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Kim JJ, Lee SY, Hwang Y, Kim S, Chung JM, Park S, Yoon J, Yun H, Ji JH, Chae S, Cho H, Kim CG, Dawson TM, Kim H, Dawson VL, Kang HC. USP39 promotes non-homologous end-joining repair by poly(ADP-ribose)-induced liquid demixing. Nucleic Acids Res 2021; 49:11083-11102. [PMID: 34614178 PMCID: PMC8565343 DOI: 10.1093/nar/gkab892] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 12/18/2022] Open
Abstract
Mutual crosstalk among poly(ADP-ribose) (PAR), activated PAR polymerase 1 (PARP1) metabolites, and DNA repair machinery has emerged as a key regulatory mechanism of the DNA damage response (DDR). However, there is no conclusive evidence of how PAR precisely controls DDR. Herein, six deubiquitinating enzymes (DUBs) associated with PAR-coupled DDR were identified, and the role of USP39, an inactive DUB involved in spliceosome assembly, was characterized. USP39 rapidly localizes to DNA lesions in a PAR-dependent manner, where it regulates non-homologous end-joining (NHEJ) via a tripartite RG motif located in the N-terminus comprising 46 amino acids (N46). Furthermore, USP39 acts as a molecular trigger for liquid demixing in a PAR-coupled N46-dependent manner, thereby directly interacting with the XRCC4/LIG4 complex during NHEJ. In parallel, the USP39-associated spliceosome complex controls homologous recombination repair in a PAR-independent manner. These findings provide mechanistic insights into how PAR chains precisely control DNA repair processes in the DDR.
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Affiliation(s)
- Jae Jin Kim
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Life Science, Hallym University, Chuncheon 24252, Republic of Korea
| | - Seo Yun Lee
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Yiseul Hwang
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Soyeon Kim
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Jee Min Chung
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Sangwook Park
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Junghyun Yoon
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Hansol Yun
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Jae-Hoon Ji
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Biochemistry & Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Sunyoung Chae
- Institute of Medical Science, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Hyeseong Cho
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Chan Gil Kim
- Department of Biotechnology, Konkuk University, Chungju 380-701, Republic of Korea
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hongtae Kim
- Center for Genomic Integrity Institute for Basic Science (IBS), Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.,School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ho Chul Kang
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
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2
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Immunomodulatory Roles of PARP-1 and PARP-2: Impact on PARP-Centered Cancer Therapies. Cancers (Basel) 2020; 12:cancers12020392. [PMID: 32046278 PMCID: PMC7072203 DOI: 10.3390/cancers12020392] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/03/2020] [Accepted: 02/06/2020] [Indexed: 01/11/2023] Open
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) and PARP-2 are enzymes which post-translationally modify proteins through poly(ADP-ribosyl)ation (PARylation)—the transfer of ADP-ribose chains onto amino acid residues—with a resultant modulation of protein function. Many targets of PARP-1/2-dependent PARylation are involved in the DNA damage response and hence, the loss of these proteins disrupts a wide range of biological processes, from DNA repair and epigenetics to telomere and centromere regulation. The central role of these PARPs in DNA metabolism in cancer cells has led to the development of PARP inhibitors as new cancer therapeutics, both as adjuvant treatment potentiating chemo-, radio-, and immuno-therapies and as monotherapy exploiting cancer-specific defects in DNA repair. However, a cancer is not just made up of cancer cells and the tumor microenvironment also includes multiple other cell types, particularly stromal and immune cells. Interactions between these cells—cancerous and non-cancerous—are known to either favor or limit tumorigenesis. In recent years, an important role of PARP-1 and PARP-2 has been demonstrated in different aspects of the immune response, modulating both the innate and adaptive immune system. It is now emerging that PARP-1 and PARP-2 may not only impact cancer cell biology, but also modulate the anti-tumor immune response. Understanding the immunomodulatory roles of PARP-1 and PARP-2 may provide invaluable clues to the rational development of more selective PARP-centered therapies which target both the cancer and its microenvironment.
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3
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PARP-1 Is Critical for Recruitment of Dendritic Cells to the Lung in a Mouse Model of Asthma but Dispensable for Their Differentiation and Function. Mediators Inflamm 2019; 2019:1656484. [PMID: 31178661 PMCID: PMC6507252 DOI: 10.1155/2019/1656484] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/15/2018] [Accepted: 01/02/2019] [Indexed: 02/01/2023] Open
Abstract
Dendritic cells (DCs) are critical in asthma and many other immune diseases. We previously demonstrated a role for PARP-1 in asthma. Evidence on PARP-1 playing a role in Th2-associated DC function is not clear. In this study, we examined whether PARP-1 is critical for DC differentiation and function using bone marrow progenitors and their migration to the lung in an ovalbumin-based mouse model of asthma. Results show that changes in PARP-1 levels during GM-CSF-induced DC differentiation from bone marrow progenitors were cyclic and appear to be part of an array of changes that included STAT3/STAT5/STAT6/GRAIL/RAD51. Interestingly, PARP-1 gene deletion affected primarily STAT6 and γH2AX. PARP-1 inhibition significantly reduced the migration of DCs to the lungs of ovalbumin-challenged mice, which was associated with a concomitant reduction in lung levels of the adhesion molecule VCAM-1. The requirement of PARP-1 for VCAM-1 expression was confirmed using endothelial and lung smooth muscle cells. PARP-1 expression and activity were also required for VCAM-1 in differentiated DCs. An assessment of CD11b+/CD11c+/MHCIIhigh DCs in spleens and lymph nodes of OVA-sensitized mice revealed that PARP-1 inhibition genetically or by olaparib exerted little to no effect on DC differentiation, percentage of CD80+/CD86+/CD40+-expressing cells, or their capacity to promote proliferation of ovalbumin-primed (OTII) CD4+ T cells. These findings were corroborated using GM-CSF-induced differentiation of DCs from the bone marrow. Surprisingly, the PARP-1−/− DCs exhibited a higher intrinsic capacity to induce OTII CD4+ T cell proliferation in the absence of ovalbumin. Overall, our results show that PARP-1 plays little to no role in DC differentiation and function and that the protective effect of PARP-1 inhibition against asthma is associated with a prevention of DC migration to the lung through a reduction in VCAM-1 expression. Given the current use of PARP inhibitors (e.g., olaparib) in the clinic, the present results may be of interest for the relevant therapies.
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4
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Galindo-Campos MA, Bedora-Faure M, Farrés J, Lescale C, Moreno-Lama L, Martínez C, Martín-Caballero J, Ampurdanés C, Aparicio P, Dantzer F, Cerutti A, Deriano L, Yélamos J. Coordinated signals from the DNA repair enzymes PARP-1 and PARP-2 promotes B-cell development and function. Cell Death Differ 2019; 26:2667-2681. [PMID: 30996287 DOI: 10.1038/s41418-019-0326-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 02/07/2023] Open
Abstract
Poly (ADP-ribose) polymerase (PARP)-1 and PARP-2 regulate the function of various DNA-interacting proteins by transferring ADP-ribose emerging from catalytic cleavage of cellular β-NAD+. Hence, mice lacking PARP-1 or PARP-2 show DNA perturbations ranging from altered DNA integrity to impaired DNA repair. These effects stem from the central role that PARP-1 and PARP-2 have on the cellular response to DNA damage. Failure to mount a proper response culminates in cell death. Accordingly, PARP inhibitors are emerging as promising drugs in cancer therapy. However, the full impact of these inhibitors on immunity, including B-cell antibody production, remains elusive. Given that mice carrying dual PARP-1 and PARP-2 deficiency develop early embryonic lethality, we crossed PARP-1-deficient mice with mice carrying a B-cell-conditional PARP-2 gene deletion. We found that the resulting dually PARP-1 and PARP-2-deficient mice had perturbed bone-marrow B-cell development as well as profound peripheral depletion of transitional and follicular but not marginal zone B-cells. Of note, bone-marrow B-cell progenitors and peripheral mature B-cells were conserved in mice carrying either PARP-1 or PARP-2 deficiency. In dually PARP-1 and PARP-2-deficient mice, B-cell lymphopenia was associated with increased DNA damage and accentuated death in actively proliferating B-cells. Moreover, dual PARP-1 and PARP-2 deficiency impaired antibody responses to T-independent carbohydrate but not to T-dependent protein antigens. Notwithstanding the pivotal role of PARP-1 and PARP-2 in DNA repair, combined PARP-1 and PARP-2 deficiency did not perturb the DNA-editing processes required for the generation of a protective antibody repertoire, including Ig V(D)J gene recombination and IgM-to-IgG class switching. These findings provide key information as to the potential impact of PARP inhibitors on humoral immunity, which will facilitate the development of safer PARP-targeting regimens against cancer.
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Affiliation(s)
- Miguel A Galindo-Campos
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Marie Bedora-Faure
- Genome Integrity, Immunity and Cancer Unit, Equipe Labellisée Ligue Contre le Cancer, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015, Paris, France
| | - Jordi Farrés
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Chloé Lescale
- Genome Integrity, Immunity and Cancer Unit, Equipe Labellisée Ligue Contre le Cancer, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015, Paris, France
| | - Lucia Moreno-Lama
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Carlos Martínez
- Experimental Pathology Unit, IMIB-LAIB-Arrixaca, Murcia, Spain
| | | | - Coral Ampurdanés
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Pedro Aparicio
- Department of Biochemistry, Molecular Biology and Immunology, University of Murcia, Murcia, Spain
| | - Françoise Dantzer
- Biotechnology and Cell Signaling, UMR7242-CNRS, Laboratory of Excellence Medalis, ESBS, Illkirch, France
| | - Andrea Cerutti
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain.,Inflammatory and Cardiovascular Disorders Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Ludovic Deriano
- Genome Integrity, Immunity and Cancer Unit, Equipe Labellisée Ligue Contre le Cancer, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015, Paris, France.
| | - José Yélamos
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain. .,Department of Immunology, Hospital del Mar, Barcelona, Spain.
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5
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Kolb AL, Gunn AR, Lakin ND. Redundancy between nucleases required for homologous recombination promotes PARP inhibitor resistance in the eukaryotic model organism Dictyostelium. Nucleic Acids Res 2017; 45:10056-10067. [PMID: 28973445 PMCID: PMC5622368 DOI: 10.1093/nar/gkx639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/14/2017] [Indexed: 12/21/2022] Open
Abstract
ADP-ribosyltransferases promote repair of DNA single strand breaks and disruption of this pathway by Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) is toxic to cells with defects in homologous recombination (HR). Here, we show that this relationship is conserved in the simple eukaryote Dictyostelium and exploit this organism to define mechanisms that drive resistance of the HR-deficient cells to PARPi. Dictyostelium cells disrupted in exonuclease I, a critical factor for HR, are sensitive to PARPi. Deletion of exo1 prevents the accumulation of Rad51 in chromatin induced by PARPi, resulting in DNA damage being channelled through repair by non-homologous end-joining (NHEJ). Inactivation of NHEJ supresses the sensitivity of exo1− cells to PARPi, indicating this pathway drives synthetic lethality and that in its absence alternative repair mechanisms promote cell survival. This resistance is independent of alternate-NHEJ and is instead achieved by re-activation of HR. Moreover, inhibitors of Mre11 restore sensitivity of dnapkcs−exo1− cells to PARPi, indicating redundancy between nucleases that initiate HR can drive PARPi resistance. These data inform on mechanism of PARPi resistance in HR-deficient cells and present Dictyostelium as a convenient genetic model to characterize these pathways.
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Affiliation(s)
- Anna-Lena Kolb
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Alasdair R Gunn
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Nicholas D Lakin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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6
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Site-specific ADP-ribosylation of histone H2B in response to DNA double strand breaks. Sci Rep 2017; 7:43750. [PMID: 28252050 PMCID: PMC5333086 DOI: 10.1038/srep43750] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/26/2017] [Indexed: 12/15/2022] Open
Abstract
ADP-ribosyltransferases (ARTs) modify proteins with single units or polymers of ADP-ribose to regulate DNA repair. However, the substrates for these enzymes are ill-defined. For example, although histones are modified by ARTs, the sites on these proteins ADP-ribosylated following DNA damage and the ARTs that catalyse these events are unknown. This, in part, is due to the lack of a eukaryotic model that contains ARTs, in addition to histone genes that can be manipulated to assess ADP-ribosylation events in vivo. Here we exploit the model Dictyostelium to identify site-specific histone ADP-ribosylation events in vivo and define the ARTs that mediate these modifications. Dictyostelium histones are modified in response to DNA double strand breaks (DSBs) in vivo by the ARTs Adprt1a and Adprt2. Adprt1a is a mono-ART that modifies H2BE18 in vitro, although disruption of this site allows ADP-ribosylation at H2BE19. Although redundancy between H2BE18 and H2BE19 ADP-ribosylation is also apparent following DSBs in vivo, by generating a strain with mutations at E18/E19 in the h2b locus we demonstrate these are the principal sites modified by Adprt1a/Adprt2. This identifies DNA damage induced histone mono-ADP-ribosylation sites by specific ARTs in vivo, providing a unique platform to assess how histone ADP-ribosylation regulates DNA repair.
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7
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Gunn AR, Banos-Pinero B, Paschke P, Sanchez-Pulido L, Ariza A, Day J, Emrich M, Leys D, Ponting CP, Ahel I, Lakin ND. The role of ADP-ribosylation in regulating DNA interstrand crosslink repair. J Cell Sci 2016; 129:3845-3858. [PMID: 27587838 PMCID: PMC5087659 DOI: 10.1242/jcs.193375] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/22/2016] [Indexed: 12/11/2022] Open
Abstract
ADP-ribosylation by ADP-ribosyltransferases (ARTs) has a well-established role in DNA strand break repair by promoting enrichment of repair factors at damage sites through ADP-ribose interaction domains. Here, we exploit the simple eukaryote Dictyostelium to uncover a role for ADP-ribosylation in regulating DNA interstrand crosslink repair and redundancy of this pathway with non-homologous end-joining (NHEJ). In silico searches were used to identify a protein that contains a permutated macrodomain (which we call aprataxin/APLF-and-PNKP-like protein; APL). Structural analysis reveals that this permutated macrodomain retains features associated with ADP-ribose interactions and that APL is capable of binding poly(ADP-ribose) through this macrodomain. APL is enriched in chromatin in response to cisplatin treatment, an agent that induces DNA interstrand crosslinks (ICLs). This is dependent on the macrodomain of APL and the ART Adprt2, indicating a role for ADP-ribosylation in the cellular response to cisplatin. Although adprt2− cells are sensitive to cisplatin, ADP-ribosylation is evident in these cells owing to redundant signalling by the double-strand break (DSB)-responsive ART Adprt1a, promoting NHEJ-mediated repair. These data implicate ADP-ribosylation in DNA ICL repair and identify that NHEJ can function to resolve this form of DNA damage in the absence of Adprt2. Summary: Here, we identify a role for post-translational modification ADP-ribosylation in the response to DNA interstrand crosslinks in the model Dictyostelium.
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Affiliation(s)
- Alasdair R Gunn
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Benito Banos-Pinero
- Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Peggy Paschke
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Luis Sanchez-Pulido
- MRC Human Genetics Unit, The MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Scotland, UK
| | - Antonio Ariza
- Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Joseph Day
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Mehera Emrich
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - David Leys
- Manchester Institute of Biotechnology, University of Manchester, Princess Street 131, Manchester, M1 7DN, UK
| | - Chris P Ponting
- MRC Human Genetics Unit, The MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Scotland, UK
| | - Ivan Ahel
- Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Nicholas D Lakin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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Cilli D, Mirasole C, Pennisi R, Pallotta V, D'Alessandro A, Antoccia A, Zolla L, Ascenzi P, di Masi A. Identification of the interactors of human nibrin (NBN) and of its 26 kDa and 70 kDa fragments arising from the NBN 657del5 founder mutation. PLoS One 2014; 9:e114651. [PMID: 25485873 PMCID: PMC4259352 DOI: 10.1371/journal.pone.0114651] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 11/12/2014] [Indexed: 01/17/2023] Open
Abstract
Nibrin (also named NBN or NBS1) is a component of the MRE11/RAD50/NBN complex, which is involved in early steps of DNA double strand breaks sensing and repair. Mutations within the NBN gene are responsible for the Nijmegen breakage syndrome (NBS). The 90% of NBS patients are homozygous for the 657del5 mutation, which determines the synthesis of two truncated proteins of 26 kDa (p26) and 70 kDa (p70). Here, HEK293 cells have been exploited to transiently express either the full-length NBN protein or the p26 or p70 fragments, followed by affinity chromatography enrichment of the eluates. The application of an unsupervised proteomics approach, based upon SDS-PAGE separation and shotgun digestion of protein bands followed by MS/MS protein identification, indicates the occurrence of previously unreported protein interacting partners of the full-length NBN protein and the p26 fragment containing the FHA/BRCT1 domains, especially after cell irradiation. In particular, results obtained shed light on new possible roles of NBN and of the p26 fragment in ROS scavenging, in the DNA damage response, and in protein folding and degradation. In particular, here we show that p26 interacts with PARP1 after irradiation, and this interaction exerts an inhibitory effect on PARP1 activity as measured by NAD+ levels. Furthermore, the p26-PARP1 interaction seems to be responsible for the persistence of ROS, and in turn of DSBs, at 24 h from IR. Since some of the newly identified interactors of the p26 and p70 fragments have not been found to interact with the full-length NBN, these interactions may somehow contribute to the key biological phenomena underpinning NBS.
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Affiliation(s)
| | - Cristiana Mirasole
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Rosa Pennisi
- Department of Science, Roma Tre University, Rome, Italy
| | - Valeria Pallotta
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Angelo D'Alessandro
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Antonio Antoccia
- Department of Science, Roma Tre University, Rome, Italy
- Istituto Nazionale Biostrutture e Biosistemi – Consorzio Interuniversitario, Rome, Italy
| | - Lello Zolla
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Paolo Ascenzi
- Istituto Nazionale Biostrutture e Biosistemi – Consorzio Interuniversitario, Rome, Italy
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Rome, Italy
| | - Alessandra di Masi
- Department of Science, Roma Tre University, Rome, Italy
- Istituto Nazionale Biostrutture e Biosistemi – Consorzio Interuniversitario, Rome, Italy
- * E-mail:
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9
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Rosado MM, Bennici E, Novelli F, Pioli C. Beyond DNA repair, the immunological role of PARP-1 and its siblings. Immunology 2013; 139:428-37. [PMID: 23489378 DOI: 10.1111/imm.12099] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Revised: 02/16/2013] [Accepted: 03/11/2013] [Indexed: 12/14/2022] Open
Abstract
ADP-ribosylation is the addition of one or more (up to some hundreds) ADP-ribose moieties to acceptor proteins. There are two major families of enzymes that catalyse this reaction: extracellular ADP-ribosyl-transferases (ARTs), which are bound to the cell membrane by a glycosylphosphatidylinositol anchor or are secreted, and poly(ADP-ribose)-polymerases (PARPs), which are present in the cell nucleus and/or cytoplasm. Recent findings revealed a wide immunological role for ADP-ribosylating enzymes. ARTs, by sensing extracellular NAD concentration, can act as danger detectors. PARP-1, the prototypical representative of the PARP family, known to protect cells from genomic instability, is involved in the development of inflammatory responses and several forms of cell death. PARP-1 also plays a role in adaptive immunity by modulating the ability of dendritic cells to stimulate T cells or by directly affecting the differentiation and functions of T and B cells. Both PARP-1 and PARP-14 (CoaSt6) knockout mice were described to display reduced T helper type 2 cell differentiation and allergic responses. Our recent findings showed that PARP-1 is involved in the differentiation of Foxp3+ regulatory T (Treg) cells, suggesting a role for PARP-1 in tolerance induction. Also ARTs regulate Treg cell homeostasis by promoting Treg cell apoptosis during inflammatory responses. PARP inhibitors ameliorate immune-mediated diseases in several experimental models, including rheumatoid arthritis, colitis, experimental autoimmune encephalomyelitis and allergy. Together these findings show that ADP-ribosylating enzymes, in particular PARP-1, play a pivotal role in the regulation of immune responses and may represent a good target for new therapeutic approaches in immune-mediated diseases.
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Affiliation(s)
- Maria Manuela Rosado
- Laboratory of B cell development, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
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10
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Couto CAM, Hsu DW, Teo R, Rakhimova A, Lempidaki S, Pears CJ, Lakin ND. Nonhomologous end-joining promotes resistance to DNA damage in the absence of an ADP-ribosyltransferase that signals DNA single strand breaks. J Cell Sci 2013; 126:3452-61. [DOI: 10.1242/jcs.128769] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
ADP-ribosylation of proteins at DNA lesions by ADP-ribosyltransferases (ARTs) is an early response to DNA damage. The best defined role of ADP-ribosylation in the DNA damage response is in repair of single strand breaks (SSBs). Recently, we initiated a study of how ADP-ribosylation regulates DNA repair in Dictyostelium and found that whilst two ARTs (Adprt1b and Adprt2) are required for tolerance of cells to SSBs, a third ART (Adprt1a) promotes nonhomologous end-joining (NHEJ). Here we report that disruption of adprt2 results in accumulation of DNA damage throughout the cell cycle following exposure to agents that induce base damage and DNA SSBs. Although ADP-ribosylation is evident in adprt2− cells exposed to MMS, disruption of adprt1a and adprt2 in combination abrogates this response and further sensitises cells to this agent, indicating that in the absence of Adprt2, Adprt1a signals MMS-induced DNA lesions to promote resistance of cells to DNA damage. As a consequence of defective signalling of SSBs by Adprt2, Adprt1a is required to assemble NHEJ factors in chromatin and disruption of the NHEJ pathway in combination with adprt2 increases sensitivity of cells to MMS. Taken together, these data indicate overlapping functions between different ARTs in signalling DNA damage and illustrate a critical requirement for NHEJ in maintaining cell viability in the absence of an effective SSB response.
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11
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Pears CJ, Couto CAM, Wang HY, Borer C, Kiely R, Lakin ND. The role of ADP-ribosylation in regulating DNA double-strand break repair. Cell Cycle 2012; 11:48-56. [PMID: 22186780 DOI: 10.4161/cc.11.1.18793] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
ADP-ribosylation is the post translational modification of proteins catalysed by ADP-ribosyltransferases (ARTs). ADP-ribosylation has been implicated in a wide variety of cellular processes including cell growth and differentiation, apoptosis and transcriptional regulation. Perhaps the best characterised role, however, is in DNA repair and genome stability where ADP-ribosylation promotes resolution of DNA single strand breaks. Although ADP-ribosylation also occurs at DNA double strand breaks (DSBs), which ARTs catalyse this reaction and the molecular basis of how this modification regulates their repair remains a matter of debate. Here we review recent advances in our understanding of how ADP-ribosylation regulates DSB repair. Specifically, we highlight studies using the genetic model organism Dictyostelium, in addition to vertebrate cells that identify a third ART that accelerates DSB repair by non-homologous end-joining through promoting the interaction of repair factors with DNA lesions. The implications of these data with regards to how ADP-ribosylation regulates DNA repair and genome stability are discussed.
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12
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Della-Maria J, Zhou Y, Tsai MS, Kuhnlein J, Carney JP, Paull TT, Tomkinson AE. Human Mre11/human Rad50/Nbs1 and DNA ligase IIIalpha/XRCC1 protein complexes act together in an alternative nonhomologous end joining pathway. J Biol Chem 2011; 286:33845-53. [PMID: 21816818 PMCID: PMC3190819 DOI: 10.1074/jbc.m111.274159] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 07/30/2011] [Indexed: 11/06/2022] Open
Abstract
Recent studies have implicated a poorly defined alternative pathway of nonhomologous end joining (alt-NHEJ) in the generation of large deletions and chromosomal translocations that are frequently observed in cancer cells. Here, we describe an interaction between two factors, hMre11/hRad50/Nbs1 (MRN) and DNA ligase IIIα/XRCC1, that have been linked with alt-NHEJ. Expression of DNA ligase IIIα and the association between MRN and DNA ligase IIIα/XRCC1 are altered in cell lines defective in the major NHEJ pathway. Most notably, DNA damage induced the association of these factors in DNA ligase IV-deficient cells. MRN interacts with DNA ligase IIIα/XRCC1, stimulating intermolecular ligation, and together these proteins join incompatible DNA ends in a reaction that mimics alt-NHEJ. Thus, our results provide novel mechanistic insights into the alt-NHEJ pathway that not only contributes to genome instability in cancer cells but may also be a therapeutic target.
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Affiliation(s)
- Julie Della-Maria
- From the Radiation Oncology Research Laboratory, Department of Radiation Oncology and The Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Yi Zhou
- the Howard Hughes Medical Institute and the Department of Molecular Genetics and Microbiology, University of Texas, Austin, Texas 78712, and
| | - Miaw-Sheue Tsai
- the Ernest Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720
| | - Jeff Kuhnlein
- the Howard Hughes Medical Institute and the Department of Molecular Genetics and Microbiology, University of Texas, Austin, Texas 78712, and
| | - James P. Carney
- From the Radiation Oncology Research Laboratory, Department of Radiation Oncology and The Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Tanya T. Paull
- the Howard Hughes Medical Institute and the Department of Molecular Genetics and Microbiology, University of Texas, Austin, Texas 78712, and
| | - Alan E. Tomkinson
- From the Radiation Oncology Research Laboratory, Department of Radiation Oncology and The Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201
- the Department of Internal Medicine and University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico 87131
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13
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Cheng Q, Barboule N, Frit P, Gomez D, Bombarde O, Couderc B, Ren GS, Salles B, Calsou P. Ku counteracts mobilization of PARP1 and MRN in chromatin damaged with DNA double-strand breaks. Nucleic Acids Res 2011; 39:9605-19. [PMID: 21880593 PMCID: PMC3239177 DOI: 10.1093/nar/gkr656] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
In mammalian cells, the main pathway for DNA double-strand breaks (DSBs) repair is classical non-homologous end joining (C-NHEJ). An alternative or back-up NHEJ (B-NHEJ) pathway has emerged which operates preferentially under C-NHEJ defective conditions. Although B-NHEJ appears particularly relevant to genomic instability associated with cancer, its components and regulation are still largely unknown. To get insights into this pathway, we have knocked-down Ku, the main contributor to C-NHEJ. Thus, models of human cell lines have been engineered in which the expression of Ku70/80 heterodimer can be significantly lowered by the conditional induction of a shRNA against Ku70. On Ku reduction in cells, resulting NHEJ competent protein extracts showed a shift from C- to B-NHEJ that could be reversed by addition of purified Ku protein. Using a cellular fractionation protocol after treatment with a strong DSBs inducer followed by western blotting or immunostaining, we established that, among C-NHEJ factors, Ku is the main counteracting factor against mobilization of PARP1 and the MRN complex to damaged chromatin. In addition, Ku limits PAR synthesis and single-stranded DNA production in response to DSBs. These data support the involvement of PARP1 and the MRN proteins in the B-NHEJ route for the repair of DNA DSBs.
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Affiliation(s)
- Qiao Cheng
- CNRS, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France
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14
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Lee JS, Kim JH, Park BL, Cheong HS, Koh I, Kim JYH, Park TJ, Pasaje CF, Bae JS, Lee HS, Kim YJ, Shin HD. No associations of polymorphisms in ADPRT with hepatitis B virus clearance and hepatocellular carcinoma occurrence in a Korean population. Hepatol Res 2011; 41:250-7. [PMID: 21276153 DOI: 10.1111/j.1872-034x.2010.00772.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
AIM The human adenosine diphosphate ribosyl transferase (ADPRT) gene might significantly affect cancer by encoding poly(ADP-ribose) polymerase 1 enzyme (PARP-1) and promoting an important role in cellular responses to DNA damage, genomic stabilization and regulation of tumor suppressor genes. We explored whether polymorphisms of ADPRT affect clearance of hepatitis B virus (HBV) infection or risk of hepatocellular carcinoma (HCC) occurrence in a Korean HBV cohort. METHODS Genotyping was performed in a total of 1066 subjects composed of 434 spontaneously recovered (SR) subjects as normal controls and 632 chronic carriers (CC) of HBV who were further classified into 325 patients with liver cirrhosis (LC)/chronic hepatitis (CH) and 307 patients with HCC. RESULTS Logistic analyses of six common single nucleotide polymorphisms (SNP) and their haplotypes revealed that none of the polymorphisms were significantly associated with clearance of HBV infection and HCC occurrence, except for nominal evidence of association between haplotype 2 (ht2) with HBV clearance (P = 0.05). In the analysis of age of HCC occurrence which is an important factor in disease progression to HCC, results from Cox proportional hazards showed that none of the variants were significantly associated with onset age of HCC occurrence, although a nominal signal in ht4 (P = 0.03, but P(corr) > 0.05) was initially detected. CONCLUSION Although ADPRT is an important gene for cellular responses and tumor regulations, our study provides evidence that ADPRT variations do not affect HBV clearance and HCC occurrence.
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Affiliation(s)
- Jin Sol Lee
- Department of Life Science, Sogang University Department of Genetic Epidemiology, SNP Genetics Department of Physiology, College of Medicine, Hanyang University Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, Korea
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15
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Rulten SL, Fisher AEO, Robert I, Zuma MC, Rouleau M, Ju L, Poirier G, Reina-San-Martin B, Caldecott KW. PARP-3 and APLF function together to accelerate nonhomologous end-joining. Mol Cell 2011; 41:33-45. [PMID: 21211721 DOI: 10.1016/j.molcel.2010.12.006] [Citation(s) in RCA: 250] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 09/20/2010] [Accepted: 10/18/2010] [Indexed: 01/07/2023]
Abstract
PARP-3 is a member of the ADP-ribosyl transferase superfamily of unknown function. We show that PARP-3 is stimulated by DNA double-strand breaks (DSBs) in vitro and functions in the same pathway as the poly (ADP-ribose)-binding protein APLF to accelerate chromosomal DNA DSB repair. We implicate PARP-3 in the accumulation of APLF at DSBs and demonstrate that APLF promotes the retention of XRCC4/DNA ligase IV complex in chromatin, suggesting that PARP-3 and APLF accelerate DNA ligation during nonhomologous end-joining (NHEJ). Consistent with this, we show that class switch recombination in Aplf(-/-) B cells is biased toward microhomology-mediated end-joining, a pathway that operates in the absence of XRCC4/DNA ligase IV, and that the requirement for PARP-3 and APLF for NHEJ is circumvented by overexpression of XRCC4/DNA ligase IV. These data identify molecular roles for PARP-3 and APLF in chromosomal DNA double-strand break repair reactions.
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Affiliation(s)
- Stuart L Rulten
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK
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16
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Huen MSY, Chen J. Assembly of checkpoint and repair machineries at DNA damage sites. Trends Biochem Sci 2009; 35:101-8. [PMID: 19875294 DOI: 10.1016/j.tibs.2009.09.001] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 08/28/2009] [Accepted: 09/02/2009] [Indexed: 12/31/2022]
Abstract
The remarkably coordinated nature of the DNA damage response pathway relies on numerous mechanisms that facilitate the assembly of checkpoint and repair factors at DNA breaks. Post-translational modifications on and around chromatin have critical roles in allowing the timely and sequential assembly of DNA damage responsive elements at the vicinity of DNA breaks. Notably, recent advances in forward genetics and proteomics-based approaches have enabled the identification of novel components within the DNA damage response pathway, providing a more comprehensive picture of the molecular network that assists in the detection and propagation of DNA damage signals.
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Affiliation(s)
- Michael S Y Huen
- Department of Anatomy, Centre for Cancer Research, University of Hong Kong, L1-59, Laboratory Block, 21 Sassoon Road, Hong Kong SAR
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17
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Franco D, Chang Y. Accessibility of chromosomal recombination breaks in nuclei of wild-type and DNA-PKcs-deficient cells. DNA Repair (Amst) 2009; 8:813-21. [PMID: 19395319 DOI: 10.1016/j.dnarep.2009.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Revised: 02/24/2009] [Accepted: 03/23/2009] [Indexed: 01/17/2023]
Abstract
V(D)J recombination is a highly regulated process, proceeding from a site-specific cleavage to an imprecise end joining. After the DNA excision catalyzed by the recombinase encoded by recombination activating genes 1 and 2 (RAG1/2), newly generated recombination ends are believed held by a post-cleavage complex (PC) consisting of RAG1/2 proteins, and are subsequently resolved by non-homologous end joining (NHEJ) machinery. The relay of these ends from PC to NHEJ remains elusive. It has been speculated that NHEJ factors modify the RAG1/2-PC to gain access to the ends or act on free ends after the disassembly of the PC. Thus, recombination ends may either be retained in a complex throughout the recombination process or left as unprotected free ends after cleavage, a condition that may permit an alternative, non-classical NHEJ end joining pathway. To directly test these scenarios on recombination induced chromosomal breaks, we have developed a recombination end protection assay to monitor the accessibility of recombination ends to exonuclease-V in intact nuclei. We demonstrate that these ends are well protected in the nuclei of wild-type cells, suggesting a seamless cleavage-joining reaction. However, divergent end protection of coding versus signal ends was found in cells derived from severe combined immunodeficient (scid) mice that are defective in the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs). While signal ends are resistant, opened coding ends are susceptible to enzymatic modification. Our data suggests a role of DNA-PKcs in protecting chromosomal coding ends. Furthermore, using recombination inducible scid cell lines, we demonstrate that conditional protection of coding ends is inversely correlated with the level of their resolution, i.e., the greater the accessibility of the coding ends, the higher level of coding joints formed. Taken together, our findings provide important insights into the resolution of recombination ends by error-prone alternative NHEJ pathways.
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Affiliation(s)
- Daniel Franco
- Molecular and Cellular Biology Program, School of Life Sciences, Center for Infectious Diseases and Vaccinology, The Biodesign Institute at Arizona State University, BDA220, 1001 S. McAllister Avenue, Tempe, AZ 85287-5501, United States
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18
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Haince JF, McDonald D, Rodrigue A, Déry U, Masson JY, Hendzel MJ, Poirier GG. PARP1-dependent kinetics of recruitment of MRE11 and NBS1 proteins to multiple DNA damage sites. J Biol Chem 2007; 283:1197-208. [PMID: 18025084 DOI: 10.1074/jbc.m706734200] [Citation(s) in RCA: 433] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) is a nuclear enzyme that is rapidly activated by DNA strand breaks and signals the presence of DNA lesions by attaching ADP-ribose units to chromatin-associated proteins. The therapeutic applications of PARP inhibitors in potentiating the killing action of ionizing radiation have been well documented and are attracting increasing interest as a cancer treatment. However, the initial kinetics underlying the recognition of multiple DNA lesions by PARP1 and how inhibition of PARP potentiates the activity of DNA-damaging agents are unknown. Here we report the spatiotemporal dynamics of PARP1 recruitment to DNA damage induced by laser microirradiation in single living cells. We provide direct evidence that PARP1 is able to accumulate at a locally induced DNA double strand break. Most importantly, we observed that the rapid accumulation of MRE11 and NBS1 at sites of DNA damage requires PARP1. By determining the kinetics of protein assembly following DNA damage, our study reveals the cooperation between PARP1 and the double strand break sensors MRE11 and NBS1 in the close vicinity of a DNA lesion. This may explain the sensitivity of cancer cells to PARP inhibitors.
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Affiliation(s)
- Jean-François Haince
- Health and Environment Unit, Laval University Hospital Research Center, Centre Hospitalier Universitaire de Québec, Faculty of Medicine, Laval University, Quebec G1V 4G2, Canada
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19
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Abstract
Half a century ago, when the free radical theory of aging was first proposed, the damaging effects of reactive oxygen species (ROS) were in the focus of attention and considered the single most important determinant of aging. Two decades later, however, the disposable soma theory of aging redirected the attention to the potential impact of cellular maintenance and repair pathways that are both genetically and environmentally determined and are counteracting the damaging effects of ROS. In the present paper, recent experimental data linking DNA repair pathways with the aging process are summarised. Special attention is paid to poly(ADP-ribosyl)ation, a DNA-damage driven posttranslational modification of proteins.
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Affiliation(s)
- Alexander Bürkle
- Molecular Toxicology Group, University of Konstanz, Box X911, D-78457, Konstanz, Germany.
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20
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Wang M, Wu W, Wu W, Rosidi B, Zhang L, Wang H, Iliakis G. PARP-1 and Ku compete for repair of DNA double strand breaks by distinct NHEJ pathways. Nucleic Acids Res 2006; 34:6170-82. [PMID: 17088286 PMCID: PMC1693894 DOI: 10.1093/nar/gkl840] [Citation(s) in RCA: 604] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Poly(ADP-ribose)polymerase 1 (PARP-1) recognizes DNA strand interruptions in vivo and triggers its own modification as well as that of other proteins by the sequential addition of ADP-ribose to form polymers. This modification causes a release of PARP-1 from DNA ends and initiates a variety of responses including DNA repair. While PARP-1 has been firmly implicated in base excision and single strand break repair, its role in the repair of DNA double strand breaks (DSBs) remains unclear. Here, we show that PARP-1, probably together with DNA ligase III, operates in an alternative pathway of non-homologous end joining (NHEJ) that functions as backup to the classical pathway of NHEJ that utilizes DNA-PKcs, Ku, DNA ligase IV, XRCC4, XLF/Cernunnos and Artemis. PARP-1 binds to DNA ends in direct competition with Ku. However, in irradiated cells the higher affinity of Ku for DSBs and an excessive number of other forms of competing DNA lesions limit its contribution to DSB repair. When essential components of the classical pathway of NHEJ are absent, PARP-1 is recruited for DSB repair, particularly in the absence of Ku and non-DSB lesions. This form of DSB repair is sensitive to PARP-1 inhibitors. The results define the function of PARP-1 in DSB repair and characterize a candidate pathway responsible for joining errors causing genomic instability and cancer.
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Affiliation(s)
| | | | | | | | | | - Huichen Wang
- Center for Neurovirology, Temple University1900 North 12th, Philadelphia, PA 19122, USA
| | - George Iliakis
- To whom correspondence should be addressed. Tel: +49 201 723 4152; Fax: +49 201 723 5966;
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21
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Baumann C, Boehden GS, Bürkle A, Wiesmüller L. Poly(ADP-RIBOSE) polymerase-1 (Parp-1) antagonizes topoisomerase I-dependent recombination stimulation by P53. Nucleic Acids Res 2006; 34:1036-49. [PMID: 16473854 PMCID: PMC1363779 DOI: 10.1093/nar/gkj509] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PARP-1 interacts with and poly(ADP-ribosyl)ates p53 and topoisomerase I, which both participate in DNA recombination. Previously, we showed that PARP-1 downregulates homology-directed double-strand break (DSB) repair. We also discovered that, despite the well-established role of p53 as a global suppressor of error-prone recombination, p53 enhances homologous recombination (HR) at the RARα breakpoint cluster region (bcr) comprising topoisomerase I recognition sites. Using an SV40-based assay and isogenic cell lines differing in the p53 and PARP-1 status we demonstrate that PARP-1 counteracts HR enhancement by p53, although DNA replication was largely unaffected. When the same DNA element was integrated in an episomal recombination plasmid, both p53 and PARP-1 exerted anti-recombinogenic rather than stimulatory activities. Strikingly, with DNA substrates integrated into cellular chromosomes, enhancement of HR by p53 and antagonistic PARP-1 action was seen, very similar to the HR of viral minichromosomes. siRNA-mediated knockdown revealed the essential role of topoisomerase I in this regulatory mechanism. However, after I-SceI-meganuclease-mediated cleavage of the chromosomally integrated substrate, no topoisomerase I-dependent effects by p53 and PARP-1 were observed. Our data further indicate that PARP-1, probably through topoisomerase I interactions rather than poly(ADP-ribosyl)ation, prevents p53 from stimulating spontaneous HR on chromosomes via topoisomerase I activity.
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Affiliation(s)
- Cindy Baumann
- Universitätsfrauenklinik, Prittwitzstrasse 43D-89075 Ulm, Germany
| | - Gisa S. Boehden
- Universitätsfrauenklinik, Prittwitzstrasse 43D-89075 Ulm, Germany
- Heinrich-Pette-Institut für Experimentelle Virologie und Immunologie an der Universität HamburgMartinistraße 52, D-20251 Hamburg, Germany
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, University of KonstanzD-78457 Konstanz, Germany
| | - Lisa Wiesmüller
- Universitätsfrauenklinik, Prittwitzstrasse 43D-89075 Ulm, Germany
- Heinrich-Pette-Institut für Experimentelle Virologie und Immunologie an der Universität HamburgMartinistraße 52, D-20251 Hamburg, Germany
- To whom correspondence should be addressed. Tel: +49 731 500 27640; Fax: +49 731 500 26674;
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22
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Abstract
Poly(ADP-ribosyl)ation, which is the posttranslational modification of proteins with poly(ADP-ribose), is catalysed by poly(ADP-ribose) polymerases. DNA-strand break induced catalytic activation of two PARP isoforms, namely PARP-1 and -2, are in involved in DNA base-excision repair and other repair pathways. A body of correlative data suggests a link between DNA-damage induced poly(ADP-ribosyl)ation and mammalian longevity. This notion was reinforced by recently published evidence for interactions between PARP-1 and the Werner syndrome protein, deficiency of which causes premature ageing in humans. Recent research on PARPs and poly(ADP-ribose) provides several candidate mechanisms through which poly(ADP-ribosyl)ation might contribute to keeping the ageing process at slow pace.
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Affiliation(s)
- Alexander Bürkle
- Molecular Toxicology Group, Box X911, University of Konstanz, D-78457 Konstanz, Germany.
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23
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Kaul-Ghanekar R, Majumdar S, Jalota A, Gulati N, Dubey N, Saha B, Chattopadhyay S. Abnormal V(D)J recombination of T cell receptor beta locus in SMAR1 transgenic mice. J Biol Chem 2004; 280:9450-9. [PMID: 15623522 DOI: 10.1074/jbc.m412206200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Scaffold/matrix-associated region-1-binding protein (SMAR1) specifically interacts with the MARbeta sequence, which is located 400-bp upstream of the murine TCRbeta enhancer and is highly expressed during the DP stage of thymocyte development. To further analyze the functions of SMAR1, transgenic mice were generated that express SMAR1 in a tissue-independent manner. SMAR1-overexpressing mice exhibit severely altered frequency of the T cells expressing commonly used Vbetas (Vbeta5.1/5.2 and Vbeta8.1/8.2/8.3). The rearrangements of Vbeta5.1/5.2, Vbeta8.1/8.2/8.3 loci are also reduced in SMAR1 transgenic mice. The T cells in SMAR1 transgenic mice exhibit a mild perturbation at the early DN stage. SMAR1 transgenic mice exhibit hypercellular lymph nodes and spleen accompanied with prominent architectural defects in these organs. These results indicate that SMAR1 plays an important role in the regulation of T cell development as well as V(D)J recombination besides maintaining the architecture of the lymphoid organs.
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Affiliation(s)
- Ruchika Kaul-Ghanekar
- National Center for Cell Science, Pune University Campus, Ganeshkhind, Pune 411007, India
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24
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Audebert M, Salles B, Calsou P. Involvement of Poly(ADP-ribose) Polymerase-1 and XRCC1/DNA Ligase III in an Alternative Route for DNA Double-strand Breaks Rejoining. J Biol Chem 2004; 279:55117-26. [PMID: 15498778 DOI: 10.1074/jbc.m404524200] [Citation(s) in RCA: 518] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The efficient repair of DNA double-strand breaks (DSBs) is critical for the maintenance of genomic integrity. In mammalian cells, the nonhomologous end-joining process that represents the predominant repair pathway relies on the DNA-dependent protein kinase (DNA-PK) and the XRCC4-DNA ligase IV complex. Nonetheless, several in vitro and in vivo results indicate that mammalian cells use more than a single end-joining mechanism. While searching for a DNA-PK-independent end-joining activity, we found that the pretreatment of DNA-PK-proficient and -deficient rodent cells with an inhibitor of the poly(ADP-ribose) polymerase-1 enzyme (PARP-1) led to increased cytotoxicity of the highly efficient DNA double-strand breaking compound calicheamicin gamma1. In addition, the repair kinetics of the DSBs induced by calicheamicin gamma1 was delayed both in PARP-1-proficient cells pretreated with the PARP-1 inhibitor and in PARP-1-deficient cells. In order to get new insights into the mechanism of an alternative route for DSBs repair, we have established a new synapsis and end-joining two-step assay in vitro, operating on DSBs with either nuclear protein extracts or recombinant proteins. We found an end-joining activity independent of the DNA-PK/XRCC4-ligase IV complex but that actually required a novel synapsis activity of PARP-1 and the ligation activity of the XRCC1-DNA ligase III complex, proteins otherwise involved in the base excision repair pathway. Taken together, these results strongly suggest that a PARP-1-dependent DSBs end-joining activity may exist in mammalian cells. We propose that this mechanism could act as an alternative route of DSBs repair that complements the DNA-PK/XRCC4/ligase IV-dependent nonhomologous end-joining.
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Affiliation(s)
- Marc Audebert
- Institut de Pharmacologie et de Biologie Structurale, CNRS UMR 5089, 205 route de Narbonne, F-31077 Toulouse Cedex, France
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25
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Yant SR, Kay MA. Nonhomologous-end-joining factors regulate DNA repair fidelity during Sleeping Beauty element transposition in mammalian cells. Mol Cell Biol 2003; 23:8505-18. [PMID: 14612396 PMCID: PMC262663 DOI: 10.1128/mcb.23.23.8505-8518.2003] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Herein, we report that the DNA-dependent protein kinase (DNA-PK) regulates the DNA damage introduced during Sleeping Beauty (SB) element excision and reinsertion in mammalian cells. Using both plasmid- and chromosome-based mobility assays, we analyzed the repair of transposase-induced double-stranded DNA breaks in cells deficient in either the DNA-binding subunit of DNA-PK (Ku) or its catalytic subunit (DNA-PKcs). We found that the free 3' overhangs left after SB element excision were efficiently and accurately processed by the major Ku-dependent nonhomologous-end-joining pathway. Rejoining of broken DNA molecules in the absence of Ku resulted in extensive end degradation at the donor site and greatly increased the frequency of recombination with ectopic templates. Therefore, the major DNA-PK-dependent DNA damage response predominates over more-error-prone repair pathways and thereby facilitates high-fidelity DNA repair during transposon mobilization in mammalian cells. Although transposable elements were not found to be efficiently circularized after transposase-mediated excision, DNA-PK deficiency supported more-frequent transposase-mediated element insertion than was found in wild-type controls. We conclude that, based on its ability to regulate excision site junctional diversity and transposon insertion frequency, DNA-PK serves an important protective role during transpositional recombination in mammals.
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Affiliation(s)
- Stephen R Yant
- Departments of Pediatrics and Genetics, Stanford University School of Medicine, Stanford, California 94305-5208, USA
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Noël G, Giocanti N, Fernet M, Mégnin-Chanet F, Favaudon V. Poly(ADP-ribose) polymerase (PARP-1) is not involved in DNA double-strand break recovery. BMC Cell Biol 2003; 4:7. [PMID: 12866953 PMCID: PMC179890 DOI: 10.1186/1471-2121-4-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2003] [Accepted: 07/16/2003] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The cytotoxicity and the rejoining of DNA double-strand breaks induced by gamma-rays, H2O2 and neocarzinostatin, were investigated in normal and PARP-1 knockout mouse 3T3 fibroblasts to determine the role of poly(ADP-ribose) polymerase (PARP-1) in DNA double-strand break repair. RESULTS PARP-1-/- were considerably more sensitive than PARP-1+/+ 3T3s to induced cell kill by gamma-rays and H2O2. However, the two cell lines did not show any significant difference in the susceptibility to neocarzinostatin below 1.5 nM drug. Restoration of PARP-1 expression in PARP-1-/- 3T3s by retroviral transfection of the full PARP-1 cDNA did not induce any change in neocarzinostatin response. Moreover the incidence and the rejoining kinetics of neocarzinostatin-induced DNA double-strand breaks were identical in PARP-1+/+ and PARP-1-/- 3T3s. Poly(ADP-ribose) synthesis following gamma-rays and H2O2 was observed in PARP-1-proficient cells only. In contrast neocarzinostatin, even at supra-lethal concentration, was unable to initiate PARP-1 activation yet it induced H2AX histone phosphorylation in both PARP1+/+ and PARP-1-/- 3T3s as efficiently as gamma-rays and H2O2. CONCLUSIONS The results show that PARP-1 is not a major determinant of DNA double-strand break recovery with either strand break rejoining or cell survival as an endpoint. Even though both PARP-1 and ATM activation are major determinants of the cell response to gamma-rays and H2O2, data suggest that PARP-1-dependent poly(ADP-ribose) synthesis and ATM-dependent H2AX phosphorylation, are not inter-related in the repair pathway of neocarzinostatin-induced DNA double-strand breaks.
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Affiliation(s)
- Georges Noël
- Unité 350 INSERM, Institut Curie-Recherche, Bâts. 110-112, Centre Universitaire, 91405 Orsay Cedex, France
- Centre de Protonthérapie d'Orsay, Bât. 101, Centre Universitaire, BP 65, 91402 Orsay Cedex, France
| | - Nicole Giocanti
- Unité 350 INSERM, Institut Curie-Recherche, Bâts. 110-112, Centre Universitaire, 91405 Orsay Cedex, France
| | - Marie Fernet
- Unité 350 INSERM, Institut Curie-Recherche, Bâts. 110-112, Centre Universitaire, 91405 Orsay Cedex, France
- Present address: DNA Repair Group, International Agency for Research on Cancer, 150 cours Albert Thomas, 69372 Lyon Cedex 08, France
| | - Frédérique Mégnin-Chanet
- Unité 350 INSERM, Institut Curie-Recherche, Bâts. 110-112, Centre Universitaire, 91405 Orsay Cedex, France
| | - Vincent Favaudon
- Unité 350 INSERM, Institut Curie-Recherche, Bâts. 110-112, Centre Universitaire, 91405 Orsay Cedex, France
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