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Sobol RW. Mouse models to explore the biological and organismic role of DNA polymerase beta. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024; 65 Suppl 1:57-71. [PMID: 38619421 PMCID: PMC11027944 DOI: 10.1002/em.22593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/16/2024]
Abstract
Gene knock-out (KO) mouse models for DNA polymerase beta (Polβ) revealed that loss of Polβ leads to neonatal lethality, highlighting the critical organismic role for this DNA polymerase. While biochemical analysis and gene KO cell lines have confirmed its biochemical role in base excision repair and in TET-mediated demethylation, more long-lived mouse models continue to be developed to further define its organismic role. The Polb-KO mouse was the first of the Cre-mediated tissue-specific KO mouse models. This technology was exploited to investigate roles for Polβ in V(D)J recombination (variable-diversity-joining rearrangement), DNA demethylation, gene complementation, SPO11-induced DNA double-strand break repair, germ cell genome stability, as well as neuronal differentiation, susceptibility to genotoxin-induced DNA damage, and cancer onset. The revolution in knock-in (KI) mouse models was made possible by CRISPR/cas9-mediated gene editing directly in C57BL/6 zygotes. This technology has helped identify phenotypes associated with germline or somatic mutants of Polβ. Such KI mouse models have helped uncover the importance of key Polβ active site residues or specific Polβ enzyme activities, such as the PolbY265C mouse that develops lupus symptoms. More recently, we have used this KI technology to mutate the Polb gene with two codon changes, yielding the PolbL301R/V303R mouse. In this KI mouse model, the expressed Polβ protein cannot bind to its obligate heterodimer partner, Xrcc1. Although the expressed mutant Polβ protein is proteolytically unstable and defective in recruitment to sites of DNA damage, the homozygous PolbL301R/V303R mouse is viable and fertile, yet small in stature. We expect that this and additional targeted mouse models under development are poised to reveal new biological and organismic roles for Polβ.
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Affiliation(s)
- Robert W. Sobol
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912
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2
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Liu QW, Yang ZW, Tang QH, Wang WE, Chu DS, Ji JF, Fan QY, Jiang H, Yang QX, Zhang H, Liu XY, Xu XS, Wang XF, Liu JB, Fu D, Tao K, Yu H. The power and the promise of synthetic lethality for clinical application in cancer treatment. Biomed Pharmacother 2024; 172:116288. [PMID: 38377739 DOI: 10.1016/j.biopha.2024.116288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/08/2024] [Accepted: 02/17/2024] [Indexed: 02/22/2024] Open
Abstract
Synthetic lethality is a phenomenon wherein the simultaneous deficiency of two or more genes results in cell death, while the deficiency of any individual gene does not lead to cell death. In recent years, synthetic lethality has emerged as a significant topic in the field of targeted cancer therapy, with certain drugs based on this concept exhibiting promising outcomes in clinical trials. Nevertheless, the presence of tumor heterogeneity and the intricate DNA repair mechanisms pose challenges to the effective implementation of synthetic lethality. This review aims to explore the concepts, development, and ethical quandaries surrounding synthetic lethality. Additionally, it will provide an in-depth analysis of the clinical application and underlying mechanism of synthetic lethality.
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Affiliation(s)
- Qian-Wen Liu
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province 225300, China; General Surgery, Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Zhi-Wen Yang
- Department of Pharmacy, Changning Maternity and Infant Health Hospital, East China Normal University, Shanghai, Shanghai 200050, China
| | - Qing-Hai Tang
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region and College of Life Sciences, Hengyang Normal University, Hengyang, Hunan Province 421008, China
| | - Wen-Er Wang
- General Surgery, the Fourth Hospital Of Changsha, Changsha Hospital Of Hunan Normal University, Changsha, Hunan Province 410006, China
| | - Da-Sheng Chu
- Second Cadre Rest Medical and Health Center of Changning District, Shanghai Garrison, Shanghai226631, China
| | - Jin-Feng Ji
- Department of Integrated Traditional Chinese and Western Internal Medicine, Affiliated Tumor Hospital of Nantong University, Nantong Tumor Hospital, Nantong, Jiangsu Province 226631, China
| | - Qi-Yu Fan
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu Province 226631, China
| | - Hong Jiang
- Department of Thoracic Surgery, the 905th Hospital of Chinese People's Liberation Army Navy, Shanghai 200050, China
| | - Qin-Xin Yang
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province 225300, China
| | - Hui Zhang
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu Province 226631, China
| | - Xin-Yun Liu
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province 225300, China
| | - Xiao-Sheng Xu
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China.
| | - Xiao-Feng Wang
- Department of Orthopedics, Xiamen Hospital, Zhongshan Hospital, Fudan University, Xiamen, Fujian Province 361015, China.
| | - Ji-Bin Liu
- Institute of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu Province 226631, China.
| | - Da Fu
- General Surgery, Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China.
| | - Kun Tao
- Department of Pathology, Tongji Hospital, School of Medicine, Tongji University, Shanghai 200065, China.
| | - Hong Yu
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu Province 225300, China; Department of Pathology, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, Jiangsu Province 225300, China.
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3
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Moccia M, Pascucci B, Saviano M, Cerasa MT, Terzidis MA, Chatgilialoglu C, Masi A. Advances in Nucleic Acid Research: Exploring the Potential of Oligonucleotides for Therapeutic Applications and Biological Studies. Int J Mol Sci 2023; 25:146. [PMID: 38203317 PMCID: PMC10778772 DOI: 10.3390/ijms25010146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
In recent years, nucleic acids have emerged as powerful biomaterials, revolutionizing the field of biomedicine. This review explores the multifaceted applications of nucleic acids, focusing on their pivotal role in various biomedical applications. Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), possess unique properties such as molecular recognition ability, programmability, and ease of synthesis, making them versatile tools in biosensing and for gene regulation, drug delivery, and targeted therapy. Their compatibility with chemical modifications enhances their binding affinity and resistance to degradation, elevating their effectiveness in targeted applications. Additionally, nucleic acids have found utility as self-assembling building blocks, leading to the creation of nanostructures whose high order underpins their enhanced biological stability and affects the cellular uptake efficiency. Furthermore, this review delves into the significant role of oligonucleotides (ODNs) as indispensable tools for biological studies and biomarker discovery. ODNs, short sequences of nucleic acids, have been instrumental in unraveling complex biological mechanisms. They serve as probes for studying gene expression, protein interactions, and cellular pathways, providing invaluable insights into fundamental biological processes. By examining the synergistic interplay between nucleic acids as powerful biomaterials and ODNs as indispensable tools for biological studies and biomarkers, this review highlights the transformative impact of these molecules on biomedical research. Their versatile applications not only deepen our understanding of biological systems but also are the driving force for innovation in diagnostics and therapeutics, ultimately advancing the field of biomedicine.
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Affiliation(s)
- Maria Moccia
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Strada Provinciale 35d, n. 9, 00010 Montelibretti, Italy; (M.M.); (B.P.)
| | - Barbara Pascucci
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Strada Provinciale 35d, n. 9, 00010 Montelibretti, Italy; (M.M.); (B.P.)
| | - Michele Saviano
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, URT Caserta, Via Vivaldi 43, 81100 Caserta, Italy;
| | - Maria Teresa Cerasa
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via Giovanni Amendola 122/O, 70126 Bari, Italy;
| | - Michael A. Terzidis
- Laboratory of Chemical Biology, Department of Nutritional Sciences and Dietetics, Sindos Campus, International Hellenic University, 57400 Thessaloniki, Greece;
| | - Chryssostomos Chatgilialoglu
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, 40129 Bologna, Italy;
- Center of Advanced Technologies, Adam Mickiewicz University, 61-712 Poznań, Poland
| | - Annalisa Masi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Strada Provinciale 35d, n. 9, 00010 Montelibretti, Italy; (M.M.); (B.P.)
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Carvajal-Maldonado D, Drogalis Beckham L, Wood RD, Doublié S. When DNA Polymerases Multitask: Functions Beyond Nucleotidyl Transfer. Front Mol Biosci 2022; 8:815845. [PMID: 35071329 PMCID: PMC8782244 DOI: 10.3389/fmolb.2021.815845] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
DNA polymerases catalyze nucleotidyl transfer, the central reaction in synthesis of DNA polynucleotide chains. They function not only in DNA replication, but also in diverse aspects of DNA repair and recombination. Some DNA polymerases can perform translesion DNA synthesis, facilitating damage tolerance and leading to mutagenesis. In addition to these functions, many DNA polymerases conduct biochemically distinct reactions. This review presents examples of DNA polymerases that carry out nuclease (3'-5' exonuclease, 5' nuclease, or end-trimming nuclease) or lyase (5' dRP lyase) extracurricular activities. The discussion underscores how DNA polymerases have a remarkable ability to manipulate DNA strands, sometimes involving relatively large intramolecular movement.
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Affiliation(s)
- Denisse Carvajal-Maldonado
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Center, Houston, TX, United States
| | - Lea Drogalis Beckham
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, United States
| | - Richard D Wood
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Center, Houston, TX, United States
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, United States
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Zhu W, Hu J, Chi J, Li Y, Yang B, Hu W, Chen F, Xu C, Chai L, Bao Y. Label-Free Proteomics Reveals the Molecular Mechanism of Subculture Induced Strain Degeneration and Discovery of Indicative Index for Degeneration in Pleurotus ostreatus. Molecules 2020; 25:molecules25214920. [PMID: 33114310 PMCID: PMC7660624 DOI: 10.3390/molecules25214920] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/13/2020] [Accepted: 10/19/2020] [Indexed: 11/16/2022] Open
Abstract
Pleurotus ostreatus is one of the widely cultivated edible fungi across the world. Mycelial subculture is an indispensable part in the process of cultivation and production for all kinds of edible fungi. However, successive subcultures usually lead to strain degeneration. The degenerated strains usually have a decrease in stress resistance, yield, and an alteration in fruiting time, which will subsequently result in tremendous economic loss. Through proteomic analysis, we identified the differentially expressed proteins (DEPs) in the mycelium of Pleurotus ostreatus from different subcultured generations. We found that the DNA damage repair system, especially the double-strand breaks (DSBs), repairs via homologous recombination, was impaired in the subcultured mycelium, and gradual accumulation of the DSBs would lead to the strain degeneration after successive subculture. The TUNEL assay further confirmed our finding about the DNA breaks in the subcultured mycelium. Interestingly, the enzyme activity of laccase, carboxylic ester hydrolase, α-galactosidase, and catalase directly related to passage number could be used as the characteristic index for strain degeneration determination. Our results not only reveal for the first time at the molecular level that genomic instability is the cause of degeneration, but also provide an applicable approach for monitoring strain degeneration in process of edible fungi cultivation and production.
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Affiliation(s)
- Weiwei Zhu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China;
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (J.C.); (Y.L.); (F.C.); (C.X.); (L.C.)
| | - Jinbo Hu
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; (J.H.); (B.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingliang Chi
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (J.C.); (Y.L.); (F.C.); (C.X.); (L.C.)
| | - Yang Li
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (J.C.); (Y.L.); (F.C.); (C.X.); (L.C.)
| | - Bing Yang
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; (J.H.); (B.Y.)
| | - Wenli Hu
- Core Facility Center, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China;
| | - Fei Chen
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (J.C.); (Y.L.); (F.C.); (C.X.); (L.C.)
| | - Chong Xu
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (J.C.); (Y.L.); (F.C.); (C.X.); (L.C.)
| | - Linshan Chai
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (J.C.); (Y.L.); (F.C.); (C.X.); (L.C.)
| | - Yongming Bao
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China;
- School of Ocean Science and Technology, Dalian University of Technology, Panjin 124021, China
- Correspondence: ; Tel.: +86-427-2631777; Fax: +86-411-84706365
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6
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Rajapakse A, Suraweera A, Boucher D, Naqi A, O'Byrne K, Richard DJ, Croft LV. Redox Regulation in the Base Excision Repair Pathway: Old and New Players as Cancer Therapeutic Targets. Curr Med Chem 2020; 27:1901-1921. [PMID: 31258058 DOI: 10.2174/0929867326666190430092732] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/09/2019] [Accepted: 04/05/2019] [Indexed: 01/03/2023]
Abstract
BACKGROUND Reactive Oxygen Species (ROS) are by-products of normal cellular metabolic processes, such as mitochondrial oxidative phosphorylation. While low levels of ROS are important signalling molecules, high levels of ROS can damage proteins, lipids and DNA. Indeed, oxidative DNA damage is the most frequent type of damage in the mammalian genome and is linked to human pathologies such as cancer and neurodegenerative disorders. Although oxidative DNA damage is cleared predominantly through the Base Excision Repair (BER) pathway, recent evidence suggests that additional pathways such as Nucleotide Excision Repair (NER) and Mismatch Repair (MMR) can also participate in clearance of these lesions. One of the most common forms of oxidative DNA damage is the base damage 8-oxoguanine (8-oxoG), which if left unrepaired may result in G:C to A:T transversions during replication, a common mutagenic feature that can lead to cellular transformation. OBJECTIVE Repair of oxidative DNA damage, including 8-oxoG base damage, involves the functional interplay between a number of proteins in a series of enzymatic reactions. This review describes the role and the redox regulation of key proteins involved in the initial stages of BER of 8-oxoG damage, namely Apurinic/Apyrimidinic Endonuclease 1 (APE1), human 8-oxoguanine DNA glycosylase-1 (hOGG1) and human single-stranded DNA binding protein 1 (hSSB1). Moreover, the therapeutic potential and modalities of targeting these key proteins in cancer are discussed. CONCLUSION It is becoming increasingly apparent that some DNA repair proteins function in multiple repair pathways. Inhibiting these factors would provide attractive strategies for the development of more effective cancer therapies.
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Affiliation(s)
- Aleksandra Rajapakse
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia.,School of Natural Sciences, Griffith University, Nathan, QLD, Australia
| | - Amila Suraweera
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia
| | - Didier Boucher
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia
| | - Ali Naqi
- Department of Chemistry, Pennsylvania State University, United States
| | - Kenneth O'Byrne
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia.,Cancer Services, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Derek J Richard
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia
| | - Laura V Croft
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Cancer and Ageing Research Program, Translational Research Institute, Brisbane, QLD, Australia
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Saha LK, Wakasugi M, Akter S, Prasad R, Wilson SH, Shimizu N, Sasanuma H, Huang SYN, Agama K, Pommier Y, Matsunaga T, Hirota K, Iwai S, Nakazawa Y, Ogi T, Takeda S. Topoisomerase I-driven repair of UV-induced damage in NER-deficient cells. Proc Natl Acad Sci U S A 2020; 117:14412-14420. [PMID: 32513688 PMCID: PMC7321995 DOI: 10.1073/pnas.1920165117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Nucleotide excision repair (NER) removes helix-destabilizing adducts including ultraviolet (UV) lesions, cyclobutane pyrimidine dimers (CPDs), and pyrimidine (6-4) pyrimidone photoproducts (6-4PPs). In comparison with CPDs, 6-4PPs have greater cytotoxicity and more strongly destabilizing properties of the DNA helix. It is generally believed that NER is the only DNA repair pathway that removes the UV lesions as evidenced by the previous data since no repair of UV lesions was detected in NER-deficient skin fibroblasts. Topoisomerase I (TOP1) constantly creates transient single-strand breaks (SSBs) releasing the torsional stress in genomic duplex DNA. Stalled TOP1-SSB complexes can form near DNA lesions including abasic sites and ribonucleotides embedded in chromosomal DNA. Here we show that base excision repair (BER) increases cellular tolerance to UV independently of NER in cancer cells. UV lesions irreversibly trap stable TOP1-SSB complexes near the UV damage in NER-deficient cells, and the resulting SSBs activate BER. Biochemical experiments show that 6-4PPs efficiently induce stable TOP1-SSB complexes, and the long-patch repair synthesis of BER removes 6-4PPs downstream of the SSB. Furthermore, NER-deficient cancer cell lines remove 6-4PPs within 24 h, but not CPDs, and the removal correlates with TOP1 expression. NER-deficient skin fibroblasts weakly express TOP1 and show no detectable repair of 6-4PPs. Remarkably, the ectopic expression of TOP1 in these fibroblasts led them to completely repair 6-4PPs within 24 h. In conclusion, we reveal a DNA repair pathway initiated by TOP1, which significantly contributes to cellular tolerance to UV-induced lesions particularly in malignant cancer cells overexpressing TOP1.
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Affiliation(s)
- Liton Kumar Saha
- Department of Radiation Genetics, Kyoto University, Graduate School of Medicine, 606-8501 Kyoto, Japan
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Mitsuo Wakasugi
- Laboratory of Human Molecular Genetics, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 920-1192 Kanazawa, Japan
| | - Salma Akter
- Department of Radiation Genetics, Kyoto University, Graduate School of Medicine, 606-8501 Kyoto, Japan
| | - Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709
| | - Naoto Shimizu
- Department of Radiation Genetics, Kyoto University, Graduate School of Medicine, 606-8501 Kyoto, Japan
| | - Hiroyuki Sasanuma
- Department of Radiation Genetics, Kyoto University, Graduate School of Medicine, 606-8501 Kyoto, Japan
| | - Shar-Yin Naomi Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Keli Agama
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Tsukasa Matsunaga
- Laboratory of Human Molecular Genetics, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 920-1192 Kanazawa, Japan
| | - Kouji Hirota
- Department of Chemistry, Tokyo Metropolitan University, 192-0397 Tokyo, Japan
| | - Shigenori Iwai
- Biological Chemistry Group, Graduate School of Engineering Science, Osaka University, 565-0871 Osaka, Japan
| | - Yuka Nakazawa
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, 464-8601 Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, 464-8601 Nagoya, Japan
| | - Shunichi Takeda
- Department of Radiation Genetics, Kyoto University, Graduate School of Medicine, 606-8501 Kyoto, Japan;
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8
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Rose E, Carvalho JL, Hecht M. Mechanisms of DNA repair in Trypanosoma cruzi: What do we know so far? DNA Repair (Amst) 2020; 91-92:102873. [PMID: 32505694 DOI: 10.1016/j.dnarep.2020.102873] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/27/2020] [Accepted: 05/22/2020] [Indexed: 12/13/2022]
Abstract
Trypanosoma cruzi is the etiological agent of Chagas Disease, which affects 6-7 million people worldwide. Since the early stages of infection and throughout its life cycle, the parasite is exposed to several genotoxic agents. Furthermore, DNA damage is also part of the mechanism of action of at least a few trypanocidal drugs, including Benznidazole. Thus, it is paramount for the parasite to count on an efficient DNA repair machinery to guarantee genome integrity and survival. The present work provides an up-to-date review of both the conserved and peculiar DNA repair mechanisms described in T. cruzi against oxidative stress, ultraviolet and ionizing radiation, DNA adduct-inducing agents, and Benznidazole. The comprehension of the DNA repair mechanisms of the parasite may shed light on the parasite evolution and possibly pave the way for the development of novel and more effective trypanocidal drugs.
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Affiliation(s)
- Ester Rose
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasília, Brasília, Brazil.
| | - Juliana Lott Carvalho
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasília, Brasília, Brazil; Genomic Sciences and Biotechnology Program, Catholic University of Brasília, Brasília, Brazil
| | - Mariana Hecht
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasília, Brasília, Brazil
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9
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Base excision repair pathways of bacteria: new promise for an old problem. Future Med Chem 2020; 12:339-355. [PMID: 32031026 DOI: 10.4155/fmc-2019-0267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Infectious diseases continue to be a major cause of human mortality. With the emergence of drug resistance, diseases that were long thought to have been curable by antibiotics are resurging. There is an urgent clinical need for newer antibiotics that target novel cellular pathways to overcome resistance to currently used therapeutics. The base excision repair (BER) pathways of the pathogen restore altered bases and safeguard the genomic integrity of the pathogen from the host's immune response. Although the BER machinery is of paramount importance to the survival of the pathogens, its potential as a drug target is largely unexplored. In this review, we discuss the importance of BER in different pathogenic organisms and the potential of its inhibition with small molecules.
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10
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Jaiswal AS, Williamson EA, Srinivasan G, Kong K, Lomelino CL, McKenna R, Walter C, Sung P, Narayan S, Hromas R. The splicing component ISY1 regulates APE1 in base excision repair. DNA Repair (Amst) 2019; 86:102769. [PMID: 31887540 DOI: 10.1016/j.dnarep.2019.102769] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 11/01/2019] [Accepted: 12/09/2019] [Indexed: 11/19/2022]
Abstract
The integrity of cellular genome is continuously challenged by endogenous and exogenous DNA damaging agents. If DNA damage is not removed in a timely fashion the replisome may stall at DNA lesions, causing fork collapse and genetic instability. Base excision DNA repair (BER) is the most important pathway for the removal of oxidized or mono-alkylated DNA. While the main components of the BER pathway are well defined, its regulatory mechanism is not yet understood. We report here that the splicing factor ISY1 enhances apurinic/apyrimidinic endonuclease 1 (APE1) activity, the multifunctional enzyme in BER, by promoting its 5'-3' endonuclease activity. ISY1 expression is induced by oxidative damage, which would provide an immediate up-regulation of APE1 activity in vivo and enhance BER of oxidized bases. We further found that APE1 and ISY1 interact, and ISY1 enhances the ability of APE1 to recognize abasic sites in DNA. Using purified recombinant proteins, we reconstituted BER and demonstrated that ISY1 markedly promoted APE1 activity in both the short- and long-patch BER pathways. Our study identified ISY1 as a regulator of the BER pathway, which would be of physiological relevance where suboptimal levels of APE1 are present. The interaction of ISY1 and APE1 also establishes a connection between DNA damage repair and pre-mRNA splicing.
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Affiliation(s)
- Aruna S Jaiswal
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Health Science Center, San Antonio, TX 78229 United States.
| | - Elizabeth A Williamson
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Health Science Center, San Antonio, TX 78229 United States
| | - Gayathri Srinivasan
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Health Science Center, San Antonio, TX 78229 United States
| | - Kimi Kong
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Health Science Center, San Antonio, TX 78229 United States
| | - Carrie L Lomelino
- Department of Biochemistry and Molecular Biology, University of Florida Health, Gainesville, FL 32610 United States
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida Health, Gainesville, FL 32610 United States
| | - Christi Walter
- Department of Cell Systems and Anatomy, University of Texas Health Science Center, San Antonio, TX 78229 United States
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06520 San Antonio, TX 78229 United States
| | - Satya Narayan
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32610 United States
| | - Robert Hromas
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas Health Science Center, San Antonio, TX 78229 United States.
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11
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Kay J, Thadhani E, Samson L, Engelward B. Inflammation-induced DNA damage, mutations and cancer. DNA Repair (Amst) 2019; 83:102673. [PMID: 31387777 DOI: 10.1016/j.dnarep.2019.102673] [Citation(s) in RCA: 188] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 06/15/2019] [Accepted: 07/18/2019] [Indexed: 12/22/2022]
Abstract
The relationships between inflammation and cancer are varied and complex. An important connection linking inflammation to cancer development is DNA damage. During inflammation reactive oxygen and nitrogen species (RONS) are created to combat pathogens and to stimulate tissue repair and regeneration, but these chemicals can also damage DNA, which in turn can promote mutations that initiate and promote cancer. DNA repair pathways are essential for preventing DNA damage from causing mutations and cytotoxicity, but RONS can interfere with repair mechanisms, reducing their efficacy. Further, cellular responses to DNA damage, such as damage signaling and cytotoxicity, can promote inflammation, creating a positive feedback loop. Despite coordination of DNA repair and oxidative stress responses, there are nevertheless examples whereby inflammation has been shown to promote mutagenesis, tissue damage, and ultimately carcinogenesis. Here, we discuss the DNA damage-mediated associations between inflammation, mutagenesis and cancer.
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Affiliation(s)
- Jennifer Kay
- Department of Biological Engineering, United States.
| | | | - Leona Samson
- Department of Biological Engineering, United States; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States
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12
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The Pol β variant containing exon α is deficient in DNA polymerase but has full dRP lyase activity. Sci Rep 2019; 9:9928. [PMID: 31289286 PMCID: PMC6616571 DOI: 10.1038/s41598-019-45846-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/03/2019] [Indexed: 12/28/2022] Open
Abstract
DNA polymerase (Pol) β is a key enzyme in base excision repair (BER), an important repair system for maintaining genomic integrity. We previously reported the presence of a Pol β transcript containing exon α (105-nucleotide) in normal and colon cancer cell lines. The transcript carried an insertion between exons VI and VII and was predicted to encode a ~42 kDa variant of the wild-type 39 kDa enzyme. However, little is known about the biochemical properties of the exon α-containing Pol β (exon α Pol β) variant. Here, we first obtained evidence indicating expression of the 42 kDa exon α Pol β variant in mouse embryonic fibroblasts. The exon α Pol β variant was then overexpressed in E. coli, purified, and characterized for its biochemical properties. Kinetic studies of exon α Pol β revealed that it is deficient in DNA binding to gapped DNA, has strongly reduced polymerase activity and higher Km for dNTP during gap-filling. On the other hand, the 5'-dRP lyase activity of the exon α Pol β variant is similar to that of wild-type Pol β. These results indicate the exon α Pol β variant is base excision repair deficient, but does conduct 5'-trimming of a dRP group at the gap margin. Understanding the biological implications of this Pol β variant warrants further investigation.
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13
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Trasviña-Arenas CH, David SS, Delaye L, Azuara-Liceaga E, Brieba LG. Evolution of Base Excision Repair in Entamoeba histolytica is shaped by gene loss, gene duplication, and lateral gene transfer. DNA Repair (Amst) 2019; 76:76-88. [DOI: 10.1016/j.dnarep.2019.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 01/14/2019] [Accepted: 02/19/2019] [Indexed: 12/22/2022]
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14
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Thapar U, Demple B. Deployment of DNA polymerases beta and lambda in single-nucleotide and multinucleotide pathways of mammalian base excision DNA repair. DNA Repair (Amst) 2019; 76:11-19. [PMID: 30763888 DOI: 10.1016/j.dnarep.2019.02.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/08/2019] [Accepted: 02/01/2019] [Indexed: 11/17/2022]
Abstract
There exist two major base excision DNA repair (BER) pathways, namely single-nucleotide or "short-patch" (SP-BER), and "long-patch" BER (LP-BER). Both pathways appear to be involved in the repair of small base lesions such as uracil, abasic sites and oxidized bases. In addition to DNA polymerase β (Polβ) as the main BER enzyme for repair synthesis, there is evidence for a minor role for DNA polymerase lambda (Polλ) in BER. In this study we explore the potential contribution of Polλ to both SP- and LP-BER in cell-free extracts. We measured BER activity in extracts of mouse embryonic fibroblasts using substrates with either a single uracil or the chemically stable abasic site analog tetrahydrofuran residue. The addition of purified Polλ complemented the pronounced BER deficiency of POLB-null cell extracts as efficiently as did Polβ itself. We have developed a new approach for determining the relative contributions of SP- and LP-BER pathways, exploiting mass-labeled nucleotides to distinguish single- and multinucleotide repair patches. Using this method, we found that uracil repair in wild-type and in Polβ-deficient cell extracts supplemented with Polλ was ∼80% SP-BER. The results show that recombinant Polλ can contribute to both SP- and LP-BER. However, endogenous Polλ, which is present at a level ˜50% that of Polβ in mouse embryonic fibroblasts, appears to make little contribution to BER in extracts. Thus Polλ in cells appears to be under some constraint, perhaps sequestered in a complex with other proteins, or post-translationally modified in a way that limits its ability to participate effectively in BER.
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Affiliation(s)
- Upasna Thapar
- Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY 11794, United States; Department of Pharmacological Sciences, Stony Brook University School of Medicine, Stony Brook, NY, 11794, United States
| | - Bruce Demple
- Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY 11794, United States; Department of Pharmacological Sciences, Stony Brook University School of Medicine, Stony Brook, NY, 11794, United States.
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15
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Sharpe MA, Raghavan S, Baskin DS. PAM-OBG: A monoamine oxidase B specific prodrug that inhibits MGMT and generates DNA interstrand crosslinks, potentiating temozolomide and chemoradiation therapy in intracranial glioblastoma. Oncotarget 2018; 9:23923-23943. [PMID: 29844863 PMCID: PMC5963626 DOI: 10.18632/oncotarget.25246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/08/2018] [Indexed: 12/31/2022] Open
Abstract
Via extensive analyses of genetic databases, we have characterized the DNA-repair capacity of glioblastoma with respect to patient survival. In addition to elevation of O6-methylguanine DNA methyltransferase (MGMT), down-regulation of three DNA repair pathways; canonical mismatch repair (MMR), Non-Homologous End-Joining (NHEJ), and Homologous Recombination (HR) are correlated with poor patient outcome. We have designed and tested both in vitro and in vivo, a monoamine oxidase B (MAOB) specific prodrug, PAM-OBG, that is converted by glioma MAOB into the MGMT inhibitor O6-benzylguanine (O6BG) and the DNA crosslinking agent acrolein. In cultured glioma cells, we show that PAM-OBG is converted to O6BG, inhibiting MGMT and sensitizing cells to DNA alkylating agents such as BCNU, CCNU, and Temozolomide (TMZ). In addition, we demonstrate that the acrolein generated is highly toxic in glioma treated with an inhibitor of Nucleotide Excision Repair (NER). In mouse intracranial models of primary human glioma, we show that PAM-OBG increases survival of mice treated with either BCNU or CCNU by a factor of six and that in a chemoradiation model utilizing six rounds of TMZ/2Gy radiation, pre-treatment with PAM-OBG more than doubled survival time.
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Affiliation(s)
- Martyn A Sharpe
- Department of Neurosurgery, Kenneth R. Peak Brain and Pituitary Tumor Center, Houston Methodist Hospital, TX 77030, Houston, USA
| | - Sudhir Raghavan
- Department of Neurosurgery, Kenneth R. Peak Brain and Pituitary Tumor Center, Houston Methodist Hospital, TX 77030, Houston, USA
| | - David S Baskin
- Department of Neurosurgery, Kenneth R. Peak Brain and Pituitary Tumor Center, Houston Methodist Hospital, TX 77030, Houston, USA
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16
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Zhou J, Chan J, Lambelé M, Yusufzai T, Stumpff J, Opresko PL, Thali M, Wallace SS. NEIL3 Repairs Telomere Damage during S Phase to Secure Chromosome Segregation at Mitosis. Cell Rep 2018; 20:2044-2056. [PMID: 28854357 DOI: 10.1016/j.celrep.2017.08.020] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/05/2017] [Accepted: 08/01/2017] [Indexed: 12/28/2022] Open
Abstract
Oxidative damage to telomere DNA compromises telomere integrity. We recently reported that the DNA glycosylase NEIL3 preferentially repairs oxidative lesions in telomere sequences in vitro. Here, we show that loss of NEIL3 causes anaphase DNA bridging because of telomere dysfunction. NEIL3 expression increases during S phase and reaches maximal levels in late S/G2. NEIL3 co-localizes with TRF2 and associates with telomeres during S phase, and this association increases upon oxidative stress. Mechanistic studies reveal that NEIL3 binds to single-stranded DNA via its intrinsically disordered C terminus in a telomere-sequence-independent manner. Moreover, NEIL3 is recruited to telomeres through its interaction with TRF1, and this interaction enhances the enzymatic activity of purified NEIL3. Finally, we show that NEIL3 interacts with AP Endonuclease 1 (APE1) and the long-patch base excision repair proteins PCNA and FEN1. Taken together, we propose that NEIL3 protects genome stability through targeted repair of oxidative damage in telomeres during S/G2 phase.
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Affiliation(s)
- Jia Zhou
- Department of Microbiology and Molecular Genetics, College of Medicine and College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA; Graduate Program in Cell and Molecular Biology, University of Vermont, Burlington, VT 05405, USA; Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jany Chan
- Department of Microbiology and Molecular Genetics, College of Medicine and College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Marie Lambelé
- Department of Microbiology and Molecular Genetics, College of Medicine and College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Timur Yusufzai
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jason Stumpff
- Department of Molecular Physiology and Biophysics, College of Medicine, University of Vermont, Burlington, VT 05405, USA; Graduate Program in Cell and Molecular Biology, University of Vermont, Burlington, VT 05405, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Markus Thali
- Department of Microbiology and Molecular Genetics, College of Medicine and College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA; Graduate Program in Cell and Molecular Biology, University of Vermont, Burlington, VT 05405, USA.
| | - Susan S Wallace
- Department of Microbiology and Molecular Genetics, College of Medicine and College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA; Graduate Program in Cell and Molecular Biology, University of Vermont, Burlington, VT 05405, USA.
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17
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miR-200a Modulates the Expression of the DNA Repair Protein OGG1 Playing a Role in Aging of Primary Human Keratinocytes. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:9147326. [PMID: 29765508 PMCID: PMC5889889 DOI: 10.1155/2018/9147326] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/13/2017] [Accepted: 01/22/2018] [Indexed: 12/20/2022]
Abstract
Oxidative DNA damage accumulation may induce cellular senescence. Notably, senescent cells accumulate in aged tissues and are present at the sites of age-related pathologies. Although the signaling of DNA strand breaks has been extensively studied, the role of oxidative base lesions has not fully investigated in primary human keratinocyte aging. In this study, we show that primary human keratinocytes from elderly donors are characterized by a significant accumulation of the oxidative base lesion 8-OH-dG, impairment of oxidative DNA repair, and increase of miR-200a levels. Notably, OGG1-2a, a critical enzyme for 8-OH-dG repair, is a direct target of miR-200a and its expression levels significantly decrease in aged keratinocytes. The 8-OH-dG accumulation displays a significant linear relationship with the aging biomarker p16 expression during keratinocyte senescence. Interestingly, we found that miR-200a overexpression down-modulates its putative target Bmi-1, a well-known p16 repressor, and up-regulates p16 itself. miR-200a overexpression also up-regulates the NLRP3 inflammasome and IL-1β expression. Of note, primary keratinocytes from elderly donors are characterized by NRPL3 activation and IL-1β secretion. These findings point to miR-200a as key player in primary human keratinocyte aging since it is able to reduce oxidative DNA repair activity and may induce several senescence features through p16 and IL-1β up-regulation.
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18
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Prasad R, Çağlayan M, Dai DP, Nadalutti CA, Zhao ML, Gassman NR, Janoshazi AK, Stefanick DF, Horton JK, Krasich R, Longley MJ, Copeland WC, Griffith JD, Wilson SH. DNA polymerase β: A missing link of the base excision repair machinery in mammalian mitochondria. DNA Repair (Amst) 2017; 60:77-88. [PMID: 29100041 PMCID: PMC5919216 DOI: 10.1016/j.dnarep.2017.10.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mitochondrial genome integrity is fundamental to mammalian cell viability. Since mitochondrial DNA is constantly under attack from oxygen radicals released during ATP production, DNA repair is vital in removing oxidatively generated lesions in mitochondrial DNA, but the presence of a strong base excision repair system has not been demonstrated. Here, we addressed the presence of such a system in mammalian mitochondria involving the primary base lesion repair enzyme DNA polymerase (pol) β. Pol β was localized to mammalian mitochondria by electron microscopic-immunogold staining, immunofluorescence co-localization and biochemical experiments. Extracts from purified mitochondria exhibited base excision repair activity that was dependent on pol β. Mitochondria from pol β-deficient mouse fibroblasts had compromised DNA repair and showed elevated levels of superoxide radicals after hydrogen peroxide treatment. Mitochondria in pol β-deficient fibroblasts displayed altered morphology by electron microscopy. These results indicate that mammalian mitochondria contain an efficient base lesion repair system mediated in part by pol β and thus pol β plays a role in preserving mitochondrial genome stability.
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Affiliation(s)
- Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Melike Çağlayan
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Da-Peng Dai
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Cristina A Nadalutti
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ming-Lang Zhao
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Natalie R Gassman
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA; University of South Alabama Mitchell Cancer Institute, 1660 Springhill Ave, Mobile, AL 36604, USA
| | - Agnes K Janoshazi
- Signal Transduction Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Donna F Stefanick
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Julie K Horton
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Rachel Krasich
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Matthew J Longley
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA.
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19
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Klvaňa M, Bren U, Florián J. Uniform Free-Energy Profiles of the P-O Bond Formation and Cleavage Reactions Catalyzed by DNA Polymerases β and λ. J Phys Chem B 2016; 120:13017-13030. [PMID: 27992186 PMCID: PMC5217713 DOI: 10.1021/acs.jpcb.6b08581] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Human
X-family DNA polymerases β (Polβ) and λ
(Polλ) catalyze the nucleotidyl-transfer reaction in the base
excision repair pathway of the cellular DNA damage response. Using
empirical valence bond and free-energy perturbation simulations, we
explore the feasibility of various mechanisms for the deprotonation
of the 3′-OH group of the primer DNA strand, and the subsequent
formation and cleavage of P–O bonds in four Polβ, two
truncated Polλ (tPolλ), and two tPolλ Loop1 mutant
(tPolλΔL1) systems differing in the initial X-ray crystal
structure and nascent base pair. The average calculated activation
free energies of 14, 18, and 22 kcal mol–1 for Polβ,
tPolλ, and tPolλΔL1, respectively, reproduce the
trend in the observed catalytic rate constants. The most feasible
reaction pathway consists of two successive steps: specific base (SB)
proton transfer followed by rate-limiting concerted formation and
cleavage of the P–O bonds. We identify linear free-energy relationships
(LFERs) which show that the differences in the overall activation
and reaction free energies among the eight studied systems are determined
by the reaction free energy of the SB proton transfer. We discuss
the implications of the LFERs and suggest pKa of the 3′-OH group as a predictor of the catalytic
rate of X-family DNA polymerases.
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Affiliation(s)
- Martin Klvaňa
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Technology, University of Maribor , Smetanova ulica 17, 2000 Maribor, Slovenia.,Department of Chemistry and Biochemistry, Loyola University Chicago , 1032 W. Sheridan Road, Chicago, Illinois 60660, United States
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Technology, University of Maribor , Smetanova ulica 17, 2000 Maribor, Slovenia.,Laboratory for Molecular Modeling, National Institute of Chemistry , Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
| | - Jan Florián
- Department of Chemistry and Biochemistry, Loyola University Chicago , 1032 W. Sheridan Road, Chicago, Illinois 60660, United States
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20
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Ng HZ, Ng M, Eng CM, Gao Z. Deoxyribonucleic acid glycosylase assays: Progress and prospects. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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21
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Prasad R, Poltoratsky V, Hou EW, Wilson SH. Rev1 is a base excision repair enzyme with 5'-deoxyribose phosphate lyase activity. Nucleic Acids Res 2016; 44:10824-10833. [PMID: 27683219 PMCID: PMC5159550 DOI: 10.1093/nar/gkw869] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/16/2016] [Accepted: 09/21/2016] [Indexed: 12/28/2022] Open
Abstract
Rev1 is a member of the Y-family of DNA polymerases and is known for its deoxycytidyl transferase activity that incorporates dCMP into DNA and its ability to function as a scaffold factor for other Y-family polymerases in translesion bypass events. Rev1 also is involved in mutagenic processes during somatic hypermutation of immunoglobulin genes. In light of the mutation pattern consistent with dCMP insertion observed earlier in mouse fibroblast cells treated with a base excision repair-inducing agent, we questioned whether Rev1 could also be involved in base excision repair (BER). Here, we uncovered a weak 5′-deoxyribose phosphate (5′-dRP) lyase activity in mouse Rev1 and demonstrated the enzyme can mediate BER in vitro. The full-length Rev1 protein and its catalytic core domain are similar in their ability to support BER in vitro. The dRP lyase activity in both of these proteins was confirmed by NaBH4 reduction of the Schiff base intermediate and kinetics studies. Limited proteolysis, mass spectrometry and deletion analysis localized the dRP lyase active site to the C-terminal segment of Rev1's catalytic core domain. These results suggest that Rev1 could serve as a backup polymerase in BER and could potentially contribute to AID-initiated antibody diversification through this activity.
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Affiliation(s)
- Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, PO Box 12233, MD F3-01, Research Triangle Park, NC 27709, USA
| | - Vladimir Poltoratsky
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, PO Box 12233, MD F3-01, Research Triangle Park, NC 27709, USA
| | - Esther W Hou
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, PO Box 12233, MD F3-01, Research Triangle Park, NC 27709, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, PO Box 12233, MD F3-01, Research Triangle Park, NC 27709, USA
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22
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The Response to Oxidative DNA Damage in Neurons: Mechanisms and Disease. Neural Plast 2016; 2016:3619274. [PMID: 26942017 PMCID: PMC4752990 DOI: 10.1155/2016/3619274] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 12/24/2015] [Indexed: 11/26/2022] Open
Abstract
There is a growing body of evidence indicating that the mechanisms that control genome stability are of key importance in the development and function of the nervous system. The major threat for neurons is oxidative DNA damage, which is repaired by the base excision repair (BER) pathway. Functional mutations of enzymes that are involved in the processing of single-strand breaks (SSB) that are generated during BER have been causally associated with syndromes that present important neurological alterations and cognitive decline. In this review, the plasticity of BER during neurogenesis and the importance of an efficient BER for correct brain function will be specifically addressed paying particular attention to the brain region and neuron-selectivity in SSB repair-associated neurological syndromes and age-related neurodegenerative diseases.
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23
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Narayan S, Sharma R. Molecular mechanism of adenomatous polyposis coli-induced blockade of base excision repair pathway in colorectal carcinogenesis. Life Sci 2015; 139:145-52. [PMID: 26334567 DOI: 10.1016/j.lfs.2015.08.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 07/31/2015] [Accepted: 08/23/2015] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is the third leading cause of death in both men and women in North America. Despite chemotherapeutic efforts, CRC is associated with a high degree of morbidity and mortality. Thus, to develop effective treatment strategies for CRC, one needs knowledge of the pathogenesis of cancer development and cancer resistance. It is suggested that colonic tumors or cell lines harbor truncated adenomatous polyposis coli (APC) without DNA repair inhibitory (DRI)-domain. It is also thought that the product of the APC gene can modulate base excision repair (BER) pathway through an interaction with DNA polymerase β (Pol-β) and flap endonuclease 1 (Fen-1) to mediate CRC cell apoptosis. The proposed therapy with temozolomide (TMZ) exploits this particular pathway; however, a high percentage of colorectal tumors continue to develop resistance to chemotherapy due to mismatch repair (MMR)-deficiency. In the present communication, we have comprehensively reviewed a critical issue that has not been addressed previously: a novel mechanism by which APC-induced blockage of single nucleotide (SN)- and long-patch (LP)-BER play role in DNA-alkylation damage-induced colorectal carcinogenesis.
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Affiliation(s)
- Satya Narayan
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32610 United States.
| | - Ritika Sharma
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32610 United States
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24
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Prasad R, Dyrkheeva N, Williams J, Wilson SH. Mammalian Base Excision Repair: Functional Partnership between PARP-1 and APE1 in AP-Site Repair. PLoS One 2015; 10:e0124269. [PMID: 26020771 PMCID: PMC4447435 DOI: 10.1371/journal.pone.0124269] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/11/2015] [Indexed: 01/09/2023] Open
Abstract
The apurinic/apyrimidinic- (AP-) site in genomic DNA arises through spontaneous base loss and base removal by DNA glycosylases and is considered an abundant DNA lesion in mammalian cells. The base excision repair (BER) pathway repairs the AP-site lesion by excising and replacing the site with a normal nucleotide via template directed gap-filling DNA synthesis. The BER pathway is mediated by a specialized group of proteins, some of which can be found in multiprotein complexes in cultured mouse fibroblasts. Using a DNA polymerase (pol) β immunoaffinity-capture technique to isolate such a complex, we identified five tightly associated and abundant BER factors in the complex: PARP-1, XRCC1, DNA ligase III, PNKP, and Tdp1. AP endonuclease 1 (APE1), however, was not present. Nevertheless, the complex was capable of BER activity, since repair was initiated by PARP-1’s AP lyase strand incision activity. Addition of purified APE1 increased the BER activity of the pol β complex. Surprisingly, the pol β complex stimulated the strand incision activity of APE1. Our results suggested that PARP-1 was responsible for this effect, whereas other proteins in the complex had no effect on APE1 strand incision activity. Studies of purified PARP-1 and APE1 revealed that PARP-1 was able to stimulate APE1 strand incision activity. These results illustrate roles of PARP-1 in BER including a functional partnership with APE1.
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Affiliation(s)
- Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Nadezhda Dyrkheeva
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Jason Williams
- Epigenetics and Stem Cell Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Samuel H. Wilson
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
- * E-mail:
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Yamamoto R, Umetsu M, Yamamoto M, Matsuyama S, Takenaka S, Ide H, Kubo K. AP endonuclease knockdown enhances methyl methanesulfonate hypersensitivity of DNA polymerase β knockout mouse embryonic fibroblasts. JOURNAL OF RADIATION RESEARCH 2015; 56:462-466. [PMID: 25724755 PMCID: PMC4426919 DOI: 10.1093/jrr/rru125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 12/07/2014] [Accepted: 12/17/2014] [Indexed: 06/04/2023]
Abstract
Apurinic/apyrimidinic (AP) endonuclease (Apex) is required for base excision repair (BER), which is the major mechanism of repair for small DNA lesions such as alkylated bases. Apex incises the DNA strand at an AP site to leave 3'-OH and 5'-deoxyribose phosphate (5'-dRp) termini. DNA polymerase β (PolB) plays a dominant role in single nucleotide (Sn-) BER by incorporating a nucleotide and removing 5'-dRp. Methyl methanesulfonate (MMS)-induced damage is repaired by Sn-BER, and thus mouse embryonic fibroblasts (MEFs) deficient in PolB show significantly increased sensitivity to MMS. However, the survival curve for PolB-knockout MEFs (PolBKOs) has a shoulder, and increased sensitivity is only apparent at relatively high MMS concentrations. In this study, we prepared Apex-knockdown/PolB-knockout MEFs (AKDBKOs) to examine whether BER is related to the apparent resistance of PolBKOs at low MMS concentrations. The viability of PolBKOs immediately after MMS treatment was significantly lower than that of wild-type MEFs, but there was essentially no effect of Apex-knockdown on cell viability in the presence or absence of PolB. In contrast, relative counts of MEFs after repair were decreased by Apex knockdown. Parental PolBKOs showed especially high sensitivity at >1.5 mM MMS, suggesting that PolBKOs have another repair mechanism in addition to PolB-dependent Sn-BER, and that the back-up mechanism is unable to repair damage induced by high MMS concentrations. Interestingly, AKDBKOs were hypersensitive to MMS in a relative cell growth assay, suggesting that MMS-induced damage in PolB-knockout MEFs is repaired by Apex-dependent repair mechanisms, presumably including long-patch BER.
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Affiliation(s)
- Ryohei Yamamoto
- Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku Ourai Kita, Izumisano, Osaka 598-8531, Japan
| | - Makio Umetsu
- Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku Ourai Kita, Izumisano, Osaka 598-8531, Japan
| | - Mizuki Yamamoto
- Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku Ourai Kita, Izumisano, Osaka 598-8531, Japan
| | - Satoshi Matsuyama
- Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku Ourai Kita, Izumisano, Osaka 598-8531, Japan
| | - Shigeo Takenaka
- Department of Integrated Functional Biosciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku Ourai Kita, Izumisano, Osaka 598-8531, Japan
| | - Hiroshi Ide
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Kihei Kubo
- Department of Advanced Pathobiology, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku Ourai Kita, Izumisano, Osaka 598-8531, Japan
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26
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Dutta A, Yang C, Sengupta S, Mitra S, Hegde ML. New paradigms in the repair of oxidative damage in human genome: mechanisms ensuring repair of mutagenic base lesions during replication and involvement of accessory proteins. Cell Mol Life Sci 2015; 72:1679-98. [PMID: 25575562 DOI: 10.1007/s00018-014-1820-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/19/2014] [Accepted: 12/22/2014] [Indexed: 11/30/2022]
Abstract
Oxidized bases in the mammalian genome, which are invariably mutagenic due to their mispairing property, are continuously induced by endogenous reactive oxygen species and more abundantly after oxidative stress. Unlike bulky base adducts induced by UV and other environmental mutagens in the genome that block replicative DNA polymerases, oxidatively damaged bases such as 5-hydroxyuracil, produced by oxidative deamination of cytosine in the template strand, do not block replicative polymerases and thus need to be repaired prior to replication to prevent mutation. Following up our earlier studies, which showed that the Nei endonuclease VIII like 1 (NEIL1) DNA glycosylase, one of the five base excision repair (BER)-initiating enzymes in mammalian cells, has enhanced expression during the S-phase and higher affinity for replication fork-mimicking single-stranded (ss) DNA substrates, we recently provided direct experimental evidence for NEIL1's role in replicating template strand repair. The key requirement for this event, which we named as the 'cow-catcher' mechanism of pre-replicative BER, is NEIL1's non-productive binding (substrate binding without product formation) to the lesion base in ss DNA template to stall DNA synthesis, causing fork regression. Repair of the lesion in reannealed duplex is then carried out by NEIL1 in association with the DNA replication proteins. NEIL1 (and other BER-initiating enzymes) also interact with several accessory and non-canonical proteins including the heterogeneous nuclear ribonucleoprotein U and Y-box-binding protein 1 as well as high mobility group box 1 protein, whose precise roles in BER are still obscure. In this review, we have discussed the recent advances in our understanding of oxidative genome damage repair pathways with particular focus on the pre-replicative template strand repair and the role of scaffold factors like X-ray repairs cross-complementing protein 1 and poly (ADP-ribose) polymerase 1 and other accessory proteins guiding distinct BER sub-pathways.
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Affiliation(s)
- Arijit Dutta
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX, 77030, USA
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27
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Affiliation(s)
- Donal P McLornan
- From King's College Hospital NHS Foundation Trust, London (D.P.M., G.J.M.); and Moffitt Cancer Center, Tampa, FL (A.L.)
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Rahmanian S, Taleei R, Nikjoo H. Radiation induced base excision repair (BER): a mechanistic mathematical approach. DNA Repair (Amst) 2014; 22:89-103. [PMID: 25117268 DOI: 10.1016/j.dnarep.2014.07.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 07/17/2014] [Accepted: 07/18/2014] [Indexed: 01/24/2023]
Abstract
This paper presents a mechanistic model of base excision repair (BER) pathway for the repair of single-stand breaks (SSBs) and oxidized base lesions produced by ionizing radiation (IR). The model is based on law of mass action kinetics to translate the biochemical processes involved, step-by-step, in the BER pathway to translate into mathematical equations. The BER is divided into two subpathways, short-patch repair (SPR) and long-patch repair (LPR). SPR involves in replacement of single nucleotide via Pol β and ligation of the ends via XRCC1 and Ligase III, while LPR involves in replacement of multiple nucleotides via PCNA, Pol δ/ɛ and FEN 1, and ligation via Ligase I. A hallmark of IR is the production of closely spaced lesions within a turn of DNA helix (named complex lesions), which have been attributed to a slower repair process. The model presented considers fast and slow component of BER kinetics by assigning SPR for simple lesions and LPR for complex lesions. In the absence of in vivo reaction rate constants for the BER proteins, we have deduced a set of rate constants based on different published experimental measurements including accumulation kinetics obtained from UVA irradiation, overall SSB repair kinetic experiments, and overall BER kinetics from live-cell imaging experiments. The model was further used to calculate the repair kinetics of complex base lesions via the LPR subpathway and compared to foci kinetic experiments for cells irradiated with γ rays, Si, and Fe ions. The model calculation show good agreement with experimental measurements for both overall repair and repair of complex lesions. Furthermore, using the model we explored different mechanisms responsible for inhibition of repair when higher LET and HZE particles are used and concluded that increasing the damage complexity can inhibit initiation of LPR after the AP site removal step in BER.
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Affiliation(s)
- Shirin Rahmanian
- Radiation Biophysics Group, Department of Oncology-Pathology, Karolinska Institutet, Box 260 P9-02, Stockholm 17176, Sweden
| | - Reza Taleei
- Radiation Physics, MD Anderson Cancer Center, 1515 Holcombe Blvd., Unit 94, Houston, TX 77030-4409, USA
| | - Hooshang Nikjoo
- Radiation Biophysics Group, Department of Oncology-Pathology, Karolinska Institutet, Box 260 P9-02, Stockholm 17176, Sweden.
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Szczesny B, Olah G, Walker DK, Volpi E, Rasmussen BB, Szabo C, Mitra S. Deficiency in repair of the mitochondrial genome sensitizes proliferating myoblasts to oxidative damage. PLoS One 2013; 8:e75201. [PMID: 24066171 PMCID: PMC3774773 DOI: 10.1371/journal.pone.0075201] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 08/12/2013] [Indexed: 11/18/2022] Open
Abstract
Reactive oxygen species (ROS), generated as a by-product of mitochondrial oxidative phosphorylation, are particularly damaging to the genome of skeletal muscle because of their high oxygen consumption. Proliferating myoblasts play a key role during muscle regeneration by undergoing myogenic differentiation to fuse and restore damaged muscle. This process is severely impaired during aging and in muscular dystrophies. In this study, we investigated the role of oxidatively damaged DNA and its repair in the mitochondrial genome of proliferating skeletal muscle progenitor myoblasts cells and their terminally differentiated product, myotubes. Using the C2C12 cell line as a well-established model for skeletal muscle differentiation, we show that myoblasts are highly sensitive to ROS-mediated DNA damage, particularly in the mitochondrial genome, due to deficiency in 5’ end processing at the DNA strand breaks. Ectopic expression of the mitochondrial-specific 5’ exonuclease, EXOG, a key DNA base excision/single strand break repair (BER/SSBR) enzyme, in myoblasts but not in myotubes, improves the cell’s resistance to oxidative challenge. We linked loss of myoblast viability by activation of apoptosis with deficiency in the repair of the mitochondrial genome. Moreover, the process of myoblast differentiation increases mitochondrial biogenesis and the level of total glutathione. We speculate that our data may provide a mechanistic explanation for depletion of proliferating muscle precursor cells during the development of sarcopenia, and skeletal muscle dystrophies.
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Affiliation(s)
- Bartosz Szczesny
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
- * E-mail:
| | - Gabor Olah
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Dillon K. Walker
- Department of Nutrition and Metabolism, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Elena Volpi
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Blake B. Rasmussen
- Department of Nutrition and Metabolism, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Csaba Szabo
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Sankar Mitra
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
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Gridley CL, Rangarajan S, Firbank S, Dalal S, Sweasy JB, Jaeger J. Structural changes in the hydrophobic hinge region adversely affect the activity and fidelity of the I260Q mutator DNA polymerase β. Biochemistry 2013; 52:4422-32. [PMID: 23651085 DOI: 10.1021/bi301368f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The I260Q variant of DNA polymerase β is an efficient mutator polymerase with fairly indiscriminate misincorporation activities opposite all template bases. Previous modeling studies have suggested that I260Q harbors structural variations in its hinge region. Here, we present the crystal structures of wild type and I260Q rat polymerase β in the presence and absence of substrates. Both the I260Q apoenzyme structure and the closed ternary complex with double-stranded DNA and ddTTP show ordered water molecules in the hydrophobic hinge near Gln260, whereas this is not the case in the wild type polymerase. Compared to wild type polymerase β ternary complexes, there are subtle movements around residues 260, 272, 295, and 296 in the mutant. The rearrangements in this region, coupled with side chain movements in the immediate neighborhood of the dNTP-binding pocket, namely, residues 258 and 272, provide an explanation for the altered activity and fidelity profiles observed in the I260Q mutator polymerase.
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Affiliation(s)
- Chelsea L Gridley
- Division of Genetics, Wadsworth Center, New York State Department of Health, New Scotland Avenue, Albany, New York 12208, United States
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31
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Maintenance of genomic stability in mouse embryonic stem cells: relevance in aging and disease. Int J Mol Sci 2013; 14:2617-36. [PMID: 23358251 PMCID: PMC3588006 DOI: 10.3390/ijms14022617] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 01/11/2013] [Accepted: 01/12/2013] [Indexed: 01/15/2023] Open
Abstract
Recent studies have shown that mouse embryonic stem cells (mESCs) rely on a distinctive genome caretaking network. In this review, we will discuss how mESCs functionally respond to DNA damage and describe several modifications in mESC DNA damage response, which accommodate dynamic cycling and preservation of genetic information. Subsequently, we will discuss how the transition from mESCs to adult stem/progenitor cells can be involved in the decline of tissue integrity and function in the elderly.
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32
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Prasad R, Williams JG, Hou EW, Wilson SH. Pol β associated complex and base excision repair factors in mouse fibroblasts. Nucleic Acids Res 2012; 40:11571-82. [PMID: 23042675 PMCID: PMC3526277 DOI: 10.1093/nar/gks898] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
During mammalian base excision repair (BER) of lesion-containing DNA, it is proposed that toxic strand-break intermediates generated throughout the pathway are sequestered and passed from one step to the next until repair is complete. This stepwise process is termed substrate channeling. A working model evaluated here is that a complex of BER factors may facilitate the BER process. FLAG-tagged DNA polymerase (pol) β was expressed in mouse fibroblasts carrying a deletion in the endogenous pol β gene, and the cell extract was subjected to an ‘affinity-capture’ procedure using anti-FLAG antibody. The pol β affinity-capture fraction (ACF) was found to contain several BER factors including polymerase-1, X-ray cross-complementing factor1-DNA ligase III and enzymes involved in processing 3′-blocked ends of BER intermediates, e.g. polynucleotide kinase and tyrosyl-DNA phosphodiesterase 1. In contrast, DNA glycosylases, apurinic/aprymidinic endonuclease 1 and flap endonuclease 1 and several other factors involved in BER were not present. Some of the BER factors in the pol β ACF were in a multi-protein complex as observed by sucrose gradient centrifugation. The pol β ACF was capable of substrate channeling for steps in vitro BER and was proficient in in vitro repair of substrates mimicking a 3′-blocked topoisomerase I covalent intermediate or an oxidative stress-induced 3′-blocked intermediate.
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Affiliation(s)
- Rajendra Prasad
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA
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33
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Siddiqui A, Rivera-Sánchez S, del R. Castro M, Acevedo-Torres K, Rane A, Torres-Ramos CA, Nicholls DG, Andersen JK, Ayala-Torres S. Mitochondrial DNA damage is associated with reduced mitochondrial bioenergetics in Huntington's disease. Free Radic Biol Med 2012; 53:1478-88. [PMID: 22709585 PMCID: PMC3846402 DOI: 10.1016/j.freeradbiomed.2012.06.008] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 06/06/2012] [Accepted: 06/07/2012] [Indexed: 11/25/2022]
Abstract
Oxidative stress and mitochondrial dysfunction have been implicated in the pathology of HD; however, the precise mechanisms by which mutant huntingtin modulates levels of oxidative damage in turn resulting in mitochondrial dysfunction are not known. We hypothesize that mutant huntingtin increases oxidative mtDNA damage leading to mitochondrial dysfunction. We measured nuclear and mitochondrial DNA lesions and mitochondrial bioenergetics in the STHdhQ7 and STHdhQ111 in vitro striatal model of HD. Striatal cells expressing mutant huntingtin show higher basal levels of mitochondrial-generated ROS and mtDNA lesions and a lower spare respiratory capacity. Silencing of APE1, the major mammalian apurinic/apyrimidinic (AP) endonuclease that participates in the base excision repair (BER) pathway, caused further reductions of spare respiratory capacity in the mutant huntingtin-expressing cells. Localization experiments show that APE1 increases in the mitochondria of wild-type Q7 cells but not in the mutant huntingtin Q111 cells after treatment with hydrogen peroxide. Moreover, these results are recapitulated in human HD striata and HD skin fibroblasts that show significant mtDNA damage (increased lesion frequency and mtDNA depletion) and significant decreases in spare respiratory capacity, respectively. These data suggest that mtDNA is a major target of mutant huntingtin-associated oxidative stress and may contribute to subsequent mitochondrial dysfunction and that APE1 (and, by extension, BER) is an important target in the maintenance of mitochondrial function in HD.
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Affiliation(s)
| | - Sulay Rivera-Sánchez
- Department of Biochemistry, University of Puerto Rico Medical Sciences Campus, San Juan, PR
| | - María del R. Castro
- Department of Pharmacology and Toxicology, University of Puerto Rico Medical Sciences Campus, San Juan, PR
| | - Karina Acevedo-Torres
- Department of Physiology, University of Puerto Rico Medical Sciences Campus, San Juan, PR
| | - Anand Rane
- Buck Institute for Age Research, Novato, CA
| | - Carlos A. Torres-Ramos
- Department of Physiology, University of Puerto Rico Medical Sciences Campus, San Juan, PR
| | | | | | - Sylvette Ayala-Torres
- Department of Pharmacology and Toxicology, University of Puerto Rico Medical Sciences Campus, San Juan, PR
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Schamber-Reis BLF, Nardelli S, Régis-Silva CG, Campos PC, Cerqueira PG, Lima SA, Franco GR, Macedo AM, Pena SDJ, Cazaux C, Hoffmann JS, Motta MCM, Schenkman S, Teixeira SMR, Machado CR. DNA polymerase beta from Trypanosoma cruzi is involved in kinetoplast DNA replication and repair of oxidative lesions. Mol Biochem Parasitol 2012; 183:122-31. [PMID: 22369885 DOI: 10.1016/j.molbiopara.2012.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 02/09/2012] [Accepted: 02/14/2012] [Indexed: 12/18/2022]
Abstract
Specific DNA repair pathways from Trypanosoma cruzi are believed to protect genomic DNA and kinetoplast DNA (kDNA) from mutations. Particular pathways are supposed to operate in order to repair nucleotides oxidized by reactive oxygen species (ROS) during parasite infection, being 7,8-dihydro-8-oxoguanine (8oxoG) a frequent and highly mutagenic base alteration. If unrepaired, 8oxoG can lead to cytotoxic base transversions during DNA replication. In mammals, DNA polymerase beta (Polβ) is mainly involved in base excision repair (BER) of oxidative damage. However its biological role in T. cruzi is still unknown. We show, by immunofluorescence localization, that T. cruzi DNA polymerase beta (Tcpolβ) is restricted to the antipodal sites of kDNA in replicative epimastigote and amastigote developmental stages, being strictly localized to kDNA antipodal sites between G1/S and early G2 phase in replicative epimastigotes. Nevertheless, this polymerase was detected inside the mitochondrial matrix of trypomastigote forms, which are not able to replicate in culture. Parasites over expressing Tcpolβ showed reduced levels of 8oxoG in kDNA and an increased survival after treatment with hydrogen peroxide when compared to control cells. However, this resistance was lost after treating Tcpolβ overexpressors with methoxiamine, a potent BER inhibitor. Curiously, a presumed DNA repair focus containing Tcpolβ was identified in the vicinity of kDNA of cultured wild type epimastigotes after treatment with hydrogen peroxide. Taken together our data suggest participation of Tcpolβ during kDNA replication and repair of oxidative DNA damage induced by genotoxic stress in this organelle.
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Affiliation(s)
- Bruno Luiz Fonseca Schamber-Reis
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
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35
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MIYOSHI T, NAKANO SI, NAKAMURA K, YAMANOUCHI K, NISHIHARA M. In Vivo Electroporation Induces Cell Cycle Reentry of Myonuclei in Rat Skeletal Muscle. J Vet Med Sci 2012; 74:1291-7. [DOI: 10.1292/jvms.12-0195] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Takahiro MIYOSHI
- Department of Veterinary Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Department of Veterinary Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657, Japan
| | - Shin-ichi NAKANO
- Department of Veterinary Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Department of Veterinary Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657, Japan
| | - Katsuyuki NAKAMURA
- Department of Veterinary Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Department of Veterinary Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657, Japan
| | - Keitaro YAMANOUCHI
- Department of Veterinary Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Department of Veterinary Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657, Japan
| | - Masugi NISHIHARA
- Department of Veterinary Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo
- Department of Veterinary Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657, Japan
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36
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Prasad R, Beard WA, Batra VK, Liu Y, Shock DD, Wilson SH. A review of recent experiments on step-to-step “hand-off” of the DNA intermediates in mammalian base excision repair pathways. Mol Biol 2011. [DOI: 10.1134/s0026893311040091] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Tichy ED, Liang L, Deng L, Tischfield J, Schwemberger S, Babcock G, Stambrook PJ. Mismatch and base excision repair proficiency in murine embryonic stem cells. DNA Repair (Amst) 2011; 10:445-51. [PMID: 21315663 DOI: 10.1016/j.dnarep.2011.01.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 12/20/2010] [Accepted: 01/12/2011] [Indexed: 02/02/2023]
Abstract
Accumulation of mutations in embryonic stem (ES) cells would be detrimental to an embryo derived from these cells, and would adversely affect multiple organ systems and tissue types. ES cells have evolved multiple mechanisms to preserve genomic integrity that extend beyond those found in differentiated cell types. The present study queried whether mismatch repair (MMR) and base-excision repair (BER) may play a role in the maintenance of murine ES cell genomes. The MMR proteins Msh2 and Msh6 are highly elevated in mouse ES cells compared with mouse embryo fibroblasts (MEFs), as are Pms2 and Mlh1, albeit to a lesser extent. Cells transfected with an MMR reporter plasmid showed that MMR repair capacity is low in MEFs, but highly active in wildtype ES cells. As expected, an ES cell line defective in MMR was several-fold less effective in repair level than wildtype ES cells. Like proteins that participate in MMR, the level of proteins involved in BER was elevated in ES cells compared with MEFs. When BER activity was examined biochemically using a uracil-containing oligonucleotide template, repair activity was higher in ES cells compared with MEFs. The data are consistent with the suggestion that ES cells have multiple mechanisms, including highly active MMR and BER that preserve genetic integrity and minimize the accumulation of mutations.
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Affiliation(s)
- Elisia D Tichy
- Department of Molecular Genetics, Biochemistry & Microbiology, University of Cincinnati, Cincinnati, OH 45267, USA.
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38
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Jaiswal AS, Narayan S. Assembly of the base excision repair complex on abasic DNA and role of adenomatous polyposis coli on its functional activity. Biochemistry 2011; 50:1901-9. [PMID: 21261287 DOI: 10.1021/bi102000q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The assembly and stability of base excision repair (BER) proteins in vivo with abasic DNA and the role of adenomatous polyposis coli (APC) protein in this process are currently unclear. We have studied the assembly of a multiprotein BER complex onto abasic DNA (F-DNA) and characterized the physical and functional activity of the associated proteins. We found that the BER complex contained all the essential components of the long-patch BER system, such as APE1, Pol-β, Fen1, and DNA ligase I. Interestingly, wild-type APC was also present in the BER complex. Kinetics of the assembly of BER proteins onto the F-DNA were rapid and appeared in sequential order depending upon their requirement in the repair process. The presence of wild-type APC in the BER complex caused a decrease in the level of assembly of BER proteins and negatively affected long-patch BER. These results suggest that major BER proteins in the complex are assembled onto F-DNA and are competent in performing DNA repair. Wild-type APC in the BER complex reduces the repair activity, probably because of interaction with multiple components of the system.
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Affiliation(s)
- Aruna S Jaiswal
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida 32610, United States.
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Rastogi RP, Richa, Kumar A, Tyagi MB, Sinha RP. Molecular mechanisms of ultraviolet radiation-induced DNA damage and repair. J Nucleic Acids 2010; 2010:592980. [PMID: 21209706 PMCID: PMC3010660 DOI: 10.4061/2010/592980] [Citation(s) in RCA: 587] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 08/15/2010] [Accepted: 09/28/2010] [Indexed: 11/20/2022] Open
Abstract
DNA is one of the prime molecules, and its stability is of utmost importance for proper functioning and existence of all living systems. Genotoxic chemicals and radiations exert adverse effects on genome stability. Ultraviolet radiation (UVR) (mainly UV-B: 280-315 nm) is one of the powerful agents that can alter the normal state of life by inducing a variety of mutagenic and cytotoxic DNA lesions such as cyclobutane-pyrimidine dimers (CPDs), 6-4 photoproducts (6-4PPs), and their Dewar valence isomers as well as DNA strand breaks by interfering the genome integrity. To counteract these lesions, organisms have developed a number of highly conserved repair mechanisms such as photoreactivation, base excision repair (BER), nucleotide excision repair (NER), and mismatch repair (MMR). Additionally, double-strand break repair (by homologous recombination and nonhomologous end joining), SOS response, cell-cycle checkpoints, and programmed cell death (apoptosis) are also operative in various organisms with the expense of specific gene products. This review deals with UV-induced alterations in DNA and its maintenance by various repair mechanisms.
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Affiliation(s)
- Rajesh P Rastogi
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
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40
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van Loon B, Markkanen E, Hübscher U. Oxygen as a friend and enemy: How to combat the mutational potential of 8-oxo-guanine. DNA Repair (Amst) 2010; 9:604-16. [PMID: 20399712 DOI: 10.1016/j.dnarep.2010.03.004] [Citation(s) in RCA: 234] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 03/17/2010] [Indexed: 12/20/2022]
Abstract
The maintenance of genetic stability is of crucial importance for any form of life. Prior to cell division in each mammalian cell, the process of DNA replication must faithfully duplicate the three billion bases with an absolute minimum of mistakes. Various environmental and endogenous agents, such as reactive oxygen species (ROS), can modify the structural properties of DNA bases and thus damage the DNA. Upon exposure of cells to oxidative stress, an often generated and highly mutagenic DNA damage is 7,8-dihydro-8-oxo-guanine (8-oxo-G). The estimated steady-state level of 8-oxo-G lesions is about 10(3) per cell/per day in normal tissues and up to 10(5) lesions per cell/per day in cancer tissues. The presence of 8-oxo-G on the replicating strand leads to frequent (10-75%) misincorporations of adenine opposite the lesion (formation of A:8-oxo-G mispairs), subsequently resulting in C:G to A:T transversion mutations. These mutations are among the most predominant somatic mutations in lung, breast, ovarian, gastric and colorectal cancers. Thus, in order to reduce the mutational burden of ROS, human cells have evolved base excision repair (BER) pathways ensuring (i) the correct and efficient repair of A:8-oxo-G mispairs and (ii) the removal of 8-oxo-G lesions from the genome. Very recently it was shown that MutY glycosylase homologue (MUTYH) and DNA polymerase lambda play a crucial role in the accurate repair of A:8-oxo-G mispairs. Here we review the importance of accurate BER of 8-oxo-G damage and its regulation in prevention of cancer.
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Affiliation(s)
- Barbara van Loon
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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Brown JA, Pack LR, Sanman LE, Suo Z. Efficiency and fidelity of human DNA polymerases λ and β during gap-filling DNA synthesis. DNA Repair (Amst) 2010; 10:24-33. [PMID: 20961817 DOI: 10.1016/j.dnarep.2010.09.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 09/14/2010] [Accepted: 09/16/2010] [Indexed: 12/31/2022]
Abstract
The base excision repair (BER) pathway coordinates the replacement of 1-10 nucleotides at sites of single-base lesions. This process generates DNA substrates with various gap sizes which can alter the catalytic efficiency and fidelity of a DNA polymerase during gap-filling DNA synthesis. Here, we quantitatively determined the substrate specificity and base substitution fidelity of human DNA polymerase λ (Pol λ), an enzyme proposed to support the known BER DNA polymerase β (Pol β), as it filled 1-10-nucleotide gaps at 1-nucleotide intervals. Pol λ incorporated a correct nucleotide with relatively high efficiency until the gap size exceeded 9 nucleotides. Unlike Pol λ, Pol β did not have an absolute threshold on gap size as the catalytic efficiency for a correct dNTP gradually decreased as the gap size increased from 2 to 10 nucleotides and then recovered for non-gapped DNA. Surprisingly, an increase in gap size resulted in lower polymerase fidelity for Pol λ, and this downregulation of fidelity was controlled by its non-enzymatic N-terminal domains. Overall, Pol λ was up to 160-fold more error-prone than Pol β, thereby suggesting Pol λ would be more mutagenic during long gap-filling DNA synthesis. In addition, dCTP was the preferred misincorporation for Pol λ and its N-terminal domain truncation mutants. This nucleotide preference was shown to be dependent upon the identity of the adjacent 5'-template base. Our results suggested that both Pol λ and Pol β would catalyze nucleotide incorporation with the highest combination of efficiency and accuracy when the DNA substrate contains a single-nucleotide gap. Thus, Pol λ, like Pol β, is better suited to catalyze gap-filling DNA synthesis during short-patch BER in vivo, although, Pol λ may play a role in long-patch BER.
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Affiliation(s)
- Jessica A Brown
- Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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42
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Prasad R, Shock DD, Beard WA, Wilson SH. Substrate channeling in mammalian base excision repair pathways: passing the baton. J Biol Chem 2010; 285:40479-88. [PMID: 20952393 DOI: 10.1074/jbc.m110.155267] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The current model for base excision repair (BER) involves two general sub-pathways termed single-nucleotide BER and long patch BER that are distinguished by their repair patch sizes and the enzymes/co-factors involved. Both sub-pathways involve a series of sequential steps from initiation to completion of repair. The BER sub-pathways are designed to sequester the various intermediates, passing them along from one step to the next without allowing these toxic molecules to trigger cell cycle arrest, necrotic cell death, or apoptosis. Although a variety of DNA-protein and protein-protein interactions are known for the BER intermediates and enzymes/co-factors, the molecular mechanisms accounting for step-to-step coordination are not well understood. In the present study we designed an in vitro assay to explore the question of whether there is a channeling or "hand-off" of the repair intermediates during BER in vitro. The results show that when BER enzymes are pre-bound to the initial single-nucleotide BER intermediate, the DNA is channeled from apurinic/apyrimidinic endonuclease 1 to DNA polymerase β and then to DNA ligase. In the long patch BER subpathway, where the 5'-end of the incised strand is blocked, the intermediate after DNA polymerase β gap filling is not channeled to the subsequent enzyme, flap endonuclease 1. Instead, flap endonuclease 1 must recognize and bind to the intermediate in competition with other molecules.
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Affiliation(s)
- Rajendra Prasad
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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43
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Morita R, Nakane S, Shimada A, Inoue M, Iino H, Wakamatsu T, Fukui K, Nakagawa N, Masui R, Kuramitsu S. Molecular mechanisms of the whole DNA repair system: a comparison of bacterial and eukaryotic systems. J Nucleic Acids 2010; 2010:179594. [PMID: 20981145 PMCID: PMC2957137 DOI: 10.4061/2010/179594] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 07/27/2010] [Indexed: 11/20/2022] Open
Abstract
DNA is subjected to many endogenous and exogenous damages. All organisms have developed a complex network of DNA repair mechanisms. A variety of different DNA repair pathways have been reported: direct reversal, base excision repair, nucleotide excision repair, mismatch repair, and recombination repair pathways. Recent studies of the fundamental mechanisms for DNA repair processes have revealed a complexity beyond that initially expected, with inter- and intrapathway complementation as well as functional interactions between proteins involved in repair pathways. In this paper we give a broad overview of the whole DNA repair system and focus on the molecular basis of the repair machineries, particularly in Thermus thermophilus HB8.
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Affiliation(s)
- Rihito Morita
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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44
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Jelezcova E, Trivedi RN, Wang XH, Tang JB, Brown AR, Goellner EM, Schamus S, Fornsaglio JL, Sobol RW. Parp1 activation in mouse embryonic fibroblasts promotes Pol beta-dependent cellular hypersensitivity to alkylation damage. Mutat Res 2010; 686:57-67. [PMID: 20096707 DOI: 10.1016/j.mrfmmm.2010.01.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Revised: 01/10/2010] [Accepted: 01/14/2010] [Indexed: 11/18/2022]
Abstract
Alkylating agents induce cell death in wild-type (WT) mouse embryonic fibroblasts (MEFs) by multiple mechanisms, including apoptosis, autophagy and necrosis. DNA polymerase beta (Pol beta) knockout (KO) MEFs are hypersensitive to the cytotoxic effect of alkylating agents, as compared to WT MEFs. To test the hypothesis that Parp1 is preferentially activated by methyl methanesulfonate (MMS) exposure of Pol beta KO MEFs, we have examined the relationship between Pol beta expression, Parp1 activation and cell survival following MMS exposure in a series of WT and Pol beta deficient MEF cell lines. Consistent with our hypothesis, we observed elevated Parp1 activation in Pol beta KO MEFs as compared to matched WT MEFs. Both the MMS-induced activation of Parp1 and the MMS-induced cytotoxicity of Pol beta KO MEFs are attenuated by pre-treatment with the Parp1/Parp2 inhibitor PJ34. Further, elevated Parp1 activation is observed following knockdown (KD) of endogenous Pol beta, as compared to WT cells. Pol beta KD MEFs are hypersensitive to MMS and both the MMS-induced hypersensitivity and Parp1 activation is prevented by pre-treatment with PJ34. In addition, the MMS-induced cellular sensitivity of Pol beta KO MEFs is reversed when Parp1 is also deleted (Pol beta/Parp1 double KO MEFs) and we observe no MMS sensitivity differential between Pol beta/Parp1 double KO MEFs and those that express recombinant mouse Pol beta. These studies suggest that Parp1 may function as a sensor of BER to initiate cell death when BER is aborted or fails. Parp1 may therefore function in BER as a tumor suppressor by initiating cell death and preventing the accumulation of cells with chromosomal damage due to a BER defect.
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Affiliation(s)
- Elena Jelezcova
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine & University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
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45
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Asagoshi K, Liu Y, Masaoka A, Lan L, Prasad R, Horton JK, Brown AR, Wang XH, Bdour HM, Sobol RW, Taylor JS, Yasui A, Wilson SH. DNA polymerase beta-dependent long patch base excision repair in living cells. DNA Repair (Amst) 2009; 9:109-19. [PMID: 20006562 DOI: 10.1016/j.dnarep.2009.11.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 10/29/2009] [Accepted: 11/03/2009] [Indexed: 11/16/2022]
Abstract
We examined a role for DNA polymerase beta (Pol beta) in mammalian long patch base excision repair (LP BER). Although a role for Pol beta is well known in single-nucleotide BER, information on this enzyme in the context of LP BER has been limited. To examine the question of Pol beta involvement in LP BER, we made use of nucleotide excision repair-deficient human XPA cells expressing UVDE (XPA-UVDE), which introduces a nick directly 5' to the cyclobutane pyrimidine dimer or 6-4 photoproduct, leaving ends with 3'-OH and 5'-phosphorylated UV lesion. We observed recruitment of GFP-fused Pol beta to focal sites of nuclear UV irradiation, consistent with a role of Pol beta in repair of UV-induced photoproducts adjacent to a strand break. This was the first evidence of Pol beta recruitment in LP BER in vivo. In cell extract, a 5'-blocked oligodeoxynucleotide substrate containing a nicked 5'-cyclobutane pyrimidine dimer was repaired by Pol beta-dependent LP BER. We also demonstrated Pol beta involvement in LP BER by making use of mouse cells that are double null for XPA and Pol beta. These results were extended by experiments with oligodeoxynucleotide substrates and purified human Pol beta.
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Affiliation(s)
- Kenjiro Asagoshi
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
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Swift RV, Amaro RE. Discovery and design of DNA and RNA ligase inhibitors in infectious microorganisms. Expert Opin Drug Discov 2009; 4:1281-1294. [PMID: 20354588 DOI: 10.1517/17460440903373617] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
BACKGROUND: Members of the nucleotidyltransferase superfamily known as DNA and RNA ligases carry out the enzymatic process of polynucleotide ligation. These guardians of genomic integrity share a three-step ligation mechanism, as well as common core structural elements. Both DNA and RNA ligases have experienced a surge of recent interest as chemotherapeutic targets for the treatment of a range of diseases, including bacterial infection, cancer, and the diseases caused by the protozoan parasites known as trypanosomes. OBJECTIVE: In this review, we will focus on efforts targeting pathogenic microorganisms; specifically, bacterial NAD(+)-dependent DNA ligases, which are promising broad-spectrum antibiotic targets, and ATP-dependent RNA editing ligases from Trypanosoma brucei, the species responsible for the devastating neurodegenerative disease, African sleeping sickness. CONCLUSION: High quality crystal structures of both NAD(+)-dependent DNA ligase and the Trypanosoma brucei RNA editing ligase have facilitated the development of a number of promising leads. For both targets, further progress will require surmounting permeability issues and improving selectivity and affinity.
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Affiliation(s)
- Robert V Swift
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
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Darwanto A, Farrel A, Rogstad DK, Sowers LC. Characterization of DNA glycosylase activity by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Biochem 2009; 394:13-23. [PMID: 19607800 PMCID: PMC3990469 DOI: 10.1016/j.ab.2009.07.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 07/07/2009] [Accepted: 07/09/2009] [Indexed: 11/25/2022]
Abstract
The DNA of all organisms is persistently damaged by endogenous reactive molecules. Most of the single-base endogenous damage is repaired through the base excision repair (BER) pathway that is initiated by members of the DNA glycosylase family. Although the BER pathway is often considered to proceed through a common abasic site intermediate, emerging evidence indicates that there are likely distinct branches reflected by the multitude of chemically different 3' and 5' ends generated at the repair site. In this study, we have applied matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) to the analysis of model DNA substrates acted on by recombinant glycosylases. We examine the chemical identity of several possible abasic site and nicked intermediates generated by monofunctional and bifunctional glycosylases. Our results suggest that the intermediate from endoIII/Nth might not be a simple beta-elimination product as described previously. On the basis of (18)O incorporation experiments, we propose a new mechanism for the endoIII/Nth family of glycosylases that may resolve several of the previous controversies. We further demonstrate that the use of an array of lesion-containing oligonucleotides can be used to rapidly examine the substrate preferences of a given glycosylase. Some of the lesions examined here can be acted on by more than one glycosylase, resulting in a spectrum of damaged intermediates for each lesion, suggesting that the sequence and coordination of repair activities that act on these lesions may influence the biological outcome of damage repair.
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Affiliation(s)
- Agus Darwanto
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Alvin Farrel
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Daniel K. Rogstad
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Lawrence C. Sowers
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
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An 8-oxo-guanine repair pathway coordinated by MUTYH glycosylase and DNA polymerase lambda. Proc Natl Acad Sci U S A 2009; 106:18201-6. [PMID: 19820168 DOI: 10.1073/pnas.0907280106] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Reactive oxygen species (ROS) interact with DNA, frequently generating highly mutagenic 7,8-dihydro-8-oxoguanine (8-oxo-G) lesions. Replicative DNA polymerases (pols) often misincorporate adenine opposite 8-oxo-G. The subsequent repair mechanism allowing the removal of adenine and formation of C:8-oxo-G base pair is essential to prevent C:G to A:T transversion mutations. Here, we show by immunofluorescence experiments, in cells exposed to ROS, the involvement of MutY glycosylase homologue (MUTYH) and DNA pol lambda in the repair of A:8-oxo-G mispairs. We observe specific recruitment of MUTYH, DNA pol lambda, proliferating cell nuclear antigen (PCNA), flap endonuclease 1 (FEN1) and DNA ligases I and III from human cell extracts to A:8-oxo-G DNA, but not to undamaged DNA. Using purified human proteins and a DNA template, we reconstitute the full pathway for the faithful repair of A:8-oxo-G mispairs involving MUTYH, DNA pol lambda, FEN1, and DNA ligase I. These results reveal a cellular response pathway to ROS, important to sustain genomic stability and modulate carcinogenesis.
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Masaoka A, Horton JK, Beard WA, Wilson SH. DNA polymerase beta and PARP activities in base excision repair in living cells. DNA Repair (Amst) 2009; 8:1290-9. [PMID: 19748837 DOI: 10.1016/j.dnarep.2009.08.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 07/29/2009] [Accepted: 08/14/2009] [Indexed: 01/08/2023]
Abstract
To examine base excision repair (BER) capacity in the context of living cells, we developed and applied a plasmid-based reporter assay. Non-replicating plasmids containing unique DNA base lesions were designed to express luciferase only after lesion repair had occurred, and luciferase expression in transfected cells was measured continuously during a repair period of 14 h. Two types of DNA lesions were examined: uracil opposite T reflecting repair primarily by the single-nucleotide BER sub-pathway, and the abasic site analogue tetrahydrofuran (THF) opposite C reflecting repair by long-patch BER. We found that the repair capacity for uracil-DNA in wild type mouse fibroblasts was very strong, whereas the repair capacity for THF-DNA, although strong, was slightly weaker. Repair capacity in DNA polymerase beta (Pol beta) null cells for uracil-DNA and THF-DNA was reduced by approximately 15% and 20%, respectively, compared to that in wild type cells. In both cases, the repair deficiency was fully complemented in Pol beta null cells expressing recombinant Pol beta. The effect of inhibition of poly(ADP-ribose) polymerase (PARP) activity on repair capacity was examined by treatment of cells with the inhibitor 4-amino-1,8-naphthalimide (4-AN). PARP inhibition decreased the repair capacity for both lesions in wild type cells, and this reduction was to the same level as that seen in Pol beta null cells. In contrast, 4-AN had no effect on repair in Pol beta null cells. The results highlight that Pol beta and PARP function in the same repair pathway, but also suggest that there is repair independent of both Pol beta and PARP activities. Thus, before the BER capacity of a cell can be predicted or modulated, a better understanding of Pol beta and PARP activity-independent BER pathways is required.
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Affiliation(s)
- Aya Masaoka
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
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50
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Ubiquitin ligase ARF-BP1/Mule modulates base excision repair. EMBO J 2009; 28:3207-15. [PMID: 19713937 DOI: 10.1038/emboj.2009.243] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Accepted: 07/23/2009] [Indexed: 11/08/2022] Open
Abstract
Base excision repair (BER) is the major cellular pathway involved in removal of endogenous/spontaneous DNA lesions. Here, we study the mechanism that controls the steady-state levels of BER enzymes in human cells. By fractionating human cell extract, we purified the E3 ubiquitin ligase Mule (ARF-BP1/HectH9) as an enzyme that can ubiquitylate DNA polymerase beta (Pol beta), the major BER DNA polymerase. We identified lysines 41, 61 and 81 as the major sites of modification and show that replacement of these lysines to arginines leads to increased protein stability. We further show that the cellular levels of Pol beta and its ubiquitylated derivative are modulated by Mule and ARF and siRNA knockdown of Mule leads to accumulation of Pol beta and increased DNA repair. Our findings provide a novel mechanism regulating steady-state levels of BER proteins.
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