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Theofilatos D, Ho T, Waitt G, Äijö T, Schiapparelli LM, Soderblom EJ, Tsagaratou A. Deciphering the TET3 interactome in primary thymic developing T cells. iScience 2024; 27:109782. [PMID: 38711449 PMCID: PMC11070343 DOI: 10.1016/j.isci.2024.109782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 03/04/2024] [Accepted: 04/15/2024] [Indexed: 05/08/2024] Open
Abstract
Ten-eleven translocation (TET) proteins are DNA dioxygenases that mediate active DNA demethylation. TET3 is the most highly expressed TET protein in thymic developing T cells. TET3, either independently or in cooperation with TET1 or TET2, has been implicated in T cell lineage specification by regulating DNA demethylation. However, TET-deficient mice exhibit complex phenotypes, suggesting that TET3 exerts multifaceted roles, potentially by interacting with other proteins. We performed liquid chromatography with tandem mass spectrometry in primary developing T cells to identify TET3 interacting partners in endogenous, in vivo conditions. We discover TET3 interacting partners. Our data establish that TET3 participates in a plethora of fundamental biological processes, such as transcriptional regulation, RNA polymerase elongation, splicing, DNA repair, and DNA replication. This resource brings in the spotlight emerging functions of TET3 and sets the stage for systematic studies to dissect the precise mechanistic contributions of TET3 in shaping T cell biology.
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Affiliation(s)
- Dimitris Theofilatos
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tricia Ho
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Greg Waitt
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Tarmo Äijö
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Erik J. Soderblom
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Cell Biology, Duke University, Durham, NC, USA
| | - Ageliki Tsagaratou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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2
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Nie L, Wang C, Huang M, Liu X, Feng X, Tang M, Li S, Hang Q, Teng H, Shen X, Ma L, Gan B, Chen J. DePARylation is critical for S phase progression and cell survival. eLife 2024; 12:RP89303. [PMID: 38578205 PMCID: PMC10997334 DOI: 10.7554/elife.89303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024] Open
Abstract
Poly(ADP-ribose)ylation or PARylation by PAR polymerase 1 (PARP1) and dePARylation by poly(ADP-ribose) glycohydrolase (PARG) are equally important for the dynamic regulation of DNA damage response. PARG, the most active dePARylation enzyme, is recruited to sites of DNA damage via pADPr-dependent and PCNA-dependent mechanisms. Targeting dePARylation is considered an alternative strategy to overcome PARP inhibitor resistance. However, precisely how dePARylation functions in normal unperturbed cells remains elusive. To address this challenge, we conducted multiple CRISPR screens and revealed that dePARylation of S phase pADPr by PARG is essential for cell viability. Loss of dePARylation activity initially induced S-phase-specific pADPr signaling, which resulted from unligated Okazaki fragments and eventually led to uncontrolled pADPr accumulation and PARP1/2-dependent cytotoxicity. Moreover, we demonstrated that proteins involved in Okazaki fragment ligation and/or base excision repair regulate pADPr signaling and cell death induced by PARG inhibition. In addition, we determined that PARG expression is critical for cellular sensitivity to PARG inhibition. Additionally, we revealed that PARG is essential for cell survival by suppressing pADPr. Collectively, our data not only identify an essential role for PARG in normal proliferating cells but also provide a potential biomarker for the further development of PARG inhibitors in cancer therapy.
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Affiliation(s)
- Litong Nie
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Chao Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Min Huang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Xiaoguang Liu
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Xu Feng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Siting Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Qinglei Hang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Hongqi Teng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Xi Shen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Li Ma
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Boyi Gan
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
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3
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Duma L, Ahel I. The function and regulation of ADP-ribosylation in the DNA damage response. Biochem Soc Trans 2023; 51:995-1008. [PMID: 37171085 PMCID: PMC10317172 DOI: 10.1042/bst20220749] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023]
Abstract
ADP-ribosylation is a post-translational modification involved in DNA damage response (DDR). In higher organisms it is synthesised by PARP 1-3, DNA strand break sensors. Recent advances have identified serine residues as the most common targets for ADP-ribosylation during DDR. To ADP-ribosylate serine, PARPs require an accessory factor, HPF1 which completes the catalytic domain. Through ADP-ribosylation, PARPs recruit a variety of factors to the break site and control their activities. However, the timely removal of ADP-ribosylation is also key for genome stability and is mostly performed by two hydrolases: PARG and ARH3. Here, we describe the key writers, readers and erasers of ADP-ribosylation and their contribution to the mounting of the DDR. We also discuss the use of PARP inhibitors in cancer therapy and the ways to tackle PARPi treatment resistance.
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Affiliation(s)
- Lena Duma
- Sir William Dunn School of Pathology, University of Oxford, Oxford, U.K
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, U.K
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4
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Wicks AJ, Krastev DB, Pettitt SJ, Tutt ANJ, Lord CJ. Opinion: PARP inhibitors in cancer-what do we still need to know? Open Biol 2022; 12:220118. [PMID: 35892198 PMCID: PMC9326299 DOI: 10.1098/rsob.220118] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/08/2022] [Indexed: 02/07/2023] Open
Abstract
PARP inhibitors (PARPi) have been demonstrated to exhibit profound anti-tumour activity in individuals whose cancers have a defect in the homologous recombination DNA repair pathway. Here, we describe the current consensus as to how PARPi work and how drug resistance to these agents emerges. We discuss the need to refine the current repertoire of clinical-grade companion biomarkers to be used with PARPi, so that patient stratification can be improved, the early emergence of drug resistance can be detected and dose-limiting toxicity can be predicted. We also highlight current thoughts about how PARPi resistance might be treated.
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Affiliation(s)
- Andrew J. Wicks
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Dragomir B. Krastev
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Stephen J. Pettitt
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Andrew N. J. Tutt
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Christopher J. Lord
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK
- Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
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5
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Bai W, Zhao B, Gu M, Dong J. Alternative end-joining in BCR gene rearrangements and translocations. Acta Biochim Biophys Sin (Shanghai) 2022; 54:782-795. [PMID: 35593472 PMCID: PMC9828324 DOI: 10.3724/abbs.2022051] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Programmed DNA double-strand breaks (DSBs) occur during antigen receptor gene recombination, namely V(D)J recombination in developing B lymphocytes and class switch recombination (CSR) in mature B cells. Repair of these DSBs by classical end-joining (c-NHEJ) enables the generation of diverse BCR repertoires for efficient humoral immunity. Deletion of or mutation in c-NHEJ genes in mice and humans confer various degrees of primary immune deficiency and predisposition to lymphoid malignancies that often harbor oncogenic chromosomal translocations. In the absence of c-NHEJ, alternative end-joining (A-EJ) catalyzes robust CSR and to a much lesser extent, V(D)J recombination, but the mechanisms of A-EJ are only poorly defined. In this review, we introduce recent advances in the understanding of A-EJ in the context of V(D)J recombination and CSR with emphases on DSB end processing, DNA polymerases and ligases, and discuss the implications of A-EJ to lymphoid development and chromosomal translocations.
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Affiliation(s)
- Wanyu Bai
- Department of ImmunologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China,Key Laboratory of Tropical Disease Control (Sun Yat-sen University)Ministry of EducationGuangzhou510080China
| | - Bo Zhao
- Department of ImmunologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China,Key Laboratory of Tropical Disease Control (Sun Yat-sen University)Ministry of EducationGuangzhou510080China
| | - Mingyu Gu
- Department of ImmunologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China,Key Laboratory of Tropical Disease Control (Sun Yat-sen University)Ministry of EducationGuangzhou510080China
| | - Junchao Dong
- Department of ImmunologyZhongshan School of MedicineSun Yat-sen UniversityGuangzhou510080China,Key Laboratory of Tropical Disease Control (Sun Yat-sen University)Ministry of EducationGuangzhou510080China,Correspondence address. Tel: +86-20-87330571; E-mail:
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6
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Crewe M, Madabhushi R. Topoisomerase-Mediated DNA Damage in Neurological Disorders. Front Aging Neurosci 2021; 13:751742. [PMID: 34899270 PMCID: PMC8656403 DOI: 10.3389/fnagi.2021.751742] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/23/2021] [Indexed: 12/12/2022] Open
Abstract
The nervous system is vulnerable to genomic instability and mutations in DNA damage response factors lead to numerous developmental and progressive neurological disorders. Despite this, the sources and mechanisms of DNA damage that are most relevant to the development of neuronal dysfunction are poorly understood. The identification of primarily neurological abnormalities in patients with mutations in TDP1 and TDP2 suggest that topoisomerase-mediated DNA damage could be an important underlying source of neuronal dysfunction. Here we review the potential sources of topoisomerase-induced DNA damage in neurons, describe the cellular mechanisms that have evolved to repair such damage, and discuss the importance of these repair mechanisms for preventing neurological disorders.
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Affiliation(s)
| | - Ram Madabhushi
- Departments of Psychiatry, Neuroscience, and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, United States
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7
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Adamowicz M, Hailstone R, Demin AA, Komulainen E, Hanzlikova H, Brazina J, Gautam A, Wells SE, Caldecott KW. XRCC1 protects transcription from toxic PARP1 activity during DNA base excision repair. Nat Cell Biol 2021; 23:1287-1298. [PMID: 34811483 PMCID: PMC8683375 DOI: 10.1038/s41556-021-00792-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 10/11/2021] [Indexed: 11/22/2022]
Abstract
Genetic defects in the repair of DNA single-strand breaks (SSBs) can result in neurological disease triggered by toxic activity of the single-strand-break sensor protein PARP1. However, the mechanism(s) by which this toxic PARP1 activity triggers cellular dysfunction are unclear. Here we show that human cells lacking XRCC1 fail to rapidly recover transcription following DNA base damage, a phenotype also observed in patient-derived fibroblasts with XRCC1 mutations and Xrcc1−/− mouse neurons. This defect is caused by excessive/aberrant PARP1 activity during DNA base excision repair, resulting from the loss of PARP1 regulation by XRCC1. We show that aberrant PARP1 activity suppresses transcriptional recovery during base excision repair by promoting excessive recruitment and activity of the ubiquitin protease USP3, which as a result reduces the level of monoubiquitinated histones important for normal transcriptional regulation. Importantly, inhibition and/or deletion of PARP1 or USP3 restores transcriptional recovery in XRCC1−/− cells, highlighting PARP1 and USP3 as possible therapeutic targets in neurological disease. Adamowicz et al. report that toxic PARP1 activity, induced by ataxia-associated mutations in XRCC1, impairs the recovery of global transcription during DNA base excision repair by promoting aberrant recruitment and activity of the histone ubiquitin protease USP3.
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Affiliation(s)
- Marek Adamowicz
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Richard Hailstone
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Annie A Demin
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Emilia Komulainen
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Hana Hanzlikova
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK.,Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Science, Prague, Czech Republic
| | - Jan Brazina
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Amit Gautam
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Sophie E Wells
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Keith W Caldecott
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK. .,Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Science, Prague, Czech Republic.
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8
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Kumamoto S, Nishiyama A, Chiba Y, Miyashita R, Konishi C, Azuma Y, Nakanishi M. HPF1-dependent PARP activation promotes LIG3-XRCC1-mediated backup pathway of Okazaki fragment ligation. Nucleic Acids Res 2021; 49:5003-5016. [PMID: 33872376 PMCID: PMC8136790 DOI: 10.1093/nar/gkab269] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/29/2021] [Accepted: 04/01/2021] [Indexed: 12/20/2022] Open
Abstract
DNA ligase 1 (LIG1) is known as the major DNA ligase responsible for Okazaki fragment joining. Recent studies have implicated LIG3 complexed with XRCC1 as an alternative player in Okazaki fragment joining in cases where LIG1 is not functional, although the underlying mechanisms are largely unknown. Here, using a cell-free system derived from Xenopus egg extracts, we demonstrated the essential role of PARP1-HPF1 in LIG3-dependent Okazaki fragment joining. We found that Okazaki fragments were eventually ligated even in the absence of LIG1, employing in its place LIG3-XRCC1, which was recruited onto chromatin. Concomitantly, LIG1 deficiency induces ADP-ribosylation of histone H3 in a PARP1-HPF1-dependent manner. The depletion of PARP1 or HPF1 resulted in a failure to recruit LIG3 onto chromatin and a subsequent failure in Okazaki fragment joining in LIG1-depleted extracts. Importantly, Okazaki fragments were not ligated at all when LIG1 and XRCC1 were co-depleted. Our results suggest that a unique form of ADP-ribosylation signaling promotes the recruitment of LIG3 on chromatin and its mediation of Okazaki fragment joining as a backup system for LIG1 perturbation.
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Affiliation(s)
- Soichiro Kumamoto
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yoshie Chiba
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Ryota Miyashita
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Chieko Konishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yoshiaki Azuma
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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9
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XRCC1 prevents toxic PARP1 trapping during DNA base excision repair. Mol Cell 2021; 81:3018-3030.e5. [PMID: 34102106 PMCID: PMC8294329 DOI: 10.1016/j.molcel.2021.05.009] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/08/2021] [Accepted: 05/10/2021] [Indexed: 01/12/2023]
Abstract
Mammalian DNA base excision repair (BER) is accelerated by poly(ADP-ribose) polymerases (PARPs) and the scaffold protein XRCC1. PARPs are sensors that detect single-strand break intermediates, but the critical role of XRCC1 during BER is unknown. Here, we show that protein complexes containing DNA polymerase β and DNA ligase III that are assembled by XRCC1 prevent excessive engagement and activity of PARP1 during BER. As a result, PARP1 becomes "trapped" on BER intermediates in XRCC1-deficient cells in a manner similar to that induced by PARP inhibitors, including in patient fibroblasts from XRCC1-mutated disease. This excessive PARP1 engagement and trapping renders BER intermediates inaccessible to enzymes such as DNA polymerase β and impedes their repair. Consequently, PARP1 deletion rescues BER and resistance to base damage in XRCC1-/- cells. These data reveal excessive PARP1 engagement during BER as a threat to genome integrity and identify XRCC1 as an "anti-trapper" that prevents toxic PARP1 activity.
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10
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Rapid Detection and Signaling of DNA Damage by PARP-1. Trends Biochem Sci 2021; 46:744-757. [PMID: 33674152 DOI: 10.1016/j.tibs.2021.01.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/14/2021] [Accepted: 01/29/2021] [Indexed: 12/16/2022]
Abstract
Poly(ADP-ribosyl) polymerase-1 (PARP-1) is an abundant ADP-ribosyl transferase that regulates various biological processes. PARP-1 is widely recognized as a first-line responder molecule in DNA damage response (DDR). Here, we review the full cycle of detecting DNA damage by PARP-1, PARP-1 activation upon DNA binding, and PARP-1 release from a DNA break. We also discuss the allosteric consequence upon binding of PARP inhibitors (PARPi) and the opportunity to tune its release from a DNA break. It is now possible to harness this new understanding to design novel PARPi for treating diseases where cell toxicity caused by PARP-1 'trapping' on DNA is either the desired consequence or entirely counterproductive.
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11
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Kutuzov MM, Belousova EA, Kurgina TA, Ukraintsev AA, Vasil’eva IA, Khodyreva SN, Lavrik OI. The contribution of PARP1, PARP2 and poly(ADP-ribosyl)ation to base excision repair in the nucleosomal context. Sci Rep 2021; 11:4849. [PMID: 33649352 PMCID: PMC7921663 DOI: 10.1038/s41598-021-84351-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/11/2021] [Indexed: 01/31/2023] Open
Abstract
The regulation of repair processes including base excision repair (BER) in the presence of DNA damage is implemented by a cellular signal: poly(ADP-ribosyl)ation (PARylation), which is catalysed by PARP1 and PARP2. Despite ample studies, it is far from clear how BER is regulated by PARPs and how the roles are distributed between the PARPs. Here, we investigated the effects of PARP1, PARP2 and PARylation on activities of the main BER enzymes (APE1, DNA polymerase β [Polβ] and DNA ligase IIIα [LigIIIα]) in combination with BER scaffold protein XRCC1 in the nucleosomal context. We constructed nucleosome core particles with midward- or outward-oriented damage. It was concluded that in most cases, the presence of PARP1 leads to the suppression of the activities of APE1, Polβ and to a lesser extent LigIIIα. PARylation by PARP1 attenuated this effect to various degrees depending on the enzyme. PARP2 had an influence predominantly on the last stage of BER: DNA sealing. Nonetheless, PARylation by PARP2 led to Polβ inhibition and to significant stimulation of LigIIIα activities in a NAD+-dependent manner. On the basis of the obtained and literature data, we suggest a hypothetical model of the contribution of PARP1 and PARP2 to BER.
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Affiliation(s)
- M. M. Kutuzov
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - E. A. Belousova
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - T. A. Kurgina
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia ,grid.4605.70000000121896553Novosibirsk State University, Novosibirsk, Russia
| | - A. A. Ukraintsev
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - I. A. Vasil’eva
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - S. N. Khodyreva
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - O. I. Lavrik
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia ,grid.4605.70000000121896553Novosibirsk State University, Novosibirsk, Russia
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12
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Jurkiw TJ, Tumbale PP, Schellenberg MJ, Cunningham-Rundles C, Williams RS, O’Brien PJ. LIG1 syndrome mutations remodel a cooperative network of ligand binding interactions to compromise ligation efficiency. Nucleic Acids Res 2021; 49:1619-1630. [PMID: 33444456 PMCID: PMC7897520 DOI: 10.1093/nar/gkaa1297] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/28/2020] [Accepted: 01/06/2021] [Indexed: 11/14/2022] Open
Abstract
Human DNA ligase I (LIG1) is the main replicative ligase and it also seals DNA breaks to complete DNA repair and recombination pathways. Immune compromised patients harbor hypomorphic LIG1 alleles encoding substitutions of conserved arginine residues, R771W and R641L, that compromise LIG1 activity through poorly defined mechanisms. To understand the molecular basis of LIG1 syndrome mutations, we determined high resolution X-ray structures and performed systematic biochemical characterization of LIG1 mutants using steady-state and pre-steady state kinetic approaches. Our results unveil a cooperative network of plastic DNA-LIG1 interactions that connect DNA substrate engagement with productive binding of Mg2+ cofactors for catalysis. LIG1 syndrome mutations destabilize this network, compromising Mg2+ binding affinity, decreasing ligation efficiency, and leading to elevated abortive ligation that may underlie the disease pathology. These findings provide novel insights into the fundamental mechanism by which DNA ligases engage with a nicked DNA substrate, and they suggest that disease pathology of LIG1 syndrome could be modulated by Mg2+ levels.
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Affiliation(s)
- Thomas J Jurkiw
- Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Percy P Tumbale
- Structural Cell Biology group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Matthew J Schellenberg
- Structural Cell Biology group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Charlotte Cunningham-Rundles
- Division of Clinical Immunology, Departments of Medicine and Pediatrics, and Graduate School of Biomedical Sciences, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - R Scott Williams
- Structural Cell Biology group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Patrick J O’Brien
- Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
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13
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Tomkinson AE, Naila T, Khattri Bhandari S. Altered DNA ligase activity in human disease. Mutagenesis 2021; 35:51-60. [PMID: 31630206 DOI: 10.1093/mutage/gez026] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/09/2019] [Indexed: 12/18/2022] Open
Abstract
The joining of interruptions in the phosphodiester backbone of DNA is critical to maintain genome stability. These breaks, which are generated as part of normal DNA transactions, such as DNA replication, V(D)J recombination and meiotic recombination as well as directly by DNA damage or due to DNA damage removal, are ultimately sealed by one of three human DNA ligases. DNA ligases I, III and IV each function in the nucleus whereas DNA ligase III is the sole enzyme in mitochondria. While the identification of specific protein partners and the phenotypes caused either by genetic or chemical inactivation have provided insights into the cellular functions of the DNA ligases and evidence for significant functional overlap in nuclear DNA replication and repair, different results have been obtained with mouse and human cells, indicating species-specific differences in the relative contributions of the DNA ligases. Inherited mutations in the human LIG1 and LIG4 genes that result in the generation of polypeptides with partial activity have been identified as the causative factors in rare DNA ligase deficiency syndromes that share a common clinical symptom, immunodeficiency. In the case of DNA ligase IV, the immunodeficiency is due to a defect in V(D)J recombination whereas the cause of the immunodeficiency due to DNA ligase I deficiency is not known. Overexpression of each of the DNA ligases has been observed in cancers. For DNA ligase I, this reflects increased proliferation. Elevated levels of DNA ligase III indicate an increased dependence on an alternative non-homologous end-joining pathway for the repair of DNA double-strand breaks whereas elevated level of DNA ligase IV confer radioresistance due to increased repair of DNA double-strand breaks by the major non-homologous end-joining pathway. Efforts to determine the potential of DNA ligase inhibitors as cancer therapeutics are on-going in preclinical cancer models.
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Affiliation(s)
- Alan E Tomkinson
- Departments of Internal Medicine and Molecular Genetics and Microbiology, and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Tasmin Naila
- Departments of Internal Medicine and Molecular Genetics and Microbiology, and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Seema Khattri Bhandari
- Departments of Internal Medicine and Molecular Genetics and Microbiology, and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
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14
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Hammel M, Rashid I, Sverzhinsky A, Pourfarjam Y, Tsai MS, Ellenberger T, Pascal JM, Kim IK, Tainer JA, Tomkinson AE. An atypical BRCT-BRCT interaction with the XRCC1 scaffold protein compacts human DNA Ligase IIIα within a flexible DNA repair complex. Nucleic Acids Res 2021; 49:306-321. [PMID: 33330937 PMCID: PMC7797052 DOI: 10.1093/nar/gkaa1188] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 11/21/2020] [Accepted: 12/13/2020] [Indexed: 01/08/2023] Open
Abstract
The XRCC1–DNA ligase IIIα complex (XL) is critical for DNA single-strand break repair, a key target for PARP inhibitors in cancer cells deficient in homologous recombination. Here, we combined biophysical approaches to gain insights into the shape and conformational flexibility of the XL as well as XRCC1 and DNA ligase IIIα (LigIIIα) alone. Structurally-guided mutational analyses based on the crystal structure of the human BRCT–BRCT heterodimer identified the network of salt bridges that together with the N-terminal extension of the XRCC1 C-terminal BRCT domain constitute the XL molecular interface. Coupling size exclusion chromatography with small angle X-ray scattering and multiangle light scattering (SEC-SAXS–MALS), we determined that the XL is more compact than either XRCC1 or LigIIIα, both of which form transient homodimers and are highly disordered. The reduced disorder and flexibility allowed us to build models of XL particles visualized by negative stain electron microscopy that predict close spatial organization between the LigIIIα catalytic core and both BRCT domains of XRCC1. Together our results identify an atypical BRCT–BRCT interaction as the stable nucleating core of the XL that links the flexible nick sensing and catalytic domains of LigIIIα to other protein partners of the flexible XRCC1 scaffold.
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Affiliation(s)
- Michal Hammel
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ishtiaque Rashid
- Departments of Internal Medicine, Molecular Genetics & Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA
| | - Aleksandr Sverzhinsky
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Yasin Pourfarjam
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct, Cincinnati, OH 45221, USA
| | - Miaw-Sheue Tsai
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tom Ellenberger
- Department of Biochemistry, Washington University, St. Louis, MO, USA
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - In-Kwon Kim
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct, Cincinnati, OH 45221, USA
| | - John A Tainer
- Departments of Cancer Biology and Molecular & Cellular Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alan E Tomkinson
- Departments of Internal Medicine, Molecular Genetics & Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA
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15
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Ligand-induced gene activation is associated with oxidative genome damage whose repair is required for transcription. Proc Natl Acad Sci U S A 2020; 117:22183-22192. [PMID: 32826329 PMCID: PMC7486736 DOI: 10.1073/pnas.1919445117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The endogenous genome damage induced by mitochondrial/cytosolic reactive oxygen species (ROS) is well recognized. However, similar damage induced by nuclear ROS generated via histone/cytosine-phosphate-guanine (CpG) demethylation during transcription has not been scrupulously investigated. This report documents the formation of genomic oxidized bases and single-strand breaks during ligand-induced gene activation via histone/CpG demethylation. That repair of these damages occurs preferentially in promoters and is essential for transcriptional activation underscore the essentiality of promoter-specific repair for transcription. In contrast, heat shock (HS) induction generates double-strand breaks, the repair of which is essential for the activation of HS-responsive genes. This study thus implies gross underestimation of endogenous oxidative genome damage and highlights the intrinsic diversity of damage and distinct repair processes associated with transcription. Among several reversible epigenetic changes occurring during transcriptional activation, only demethylation of histones and cytosine-phosphate-guanines (CpGs) in gene promoters and other regulatory regions by specific demethylase(s) generates reactive oxygen species (ROS), which oxidize DNA and other cellular components. Here, we show induction of oxidized bases and single-strand breaks (SSBs), but not direct double-strand breaks (DSBs), in the genome during gene activation by ligands of the nuclear receptor superfamily. We observed that these damages were preferentially repaired in promoters via the base excision repair (BER)/single-strand break repair (SSBR) pathway. Interestingly, BER/SSBR inhibition suppressed gene activation. Constitutive association of demethylases with BER/SSBR proteins in multiprotein complexes underscores the coordination of histone/DNA demethylation and genome repair during gene activation. However, ligand-independent transcriptional activation occurring during heat shock (HS) induction is associated with the generation of DSBs, the repair of which is likewise essential for the activation of HS-responsive genes. These observations suggest that the repair of distinct damages induced during diverse transcriptional activation is a universal prerequisite for transcription initiation. Because of limited investigation of demethylation-induced genome damage during transcription, this study suggests that the extent of oxidative genome damage resulting from various cellular processes is substantially underestimated.
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16
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Displacement of Slow-Turnover DNA Glycosylases by Molecular Traffic on DNA. Genes (Basel) 2020; 11:genes11080866. [PMID: 32751599 PMCID: PMC7465369 DOI: 10.3390/genes11080866] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/25/2020] [Accepted: 07/28/2020] [Indexed: 12/20/2022] Open
Abstract
In the base excision repair pathway, the initiating enzymes, DNA glycosylases, remove damaged bases and form long-living complexes with the abasic DNA product, but can be displaced by AP endonucleases. However, many nuclear proteins can move along DNA, either actively (such as DNA or RNA polymerases) or by passive one-dimensional diffusion. In most cases, it is not clear whether this movement is disturbed by other bound proteins or how collisions with moving proteins affect the bound proteins, including DNA glycosylases. We have used a two-substrate system to study the displacement of human OGG1 and NEIL1 DNA glycosylases by DNA polymerases in both elongation and diffusion mode and by D4, a passively diffusing subunit of a viral DNA polymerase. The OGG1–DNA product complex was disrupted by DNA polymerase β (POLβ) in both elongation and diffusion mode, Klenow fragment (KF) in the elongation mode and by D4. NEIL1, which has a shorter half-life on DNA, was displaced more efficiently. Hence, both possibly specific interactions with POLβ and nonspecific collisions (KF, D4) can displace DNA glycosylases from DNA. The protein movement along DNA was blocked by very tightly bound Cas9 RNA-targeted nuclease, providing an upper limit on the efficiency of obstacle clearance.
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17
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Stratigopoulou M, van Dam TP, Guikema JEJ. Base Excision Repair in the Immune System: Small DNA Lesions With Big Consequences. Front Immunol 2020; 11:1084. [PMID: 32547565 PMCID: PMC7272602 DOI: 10.3389/fimmu.2020.01084] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022] Open
Abstract
The integrity of the genome is under constant threat of environmental and endogenous agents that cause DNA damage. Endogenous damage is particularly pervasive, occurring at an estimated rate of 10,000–30,000 per cell/per day, and mostly involves chemical DNA base lesions caused by oxidation, depurination, alkylation, and deamination. The base excision repair (BER) pathway is primary responsible for removing and repairing these small base lesions that would otherwise lead to mutations or DNA breaks during replication. Next to preventing DNA mutations and damage, the BER pathway is also involved in mutagenic processes in B cells during immunoglobulin (Ig) class switch recombination (CSR) and somatic hypermutation (SHM), which are instigated by uracil (U) lesions derived from activation-induced cytidine deaminase (AID) activity. BER is required for the processing of AID-induced lesions into DNA double strand breaks (DSB) that are required for CSR, and is of pivotal importance for determining the mutagenic outcome of uracil lesions during SHM. Although uracils are generally efficiently repaired by error-free BER, this process is surprisingly error-prone at the Ig loci in proliferating B cells. Breakdown of this high-fidelity process outside of the Ig loci has been linked to mutations observed in B-cell tumors and DNA breaks and chromosomal translocations in activated B cells. Next to its role in preventing cancer, BER has also been implicated in immune tolerance. Several defects in BER components have been associated with autoimmune diseases, and animal models have shown that BER defects can cause autoimmunity in a B-cell intrinsic and extrinsic fashion. In this review we discuss the contribution of BER to genomic integrity in the context of immune receptor diversification, cancer and autoimmune diseases.
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Affiliation(s)
- Maria Stratigopoulou
- Department of Pathology, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Tijmen P van Dam
- Department of Pathology, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Jeroen E J Guikema
- Department of Pathology, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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18
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Khanam T, Afsar M, Shukla A, Alam F, Kumar S, Soyar H, Dolma K, Pasupuleti M, Srivastava KK, Ampapathi RS, Ramachandran R. M. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision repair. Nucleic Acids Res 2020; 48:4325-4343. [PMID: 32232338 PMCID: PMC7530888 DOI: 10.1093/nar/gkaa188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/24/2020] [Accepted: 03/27/2020] [Indexed: 12/19/2022] Open
Abstract
Class-II AP-endonuclease (XthA) and NAD+-dependent DNA ligase (LigA) are involved in initial and terminal stages of bacterial DNA base excision repair (BER), respectively. XthA acts on abasic sites of damaged DNA to create nicks with 3′OH and 5′-deoxyribose phosphate (5′-dRP) moieties. Co-immunoprecipitation using mycobacterial cell-lysate, identified MtbLigA-MtbXthA complex formation. Pull-down experiments using purified wild-type, and domain-deleted MtbLigA mutants show that LigA-XthA interactions are mediated by the BRCT-domain of LigA. Small-Angle-X-ray scattering, 15N/1H-HSQC chemical shift perturbation experiments and mutational analysis identified the BRCT-domain region that interacts with a novel 104DGQPSWSGKP113 motif on XthA for complex-formation. Isothermal-titration calorimetry experiments show that a synthetic peptide with this sequence interacts with MtbLigA and disrupts XthA–LigA interactions. In vitro assays involving DNA substrate and product analogs show that LigA can efficiently reseal 3′OH and 5′dRP DNA termini created by XthA at abasic sites. Assays and SAXS experiments performed in the presence and absence of DNA, show that XthA inhibits LigA by specifically engaging with the latter's BRCT-domain to prevent it from encircling substrate DNA. Overall, the study suggests a coordinating function for XthA whereby it engages initially with LigA to prevent the undesirable consequences of futile cleavage and ligation cycles that might derail bacterial BER.
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Affiliation(s)
- Taran Khanam
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Mohammad Afsar
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Ankita Shukla
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Faiyaz Alam
- Sophisticated Analytical Instruments Based Facility and Research Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Sanjay Kumar
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Horam Soyar
- Microbiology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Kunzes Dolma
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Mukesh Pasupuleti
- Microbiology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Kishore Kumar Srivastava
- Microbiology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Ravi Sankar Ampapathi
- Sophisticated Analytical Instruments Based Facility and Research Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
| | - Ravishankar Ramachandran
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow 226031, Uttar Pradesh, India
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19
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Abstract
Exposure to arsenic in contaminated drinking water is an emerging public health problem that impacts more than 200 million people worldwide. Accumulating lines of evidence from epidemiological studies revealed that chronic exposure to arsenic can result in various human diseases including cancer, type 2 diabetes, and neurodegenerative disorders. Arsenic is also classified as a Group I human carcinogen. In this review, we survey extensively different modes of action for arsenic-induced carcinogenesis, with focus being placed on arsenic-mediated impairment of DNA repair pathways. Inorganic arsenic can be bioactivated by methylation, and the ensuing products are highly genotoxic. Bioactivation of arsenicals also elicits the production of reactive oxygen and nitrogen species (ROS and RNS), which can directly damage DNA and modify cysteine residues in proteins. Results from recent studies suggest zinc finger proteins as crucial molecular targets for direct binding to As3+ or for modifications by arsenic-induced ROS/RNS, which may constitute a common mechanism underlying arsenic-induced perturbations of DNA repair.
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20
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Abstract
Effective maintenance and stability of our genomes is essential for normal cell division, tissue homeostasis, and cellular and organismal fitness. The processes of chromosome replication and segregation require continual surveillance to insure fidelity. Accurate and efficient repair of DNA damage preserves genome integrity, which if lost can lead to multiple diseases, including cancer. Poly(ADP-ribose) a dynamic and reversible posttranslational modification and the enzymes that catalyze it (PARP1, PARP2, tankyrase 1, and tankyrase 2) function to maintain genome stability through diverse mechanisms. Here we review the role of these enzymes and the modification in genome repair, replication, and resolution in human cells.
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Affiliation(s)
- Kameron Azarm
- Department of Pathology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Susan Smith
- Department of Pathology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
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21
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Zhang H, Cai B, Geng A, Tang H, Zhang W, Li S, Jiang Y, Tan R, Wan X, Mao Z. Base excision repair but not DNA double-strand break repair is impaired in aged human adipose-derived stem cells. Aging Cell 2020; 19:e13062. [PMID: 31782607 PMCID: PMC6996963 DOI: 10.1111/acel.13062] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 08/21/2019] [Accepted: 10/11/2019] [Indexed: 02/06/2023] Open
Abstract
The decline in DNA repair capacity contributes to the age-associated decrease in genome integrity in somatic cells of different species. However, due to the lack of clinical samples and appropriate tools for studying DNA repair, whether and how age-associated changes in DNA repair result in a loss of genome integrity of human adult stem cells remains incompletely characterized. Here, we isolated 20 eyelid adipose-derived stem cell (ADSC) lines from healthy individuals (young: 10 donors with ages ranging 17-25 years; old: 10 donors with ages ranging 50-59 years). Using these cell lines, we systematically compared the efficiency of base excision repair (BER) and two DNA double-strand break (DSB) repair pathways-nonhomologous end joining (NHEJ) and homologous recombination (HR)-between the young and old groups. Surprisingly, we found that the efficiency of BER but not NHEJ or HR is impaired in aged human ADSCs, which is in contrast to previous findings that DSB repair declines with age in human fibroblasts. We also demonstrated that BER efficiency is negatively associated with tail moment, which reflects a loss of genome integrity in human ADSCs. Mechanistic studies indicated that at the protein level XRCC1, but not other BER factors, exhibited age-associated decline. Overexpression of XRCC1 reversed the decline of BER efficiency and genome integrity, indicating that XRCC1 is a potential therapeutic target for stabilizing genomes in aged ADSCs.
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Affiliation(s)
- Haiping Zhang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital Shanghai Key Laboratory of Signaling and Disease Research School of Life Sciences and Technology Tongji University Shanghai China
| | - Bailian Cai
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital Shanghai Key Laboratory of Signaling and Disease Research School of Life Sciences and Technology Tongji University Shanghai China
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital School of Medicine Tongji University Shanghai China
| | - Anke Geng
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital Shanghai Key Laboratory of Signaling and Disease Research School of Life Sciences and Technology Tongji University Shanghai China
| | - Huanyin Tang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital Shanghai Key Laboratory of Signaling and Disease Research School of Life Sciences and Technology Tongji University Shanghai China
| | - Wenjun Zhang
- Department of Plastic Surgery Changzheng Hospital Shanghai China
| | - Sheng Li
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital Shanghai Key Laboratory of Signaling and Disease Research School of Life Sciences and Technology Tongji University Shanghai China
| | - Ying Jiang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital Shanghai Key Laboratory of Signaling and Disease Research School of Life Sciences and Technology Tongji University Shanghai China
| | - Rong Tan
- Center for Molecular Medicine Xiangya Hospital Central South University Changsha China
| | - Xiaoping Wan
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital Shanghai Key Laboratory of Signaling and Disease Research School of Life Sciences and Technology Tongji University Shanghai China
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital School of Medicine Tongji University Shanghai China
| | - Zhiyong Mao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital Shanghai Key Laboratory of Signaling and Disease Research School of Life Sciences and Technology Tongji University Shanghai China
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital School of Medicine Tongji University Shanghai China
- State Key Laboratory of Natural Medicines China Pharmaceutical University Nanjing China
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22
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Çağlayan M. Interplay between DNA Polymerases and DNA Ligases: Influence on Substrate Channeling and the Fidelity of DNA Ligation. J Mol Biol 2019; 431:2068-2081. [PMID: 31034893 DOI: 10.1016/j.jmb.2019.04.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/18/2019] [Accepted: 04/18/2019] [Indexed: 02/06/2023]
Abstract
DNA ligases are a highly conserved group of nucleic acid enzymes that play an essential role in DNA repair, replication, and recombination. This review focuses on functional interaction between DNA polymerases and DNA ligases in the repair of single- and double-strand DNA breaks, and discusses the notion that the substrate channeling during DNA polymerase-mediated nucleotide insertion coupled to DNA ligation could be a mechanism to minimize the release of potentially mutagenic repair intermediates. Evidence suggesting that DNA ligases are essential for cell viability includes the fact that defects or insufficiency in DNA ligase are casually linked to genome instability. In the future, it may be possible to develop small molecule inhibitors of mammalian DNA ligases and/or their functional protein partners that potentiate the effects of chemotherapeutic compounds and improve cancer treatment outcomes.
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Affiliation(s)
- Melike Çağlayan
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.
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23
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Kordon MM, Szczurek A, Berniak K, Szelest O, Solarczyk K, Tworzydło M, Wachsmann-Hogiu S, Vaahtokari A, Cremer C, Pederson T, Dobrucki JW. PML-like subnuclear bodies, containing XRCC1, juxtaposed to DNA replication-based single-strand breaks. FASEB J 2019; 33:2301-2313. [PMID: 30260704 PMCID: PMC6993927 DOI: 10.1096/fj.201801379r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/27/2018] [Indexed: 12/14/2022]
Abstract
DNA lesions induce recruitment and accumulation of various repair factors, resulting in formation of discrete nuclear foci. Using superresolution fluorescence microscopy as well as live cell and quantitative imaging, we demonstrate that X-ray repair cross-complementing protein 1 (XRCC1), a key factor in single-strand break and base excision repair, is recruited into nuclear bodies formed in response to replication-related single-strand breaks. Intriguingly, these bodies are assembled immediately in the vicinity of these breaks and never fully colocalize with replication foci. They are structurally organized, containing canonical promyelocytic leukemia (PML) nuclear body protein SP100 concentrated in a peripheral layer, and XRCC1 in the center. They also contain other factors, including PML, poly(ADP-ribose) polymerase 1 (PARP1), ligase IIIα, and origin recognition complex subunit 5. The breast cancer 1 and -2 C terminus domains of XRCC1 are essential for formation of these repair foci. These results reveal that XRCC1-contaning foci constitute newly recognized PML-like nuclear bodies that accrete and locally deliver essential factors for repair of single-strand DNA breaks in replication regions.-Kordon, M. M., Szczurek, A., Berniak, K., Szelest, O., Solarczyk, K., Tworzydło, M., Wachsmann-Hogiu, S., Vaahtokari, A., Cremer, C., Pederson, T., Dobrucki, J. W. PML-like subnuclear bodies, containing XRCC1, juxtaposed to DNA replication-based single-strand breaks.
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Affiliation(s)
- Magdalena M. Kordon
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Aleksander Szczurek
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
- Superresolution Microscopy Group, Institute of Molecular Biology, Mainz, Germany
| | - Krzysztof Berniak
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Oskar Szelest
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Kamil Solarczyk
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Magdalena Tworzydło
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Sebastian Wachsmann-Hogiu
- Department of Pathology and Laboratory Medicine, University of California at Davis, Davis, California, USA
| | - Anne Vaahtokari
- The Francis Crick Institute, Cancer Research UK, London, United Kingdom; and
| | - Christoph Cremer
- Superresolution Microscopy Group, Institute of Molecular Biology, Mainz, Germany
| | - Thoru Pederson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jurek W. Dobrucki
- Department of Cell Biophysics, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
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24
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Polo LM, Xu Y, Hornyak P, Garces F, Zeng Z, Hailstone R, Matthews SJ, Caldecott KW, Oliver AW, Pearl LH. Efficient Single-Strand Break Repair Requires Binding to Both Poly(ADP-Ribose) and DNA by the Central BRCT Domain of XRCC1. Cell Rep 2019; 26:573-581.e5. [PMID: 30650352 PMCID: PMC6334254 DOI: 10.1016/j.celrep.2018.12.082] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/26/2018] [Accepted: 12/18/2018] [Indexed: 12/11/2022] Open
Abstract
XRCC1 accelerates repair of DNA single-strand breaks by acting as a scaffold protein for the recruitment of Polβ, LigIIIα, and end-processing factors, such as PNKP and APTX. XRCC1 itself is recruited to DNA damage through interaction of its central BRCT domain with poly(ADP-ribose) chains generated by PARP1 or PARP2. XRCC1 is believed to interact directly with DNA at sites of damage, but the molecular basis for this interaction within XRCC1 remains unclear. We now show that the central BRCT domain simultaneously mediates interaction of XRCC1 with poly(ADP-ribose) and DNA, through separate and non-overlapping binding sites on opposite faces of the domain. Mutation of residues within the DNA binding site, which includes the site of a common disease-associated human polymorphism, affects DNA binding of this XRCC1 domain in vitro and impairs XRCC1 recruitment and retention at DNA damage and repair of single-strand breaks in vivo.
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Affiliation(s)
- Luis M Polo
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Yingqi Xu
- Cross-Faculty NMR Centre, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Peter Hornyak
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK; Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Fernando Garces
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Zhihong Zeng
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Richard Hailstone
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Steve J Matthews
- Cross-Faculty NMR Centre, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Keith W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
| | - Antony W Oliver
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
| | - Laurence H Pearl
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK; Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW1E 6BT, UK.
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25
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Steinacher R, Barekati Z, Botev P, Kuśnierczyk A, Slupphaug G, Schär P. SUMOylation coordinates BERosome assembly in active DNA demethylation during cell differentiation. EMBO J 2018; 38:embj.201899242. [PMID: 30523148 DOI: 10.15252/embj.201899242] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 11/05/2018] [Accepted: 11/09/2018] [Indexed: 11/09/2022] Open
Abstract
During active DNA demethylation, 5-methylcytosine (5mC) is oxidized by TET proteins to 5-formyl-/5-carboxylcytosine (5fC/5caC) for replacement by unmethylated C by TDG-initiated DNA base excision repair (BER). Base excision generates fragile abasic sites (AP-sites) in DNA and has to be coordinated with subsequent repair steps to limit accumulation of genome destabilizing secondary DNA lesions. Here, we show that 5fC/5caC is generated at a high rate in genomes of differentiating mouse embryonic stem cells and that SUMOylation and the BER protein XRCC1 play critical roles in orchestrating TDG-initiated BER of these lesions. SUMOylation of XRCC1 facilitates physical interaction with TDG and promotes the assembly of a TDG-BER core complex. Within this TDG-BERosome, SUMO is transferred from XRCC1 and coupled to the SUMO acceptor lysine in TDG, promoting its dissociation while assuring the engagement of the BER machinery to complete demethylation. Although well-studied, the biological importance of TDG SUMOylation has remained obscure. Here, we demonstrate that SUMOylation of TDG suppresses DNA strand-break accumulation and toxicity to PARP inhibition in differentiating mESCs and is essential for neural lineage commitment.
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Affiliation(s)
| | - Zeinab Barekati
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Petar Botev
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Anna Kuśnierczyk
- Department of Cancer Research and Molecular Medicine, Proteomics and Metabolomics Core Facility, PROMEC, Norwegian University of Science and Technology, Trondheim, Norway
| | - Geir Slupphaug
- Department of Cancer Research and Molecular Medicine, Proteomics and Metabolomics Core Facility, PROMEC, Norwegian University of Science and Technology, Trondheim, Norway
| | - Primo Schär
- Department of Biomedicine, University of Basel, Basel, Switzerland
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26
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Mani RS, Mermershtain I, Abdou I, Fanta M, Hendzel MJ, Glover JNM, Weinfeld M. Domain analysis of PNKP-XRCC1 interactions: Influence of genetic variants of XRCC1. J Biol Chem 2018; 294:520-530. [PMID: 30446622 DOI: 10.1074/jbc.ra118.004262] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 11/05/2018] [Indexed: 12/28/2022] Open
Abstract
Polynucleotide kinase/phosphatase (PNKP) and X-ray repair cross-complementing 1 (XRCC1) are key proteins in the single-strand DNA break repair pathway. Phosphorylated XRCC1 stimulates PNKP by binding to its forkhead-associated (FHA) domain, whereas nonphosphorylated XRCC1 stimulates PNKP by interacting with the PNKP catalytic domain. Here, we have further studied the interactions between these two proteins, including two variants of XRCC1 (R194W and R280H) arising from single-nucleotide polymorphisms (SNPs) that have been associated with elevated cancer risk in some reports. We observed that interaction of the PNKP FHA domain with phosphorylated XRCC1 extends beyond the immediate, well-characterized phosphorylated region of XRCC1 (residues 515-526). We also found that an XRCC1 fragment, comprising residues 166-436, binds tightly to PNKP and DNA and efficiently activates PNKP's kinase activity. However, interaction of either of the SNP-derived variants of this fragment with PNKP was considerably weaker, and their stimulation of PNKP was severely reduced, although they still could bind DNA effectively. Laser microirradiation revealed reduced recruitment of PNKP to damaged DNA in cells expressing either XRCC1 variant compared with PNKP recruitment in cells expressing WT XRCC1 even though WT and variant XRCC1s were equally efficient at localizing to the damaged DNA. These findings suggest that the elevated risk of cancer associated with these XRCC1 SNPs reported in some studies may be due in part to the reduced ability of these XRCC1 variants to recruit PNKP to damaged DNA.
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Affiliation(s)
- Rajam S Mani
- From the Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2 and
| | - Inbal Mermershtain
- the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Ismail Abdou
- From the Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2 and
| | - Mesfin Fanta
- From the Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2 and
| | - Michael J Hendzel
- From the Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2 and
| | - J N Mark Glover
- the Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Michael Weinfeld
- From the Department of Oncology, University of Alberta, Edmonton, Alberta T6G 1Z2 and
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27
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Hanzlikova H, Kalasova I, Demin AA, Pennicott LE, Cihlarova Z, Caldecott KW. The Importance of Poly(ADP-Ribose) Polymerase as a Sensor of Unligated Okazaki Fragments during DNA Replication. Mol Cell 2018; 71:319-331.e3. [PMID: 29983321 PMCID: PMC6060609 DOI: 10.1016/j.molcel.2018.06.004] [Citation(s) in RCA: 242] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/11/2018] [Accepted: 06/01/2018] [Indexed: 01/08/2023]
Abstract
Poly(ADP-ribose) is synthesized by PARP enzymes during the repair of stochastic DNA breaks. Surprisingly, however, we show that most if not all endogenous poly(ADP-ribose) is detected in normal S phase cells at sites of DNA replication. This S phase poly(ADP-ribose) does not result from damaged or misincorporated nucleotides or from DNA replication stress. Rather, perturbation of the DNA replication proteins LIG1 or FEN1 increases S phase poly(ADP-ribose) more than 10-fold, implicating unligated Okazaki fragments as the source of S phase PARP activity. Indeed, S phase PARP activity is ablated by suppressing Okazaki fragment formation with emetine, a DNA replication inhibitor that selectively inhibits lagging strand synthesis. Importantly, PARP activation during DNA replication recruits the single-strand break repair protein XRCC1, and human cells lacking PARP activity and/or XRCC1 are hypersensitive to FEN1 perturbation. Collectively, our data indicate that PARP1 is a sensor of unligated Okazaki fragments during DNA replication and facilitates their repair.
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Affiliation(s)
- Hana Hanzlikova
- Genome Damage and Stability Centre & Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK; Department of Genome Dynamics, Institute of Molecular Genetics of the ASCR, v.v.i., 142 20 Prague 4, Czech Republic.
| | - Ilona Kalasova
- Department of Genome Dynamics, Institute of Molecular Genetics of the ASCR, v.v.i., 142 20 Prague 4, Czech Republic
| | - Annie A Demin
- Genome Damage and Stability Centre & Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Lewis E Pennicott
- Genome Damage and Stability Centre & Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Zuzana Cihlarova
- Department of Genome Dynamics, Institute of Molecular Genetics of the ASCR, v.v.i., 142 20 Prague 4, Czech Republic
| | - Keith W Caldecott
- Genome Damage and Stability Centre & Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK; Department of Genome Dynamics, Institute of Molecular Genetics of the ASCR, v.v.i., 142 20 Prague 4, Czech Republic.
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28
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Kim K, Pedersen LC, Kirby TW, DeRose EF, London RE. Characterization of the APLF FHA-XRCC1 phosphopeptide interaction and its structural and functional implications. Nucleic Acids Res 2017; 45:12374-12387. [PMID: 29059378 PMCID: PMC5716189 DOI: 10.1093/nar/gkx941] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/05/2017] [Indexed: 02/07/2023] Open
Abstract
Aprataxin and PNKP-like factor (APLF) is a DNA repair factor containing a forkhead-associated (FHA) domain that supports binding to the phosphorylated FHA domain binding motifs (FBMs) in XRCC1 and XRCC4. We have characterized the interaction of the APLF FHA domain with phosphorylated XRCC1 peptides using crystallographic, NMR, and fluorescence polarization studies. The FHA–FBM interactions exhibit significant pH dependence in the physiological range as a consequence of the atypically high pK values of the phosphoserine and phosphothreonine residues and the preference for a dianionic charge state of FHA-bound pThr. These high pK values are characteristic of the polyanionic peptides typically produced by CK2 phosphorylation. Binding affinity is greatly enhanced by residues flanking the crystallographically-defined recognition motif, apparently as a consequence of non-specific electrostatic interactions, supporting the role of XRCC1 in nuclear cotransport of APLF. The FHA domain-dependent interaction of XRCC1 with APLF joins repair scaffolds that support single-strand break repair and non-homologous end joining (NHEJ). It is suggested that for double-strand DNA breaks that have initially formed a complex with PARP1 and its binding partner XRCC1, this interaction acts as a backup attempt to intercept the more error-prone alternative NHEJ repair pathway by recruiting Ku and associated NHEJ factors.
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Affiliation(s)
- Kyungmin Kim
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Thomas W Kirby
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Eugene F DeRose
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Robert E London
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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29
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Yang L, Sun L, Teng Y, Chen H, Gao Y, Levine AS, Nakajima S, Lan L. Tankyrase1-mediated poly(ADP-ribosyl)ation of TRF1 maintains cell survival after telomeric DNA damage. Nucleic Acids Res 2017; 45:3906-3921. [PMID: 28160604 PMCID: PMC5397190 DOI: 10.1093/nar/gkx083] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/27/2017] [Indexed: 12/17/2022] Open
Abstract
Oxidative DNA damage triggers telomere erosion and cellular senescence. However, how repair is initiated at telomeres is largely unknown. Here, we found unlike PARP1-mediated Poly-ADP-Ribosylation (PARylation) at genomic damage sites, PARylation at telomeres is mainly dependent on tankyrase1 (TNKS1). TNKS1 is recruited to damaged telomeres via its interaction with TRF1, which subsequently facilitates the PARylation of TRF1 after damage. TNKS inhibition abolishes the recruitment of the repair proteins XRCC1 and polymerase β at damaged telomeres, while the PARP1/2 inhibitor only has such an effect at non-telomeric damage sites. The ANK domain of TNKS1 is essential for the telomeric damage response and TRF1 interaction. Mutation of the tankyrase-binding motif (TBM) on TRF1 (13R/18G to AA) disrupts its interaction with TNKS1 concomitant recruitment of TNKS1 and repair proteins after damage. Either TNKS1 inhibition or TBM mutated TRF1 expression markedly sensitizes cells to telomere oxidative damage as well as XRCC1 inhibition. Together, our data reveal a novel role of TNKS1 in facilitating SSBR at damaged telomeres through PARylation of TRF1, thereby protecting genome stability and cell viability.
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Affiliation(s)
- Lu Yang
- School of Medicine, Tsinghua University, No.1 Tsinghua Yuan, Haidian District, Beijing 100084, China.,University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Luxi Sun
- School of Medicine, Tsinghua University, No.1 Tsinghua Yuan, Haidian District, Beijing 100084, China.,University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Yaqun Teng
- School of Medicine, Tsinghua University, No.1 Tsinghua Yuan, Haidian District, Beijing 100084, China.,University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Hao Chen
- School of Medicine, Tsinghua University, No.1 Tsinghua Yuan, Haidian District, Beijing 100084, China.,University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Ying Gao
- School of Medicine, Tsinghua University, No.1 Tsinghua Yuan, Haidian District, Beijing 100084, China.,University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Arthur S Levine
- University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Satoshi Nakajima
- University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Li Lan
- University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
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30
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Guan J, Zhao Q, Lv J, Zhang Z, Sun S, Mao W. Triptolide induces DNA breaks, activates caspase-3-dependent apoptosis and sensitizes B-cell lymphoma to poly(ADP-ribose) polymerase 1 and phosphoinositide 3-kinase inhibitors. Oncol Lett 2017; 14:4965-4970. [PMID: 29085508 DOI: 10.3892/ol.2017.6771] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 06/15/2017] [Indexed: 12/31/2022] Open
Abstract
Triptolide is the primary compound isolated from Tripterygium wilfordii, which has been reported to inhibit nucleotide excision repair as well as exhibit anti-inflammatory and antitumor activities. However, the action of triptolide in DNA breaks remains unknown. The present study investigated the effects of triptolide in the induction of DNA breaks and apoptosis in a murine B-cell lymphoma cell line, CH12F3. An MTT assay revealed that X-ray repair cross-complementing protein 1 (XRCC1)-/- CH12F3 cells were more sensitive to 6 nM triptolide compared with the wild-type CH12F3 cells, which suggests that low levels of triptolide induce DNA breaks in a manner that is dependent on the XRCC1-mediated repair pathway. Flow cytometric analysis identified that 50 nM triptolide increased the phospho-histone H2AX level, demonstrating that triptolide induces double-strand breaks. Western blot analysis revealed that triptolide up-regulated Rad51 and nuclear proliferating cell nuclear antigen. Annexin V/propidium iodide staining identified that triptolide promoted apoptosis and western blot analysis confirmed that triptolide activated caspase-3-dependent apoptosis. The results of the present study also demonstrated that 5 nM triptolide sensitized CH12F3 lymphoma cells to poly(ADP-ribose) polymerase 1 and phosphoinositide 3-kinase inhibitors, suggesting that triptolide may be a potent antitumor drug for sensitizing lymphoma cells to chemotherapeutic agents.
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Affiliation(s)
- Jiawei Guan
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Qian Zhao
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Jian Lv
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Zhiwei Zhang
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Shijie Sun
- Department of Immunology, College of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Weifeng Mao
- Department of Biotechnology, College of Basic Medical Sciences, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
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31
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Breslin C, Mani RS, Fanta M, Hoch N, Weinfeld M, Caldecott KW. The Rev1 interacting region (RIR) motif in the scaffold protein XRCC1 mediates a low-affinity interaction with polynucleotide kinase/phosphatase (PNKP) during DNA single-strand break repair. J Biol Chem 2017; 292:16024-16031. [PMID: 28821613 PMCID: PMC5625035 DOI: 10.1074/jbc.m117.806638] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/15/2017] [Indexed: 11/22/2022] Open
Abstract
The scaffold protein X-ray repair cross-complementing 1 (XRCC1) interacts with multiple enzymes involved in DNA base excision repair and single-strand break repair (SSBR) and is important for genetic integrity and normal neurological function. One of the most important interactions of XRCC1 is that with polynucleotide kinase/phosphatase (PNKP), a dual-function DNA kinase/phosphatase that processes damaged DNA termini and that, if mutated, results in ataxia with oculomotor apraxia 4 (AOA4) and microcephaly with early-onset seizures and developmental delay (MCSZ). XRCC1 and PNKP interact via a high-affinity phosphorylation-dependent interaction site in XRCC1 and a forkhead-associated domain in PNKP. Here, we identified using biochemical and biophysical approaches a second PNKP interaction site in XRCC1 that binds PNKP with lower affinity and independently of XRCC1 phosphorylation. However, this interaction nevertheless stimulated PNKP activity and promoted SSBR and cell survival. The low-affinity interaction site required the highly conserved Rev1-interacting region (RIR) motif in XRCC1 and included three critical and evolutionarily invariant phenylalanine residues. We propose a bipartite interaction model in which the previously identified high-affinity interaction acts as a molecular tether, holding XRCC1 and PNKP together and thereby promoting the low-affinity interaction identified here, which then stimulates PNKP directly.
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Affiliation(s)
- Claire Breslin
- From the Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Science Park Road, Falmer, Brighton BN19RQ, United Kingdom
| | - Rajam S Mani
- the Department of Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada, and
| | - Mesfin Fanta
- the Department of Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada, and
| | - Nicolas Hoch
- From the Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Science Park Road, Falmer, Brighton BN19RQ, United Kingdom.,the CAPES Foundation, Ministry of Education of Brazil, Brasilia/DF 70040-020, Brazil
| | - Michael Weinfeld
- the Department of Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada, and
| | - Keith W Caldecott
- From the Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Science Park Road, Falmer, Brighton BN19RQ, United Kingdom,
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32
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McNally JR, O'Brien PJ. Kinetic analyses of single-stranded break repair by human DNA ligase III isoforms reveal biochemical differences from DNA ligase I. J Biol Chem 2017; 292:15870-15879. [PMID: 28751376 DOI: 10.1074/jbc.m117.804625] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 07/21/2017] [Indexed: 01/09/2023] Open
Abstract
Humans have three genes encoding DNA ligases with conserved structural features and activities, but they also have notable differences. The LIG3 gene encodes a ubiquitous isoform in all tissues (LIG3α) and a germ line-specific splicing isoform (LIG3β) that differs in the C-terminal domain. Both isoforms are found in the nucleus and the mitochondria. Here, we determined the kinetics and thermodynamics of single-stranded break ligation by LIG3α and LIG3β and compared this framework to that of LIG1, the nuclear replicative ligase. The kinetic parameters of the LIG3 isoforms are nearly identical under all tested conditions, indicating that the BRCA1 C terminal (BRCT) domain specific to LIG3α does not alter ligation kinetics. Although LIG3 is only 22% identical to LIG1 across their conserved domains, the two enzymes had very similar maximal ligation rates. Comparison of the rate and equilibrium constants for LIG3 and LIG1 nevertheless revealed important differences. The LIG3 isoforms were seven times more efficient than LIG1 at ligating nicked DNA under optimal conditions, mainly because of their lower Km value for the DNA substrate. This could explain why LIG3 is less prone to abortive ligation than LIG1. Surprisingly, the affinity of LIG3 for Mg2+ was ten times weaker than that of LIG1, suggesting that Mg2+ availability regulates DNA ligation in vivo, because Mg2+ levels are higher in the mitochondria than in the nucleus. The biochemical differences between the LIG3 isoforms and LIG1 identified here will guide the understanding of both unique and overlapping biological roles of these critical enzymes.
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Affiliation(s)
- Justin R McNally
- From the Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, Michigan 48109
| | - Patrick J O'Brien
- From the Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, Michigan 48109
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33
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Abstract
Cells are exposed to various endogenous and exogenous insults that induce DNA damage, which, if unrepaired, impairs genome integrity and leads to the development of various diseases, including cancer. Recent evidence has implicated poly(ADP-ribose) polymerase 1 (PARP1) in various DNA repair pathways and in the maintenance of genomic stability. The inhibition of PARP1 is therefore being exploited clinically for the treatment of various cancers, which include DNA repair-deficient ovarian, breast and prostate cancers. Understanding the role of PARP1 in maintaining genome integrity is not only important for the design of novel chemotherapeutic agents, but is also crucial for gaining insights into the mechanisms of chemoresistance in cancer cells. In this Review, we discuss the roles of PARP1 in mediating various aspects of DNA metabolism, such as single-strand break repair, nucleotide excision repair, double-strand break repair and the stabilization of replication forks, and in modulating chromatin structure.
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34
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Limpose KL, Corbett AH, Doetsch PW. BERing the burden of damage: Pathway crosstalk and posttranslational modification of base excision repair proteins regulate DNA damage management. DNA Repair (Amst) 2017. [PMID: 28629773 DOI: 10.1016/j.dnarep.2017.06.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
DNA base damage and non-coding apurinic/apyrimidinic (AP) sites are ubiquitous types of damage that must be efficiently repaired to prevent mutations. These damages can occur in both the nuclear and mitochondrial genomes. Base excision repair (BER) is the frontline pathway for identifying and excising damaged DNA bases in both of these cellular compartments. Recent advances demonstrate that BER does not operate as an isolated pathway but rather dynamically interacts with components of other DNA repair pathways to modulate and coordinate BER functions. We define the coordination and interaction between DNA repair pathways as pathway crosstalk. Numerous BER proteins are modified and regulated by post-translational modifications (PTMs), and PTMs could influence pathway crosstalk. Here, we present recent advances on BER/DNA repair pathway crosstalk describing specific examples and also highlight regulation of BER components through PTMs. We have organized and reported functional interactions and documented PTMs for BER proteins into a consolidated summary table. We further propose the concept of DNA repair hubs that coordinate DNA repair pathway crosstalk to identify central protein targets that could play a role in designing future drug targets.
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Affiliation(s)
- Kristin L Limpose
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA, 30322, United States
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA, 30322, United States; Winship Cancer Institute, Emory University, Atlanta, GA 30322, United States.
| | - Paul W Doetsch
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA, 30322, United States; Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, 30322, United States; Winship Cancer Institute, Emory University, Atlanta, GA 30322, United States; Department of Biochemistry, Emory University, Atlanta, GA, 30322, United States.
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35
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Abbotts R, Wilson DM. Coordination of DNA single strand break repair. Free Radic Biol Med 2017; 107:228-244. [PMID: 27890643 PMCID: PMC5443707 DOI: 10.1016/j.freeradbiomed.2016.11.039] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/21/2016] [Accepted: 11/23/2016] [Indexed: 12/28/2022]
Abstract
The genetic material of all organisms is susceptible to modification. In some instances, these changes are programmed, such as the formation of DNA double strand breaks during meiotic recombination to generate gamete variety or class switch recombination to create antibody diversity. However, in most cases, genomic damage is potentially harmful to the health of the organism, contributing to disease and aging by promoting deleterious cellular outcomes. A proportion of DNA modifications are caused by exogenous agents, both physical (namely ultraviolet sunlight and ionizing radiation) and chemical (such as benzopyrene, alkylating agents, platinum compounds and psoralens), which can produce numerous forms of DNA damage, including a range of "simple" and helix-distorting base lesions, abasic sites, crosslinks and various types of phosphodiester strand breaks. More significant in terms of frequency are endogenous mechanisms of modification, which include hydrolytic disintegration of DNA chemical bonds, attack by reactive oxygen species and other byproducts of normal cellular metabolism, or incomplete or necessary enzymatic reactions (such as topoisomerases or repair nucleases). Both exogenous and endogenous mechanisms are associated with a high risk of single strand breakage, either produced directly or generated as intermediates of DNA repair. This review will focus upon the creation, consequences and resolution of single strand breaks, with a particular focus on two major coordinating repair proteins: poly(ADP-ribose) polymerase 1 (PARP1) and X-ray repair cross-complementing protein 1 (XRCC1).
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Affiliation(s)
- Rachel Abbotts
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - David M Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
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Valdez BC, Li Y, Murray D, Liu Y, Nieto Y, Champlin RE, Andersson BS. The PARP inhibitor olaparib enhances the cytotoxicity of combined gemcitabine, busulfan and melphalan in lymphoma cells. Leuk Lymphoma 2017; 58:2705-2716. [PMID: 28394191 DOI: 10.1080/10428194.2017.1306647] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The combination of gemcitabine (Gem), busulfan (Bu), and melphalan (Mel) is a promising regimen for autologous stem-cell transplantation (SCT) for lymphomas. To further improve the efficacy of [Gem + Bu + Mel], we added poly(ADP-ribose) polymerase (PARP) inhibitor olaparib (Ola). We hypothesized that Ola would inhibit the repair of damaged DNA caused by [Gem + Bu + Mel]. Exposure of J45.01 and Toledo cell lines to IC10-20 of individual drug inhibited proliferation by 6-16%; [Gem + Bu + Mel] by 20-27%; and [Gem + Bu + Mel + Ola] by 61-67%. The synergistic cytotoxicity of the four-drug combination may be attributed to activation of the DNA-damage response, inhibition of PARP activity and DNA repair, decreased mitochondrial membrane potential, increased production of reactive oxygen species, and activation of the SAPK/JNK stress signaling pathway, all of which may enhance apoptosis. Similar observations were obtained using mononuclear cells isolated from patients with T-cell lymphocytic leukemia. Our results provide a rationale for undertaking clinical trials of this drug combination for lymphoma patients undergoing SCT.
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Affiliation(s)
- Benigno C Valdez
- a Department of Stem Cell Transplantation and Cellular Therapy , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Yang Li
- a Department of Stem Cell Transplantation and Cellular Therapy , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - David Murray
- b Department of Experimental Oncology , Cross Cancer Institute , Edmonton , Canada
| | - Yan Liu
- a Department of Stem Cell Transplantation and Cellular Therapy , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Yago Nieto
- a Department of Stem Cell Transplantation and Cellular Therapy , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Richard E Champlin
- a Department of Stem Cell Transplantation and Cellular Therapy , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Borje S Andersson
- a Department of Stem Cell Transplantation and Cellular Therapy , The University of Texas MD Anderson Cancer Center , Houston , TX , USA
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Sawant A, Floyd AM, Dangeti M, Lei W, Sobol RW, Patrick SM. Differential role of base excision repair proteins in mediating cisplatin cytotoxicity. DNA Repair (Amst) 2017; 51:46-59. [PMID: 28110804 DOI: 10.1016/j.dnarep.2017.01.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/01/2016] [Accepted: 01/03/2017] [Indexed: 02/04/2023]
Abstract
Interstrand crosslinks (ICLs) are covalent lesions formed by cisplatin. The mechanism for the processing and removal of ICLs by DNA repair proteins involves nucleotide excision repair (NER), homologous recombination (HR) and fanconi anemia (FA) pathways. In this report, we monitored the processing of a flanking uracil adjacent to a cisplatin ICL by the proteins involved in the base excision repair (BER) pathway. Using a combination of extracts, purified proteins, inhibitors, functional assays and cell culture studies, we determined the specific BER proteins required for processing a DNA substrate with a uracil adjacent to a cisplatin ICL. Uracil DNA glycosylase (UNG) is the primary glycosylase responsible for the removal of uracils adjacent to cisplatin ICLs, whereas other uracil glycosylases can process uracils in the context of undamaged DNA. Repair of the uracil adjacent to cisplatin ICLs proceeds through the classical BER pathway, highlighting the importance of specific proteins in this redundant pathway. Removal of uracil is followed by the generation of an abasic site and subsequent cleavage by AP endonuclease 1 (APE1). Inhibition of either the repair or redox domain of APE1 gives rise to cisplatin resistance. Inhibition of the lyase domain of Polymerase β (Polβ) does not influence cisplatin cytotoxicity. In addition, lack of XRCC1 leads to increased DNA damage and results in increased cisplatin cytotoxicity. Our results indicate that BER activation at cisplatin ICLs influences crosslink repair and modulates cisplatin cytotoxicity via specific UNG, APE1 and Polβ polymerase functions.
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Affiliation(s)
- Akshada Sawant
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, United States
| | - Ashley M Floyd
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, United States
| | - Mohan Dangeti
- Department of Biochemistry and Cancer Biology, University of Toledo - Health Science Campus, Toledo, OH 43614, United States
| | - Wen Lei
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, United States
| | - Robert W Sobol
- Department of Oncologic Sciences, Molecular & Metabolic Oncology Program, Mitchell Cancer Institute, University of South Alabama,1660 Springhill Avenue, Mobile, AL 36604, United States
| | - Steve M Patrick
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, United States.
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38
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Grindel A, Guggenberger B, Eichberger L, Pöppelmeyer C, Gschaider M, Tosevska A, Mare G, Briskey D, Brath H, Wagner KH. Oxidative Stress, DNA Damage and DNA Repair in Female Patients with Diabetes Mellitus Type 2. PLoS One 2016; 11:e0162082. [PMID: 27598300 PMCID: PMC5012603 DOI: 10.1371/journal.pone.0162082] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 08/17/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Diabetes mellitus type 2 (T2DM) is associated with oxidative stress which in turn can lead to DNA damage. The aim of the present study was to analyze oxidative stress, DNA damage and DNA repair in regard to hyperglycemic state and diabetes duration. METHODS Female T2DM patients (n = 146) were enrolled in the MIKRODIAB study and allocated in two groups regarding their glycated hemoglobin (HbA1c) level (HbA1c≤7.5%, n = 74; HbA1c>7.5%, n = 72). In addition, tertiles according to diabetes duration (DD) were created (DDI = 6.94±3.1 y, n = 49; DDII = 13.35±1.1 y, n = 48; DDIII = 22.90±7.3 y, n = 49). Oxidative stress parameters, including ferric reducing ability potential, malondialdehyde, oxidized and reduced glutathione, reduced thiols, oxidized LDL and F2-Isoprostane as well as the activity of antioxidant enzymes superoxide dismutase, catalase and glutathione peroxidase were measured. Damage to DNA was analyzed in peripheral blood mononuclear cells and whole blood with single cell gel electrophoresis. DNA base excision repair capacity was tested with the modified comet repair assay. Additionally, mRNA expressions of nine genes related to base excision repair were analyzed in a subset of 46 matched individuals. RESULTS No significant differences in oxidative stress parameters, antioxidant enzyme activities, damage to DNA and base excision repair capacity, neither between a HbA1c cut off />7.5%, nor between diabetes duration was found. A significant up-regulation in mRNA expression was found for APEX1, LIG3 and XRCC1 in patients with >7.5% HbA1c. Additionally, we observed higher total cholesterol, LDL-cholesterol, LDL/HDL-cholesterol, triglycerides, Framingham risk score, systolic blood pressure, BMI and lower HDL-cholesterol in the hyperglycemic group. CONCLUSION BMI, blood pressure and blood lipid status were worse in hyperglycemic individuals. However, no major disparities regarding oxidative stress, damage to DNA and DNA repair were present which might be due to good medical treatment with regular health checks in T2DM patients in Austria.
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Affiliation(s)
- Annemarie Grindel
- Department of Nutritional Sciences, Emerging Field Oxidative Stress and DNA Stability, University of Vienna, Vienna, Austria
- Research Platform Active Ageing, University of Vienna, Vienna, Austria
| | - Bianca Guggenberger
- Department of Nutritional Sciences, Emerging Field Oxidative Stress and DNA Stability, University of Vienna, Vienna, Austria
| | - Lukas Eichberger
- Department of Nutritional Sciences, Emerging Field Oxidative Stress and DNA Stability, University of Vienna, Vienna, Austria
| | - Christina Pöppelmeyer
- Department of Nutritional Sciences, Emerging Field Oxidative Stress and DNA Stability, University of Vienna, Vienna, Austria
| | - Michaela Gschaider
- Department of Nutritional Sciences, Emerging Field Oxidative Stress and DNA Stability, University of Vienna, Vienna, Austria
| | - Anela Tosevska
- Department of Nutritional Sciences, Emerging Field Oxidative Stress and DNA Stability, University of Vienna, Vienna, Austria
| | - George Mare
- Department of Nutritional Sciences, Emerging Field Oxidative Stress and DNA Stability, University of Vienna, Vienna, Austria
| | - David Briskey
- School of Human Movement and Nutrition Sciences, University of Queensland, St Lucia, QLD, Australia
| | - Helmut Brath
- Diabetes Outpatient Clinic, Health Centre South, Vienna, Austria
| | - Karl-Heinz Wagner
- Department of Nutritional Sciences, Emerging Field Oxidative Stress and DNA Stability, University of Vienna, Vienna, Austria
- Research Platform Active Ageing, University of Vienna, Vienna, Austria
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Genetic Polymorphisms of X-ray Repair Cross-Complementing Group 1 and Apurinic/Apyrimidinic Endonuclease-1 in Chronic Obstructive Pulmonary Disease. Inflammation 2016; 39:1198-204. [PMID: 27107596 DOI: 10.1007/s10753-016-0355-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a heterogeneous collection of conditions characterized by irreversible expiratory airflow limitation. The disease is interspersed with exacerbations; periods of acute symptomatic, physiological, and functional deterioration. The present study was designed to investigate the role of X-ray cross-complementing group 1 (XRCC1) and apurinic/apyrimidinic endonuclease 1 (APE1) polymorphisms and the risk of COPD. Blood samples from 354 unrelated subject (age range 18-60 years; 156 with COPD, 198 healthy controls) were collected. Genomic DNA was isolated and genotyped for XRCC1 Arg399Gln and APE1 Asp148Glu using a confronting two pair primers polymerase chain reaction. GA genotype of XRCC1 gene was found to be predominant in the COPD group compared to controls with 1.86-fold increased risk for COPD (OR 1.86, 95 % CI 1.20-2.88, p = 0.0013). TG genotype of APE1 was found to be predominant in COPD group compared to controls with the difference being statistically significant (OR 1.68, 95 % CI 1.08-2.61, p = 0.0043). The GA haplotype was found to be predominant in COPD than controls with a 2.19-fold significant increase (OR 2.19, 95 % CI 1.46-3.28, p = 0.003). Polymorphism in XRCC1 and APE1 gene is associated with an increased risk of COPD.
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Bee L, Nasca A, Zanolini A, Cendron F, d'Adamo P, Costa R, Lamperti C, Celotti L, Ghezzi D, Zeviani M. A nonsense mutation of human XRCC4 is associated with adult-onset progressive encephalocardiomyopathy. EMBO Mol Med 2016; 7:918-29. [PMID: 25872942 PMCID: PMC4520657 DOI: 10.15252/emmm.201404803] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
We studied two monozygotic twins, born to first cousins, affected by a multisystem disease. At birth, they both presented with bilateral cryptorchidism and malformations. Since early adulthood, they developed a slowly progressive neurological syndrome, with cerebellar and pyramidal signs, cognitive impairment, and depression. Dilating cardiomyopathy is also present in both. By whole-exome sequencing, we found a homozygous nucleotide change in XRCC4 (c.673C>T), predicted to introduce a premature stop codon (p.R225*). XRCC4 transcript levels were profoundly reduced, and the protein was undetectable in patients' skin fibroblasts. XRCC4 plays an important role in non-homologous end joining of DNA double-strand breaks (DSB), a system that is involved in repairing DNA damage from, for example, ionizing radiations. Gamma-irradiated mutant cells demonstrated reduction, but not abolition, of DSB repair. In contrast with embryonic lethality of the Xrcc4 KO mouse, nonsense mutations in human XRCC4 have recently been associated with primordial dwarfism and, in our cases, with adult-onset neurological impairment, suggesting an important role for DNA repair in the brain. Surprisingly, neither immunodeficiency nor predisposition to malignancy was reported in these patients.
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Affiliation(s)
- Leonardo Bee
- Department of Biology, University of Padua, Padua, Italy
| | - Alessia Nasca
- Molecular Neurogenetics Unit, Foundation IRCCS Institute of Neurology "Carlo Besta", Milan, Italy
| | - Alice Zanolini
- Molecular Neurogenetics Unit, Foundation IRCCS Institute of Neurology "Carlo Besta", Milan, Italy
| | | | - Pio d'Adamo
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Rodolfo Costa
- Department of Biology, University of Padua, Padua, Italy
| | - Costanza Lamperti
- Molecular Neurogenetics Unit, Foundation IRCCS Institute of Neurology "Carlo Besta", Milan, Italy
| | - Lucia Celotti
- Department of Biology, University of Padua, Padua, Italy
| | - Daniele Ghezzi
- Molecular Neurogenetics Unit, Foundation IRCCS Institute of Neurology "Carlo Besta", Milan, Italy
| | - Massimo Zeviani
- Molecular Neurogenetics Unit, Foundation IRCCS Institute of Neurology "Carlo Besta", Milan, Italy MRC Mitochondrial Biology Unit, CB2 0XY, Cambridge, UK
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41
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Reprint of "Oxidant and environmental toxicant-induced effects compromise DNA ligation during base excision DNA repair". DNA Repair (Amst) 2015; 36:86-90. [PMID: 26596511 DOI: 10.1016/j.dnarep.2015.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
DNA lesions arise from many endogenous and environmental agents, and such lesions can promote deleterious events leading to genomic instability and cell death. Base excision repair (BER) is the main DNA repair pathway responsible for repairing single strand breaks, base lesions and abasic sites in mammalian cells. During BER, DNA substrates and repair intermediates are channeled from one step to the next in a sequential fashion so that release of toxic repair intermediates is minimized. This includes handoff of the product of gap-filling DNA synthesis to the DNA ligation step. The conformational differences in DNA polymerase β (pol β) associated with incorrect or oxidized nucleotide (8-oxodGMP) insertion could impact channeling of the repair intermediate to the final step of BER, i.e., DNA ligation by DNA ligase I or the DNA Ligase III/XRCC1 complex. Thus, modified DNA ligase substrates produced by faulty pol β gap-filling could impair coordination between pol β and DNA ligase. Ligation failure is associated with 5'-AMP addition to the repair intermediate and accumulation of strand breaks that could be more toxic than the initial DNA lesions. Here, we provide an overview of the consequences of ligation failure in the last step of BER. We also discuss DNA-end processing mechanisms that could play roles in reversal of impaired BER.
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42
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Cherry AL, Nott TJ, Kelly G, Rulten SL, Caldecott KW, Smerdon SJ. Versatility in phospho-dependent molecular recognition of the XRCC1 and XRCC4 DNA-damage scaffolds by aprataxin-family FHA domains. DNA Repair (Amst) 2015; 35:116-25. [PMID: 26519825 PMCID: PMC4655838 DOI: 10.1016/j.dnarep.2015.10.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/05/2015] [Accepted: 10/05/2015] [Indexed: 11/11/2022]
Abstract
Aprataxin, aprataxin and PNKP-like factor (APLF) and polynucleotide kinase phosphatase (PNKP) are key DNA-repair proteins with diverse functions but which all contain a homologous forkhead-associated (FHA) domain. Their primary binding targets are casein kinase 2-phosphorylated forms of the XRCC1 and XRCC4 scaffold molecules which respectively coordinate single-stranded and double-stranded DNA break repair pathways. Here, we present the high-resolution X-ray structure of a complex of phosphorylated XRCC4 with APLF, the most divergent of the three FHA domain family members. This, combined with NMR and biochemical analysis of aprataxin and APLF binding to singly and multiply-phosphorylated forms of XRCC1 and XRCC4, and comparison with PNKP reveals a pattern of distinct but overlapping binding specificities that are differentially modulated by multi-site phosphorylation. Together, our data illuminate important differences between activities of the three phospho-binding domains, in spite of a close evolutionary relationship between them.
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Affiliation(s)
- Amy L Cherry
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Timothy J Nott
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Geoffrey Kelly
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - Stuart L Rulten
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - Keith W Caldecott
- MRC Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - Stephen J Smerdon
- Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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Wójcik KA, Synowiec E, Polakowski P, Błasiak J, Szaflik J, Szaflik JP. Variation in DNA Base Excision Repair Genes in Fuchs Endothelial Corneal Dystrophy. Med Sci Monit 2015; 21:2809-27. [PMID: 26388025 PMCID: PMC4582917 DOI: 10.12659/msm.894273] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Fuchs endothelial corneal dystrophy (FECD) is a corneal disease characterized by abnormalities in the Descemet membrane and the corneal endothelium. The etiology of this disease is poorly understood. An increased level of oxidative DNA damage reported in FECD corneas suggests a role of DNA base excision repair (BER) genes in its pathogenesis. In this work, we searched for the association between variation of the PARP-1, NEIL1, POLG, and XRCC1 genes and FECD occurrence. MATERIAL AND METHODS This study was conducted on 250 FECD patients and 353 controls using polymerase chain reaction-restriction fragment length polymorphism, high-resolution melting analysis, and the TaqMan® SNP Genotyping Assay. RESULTS We observed that the A/A genotype and the A allele of the c.1196A>G polymorphism of the XRCC1 gene were positively correlated with an increased FECD occurrence, whereas the G allele had the opposite effect. A weak association between the C/G genotype of the g.46438521G>C polymorphism of the NEIL1 gene and an increased incidence of FECD was also detected. Haplotypes of both polymorphisms of the XRCC1 were associated with FECD occurrence. No association of the c.2285T>C, c.-1370T>A and c.580C>T polymorphisms of the PARP-1, POLG and XRCC1 genes, respectively, with FECD occurrence was observed. CONCLUSIONS Our results suggest that the c.1196A>G polymorphism in the XRCC1 gene may be an independent genetic risk factor for FECD.
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Affiliation(s)
| | - Ewelina Synowiec
- Department of Molecular Genetics, University of Łódź, Łódź, Poland
| | - Piotr Polakowski
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland
| | - Janusz Błasiak
- Department of Molecular Genetics, University of Łódź, Łódź, Poland
| | - Jerzy Szaflik
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland
| | - Jacek P Szaflik
- Department of Ophthalmology, Medical University of Warsaw, Warszawa, Poland
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44
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Balliano AJ, Hayes JJ. Base excision repair in chromatin: Insights from reconstituted systems. DNA Repair (Amst) 2015; 36:77-85. [PMID: 26411876 DOI: 10.1016/j.dnarep.2015.09.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The process of base excision repair has been completely reconstituted in vitro and structural and biochemical properties of the component enzymes thoroughly studied on naked DNA templates. More recent work in this field aims to understand how BER operates on the natural substrate, chromatin [1,2]. Toward this end, a number of researchers, including the Smerdon group, have focused attention to understand how individual enzymes and reconstituted BER operate on nucleosome substrates. While nucleosomes were once thought to completely restrict access of DNA-dependent factors, the surprising finding from these studies suggests that at least some BER components can utilize target DNA bound within nucleosomes as substrates for their enzymatic processes. This data correlates well with both structural studies of these enzymes and our developing understanding of nucleosome conformation and dynamics. While more needs to be learned, these studies highlight the utility of reconstituted BER and chromatin systems to inform our understanding of in vivo biological processes.
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Affiliation(s)
- Angela J Balliano
- University of Rochester Medical Center, 601 Elmwood Ave., Box 712, Rochester, NY 14642, United States
| | - Jeffrey J Hayes
- University of Rochester Medical Center, 601 Elmwood Ave., Box 712, Rochester, NY 14642, United States.
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45
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Çağlayan M, Wilson SH. Oxidant and environmental toxicant-induced effects compromise DNA ligation during base excision DNA repair. DNA Repair (Amst) 2015; 35:85-9. [PMID: 26466358 DOI: 10.1016/j.dnarep.2015.09.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA lesions arise from many endogenous and environmental agents, and such lesions can promote deleterious events leading to genomic instability and cell death. Base excision repair (BER) is the main DNA repair pathway responsible for repairing single strand breaks, base lesions and abasic sites in mammalian cells. During BER, DNA substrates and repair intermediates are channeled from one step to the next in a sequential fashion so that release of toxic repair intermediates is minimized. This includes handoff of the product of gap-filling DNA synthesis to the DNA ligation step. The conformational differences in DNA polymerase β (pol β) associated with incorrect or oxidized nucleotide (8-oxodGMP) insertion could impact channeling of the repair intermediate to the final step of BER, i.e., DNA ligation by DNA ligase I or the DNA Ligase III/XRCC1 complex. Thus, modified DNA ligase substrates produced by faulty pol β gap-filling could impair coordination between pol β and DNA ligase. Ligation failure is associated with 5'-AMP addition to the repair intermediate and accumulation of strand breaks that could be more toxic than the initial DNA lesions. Here, we provide an overview of the consequences of ligation failure in the last step of BER. We also discuss DNA-end processing mechanisms that could play roles in reversal of impaired BER.
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Affiliation(s)
- Melike Çağlayan
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA.
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46
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Kukshal V, Kim IK, Hura GL, Tomkinson AE, Tainer JA, Ellenberger T. Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining. Nucleic Acids Res 2015; 43:7021-31. [PMID: 26130724 PMCID: PMC4538836 DOI: 10.1093/nar/gkv652] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/15/2015] [Indexed: 12/14/2022] Open
Abstract
Mammalian DNA ligase III (LigIII) functions in both nuclear and mitochondrial DNA metabolism. In the nucleus, LigIII has functional redundancy with DNA ligase I whereas LigIII is the only mitochondrial DNA ligase and is essential for the survival of cells dependent upon oxidative respiration. The unique LigIII zinc finger (ZnF) domain is not required for catalytic activity but senses DNA strand breaks and stimulates intermolecular ligation of two DNAs by an unknown mechanism. Consistent with this activity, LigIII acts in an alternative pathway of DNA double strand break repair that buttresses canonical non-homologous end joining (NHEJ) and is manifest in NHEJ-defective cancer cells, but how LigIII acts in joining intermolecular DNA ends versus nick ligation is unclear. To investigate how LigIII efficiently joins two DNAs, we developed a real-time, fluorescence-based assay of DNA bridging suitable for high-throughput screening. On a nicked duplex DNA substrate, the results reveal binding competition between the ZnF and the oligonucleotide/oligosaccharide-binding domain, one of three domains constituting the LigIII catalytic core. In contrast, these domains collaborate and are essential for formation of a DNA-bridging intermediate by adenylated LigIII that positions a pair of blunt-ended duplex DNAs for efficient and specific intermolecular ligation.
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Affiliation(s)
- Vandna Kukshal
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - In-Kwon Kim
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Gregory L Hura
- Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alan E Tomkinson
- Department of Internal Medicine and University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA
| | - John A Tainer
- Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tom Ellenberger
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
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Abstract
Scaffold proteins play a central role in DNA repair by recruiting and organizing sets of enzymes required to perform multi-step repair processes. X-ray cross complementing group 1 protein (XRCC1) forms enzyme complexes optimized for single-strand break repair, but participates in other repair pathways as well. Available structural data for XRCC1 interactions is summarized and evaluated in terms of its proposed roles in DNA repair. Mutational approaches related to the abrogation of specific XRCC1 interactions are also discussed. Although substantial progress has been made in elucidating the structural basis for XRCC1 function, the molecular mechanisms of XRCC1 recruitment related to several proposed roles of the XRCC1 DNA repair complex remain undetermined.
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Affiliation(s)
- Robert E London
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, United States.
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48
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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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Wei B, Han Q, Xu L, Zhang X, Zhu J, Wan L, Jin Y, Qian Z, Wu J, Gao Y, Zhou J, Chen X. Effects of JWA, XRCC1 and BRCA1 mRNA expression on molecular staging for personalized therapy in patients with advanced esophageal squamous cell carcinoma. BMC Cancer 2015; 15:331. [PMID: 25925371 PMCID: PMC4469327 DOI: 10.1186/s12885-015-1364-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 04/24/2015] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND DNA damage repair genes JWA, XRCC1 and BRCA1 were associated with clinical outcomes and could convert the response to the cisplatin-based therapy in some carcinomas. The synergistic effects of JWA, XRCC1 and BRCA1 mRNA expression on personalized therapy remain unknown in advanced esophageal squamous cell carcinoma (ESCC). METHODS We employed quantitative real-time polymerase chain reaction (qPCR) to determine the expression of JWA, XRCC1 and BRCA1 mRNA in paraffin-embedded specimen from 172 patients with advanced ESCC who underwent the first-line cisplatin-or docetaxel-based treatments. RESULTS High JWA or XRCC1mRNA expression was correlated with longer median overall survival (mOS) in all the patients (both P<0.001) or in subgroups with different regimens (all P<0.05), but not correlated with response rate (RR, all P>0.05). Multivariate analysis revealed that high JWA (HR 0.22; 95% CI 0.13-0.37; P<0.001) or XRCC1 (HR 0.36; 95% CI 0.21-0.63; P<0.001) mRNA expression emerged as the independent prognostic factors for ESCC patients in this cohort. But no significant difference in prognostic efficacy was found between JWA plus XRCC1 and JWA alone through ROC analysis. Further subgroup analysis showed cisplatin-based treatments could improve mOS of patients with low JWA expression (P<0.05), especially in those with low BRCA1 expression simultaneously (P<0.001); while in patients with high JWA expression, high BRCA1 mRNA expression was correlated with increased mOS in docetaxel-based treatments (P=0.044). CONCLUSION JWA, XRCC1and BRCA1 mRNA expression could be used as predictive markers in molecular staging for personalized therapy in patients with advanced ESCC who received first-line cisplatin- or docetaxel-based treatments.
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Affiliation(s)
- Bin Wei
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, 223300, China.
| | - Qin Han
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, 223300, China.
| | - Lijuan Xu
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, 223300, China.
| | - Xiaohui Zhang
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, 223300, China.
| | - Jing Zhu
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, 223300, China.
| | - Li Wan
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, 223300, China.
| | - Yan Jin
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, 223300, China.
| | - Zhaoye Qian
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, 223300, China.
| | - Jingjing Wu
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, 223300, China.
| | - Yong Gao
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, 223300, China.
| | - Jianwei Zhou
- Department of Molecular Cell Biology and Toxicology, Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment Cancer Center; School of Public Health, Nanjing Medical University, Nanjing, 210029, China.
| | - Xiaofei Chen
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, 223300, China.
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Interaction with OGG1 is required for efficient recruitment of XRCC1 to base excision repair and maintenance of genetic stability after exposure to oxidative stress. Mol Cell Biol 2015; 35:1648-58. [PMID: 25733688 DOI: 10.1128/mcb.00134-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 02/25/2015] [Indexed: 12/20/2022] Open
Abstract
XRCC1 is an essential protein required for the maintenance of genomic stability through its implication in DNA repair. The main function of XRCC1 is associated with its role in the single-strand break (SSB) and base excision repair (BER) pathways that share several enzymatic steps. We show here that the polymorphic XRCC1 variant R194W presents a defect in its interaction with the DNA glycosylase OGG1 after oxidative stress. While proficient for single-strand break repair (SSBR), this variant does not colocalize with OGG1, reflecting a defect in its involvement in BER. Consistent with a role of XRCC1 in the coordination of the BER pathway, induction of oxidative base damage in XRCC1-deficient cells complemented with the R194W variant results in increased genetic instability as revealed by the accumulation of micronuclei. These data identify a specific molecular role for the XRCC1-OGG1 interaction in BER and provide a model for the effects of the R194W variant identified in molecular cancer epidemiology studies.
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