Birbe R, Fortina P, Dicker AP, Knudsen KE, Den RB. The retinoblastoma tumor suppressor modulates DNA repair and radioresponsiveness. Clin Cancer Res 2014; 20:5468-5482. [PMID: 25165096 DOI: 10.1158/1078-0432.ccr-14-0326] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PURPOSE Perturbations in the retinoblastoma pathway are over-represented in advanced prostate cancer; retinoblastoma loss promotes bypass of first-line hormone therapy. Conversely, preliminary studies suggested that retinoblastoma-deficient tumors may become sensitized to a subset of DNA-damaging agents. Here, the molecular and in vivo consequence of retinoblastoma status was analyzed in models of clinical relevance. EXPERIMENTAL DESIGN Experimental work was performed with multiple isogenic prostate cancer cell lines (hormone sensitive: LNCaP and LAPC4 cells and hormone resistant C42, 22Rv1 cells; stable knockdown of retinoblastoma using shRNA). Multiple mechanisms were interrogated including cell cycle, apoptosis, and DNA damage repair. Transcriptome analysis was performed, validated, and mechanisms discerned. Cell survival was measured using clonogenic cell survival assay and in vivo analysis was performed in nude mice with human derived tumor xenografts. RESULTS Loss of retinoblastoma enhanced the radioresponsiveness of both hormone-sensitive and castrate-resistant prostate cancer. Hypersensitivity to ionizing radiation was not mediated by cell cycle or p53. Retinoblastoma loss led to alteration in DNA damage repair and activation of the NF-κB pathway and subsequent cellular apoptosis through PLK3. In vivo xenografts of retinoblastoma-deficient tumors exhibited diminished tumor mass, lower PSA kinetics, and decreased tumor growth after treatment with ionizing radiation (P < 0.05). CONCLUSIONS Loss of retinoblastoma confers increased radiosensitivity in prostate cancer. This hypersensitization was mediated by alterations in apoptotic signaling. Combined, these not only provide insight into the molecular consequence of retinoblastoma loss, but also credential retinoblastoma status as a putative biomarker for predicting response to radiotherapy.
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Affiliation(s)
| | - Ettickan Boopathi
- Department of Surgery, Division of Urology, Glenolden, Pennsylvania, USA
| | - Steve Ciment
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Yi Liu
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Raymond O'Neill
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Ankur Sharma
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Steve B McMahon
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.,Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Hestia Mellert
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.,Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.,Biomedical Graduate Studies, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Colorado, USA
| | - Sankar Addya
- Cancer Genomics, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.,Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Adam Ertel
- Cancer Genomics, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.,Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Ruth Birbe
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Paolo Fortina
- Cancer Genomics, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.,Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Adam P Dicker
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.,Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Karen E Knudsen
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.,Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.,Department of Urology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.,Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Robert B Den
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.,Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.,Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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25
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HU XIAOJUAN, WU XIAOHUA, HUANG YUNFEI, TONG QINGYI, TAKEDA SHUNICHI, QING YONG. Berberine induces double-strand DNA breaks in Rev3 deficient cells. Mol Med Rep 2014; 9:1883-8. [DOI: 10.3892/mmr.2014.1999] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 02/07/2014] [Indexed: 11/06/2022] Open
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26
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Bétous R, Pillaire MJ, Pierini L, van der Laan S, Recolin B, Ohl-Séguy E, Guo C, Niimi N, Grúz P, Nohmi T, Friedberg E, Cazaux C, Maiorano D, Hoffmann JS. DNA polymerase κ-dependent DNA synthesis at stalled replication forks is important for CHK1 activation. EMBO J 2013; 32:2172-85. [PMID: 23799366 PMCID: PMC3730229 DOI: 10.1038/emboj.2013.148] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 06/04/2013] [Indexed: 02/04/2023] Open
Abstract
Formation of primed single-stranded DNA at stalled replication forks triggers activation of the replication checkpoint signalling cascade resulting in the ATR-mediated phosphorylation of the Chk1 protein kinase, thus preventing genomic instability. By using siRNA-mediated depletion in human cells and immunodepletion and reconstitution experiments in Xenopus egg extracts, we report that the Y-family translesion (TLS) DNA polymerase kappa (Pol κ) contributes to the replication checkpoint response and is required for recovery after replication stress. We found that Pol κ is implicated in the synthesis of short DNA intermediates at stalled forks, facilitating the recruitment of the 9-1-1 checkpoint clamp. Furthermore, we show that Pol κ interacts with the Rad9 subunit of the 9-1-1 complex. Finally, we show that this novel checkpoint function of Pol κ is required for the maintenance of genomic stability and cell proliferation in unstressed human cells. A vertebrate translesion synthesis DNA polymerase broadly contributes to checkpoint-activating primer synthesis at stalled replication forks, a role previously ascribed only to replicative polymerases.
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Affiliation(s)
- Rémy Bétous
- Equipe Labellisée La Ligue Contre le Cancer 2013, INSERM UMR 1037, CNRS ERL 505294, CRCT (Cancer Research Center of Toulouse), Toulouse, France
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27
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Sebesta M, Burkovics P, Juhasz S, Zhang S, Szabo JE, Lee MYWT, Haracska L, Krejci L. Role of PCNA and TLS polymerases in D-loop extension during homologous recombination in humans. DNA Repair (Amst) 2013; 12:691-8. [PMID: 23731732 PMCID: PMC3744802 DOI: 10.1016/j.dnarep.2013.05.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 04/29/2013] [Accepted: 05/02/2013] [Indexed: 11/16/2022]
Abstract
Homologous recombination (HR) is essential for maintaining genomic integrity, which is challenged by a wide variety of potentially lethal DNA lesions. Regardless of the damage type, recombination is known to proceed by RAD51-mediated D-loop formation, followed by DNA repair synthesis. Nevertheless, the participating polymerases and extension mechanism are not well characterized. Here, we present a reconstitution of this step using purified human proteins. In addition to Pol δ, TLS polymerases, including Pol η and Pol κ, also can extend D-loops. In vivo characterization reveals that Pol η and Pol κ are involved in redundant pathways for HR. In addition, the presence of PCNA on the D-loop regulates the length of the extension tracks by recruiting various polymerases and might present a regulatory point for the various recombination outcomes.
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Affiliation(s)
- Marek Sebesta
- National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
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28
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Kikuchi K, Narita T, Pham VT, Iijima J, Hirota K, Keka IS, Mohiuddin, Okawa K, Hori T, Fukagawa T, Essers J, Kanaar R, Whitby MC, Sugasawa K, Taniguchi Y, Kitagawa K, Takeda S. Structure-specific endonucleases xpf and mus81 play overlapping but essential roles in DNA repair by homologous recombination. Cancer Res 2013; 73:4362-71. [PMID: 23576554 DOI: 10.1158/0008-5472.can-12-3154] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
DNA double-strand breaks (DSB) occur frequently during replication in sister chromatids and are dramatically increased when cells are exposed to chemotherapeutic agents including camptothecin. Such DSBs are efficiently repaired specifically by homologous recombination (HR) with the intact sister chromatid. HR, therefore, plays pivotal roles in cellular proliferation and cellular tolerance to camptothecin. Mammalian cells carry several structure-specific endonucleases, such as Xpf-Ercc1 and Mus81-Eme1, in which Xpf and Mus81 are the essential subunits for enzymatic activity. Here, we show the functional overlap between Xpf and Mus81 by conditionally inactivating Xpf in the chicken DT40 cell line, which has no Mus81 ortholog. Although mammalian cells deficient in either Xpf or Mus81 are viable, Xpf inactivation in DT40 cells was lethal, resulting in a marked increase in the number of spontaneous chromosome breaks. Similarly, inactivation of both Xpf and Mus81 in human HeLa cells and murine embryonic stem cells caused numerous spontaneous chromosome breaks. Furthermore, the phenotype of Xpf-deficient DT40 cells was reversed by ectopic expression of human Mus81-Eme1 or human Xpf-Ercc1 heterodimers. These observations indicate the functional overlap of Xpf-Ercc1 and Mus81-Eme1 in the maintenance of genomic DNA. Both Mus81-Eme1 and Xpf-Ercc1 contribute to the completion of HR, as evidenced by the data that the expression of Mus81-Eme1 or Xpf-Ercc1 diminished the number of camptothecin-induced chromosome breaks in Xpf-deficient DT40 cells, and to preventing early steps in HR by deleting XRCC3 suppressed the nonviability of Xpf-deficient DT40 cells. In summary, Xpf and Mus81 have a substantially overlapping function in completion of HR.
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Affiliation(s)
- Koji Kikuchi
- Department of Radiation Genetics, and Frontier Technology Center, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
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29
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Kelsall IR, Langenick J, MacKay C, Patel KJ, Alpi AF. The Fanconi anaemia components UBE2T and FANCM are functionally linked to nucleotide excision repair. PLoS One 2012; 7:e36970. [PMID: 22615860 PMCID: PMC3352854 DOI: 10.1371/journal.pone.0036970] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Accepted: 04/10/2012] [Indexed: 11/24/2022] Open
Abstract
The many proteins that function in the Fanconi anaemia (FA) monoubiquitylation pathway initiate replicative DNA crosslink repair. However, it is not clear whether individual FA genes participate in DNA repair pathways other than homologous recombination and translesion bypass. Here we show that avian DT40 cell knockouts of two integral FA genes – UBE2T and FANCM are unexpectedly sensitive to UV-induced DNA damage. Comprehensive genetic dissection experiments indicate that both of these FA genes collaborate to promote nucleotide excision repair rather than translesion bypass to protect cells form UV genotoxicity. Furthermore, UBE2T deficiency impacts on the efficient removal of the UV-induced photolesion cyclobutane pyrimidine dimer. Therefore, this work reveals that the FA pathway shares two components with nucleotide excision repair, intimating not only crosstalk between the two major repair pathways, but also potentially identifying a UBE2T-mediated ubiquitin-signalling response pathway that contributes to nucleotide excision repair.
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Affiliation(s)
- Ian R. Kelsall
- Scottish Institute for Cell Signalling, University of Dundee, Dundee, United Kingdom
| | | | - Craig MacKay
- Scottish Institute for Cell Signalling, University of Dundee, Dundee, United Kingdom
| | - Ketan J. Patel
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Arno F. Alpi
- Scottish Institute for Cell Signalling, University of Dundee, Dundee, United Kingdom
- * E-mail:
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30
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Liu X, Lee J, Ji K, Takeda S, Choi K. Potentials and mechanisms of genotoxicity of six pharmaceuticals frequently detected in freshwater environment. Toxicol Lett 2012; 211:70-6. [DOI: 10.1016/j.toxlet.2012.03.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 03/07/2012] [Accepted: 03/07/2012] [Indexed: 01/22/2023]
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31
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Requirement of Rad18 protein for replication through DNA lesions in mouse and human cells. Proc Natl Acad Sci U S A 2012; 109:7799-804. [PMID: 22547805 DOI: 10.1073/pnas.1204105109] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In yeast, the Rad6-Rad18 ubiquitin conjugating enzyme plays a critical role in promoting replication although DNA lesions by translesion synthesis (TLS). In striking contrast, a number of studies have indicated that TLS can occur in the absence of Rad18 in human and other mammalian cells, and also in chicken cells. In this study, we determine the role of Rad18 in TLS that occurs during replication in human and mouse cells, and show that in the absence of Rad18, replication of duplex plasmids containing a cis-syn TT dimer or a (6-4) TT photoproduct is severely inhibited in human cells and that mutagenesis resulting from TLS opposite cyclobutane pyrimidine dimers and (6-4) photoproducts formed at the TT, TC, and CC dipyrimidine sites in the chromosomal cII gene in UV-irradiated mouse cells is abolished. From these and other observations with Rad18, we conclude that the Rad6-Rad18 enzyme plays an essential role in promoting replication through DNA lesions by TLS in mammalian cells. In contrast, the dispensability of Rad18 for TLS in chicken DT40 cells would suggest that the role of the Rad6-Rad18 enzyme complex has diverged considerably between chicken and mammals, raising the possibility that TLS mechanisms differ among them.
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Sale JE. Competition, collaboration and coordination--determining how cells bypass DNA damage. J Cell Sci 2012; 125:1633-43. [PMID: 22499669 DOI: 10.1242/jcs.094748] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cells must overcome replication blocks that might otherwise lead to genomic instability or cell death. Classical genetic experiments have identified a series of mechanisms that cells use to replicate damaged DNA: translesion synthesis, template switching and homologous recombination. In translesion synthesis, DNA lesions are replicated directly by specialised DNA polymerases, a potentially error-prone approach. Template switching and homologous recombination use an alternative undamaged template to allow the replicative polymerases to bypass DNA lesions and, hence, are generally error free. Classically, these pathways have been viewed as alternatives, competing to ensure replication of damaged DNA templates is completed. However, this view of a series of static pathways has been blurred by recent work using a combination of genetic approaches and methodology for examining the physical intermediates of bypass reactions. These studies have revealed a much more dynamic interaction between the pathways than was initially appreciated. In this Commentary, I argue that it might be more helpful to start thinking of lesion-bypass mechanisms in terms of a series of dynamically assembled 'modules', often comprising factors from different classical pathways, whose deployment is crucially dependent on the context in which the bypass event takes place.
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Affiliation(s)
- Julian E Sale
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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Abstract
The chicken B cell line DT40 has been widely used as a model system for reverse genetics studies in higher eukaryotes, because of its advantages including efficient gene targeting and ease of chromosome manipulation. Although the genetic approach using the RNA interference technique has become the standard method particularly in human cells, DT40 still remains a powerful tool to investigate the regulation and function of genes and proteins in a vertebrate system, because of feasibility of easy, rapid, and clear genetic experiments. The use of DT40 cells for DNA repair research has several advantages. In addition to canonical assays for DNA repair, such as measurement of the sensitivities toward DNA damage reagents, it is possible to measure homologous recombination and translesion synthesis activities using activation-induced deaminase (AID)-induced diversification of the immunoglobulin locus. In this chapter, we would describe a detailed protocol for gene disruption experiments in DT40 cells.
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Affiliation(s)
- Masamichi Ishiai
- Laboratory of DNA Damage Signaling, Department of Late Effect Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan
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Sarkies P, Murat P, Phillips LG, Patel KJ, Balasubramanian S, Sale JE. FANCJ coordinates two pathways that maintain epigenetic stability at G-quadruplex DNA. Nucleic Acids Res 2011; 40:1485-98. [PMID: 22021381 PMCID: PMC3287192 DOI: 10.1093/nar/gkr868] [Citation(s) in RCA: 162] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We have previously reported that DT40 cells deficient in the Y-family polymerase REV1 are defective in replicating G-quadruplex DNA. In vivo this leads to uncoupling of DNA synthesis from redeposition of histones displaced ahead of the replication fork, which in turn leads to loss of transcriptional repression due to failure to recycle pre-existing repressive histone post-translational modifications. Here we report that a similar process can also affect transcriptionally active genes, leading to their deactivation. We use this finding to develop an assay based on loss of expression of a cell surface marker to monitor epigenetic instability at the level of single cells. This assay allows us to demonstrate G4 DNA motif-associated epigenetic instability in mutants of three helicases previously implicated in the unwinding of G-quadruplex structures, FANCJ, WRN and BLM. Transcriptional profiling of DT40 mutants reveals that FANCJ coordinates two independent mechanisms to maintain epigenetic stability near G4 DNA motifs that are dependent on either REV1 or on the WRN and BLM helicases, suggesting a model in which efficient in vivo replication of G-quadruplexes often requires the established 5'-3'-helicase activity of FANCJ acting in concert with either a specialized polymerase or helicase operating in the opposite polarity.
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Affiliation(s)
- Peter Sarkies
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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Yamamoto KN, Hirota K, Kono K, Takeda S, Sakamuru S, Xia M, Huang R, Austin CP, Witt KL, Tice RR. Characterization of environmental chemicals with potential for DNA damage using isogenic DNA repair-deficient chicken DT40 cell lines. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2011; 52:547-61. [PMID: 21538559 PMCID: PMC3278799 DOI: 10.1002/em.20656] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 03/02/2011] [Indexed: 05/23/2023]
Abstract
Included among the quantitative high throughput screens (qHTS) conducted in support of the US Tox21 program are those being evaluated for the detection of genotoxic compounds. One such screen is based on the induction of increased cytotoxicity in seven isogenic chicken DT40 cell lines deficient in DNA repair pathways compared to the parental DNA repair-proficient cell line. To characterize the utility of this approach for detecting genotoxic compounds and identifying the type(s) of DNA damage induced, we evaluated nine of 42 compounds identified as positive for differential cytotoxicity in qHTS (actinomycin D, adriamycin, alachlor, benzotrichloride, diglycidyl resorcinol ether, lovastatin, melphalan, trans-1,4-dichloro-2-butene, tris(2,3-epoxypropyl)isocyanurate) and one non-cytotoxic genotoxic compound (2-aminothiamine) for (1) clastogenicity in mutant and wild-type cells; (2) the comparative induction of γH2AX positive foci by melphalan; (3) the extent to which a 72-hr exposure duration increased assay sensitivity or specificity; (4) the use of 10 additional DT40 DNA repair-deficient cell lines to better analyze the type(s) of DNA damage induced; and (5) the involvement of reactive oxygen species in the induction of DNA damage. All compounds but lovastatin and 2-aminothiamine were more clastogenic in at least one DNA repair-deficient cell line than the wild-type cells. The differential responses across the various DNA repair-deficient cell lines provided information on the type(s) of DNA damage induced. The results demonstrate the utility of this DT40 screen for detecting genotoxic compounds, for characterizing the nature of the DNA damage, and potentially for analyzing mechanisms of mutagenesis.
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Affiliation(s)
- Kimiyo N Yamamoto
- Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo, Japan.
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Ji K, Choi K, Giesy JP, Musarrat J, Takeda S. Genotoxicity of several polybrominated diphenyl ethers (PBDEs) and hydroxylated PBDEs, and their mechanisms of toxicity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:5003-5008. [PMID: 21545137 DOI: 10.1021/es104344e] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Polybrominated diphenyl ethers (PBDEs) have been extensively utilized as flame retardants, and recently there has been concern about potential adverse effects in humans and wildlife. Their hydroxylated analogs (OH-BDEs) have received increasing attention due to their potential for endocrine and neurological toxicities. However, the potentials and mechanisms of genotoxicity of these brominated compounds have scarcely been investigated. In the present study, genotoxicity of tetra-BDEs, penta BDE, octa-BDE, deca-BDE, and tetra-OH-BDEs were investigated by use of chicken DT40 cell lines including wild-type cells and a panel of mutant cell lines deficient in DNA repair pathways. Tetra-BDEs have greater genotoxic potential than do the other BDEs tested. OH-tetra-BDEs were more genotoxic than tetra-BDEs. DT40 cells, deficient in base excision repair (Polβ(-/-)) and translesion DNA synthesis (REV3(-/-)) pathways, were hypersensitive to the genotoxic effects of tetra-BDEs and OH-tetra-BDEs. The observation of chromosomal aberrations and gamma-H2AX assay confirmed that the studied brominated compounds caused double strand breaks. Pretreatment with N-acetyl-l-cysteine (NAC) significantly rescued the Polβ(-/-) and REV3(-/-) mutants, which is consistent with the hypothesis that PBDEs and OH-BDEs cause DNA damage mediated through reactive oxygen species (ROS). Some tetra-BDEs and OH-tetra-BDEs caused base damage through ROS leading to replication blockage and subsequent chromosomal breaks.
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Affiliation(s)
- Kyunghee Ji
- School of Public Health, Seoul National University, Seoul, 151-742, Korea
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Zhang W, Qin Z, Zhang X, Xiao W. Roles of sequential ubiquitination of PCNA in DNA-damage tolerance. FEBS Lett 2011; 585:2786-94. [PMID: 21536034 DOI: 10.1016/j.febslet.2011.04.044] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 04/16/2011] [Accepted: 04/18/2011] [Indexed: 11/15/2022]
Abstract
Living organisms not only repair DNA damage induced by environmental agents and endogenous cellular metabolites, but have also developed mechanisms to survive in the presence of otherwise lethal lesions. DNA-damage tolerance (DDT) is considered such a mechanism that resumes DNA synthesis in the presence of replication-blocking lesions. Recent studies revealed that DDT in budding yeast is achieved through sequential ubiquitination of DNA polymerase processivity factor, proliferating cell nuclear antigen (PCNA). It is generally believed that monoubiquitinated PCNA promotes translesion DNA synthesis, whereas polyubiquitinated PCNA mediates an error-free mode of lesion bypass. This review will discuss how ubiquitinated PCNA modulates different means of lesion bypass.
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Affiliation(s)
- Weiwei Zhang
- College of Life Sciences, Capital Normal University, Beijing 100048, China
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Kitao H, Hirano S, Takata M. Evaluation of homologous recombinational repair in chicken B lymphoma cell line, DT40. Methods Mol Biol 2011; 745:293-309. [PMID: 21660701 DOI: 10.1007/978-1-61779-129-1_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Homologous recombination (HR) is a mode of double-strand break (DSB) repair required for cell viability in vertebrate cells. Targeted integration of homologous DNA fragment by HR is usually a very rare event in vertebrate cells; however, in chicken B lymphoma cell line DT40, the ratio of targeted to random integration is extremely high. Although the underlying mechanism of this phenotype is not fully understood, DT40 has been utilized as a model cell line for a number of genetic analyses. Here we describe three assays for evaluating homologous recombinational repair (HRR) using DT40 as a model system, measuring gene-targeting frequency, analyzing HRR process of single DSB induced by yeast homing endonuclease I-SceI, and measuring sister chromatid exchange frequency. Combined with generation of gene-disrupted DT40 mutant cell line, these assays have been highly useful to investigate the mechanisms in HRR. Using these techniques, a role of HRR of not only Rad52 epistasis group genes but also genes whose mutation cause hereditary cancer syndrome, such as Fanconi anemia, has been established.
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Affiliation(s)
- Hiroyuki Kitao
- Department of Molecular Oncology, Kyushu University, Kyushu, Japan.
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Abstract
Ultraviolet (UV) light induces specific mutations in the cellular and skin genome such as UV-signature and triplet mutations, the mechanism of which has been thought to involve translesion DNA synthesis (TLS) over UV-induced DNA base damage. Two models have been proposed: "error-free" bypass of deaminated cytosine-containing cyclobutane pyrimidine dimers (CPDs) by DNA polymerase η, and error-prone bypass of CPDs and other UV-induced photolesions by combinations of TLS and replicative DNA polymerases--the latter model has also been known as the two-step model, in which the cooperation of two (or more) DNA polymerases as misinserters and (mis)extenders is assumed. Daylight UV induces a characteristic UV-specific mutation, a UV-signature mutation occurring preferentially at methyl-CpG sites, which is also observed frequently after exposure to either UVB or UVA, but not to UVC. The wavelengths relevant to the mutation are so consistent with the composition of daylight UV that the mutation is called solar-UV signature, highlighting the importance of this type of mutation for creatures with the cytosine-methylated genome that are exposed to the sun in the natural environment. UVA has also been suggested to induce oxidative types of mutation, which would be caused by oxidative DNA damage produced through the oxidative stress after the irradiation. Indeed, UVA produces oxidative DNA damage not only in cells but also in skin, which, however, does not seem sufficient to induce mutations in the normal skin genome. In contrast, it has been demonstrated that UVA exclusively induces the solar-UV signature mutations in vivo through CPD formation.
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Affiliation(s)
- Hironobu Ikehata
- Division of Genome and Radiation Biology, Department of Cell Biology, Graduate School of Medicine, Tohoku University, Sendai, Japan.
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40
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Kohzaki M, Nishihara K, Hirota K, Sonoda E, Yoshimura M, Ekino S, Butler JE, Watanabe M, Halazonetis TD, Takeda S. DNA polymerases nu and theta are required for efficient immunoglobulin V gene diversification in chicken. J Cell Biol 2010; 189:1117-27. [PMID: 20584917 PMCID: PMC2894443 DOI: 10.1083/jcb.200912012] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Accepted: 05/26/2010] [Indexed: 01/10/2023] Open
Abstract
The chicken DT40 B lymphocyte line diversifies its immunoglobulin (Ig) V genes through translesion DNA synthesis-dependent point mutations (Ig hypermutation) and homologous recombination (HR)-dependent Ig gene conversion. The error-prone biochemical characteristic of the A family DNA polymerases Polnu and Pol led us to explore the role of these polymerases in Ig gene diversification in DT40 cells. Disruption of both polymerases causes a significant decrease in Ig gene conversion events, although POLN(-/-)/POLQ(-/-) cells exhibit no prominent defect in HR-mediated DNA repair, as indicated by no increase in sensitivity to camptothecin. Poleta has also been previously implicated in Ig gene conversion. We show that a POLH(-/-)/POLN(-/-)/POLQ(-/-) triple mutant displays no Ig gene conversion and reduced Ig hypermutation. Together, these data define a role for Polnu and Pol in recombination and suggest that the DNA synthesis associated with Ig gene conversion is accounted for by three specialized DNA polymerases.
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Affiliation(s)
- Masaoki Kohzaki
- Department of Radiation Genetics and Department of Radiation Oncology and Image-Applied Therapy, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- Research Reactor Institute, Kyoto University, Sennan-gun, Osaka 590-0494, Japan
- Department of Molecular Biology, University of Geneva, Geneva 4 CH-1211, Switzerland
| | - Kana Nishihara
- Department of Radiation Genetics and Department of Radiation Oncology and Image-Applied Therapy, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
- Department of Food and Nutrition, Kyoto Women’s University, Higashiyama-ku, Kyoto 606-8501, Japan
| | - Kouji Hirota
- Department of Radiation Genetics and Department of Radiation Oncology and Image-Applied Therapy, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Eiichiro Sonoda
- Department of Radiation Genetics and Department of Radiation Oncology and Image-Applied Therapy, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Michio Yoshimura
- Department of Radiation Genetics and Department of Radiation Oncology and Image-Applied Therapy, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shigeo Ekino
- Department of Histology, Graduate School of Medical Sciences, Kumamoto University, Honjo, Kumamoto 860-8556, Japan
| | - John E. Butler
- Department of Microbiology, University of Iowa Medical School, Iowa City, IA 52242
| | - Masami Watanabe
- Research Reactor Institute, Kyoto University, Sennan-gun, Osaka 590-0494, Japan
| | - Thanos D. Halazonetis
- Department of Molecular Biology, University of Geneva, Geneva 4 CH-1211, Switzerland
| | - Shunichi Takeda
- Department of Radiation Genetics and Department of Radiation Oncology and Image-Applied Therapy, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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Abstract
Post-translational modification by ubiquitin is best known for its role in targeting its substrates for regulated degradation. However, non-proteolytic functions of the ubiquitin system, often involving either monoubiquitylation or polyubiquitylation through Lys63-linked chains, have emerged in various cell signalling pathways. These two forms of the ubiquitin signal contribute to three different pathways related to the maintenance of genome integrity that are responsible for the processing of DNA double-strand breaks, the repair of interstrand cross links and the bypass of lesions during DNA replication.
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42
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Schmutz V, Janel-Bintz R, Wagner J, Biard D, Shiomi N, Fuchs RP, Cordonnier AM. Role of the ubiquitin-binding domain of Polη in Rad18-independent translesion DNA synthesis in human cell extracts. Nucleic Acids Res 2010; 38:6456-65. [PMID: 20529881 PMCID: PMC2965212 DOI: 10.1093/nar/gkq403] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In eukaryotic cells, the Rad6/Rad18-dependent monoubiquitination of the proliferating cell nuclear antigen (PCNA) plays an essential role in the switching between replication and translesion DNA synthesis (TLS). The DNA polymerase Polη binds to PCNA via a consensus C-terminal PCNA-interacting protein (PIP) motif. It also specifically interacts with monoubiquitinated PCNA thanks to a recently identified ubiquitin-binding domain (UBZ). To investigate whether the TLS activity of Polη is always coupled to PCNA monoubiquitination, we monitor the ability of cell-free extracts to perform DNA synthesis across different types of lesions. We observe that a cis-syn cyclobutane thymine dimer (TT-CPD), but not a N-2-acetylaminofluorene-guanine (G-AAF) adduct, is efficiently bypassed in extracts from Rad18-deficient cells, thus demonstrating the existence of a Polη-dependent and Rad18-independent TLS pathway. In addition, by complementing Polη-deficient cells with PIP and UBZ mutants, we show that each of these domains contributes to Polη activity. The finding that the bypass of a CPD lesion in vitro does not require Ub-PCNA but nevertheless depends on the UBZ domain of Polη, reveals that this domain may play a novel role in the TLS process that is not related to the monoubiquitination status of PCNA.
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Affiliation(s)
- Valérie Schmutz
- CNRS FRE3211, ESBS, Université de Strasbourg, Bld Sébastien Brandt BP 10413, 67412 Illkirch Cedex, France
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Wang X, Takenaka K, Takeda S. PTIP promotes DNA double-strand break repair through homologous recombination. Genes Cells 2010; 15:243-54. [DOI: 10.1111/j.1365-2443.2009.01379.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Nakamura K, Kogame T, Oshiumi H, Shinohara A, Sumitomo Y, Agama K, Pommier Y, Tsutsui KM, Tsutsui K, Hartsuiker E, Ogi T, Takeda S, Taniguchi Y. Collaborative action of Brca1 and CtIP in elimination of covalent modifications from double-strand breaks to facilitate subsequent break repair. PLoS Genet 2010; 6:e1000828. [PMID: 20107609 PMCID: PMC2809774 DOI: 10.1371/journal.pgen.1000828] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 12/22/2009] [Indexed: 11/29/2022] Open
Abstract
Topoisomerase inhibitors such as camptothecin and etoposide are used as anti-cancer drugs and induce double-strand breaks (DSBs) in genomic DNA in cycling cells. These DSBs are often covalently bound with polypeptides at the 3′ and 5′ ends. Such modifications must be eliminated before DSB repair can take place, but it remains elusive which nucleases are involved in this process. Previous studies show that CtIP plays a critical role in the generation of 3′ single-strand overhang at “clean” DSBs, thus initiating homologous recombination (HR)–dependent DSB repair. To analyze the function of CtIP in detail, we conditionally disrupted the CtIP gene in the chicken DT40 cell line. We found that CtIP is essential for cellular proliferation as well as for the formation of 3′ single-strand overhang, similar to what is observed in DT40 cells deficient in the Mre11/Rad50/Nbs1 complex. We also generated DT40 cell line harboring CtIP with an alanine substitution at residue Ser332, which is required for interaction with BRCA1. Although the resulting CtIPS332A/−/− cells exhibited accumulation of RPA and Rad51 upon DNA damage, and were proficient in HR, they showed a marked hypersensitivity to camptothecin and etoposide in comparison with CtIP+/−/− cells. Finally, CtIPS332A/−/−BRCA1−/− and CtIP+/−/−BRCA1−/− showed similar sensitivities to these reagents. Taken together, our data indicate that, in addition to its function in HR, CtIP plays a role in cellular tolerance to topoisomerase inhibitors. We propose that the BRCA1-CtIP complex plays a role in the nuclease-mediated elimination of oligonucleotides covalently bound to polypeptides from DSBs, thereby facilitating subsequent DSB repair. Induction of double-strand breaks (DSBs) in chromosomal DNA effectively activates a program of cellular suicide and is widely used for chemotherapy on malignant cancer cells. Cells resist such therapies by quickly repairing the DSBs. Repair is carried out by two major DSB repair pathways, homologous recombination (HR) and nonhomologous end-joining. However, these pathways cannot join DSBs if their ends are chemically modified, as seen in the DSB ends that would arise after the prolonged treatment of the cells with topoisomerase inhibitors such as camptothecin and etoposide. These anti-cancer drugs can produce the polypeptides covalently attached to the 3′ or 5′ end of DSBs. It remains elusive which enzymes eliminate these chemical modifications prior to repair. We here show evidence that the BRCA1-CtIP complex plays a role in eliminating this chemical modification, thereby facilitating subsequent DSB repair. Thus, BRCA1 and CtIP have dual functions: their previously documented roles in HR and this newly identified function. This study contributes to our ability to predict the effectiveness of chemotherapeutic agents prior to their selection by evaluating the activity of individual repair factors. Accurate prediction is crucial, because chemotherapeutic agents that cause DNA damage have such strong side effects.
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Affiliation(s)
- Kyoko Nakamura
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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45
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Ji K, Kogame T, Choi K, Wang X, Lee J, Taniguchi Y, Takeda S. A novel approach using DNA-repair-deficient chicken DT40 cell lines for screening and characterizing the genotoxicity of environmental contaminants. ENVIRONMENTAL HEALTH PERSPECTIVES 2009; 117:1737-44. [PMID: 20049126 PMCID: PMC2801191 DOI: 10.1289/ehp.0900842] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Accepted: 06/26/2009] [Indexed: 05/05/2023]
Abstract
BACKGROUND Many bacterial or mammalian cell-based test systems, such as the Ames test, chromosomal aberration assays, or gene mutation assays, are commonly used in developed countries to detect the genotoxicity of industrial chemicals. However, the specificity is generally limited and the sensitivity is not sufficiently high. In addition, most assays cannot provide information on mechanisms of genotoxicity of a given chemical. OBJECTIVES We aimed to establish a sensitive and fast screening method that is also capable of characterizing mechanisms of genotoxicity. METHODS We developed a novel bioassay employing gene-disrupted clones of the chicken DT40 B-lymphocyte line, which are designed to be deficient in several specific DNA repair pathways. Genotoxic chemicals can delay cellular proliferation in DNA-repair-deficient clones more significantly than in wild-type cells by interfering with DNA replication, thereby inducing DNA damage. In addition, we verified the validity of this assay by analyzing the genotoxicity of gamma-rays, ultraviolet (UV) light, and sodium metaarsenite (NaAsO(2)). We also characterized DNA lesions induced by NaAsO(2). RESULTS Genotoxicity of given stressors was successfully screened based on a comparison of proliferation kinetics between wild-type and DNA-repair-deficient mutants in 48 hr. We also found that NaAsO(2) apparently induces at least two types of damage: chromosomal breaks and UV photoproduct-like DNA lesions. CONCLUSION This bioassay is a reliable and sensitive screening tool for environmental mutagens as well as for further characterizing the nature of detected genotoxicity.
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Affiliation(s)
- Kyunghee Ji
- School of Public Health, Seoul National University, Seoul, Korea
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | - Kyungho Choi
- School of Public Health, Seoul National University, Seoul, Korea
| | - Xin Wang
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Jinyoung Lee
- School of Public Health, Seoul National University, Seoul, Korea
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | - Shunichi Takeda
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Address correspondence to S. Takeda, Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Konoe Yoshida, Sakyo-ku, Kyoto, 606-8501 Japan. Telephone: 81-75-753-4412. Fax: 81-75-753-4419. E-mail:
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Saladino C, Bourke E, Conroy PC, Morrison CG. Centriole separation in DNA damage-induced centrosome amplification. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2009; 50:725-732. [PMID: 19274769 DOI: 10.1002/em.20477] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Altered centrosome numbers are seen in tumor cells in response to DNA damaging treatments and are hypothesised to contribute to cancer development. The mechanism by which the centrosome and chromosome cycles become disconnected after DNA damage is not yet clear. Here, we show that centrosome amplification occurs after ionising radiation (IR) in chicken DT40 cells that lack DNA-PK, Ku70, H2AX, Xpa, and Scc1, demonstrating that these activities are not required for centrosome amplification. We show that inhibition of topoisomerase II induces Chk1-dependent centrosome amplification, a similar response to that seen after IR. In the immortalised, nontransformed hTERT-RPE1 line, we observed centriole splitting, followed by dose-dependent centrosome amplification, after IR. We found that IR results in the formation of single, not multiple, daughter centrioles during centrosome amplification in U2OS osteosarcoma cells. Analysis of BRCA1 and BRCA2 mutant tumor cells showed high levels of centriole splitting in the absence of any treatment. IR caused pronounced levels of centrosome amplification in BRCA1 mutant breast cancer cells. These data show that centrosome amplification occurs after different forms of DNA damage in chicken cells, in nontransformed human cells and in human tumor cell lines, indicating that this is a general response to DNA damaging treatments. Together, our data suggest that centriole splitting is a key step in potentiation of the centrosome amplification that is a general response to DNA damage.
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Affiliation(s)
- Chiara Saladino
- Centre for Chromosome Biology, Department of Biochemistry and NCBES, National University of Ireland-Galway, University Road, Galway, Ireland
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47
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Sale JE, Batters C, Edmunds CE, Phillips LG, Simpson LJ, Szüts D. Timing matters: error-prone gap filling and translesion synthesis in immunoglobulin gene hypermutation. Philos Trans R Soc Lond B Biol Sci 2009; 364:595-603. [PMID: 19008194 DOI: 10.1098/rstb.2008.0197] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
By temporarily deferring the repair of DNA lesions encountered during replication, the bypass of DNA damage is critical to the ability of cells to withstand genomic insults. Damage bypass can be achieved either by recombinational mechanisms that are generally accurate or by a process called translesion synthesis. Translesion synthesis involves replacing the stalled replicative polymerase with one of a number of specialized DNA polymerases whose active sites are able to tolerate a distorted or damaged DNA template. While this property allows the translesion polymerases to synthesize across damaged bases, it does so with the trade-off of an increased mutation rate. The deployment of these enzymes must therefore be carefully regulated. In addition to their important role in general DNA damage tolerance and mutagenesis, the translesion polymerases play a crucial role in converting the products of activation induced deaminase-catalysed cytidine deamination to mutations during immunoglobulin gene somatic hypermutation. In this paper, we specifically consider the control of translesion synthesis in the context of the timing of lesion bypass relative to replication fork progression and arrest at sites of DNA damage. We then examine how recent observations concerning the control of translesion synthesis might help refine our view of the mechanisms of immunoglobulin gene somatic hypermutation.
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Affiliation(s)
- Julian E Sale
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.
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Takenaka K, Miki Y. Introduction and characterization of a polymerase-dead point mutation into the POLK gene in vertebrates. FEBS Lett 2009; 583:661-4. [PMID: 19166845 DOI: 10.1016/j.febslet.2008.12.057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Revised: 12/21/2008] [Accepted: 12/24/2008] [Indexed: 11/28/2022]
Abstract
The chicken DT40 cell line is widely used for gene knock-outs. We attempted to introduce a polymerase-dead point mutation into Polkappa, a polymerase for translesion DNA synthesis, taking advantage of the highly efficient targeted integration in DT40 cells. The resulting cells (REV3(-/-)POLK(/)(pol-dead)) proliferated with the same kinetics as the parental REV3(-/-) cells. Though the mock-treated REV3(-/-)POLK(/)(mock) cells showed the same sensitivity as the parental REV3(-/-) cells to methyl methanesulfonate, the REV3(-/-)POLK(/)(pol-dead) cells demonstrated the same sensitivity as the REV3(-/-)POLK(/-) double knock-out cells. This implies that the presence of the polymerase-dead Polkappa does not interfere with other polymerases repairing monoalkylation damage.
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Affiliation(s)
- Katsuya Takenaka
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, 113-8510 Tokyo, Japan
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Takata M, Ishiai M, Kitao H. The Fanconi anemia pathway: insights from somatic cell genetics using DT40 cell line. Mutat Res 2009; 668:92-102. [PMID: 19622405 DOI: 10.1016/j.mrfmmm.2008.12.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2008] [Revised: 12/15/2008] [Accepted: 12/24/2008] [Indexed: 10/21/2022]
Abstract
The Fanconi anemia (FA) pathway is a complex phosphorylation-ubiquitination network in the DNA damage signaling, which is still poorly understood. Defects in the "FA pathway" or in the related DNA repair proteins cause FA, a hereditary disorder that accompanies compromised DNA crosslink repair, poor hematopoetic stem cell survival, genomic instability, and cancer. For molecular dissection of the FA pathway, we have been using chicken B cell line DT40 as a model system. In this review, we will summarize our current understanding of the pathway, and discuss how studies using DT40 have contributed to this rapidly evolving field.
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Affiliation(s)
- Minoru Takata
- Laboratory of DNA Damage Signaling, Department of Late Effect Studies, Radiation Biology Center, Kyoto University, Yoshida-konoe, Sakyo-ku, Kyoto 606-8501, Japan.
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Szüts D, Marcus AP, Himoto M, Iwai S, Sale JE. REV1 restrains DNA polymerase zeta to ensure frame fidelity during translesion synthesis of UV photoproducts in vivo. Nucleic Acids Res 2008; 36:6767-80. [PMID: 18953031 PMCID: PMC2588525 DOI: 10.1093/nar/gkn651] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Exposure to ultraviolet light induces a number of forms of damage in DNA, of which (6–4) photoproducts present the most formidable challenge to DNA replication. No single DNA polymerase has been shown to bypass these lesions efficiently in vitro suggesting that the coordinate use of a number of different enzymes is required in vivo. To further understand the mechanisms and control of lesion bypass in vivo, we have devised a plasmid-based system to study the replication of site-specific T–T(6–4) photoproducts in chicken DT40 cells. We show that DNA polymerase ζ is absolutely required for translesion synthesis (TLS) of this lesion, while loss of DNA polymerase η has no detectable effect. We also show that either the polymerase-binding domain of REV1 or ubiquitinated PCNA is required for the recruitment of Polζ as the catalytic TLS polymerase. Finally, we demonstrate a previously unappreciated role for REV1 in ensuring bypass synthesis remains in frame with the template. Our data therefore suggest that REV1 not only helps to coordinate the delivery of DNA polymerase ζ to a stalled primer terminus but also restrains its activity to ensure that nucleotides are incorporated in register with the template strand.
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Affiliation(s)
- Dávid Szüts
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, UK
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