101
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PARP inhibition attenuates histopathological lesion in ischemia/reperfusion renal mouse model after cold prolonged ischemia. ScientificWorldJournal 2013; 2013:486574. [PMID: 24319370 PMCID: PMC3844238 DOI: 10.1155/2013/486574] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 09/18/2013] [Indexed: 11/17/2022] Open
Abstract
We test the hypothesis that PARP inhibition can decrease acute tubular necrosis (ATN) and other renal lesions related to prolonged cold ischemia/reperfusion (IR) in kidneys preserved at 4°C in University of Wisconsin (UW) solution. Material and Methods. We used 30 male Parp1+/+ wild-type and 15 male Parp10/0 knockout C57BL/6 mice. Fifteen of these wild-type mice were pretreated with 3,4-dihydro-5-[4-(1-piperidinyl)butoxyl]-1(2H)-isoquinolinone (DPQ) at a concentration of 15 mg/kg body weight, used as PARP inhibitor. Subgroups of mice were established (A: IR 45 min/6 h; B: IR + 48 h in UW solution; and C: IR + 48 h in UW solution plus DPQ). We processed samples for morphological, immunohistochemical, ultrastructural, and western-blotting studies. Results. Prolonged cold ischemia time in UW solution increased PARP-1 expression and kidney injury. Preconditioning with PARP inhibitor DPQ plus DPQ supplementation in UW solution decreased PARP-1 nuclear expression in renal tubules and renal damage. Parp10/0 knockout mice were more resistant to IR-induced renal lesion. In conclusion, PARP inhibition attenuates ATN and other IR-related renal lesions in mouse kidneys under prolonged cold storage in UW solution. If confirmed, these data suggest that pharmacological manipulation of PARP activity may have salutary effects in cold-stored organs at transplantation.
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102
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Steffen JD, Tholey RM, Langelier MF, Planck JL, Schiewer MJ, Lal S, Bildzukewicz NA, Yeo CJ, Knudsen KE, Brody JR, Pascal JM. Targeting PARP-1 allosteric regulation offers therapeutic potential against cancer. Cancer Res 2013; 74:31-7. [PMID: 24189460 DOI: 10.1158/0008-5472.can-13-1701] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PARP-1 is a nuclear protein that has important roles in maintenance of genomic integrity. During genotoxic stress, PARP-1 recruits to sites of DNA damage where PARP-1 domain architecture initiates catalytic activation and subsequent poly(ADP-ribose)-dependent DNA repair. PARP-1 inhibition is a promising new way to selectively target cancers harboring DNA repair deficiencies. However, current inhibitors target other PARPs, raising important questions about long-term off-target effects. Here, we propose a new strategy that targets PARP-1 allosteric regulation as a selective way of inhibiting PARP-1. We found that disruption of PARP-1 domain-domain contacts through mutagenesis held no cellular consequences on recruitment to DNA damage or a model system of transcriptional regulation, but prevented DNA-damage-dependent catalytic activation. Furthermore, PARP-1 mutant overexpression in a pancreatic cancer cell line (MIA PaCa-2) increased sensitivity to platinum-based anticancer agents. These results not only highlight the potential of a synergistic drug combination of allosteric PARP inhibitors with DNA-damaging agents in genomically unstable cancer cells (regardless of homologous recombination status), but also signify important applications of selective PARP-1 inhibition. Finally, the development of a high-throughput PARP-1 assay is described as a tool to promote discovery of novel PARP-1 selective inhibitors.
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Affiliation(s)
- Jamin D Steffen
- Authors' Affiliations: Departments of Biochemistry and Molecular Biology and Surgery, Division of Surgical Research, The Jefferson Pancreas, Biliary, and Related Cancer Center; and Department of Cancer Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
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103
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Zilio N, Williamson CT, Eustermann S, Shah R, West SC, Neuhaus D, Ulrich HD. DNA-dependent SUMO modification of PARP-1. DNA Repair (Amst) 2013; 12:761-73. [PMID: 23871147 PMCID: PMC3744807 DOI: 10.1016/j.dnarep.2013.07.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 06/13/2013] [Accepted: 07/01/2013] [Indexed: 11/28/2022]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP-1) plays an important role in DNA repair, but also contributes to other aspects of nucleic acid metabolism, such as transcriptional regulation. Modification of PARP-1 with the small ubiquitin-related modifier (SUMO) affects its function as a transcriptional co-activator of hypoxia-responsive genes and promotes induction of the heat shock-induced HSP70.1 promoter. We now report that PARP-1 sumoylation is strongly influenced by DNA. Consistent with a function in transcription, we show that sumoylation in vitro is enhanced by binding to intact, but not to damaged DNA, in a manner clearly distinct from the mechanism by which DNA damage stimulates PARP-1's catalytic activity. An enhanced affinity of PARP-1 for the SUMO-conjugating enzyme Ubc9 upon binding to DNA is likely responsible for this effect. Sumoylation does not interfere with the catalytic or DNA-binding properties of PARP-1, and structural analysis reveals no significant impact of SUMO on the conformation of PARP-1's DNA-binding domain. In vivo, sumoylated PARP-1 is associated with chromatin, but the modification is not responsive to DNA damage and is not affected by PARP-1 catalytic activity. Our results suggest that PARP-1's alternative modes of DNA recognition serve as a means to differentiate between distinct aspects of the enzyme's function.
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Affiliation(s)
- Nicola Zilio
- Cancer Research UK London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms EN6 3LD, United Kingdom
| | - Chris T. Williamson
- Cancer Research UK London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms EN6 3LD, United Kingdom
| | - Sebastian Eustermann
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
| | - Rajvee Shah
- Cancer Research UK London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms EN6 3LD, United Kingdom
| | - Stephen C. West
- Cancer Research UK London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms EN6 3LD, United Kingdom
| | - David Neuhaus
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
| | - Helle D. Ulrich
- Cancer Research UK London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms EN6 3LD, United Kingdom
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
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104
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Olaparib: a promising PARP inhibitor in ovarian cancer therapy. Arch Gynecol Obstet 2013; 288:367-74. [DOI: 10.1007/s00404-013-2856-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 04/13/2013] [Indexed: 01/15/2023]
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105
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Ye N, Chen CH, Chen T, Song Z, He JX, Huan XJ, Song SS, Liu Q, Chen Y, Ding J, Xu Y, Miao ZH, Zhang A. Design, Synthesis, and Biological Evaluation of a Series of Benzo[de][1,7]naphthyridin-7(8H)-ones Bearing a Functionalized Longer Chain Appendage as Novel PARP1 Inhibitors. J Med Chem 2013; 56:2885-903. [DOI: 10.1021/jm301825t] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Na Ye
- CAS
Key Laboratory of Receptor Research, and Synthetic Organic & Medicinal
Chemistry Laboratory, ‡State Key Laboratory of Drug Research, and §CAS Key Laboratory
of Receptor Research, and Drug Discovery and Design Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China 201203
| | - Chuan-Huizi Chen
- CAS
Key Laboratory of Receptor Research, and Synthetic Organic & Medicinal
Chemistry Laboratory, ‡State Key Laboratory of Drug Research, and §CAS Key Laboratory
of Receptor Research, and Drug Discovery and Design Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China 201203
| | - TianTian Chen
- CAS
Key Laboratory of Receptor Research, and Synthetic Organic & Medicinal
Chemistry Laboratory, ‡State Key Laboratory of Drug Research, and §CAS Key Laboratory
of Receptor Research, and Drug Discovery and Design Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China 201203
| | - Zilan Song
- CAS
Key Laboratory of Receptor Research, and Synthetic Organic & Medicinal
Chemistry Laboratory, ‡State Key Laboratory of Drug Research, and §CAS Key Laboratory
of Receptor Research, and Drug Discovery and Design Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China 201203
| | - Jin-Xue He
- CAS
Key Laboratory of Receptor Research, and Synthetic Organic & Medicinal
Chemistry Laboratory, ‡State Key Laboratory of Drug Research, and §CAS Key Laboratory
of Receptor Research, and Drug Discovery and Design Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China 201203
| | - Xia-Juan Huan
- CAS
Key Laboratory of Receptor Research, and Synthetic Organic & Medicinal
Chemistry Laboratory, ‡State Key Laboratory of Drug Research, and §CAS Key Laboratory
of Receptor Research, and Drug Discovery and Design Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China 201203
| | - Shan-Shan Song
- CAS
Key Laboratory of Receptor Research, and Synthetic Organic & Medicinal
Chemistry Laboratory, ‡State Key Laboratory of Drug Research, and §CAS Key Laboratory
of Receptor Research, and Drug Discovery and Design Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China 201203
| | - Qiufeng Liu
- CAS
Key Laboratory of Receptor Research, and Synthetic Organic & Medicinal
Chemistry Laboratory, ‡State Key Laboratory of Drug Research, and §CAS Key Laboratory
of Receptor Research, and Drug Discovery and Design Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China 201203
| | - Yi Chen
- CAS
Key Laboratory of Receptor Research, and Synthetic Organic & Medicinal
Chemistry Laboratory, ‡State Key Laboratory of Drug Research, and §CAS Key Laboratory
of Receptor Research, and Drug Discovery and Design Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China 201203
| | - Jian Ding
- CAS
Key Laboratory of Receptor Research, and Synthetic Organic & Medicinal
Chemistry Laboratory, ‡State Key Laboratory of Drug Research, and §CAS Key Laboratory
of Receptor Research, and Drug Discovery and Design Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China 201203
| | - Yechun Xu
- CAS
Key Laboratory of Receptor Research, and Synthetic Organic & Medicinal
Chemistry Laboratory, ‡State Key Laboratory of Drug Research, and §CAS Key Laboratory
of Receptor Research, and Drug Discovery and Design Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China 201203
| | - Ze-Hong Miao
- CAS
Key Laboratory of Receptor Research, and Synthetic Organic & Medicinal
Chemistry Laboratory, ‡State Key Laboratory of Drug Research, and §CAS Key Laboratory
of Receptor Research, and Drug Discovery and Design Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China 201203
| | - Ao Zhang
- CAS
Key Laboratory of Receptor Research, and Synthetic Organic & Medicinal
Chemistry Laboratory, ‡State Key Laboratory of Drug Research, and §CAS Key Laboratory
of Receptor Research, and Drug Discovery and Design Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China 201203
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106
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Structural biology of the writers, readers, and erasers in mono- and poly(ADP-ribose) mediated signaling. Mol Aspects Med 2013; 34:1088-108. [PMID: 23458732 PMCID: PMC3726583 DOI: 10.1016/j.mam.2013.02.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 02/01/2013] [Accepted: 02/18/2013] [Indexed: 12/19/2022]
Abstract
ADP-ribosylation of proteins regulates protein activities in various processes including transcription control, chromatin organization, organelle assembly, protein degradation, and DNA repair. Modulating the proteins involved in the metabolism of ADP-ribosylation can have therapeutic benefits in various disease states. Protein crystal structures can help understand the biological functions, facilitate detailed analysis of single residues, as well as provide a basis for development of small molecule effectors. Here we review recent advances in our understanding of the structural biology of the writers, readers, and erasers of ADP-ribosylation.
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107
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Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition. Nat Struct Mol Biol 2013; 20:347-54. [PMID: 23396353 PMCID: PMC3897332 DOI: 10.1038/nsmb.2501] [Citation(s) in RCA: 368] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 12/26/2012] [Indexed: 12/31/2022]
Abstract
Topoisomerase I (TOP1) inhibitors are an important class of anticancer drugs. The cytotoxicity of TOP1 inhibitors can be modulated by replication fork reversal, in a process that requires PARP activity. Whether regressed forks can efficiently restart and the factors required to restart fork progression after fork reversal are still unknown. Here we combined biochemical and electron microscopy approaches with single-molecule DNA fiber analysis, to identify a key role for human RECQ1 helicase in replication fork restart after TOP1 inhibition, not shared by other human RecQ proteins. We show that the poly(ADPribosyl)ation activity of PARP1 stabilizes forks in their regressed state by limiting their restart by RECQ1. These studies provide new mechanistic insights into the roles of RECQ1 and PARP in DNA replication and offer molecular perspectives to potentiate chemotherapeutic regimens based on TOP1 inhibition.
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108
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Cantó C, Sauve AA, Bai P. Crosstalk between poly(ADP-ribose) polymerase and sirtuin enzymes. Mol Aspects Med 2013; 34:1168-201. [PMID: 23357756 DOI: 10.1016/j.mam.2013.01.004] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 01/07/2013] [Accepted: 01/17/2013] [Indexed: 01/08/2023]
Abstract
Poly(ADP-ribose) polymerases (PARPs) are NAD(+) dependent enzymes that were identified as DNA repair proteins, however, today it seems clear that PARPs are responsible for a plethora of biological functions. Sirtuins (SIRTs) are NAD(+)-dependent deacetylase enzymes involved in the same biological processes as PARPs raising the question whether PARP and SIRT enzymes may interact with each other in physiological and pathophysiological conditions. Hereby we review the current understanding of the SIRT-PARP interplay in regard to the biochemical nature of the interaction (competition for the common NAD(+) substrate, mutual posttranslational modifications and direct transcriptional effects) and the physiological or pathophysiological consequences of the interactions (metabolic events, oxidative stress response, genomic stability and aging). Finally, we give an overview of the possibilities of pharmacological intervention to modulate PARP and SIRT enzymes either directly, or through modulating NAD(+) homeostasis.
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Affiliation(s)
- Carles Cantó
- Nestlé Institute of Health Sciences, Lausanne CH-1015, Switzerland
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109
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Langelier MF, Pascal JM. PARP-1 mechanism for coupling DNA damage detection to poly(ADP-ribose) synthesis. Curr Opin Struct Biol 2013; 23:134-43. [PMID: 23333033 DOI: 10.1016/j.sbi.2013.01.003] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 12/07/2012] [Accepted: 01/03/2013] [Indexed: 12/12/2022]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP-1) regulates gene transcription, cell death signaling, and DNA repair through production of the posttranslational modification poly(ADP-ribose). During the cellular response to genotoxic stress PARP-1 rapidly associates with DNA damage, which robustly stimulates poly(ADP-ribose) production over a low basal level of PARP-1 activity. DNA damage-dependent PARP-1 activity is central to understanding PARP-1 biological function, but structural insights into the mechanisms underlying this mode of regulation have remained elusive, in part due to the highly modular six-domain architecture of PARP-1. Recent structural studies have illustrated how PARP-1 uses specialized zinc fingers to detect DNA breaks through sequence-independent interaction with exposed nucleotide bases, a common feature of damaged and abnormal DNA structures. The mechanism of coupling DNA damage detection to elevated poly(ADP-ribose) production has been elucidated based on a crystal structure of the essential domains of PARP-1 in complex with a DNA strand break. The multiple domains of PARP-1 collapse onto damaged DNA, forming a network of interdomain contacts that introduce destabilizing alterations in the catalytic domain leading to an enhanced rate of poly(ADP-ribose) production.
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Affiliation(s)
- Marie-France Langelier
- Department of Biochemistry and Molecular Biology, The Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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110
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Ye J, Montero M, Stack BC. Effects of Fusaric Acid Treatment on HEp2 and Docetaxel-Resistant HEp2 Laryngeal Squamous Cell Carcinoma. Chemotherapy 2013; 59:121-8. [DOI: 10.1159/000353718] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 06/10/2013] [Indexed: 01/08/2023]
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111
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The Sound of Silence: RNAi in Poly (ADP-Ribose) Research. Genes (Basel) 2012; 3:779-805. [PMID: 24705085 PMCID: PMC3899979 DOI: 10.3390/genes3040779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 11/05/2012] [Accepted: 11/06/2012] [Indexed: 02/07/2023] Open
Abstract
Poly(ADP-ribosyl)-ation is a nonprotein posttranslational modification of proteins and plays an integral part in cell physiology and pathology. The metabolism of poly(ADP-ribose) (PAR) is regulated by its synthesis by poly(ADP-ribose) polymerases (PARPs) and on the catabolic side by poly(ADP-ribose) glycohydrolase (PARG). PARPs convert NAD+ molecules into PAR chains that interact covalently or noncovalently with target proteins and thereby modify their structure and functions. PAR synthesis is activated when PARP1 and PARP2 bind to DNA breaks and these two enzymes account for almost all PAR formation after genotoxic stress. PARG cleaves PAR molecules into free PAR and finally ADP-ribose (ADPR) moieties, both acting as messengers in cellular stress signaling. In this review, we discuss the potential of RNAi to manipulate the levels of PARPs and PARG, and consequently those of PAR and ADPR, and compare the results with those obtained after genetic or chemical disruption.
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112
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Clark NJ, Kramer M, Muthurajan UM, Luger K. Alternative modes of binding of poly(ADP-ribose) polymerase 1 to free DNA and nucleosomes. J Biol Chem 2012; 287:32430-9. [PMID: 22854955 PMCID: PMC3463355 DOI: 10.1074/jbc.m112.397067] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Poly(ADP-ribose) polymerase 1 (PARP-1) is an abundant nuclear protein that binds chromatin and catalyzes the transfer of ADP-ribose groups to itself and to numerous target proteins upon interacting with damaged DNA. The molecular basis for the dual role of PARP-1 as a chromatin architectural protein and a first responder in DNA repair pathways remains unclear. Here, we quantified the interactions of full-length PARP-1 and its N-terminal half with different types of DNA damage and with defined nucleosome substrates. We found that full-length PARP-1 prefers nucleosomes with two linker DNA extensions over any other substrate (including several free DNA models) and that the C-terminal half of PARP-1 is necessary for this selectivity. We also measured the ability of various substrates to activate PARP-1 activity and found that the most important feature for activation is one free DNA end rather than tight interaction with the activating nucleic acid. Our data provide insight into the different modes of interaction of this multidomain protein with nucleosomes and free DNA.
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Affiliation(s)
- Nicholas J Clark
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
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113
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Tan ES, Krukenberg KA, Mitchison TJ. Large-scale preparation and characterization of poly(ADP-ribose) and defined length polymers. Anal Biochem 2012; 428:126-36. [PMID: 22743307 DOI: 10.1016/j.ab.2012.06.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 06/15/2012] [Accepted: 06/17/2012] [Indexed: 10/28/2022]
Abstract
Poly(ADP-ribose) (pADPr) is a large, structurally complex polymer of repeating ADP-ribose units. It is biosynthesized from NAD⁺ by poly(ADP-ribose) polymerases (PARPs) and degraded to ADP-ribose by poly(ADP-ribose) glycohydrolase. pADPr is involved in many cellular processes and exerts biological function through covalent modification and noncovalent binding to specific proteins. Very little is known about molecular recognition and structure-activity relationships for noncovalent interaction between pADPr and its binding proteins, in part because of lack of access to the polymer on a large scale and to units of defined lengths. We prepared polydisperse pADPr from PARP1 and tankyrase 1 at the hundreds of milligram scale by optimizing enzymatic synthesis and scaling up chromatographic purification methods. We developed and calibrated an anion exchange chromatography method to assign pADPr size and scaled it up to purify defined length polymers on the milligram scale. Furthermore, we present a pADPr profiling method to characterize the polydispersity of pADPr produced by PARPs under different reaction conditions and find that substrate proteins affect the pADPr size distribution. These methods will facilitate structural and biochemical studies of pADPr and its binding proteins.
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Affiliation(s)
- Edwin S Tan
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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114
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Wang Z, Wang F, Tang T, Guo C. The role of PARP1 in the DNA damage response and its application in tumor therapy. Front Med 2012; 6:156-64. [PMID: 22660976 DOI: 10.1007/s11684-012-0197-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 03/14/2012] [Indexed: 11/28/2022]
Abstract
Single-strand break repair protein poly(ADP-ribose) polymerase 1 (PARP1) catalyzes the poly(ADP-ribosyl)ation of many key proteins in vivo and thus plays important roles in multiple DNA damage response pathways, rendering it a promising target in cancer therapy. The tumor-suppressor effects of PARP inhibitors have attracted significant interest for development of novel cancer therapies. However, recent evidence indicated that the underlying mechanism of PARP inhibitors in tumor therapy is more complex than previously expected. The present review will focus on recent progress on the role of PARP1 in the DNA damage response and PARP inhibitors in cancer therapy. The emerging resistance of BRCA-deficient tumors to PARP inhibitors is also briefly discussed from the perspective of DNA damage and repair. These recent research advances will inform the selection of patient populations who can benefit from the PARP inhibitor treatment and development of effective drug combination strategies.
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Affiliation(s)
- Zhifeng Wang
- Laboratory of Disease Genomics and Individual Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
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115
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Gagné JP, Rouleau M, Poirier GG. Structural biology. PARP-1 activation--bringing the pieces together. Science 2012; 336:678-9. [PMID: 22582250 DOI: 10.1126/science.1221870] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Jean-Philippe Gagné
- CHUQ Research Center-CHUL, Cancer Research Unit, Laval University, Québec, Canada
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116
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Langelier MF, Planck JL, Roy S, Pascal JM. Structural basis for DNA damage-dependent poly(ADP-ribosyl)ation by human PARP-1. Science 2012; 336:728-32. [PMID: 22582261 PMCID: PMC3532513 DOI: 10.1126/science.1216338] [Citation(s) in RCA: 472] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) (ADP, adenosine diphosphate) has a modular domain architecture that couples DNA damage detection to poly(ADP-ribosyl)ation activity through a poorly understood mechanism. Here, we report the crystal structure of a DNA double-strand break in complex with human PARP-1 domains essential for activation (Zn1, Zn3, WGR-CAT). PARP-1 engages DNA as a monomer, and the interaction with DNA damage organizes PARP-1 domains into a collapsed conformation that can explain the strong preference for automodification. The Zn1, Zn3, and WGR domains collectively bind to DNA, forming a network of interdomain contacts that links the DNA damage interface to the catalytic domain (CAT). The DNA damage-induced conformation of PARP-1 results in structural distortions that destabilize the CAT. Our results suggest that an increase in CAT protein dynamics underlies the DNA-dependent activation mechanism of PARP-1.
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Affiliation(s)
- Marie-France Langelier
- Department of Biochemistry & Molecular Biology, The Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Jamie L. Planck
- Department of Biochemistry & Molecular Biology, The Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Swati Roy
- Department of Biochemistry & Molecular Biology, The Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - John M. Pascal
- Department of Biochemistry & Molecular Biology, The Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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117
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Sousa FG, Matuo R, Soares DG, Escargueil AE, Henriques JAP, Larsen AK, Saffi J. PARPs and the DNA damage response. Carcinogenesis 2012; 33:1433-40. [PMID: 22431722 DOI: 10.1093/carcin/bgs132] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Adenosine diphosphate (ADP)-ribosylation is an important posttranslational modification catalyzed by a variety of enzymes, including poly (ADP ribose) polymerases (PARPs), which use nicotinamide adenine dinucleotide (NAD(+)) as a substrate to synthesize and transfer ADP-ribose units to acceptor proteins. The PARP family members possess a variety of structural domains, span a wide range of functions and localize to various cellular compartments. Among the molecular actions attributed to PARPs, their role in the DNA damage response (DDR) has been widely documented. In particular, PARPs 1-3 are involved in several cellular processes that respond to DNA lesions, which include DNA damage recognition, signaling and repair as well as local transcriptional blockage, chromatin remodeling and cell death induction. However, how these enzymes are able to participate in such numerous and diverse mechanisms in response to DNA damage is not fully understood. Herein, the DDR functions of PARPs 1-3 and the emerging roles of poly (ADP ribose) polymers in DNA damage are reviewed. The development of PARP inhibitors, their applications and mechanisms of action are also discussed in the context of the DDR.
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Affiliation(s)
- Fabricio G Sousa
- Departamento de Biofísica, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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118
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Liu X, Shi Y, Maag DX, Palma JP, Patterson MJ, Ellis PA, Surber BW, Ready DB, Soni NB, Ladror US, Xu AJ, Iyer R, Harlan JE, Solomon LR, Donawho CK, Penning TD, Johnson EF, Shoemaker AR. Iniparib Nonselectively Modifies Cysteine-Containing Proteins in Tumor Cells and Is Not a Bona Fide PARP Inhibitor. Clin Cancer Res 2011; 18:510-23. [DOI: 10.1158/1078-0432.ccr-11-1973] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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119
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Kang J, Fang X, Chen X, Zhao G, Ren A, Xu J, Yang W. The Zinc-Dependent Fluorescence of a Synthetic GFP-Like Chromophore in Organic Solvents. Eur J Inorg Chem 2011. [DOI: 10.1002/ejic.201100605] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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120
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Loeffler PA, Cuneo MJ, Mueller GA, DeRose EF, Gabel SA, London RE. Structural studies of the PARP-1 BRCT domain. BMC STRUCTURAL BIOLOGY 2011; 11:37. [PMID: 21967661 PMCID: PMC3195086 DOI: 10.1186/1472-6807-11-37] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Accepted: 10/03/2011] [Indexed: 01/19/2023]
Abstract
Background Poly(ADP-ribose) polymerase-1 (PARP-1) is one of the first proteins localized to foci of DNA damage. Upon activation by encountering nicked DNA, the PARP-1 mediated trans-poly(ADP-ribosyl)ation of DNA binding proteins occurs, facilitating access and accumulation of DNA repair factors. PARP-1 also auto-(ADP-ribosyl)ates its central BRCT-containing domain forming part of an interaction site for the DNA repair scaffolding protein X-ray cross complementing group 1 protein (XRCC1). The co-localization of XRCC1, as well as bound DNA repair factors, to sites of DNA damage is important for cell survival and genomic integrity. Results Here we present the solution structure and biophysical characterization of the BRCT domain of rat PARP-1. The PARP-1 BRCT domain has the globular α/β fold characteristic of BRCT domains and has a thermal melting transition of 43.0°C. In contrast to a previous characterization of this domain, we demonstrate that it is monomeric in solution using both gel-filtration chromatography and small-angle X-ray scattering. Additionally, we report that the first BRCT domain of XRCC1 does not interact significantly with the PARP-1 BRCT domain in the absence of ADP-ribosylation. Moreover, none of the interactions with other longer PARP-1 constructs which previously had been demonstrated in a pull-down assay of mammalian cell extracts were detected. Conclusions The PARP-1 BRCT domain has the conserved BRCT fold that is known to be an important protein:protein interaction module in DNA repair and cell signalling pathways. Data indicating no significant protein:protein interactions between PARP-1 and XRCC1 likely results from the absence of poly(ADP-ribose) in one or both binding partners, and further implicates a poly(ADP-ribose)-dependent mechanism for localization of XRCC1 to sites of DNA damage.
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Affiliation(s)
- Paul A Loeffler
- Department of Chemistry, Sam Houston State University, Huntsville, Texas 77340, USA
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121
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Ba X, Garg NJ. Signaling mechanism of poly(ADP-ribose) polymerase-1 (PARP-1) in inflammatory diseases. THE AMERICAN JOURNAL OF PATHOLOGY 2011; 178:946-55. [PMID: 21356345 DOI: 10.1016/j.ajpath.2010.12.004] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Revised: 11/06/2010] [Accepted: 12/01/2010] [Indexed: 10/18/2022]
Abstract
Poly(ADP-ribosyl)ation, attaching the ADP-ribose polymer chain to the receptor protein, is a unique posttranslational modification. Poly(ADP-ribose) polymerase-1 (PARP-1) is a well-characterized member of the PARP family. In this review, we provide a general update on molecular structure and structure-based activity of this enzyme. However, we mainly focus on the roles of PARP-1 in inflammatory diseases. Specifically, we discuss the signaling pathway context that PARP-1 is involved in to regulate the pathogenesis of inflammation. PARP-1 facilitates diverse inflammatory responses by promoting inflammation-relevant gene expression, such as cytokines, oxidation-reduction-related enzymes, and adhesion molecules. Excessive activation of PARP-1 induces mitochondria-associated cell death in injured tissues and constitutes another mechanism for exacerbating inflammation.
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Affiliation(s)
- Xueqing Ba
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas 77555-1070, USA.
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122
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Zhou X, Sun X, Cooper KL, Wang F, Liu KJ, Hudson LG. Arsenite interacts selectively with zinc finger proteins containing C3H1 or C4 motifs. J Biol Chem 2011; 286:22855-63. [PMID: 21550982 DOI: 10.1074/jbc.m111.232926] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Arsenic inhibits DNA repair and enhances the genotoxicity of DNA-damaging agents such as benzo[a]pyrene and ultraviolet radiation. Arsenic interaction with DNA repair proteins containing functional zinc finger motifs is one proposed mechanism to account for these observations. Here, we report that arsenite binds to both CCHC DNA-binding zinc fingers of the DNA repair protein PARP-1 (poly(ADP-ribose) polymerase-1). Furthermore, trivalent arsenite coordinated with all three cysteine residues as demonstrated by MS/MS. MALDI-TOF-MS analysis of peptides harboring site-directed substitutions of cysteine with histidine residues within the PARP-1 zinc finger revealed that arsenite bound to peptides containing three or four cysteine residues, but not to peptides with two cysteines, demonstrating arsenite binding selectivity. This finding was not unique to PARP-1; arsenite did not bind to a peptide representing the CCHH zinc finger of the DNA repair protein aprataxin, but did bind to an aprataxin peptide mutated to a CCHC zinc finger. To investigate the impact of arsenite on PARP-1 zinc finger function, we measured the zinc content and DNA-binding capacity of PARP-1 immunoprecipitated from arsenite-exposed cells. PARP-1 zinc content and DNA binding were decreased by 76 and 80%, respectively, compared with protein isolated from untreated cells. We observed comparable decreases in zinc content for XPA (xeroderma pigmentosum group A) protein (CCCC zinc finger), but not SP-1 (specificity protein-1) or aprataxin (CCHH zinc finger). These findings demonstrate that PARP-1 is a direct molecular target of arsenite and that arsenite interacts selectively with zinc finger motifs containing three or more cysteine residues.
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Affiliation(s)
- Xixi Zhou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New Mexico, Albuquerque, New Mexico 87131-0001, USA
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123
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Langelier MF, Planck JL, Roy S, Pascal JM. Crystal structures of poly(ADP-ribose) polymerase-1 (PARP-1) zinc fingers bound to DNA: structural and functional insights into DNA-dependent PARP-1 activity. J Biol Chem 2011; 286:10690-701. [PMID: 21233213 PMCID: PMC3060520 DOI: 10.1074/jbc.m110.202507] [Citation(s) in RCA: 174] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 12/30/2010] [Indexed: 01/07/2023] Open
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) has two homologous zinc finger domains, Zn1 and Zn2, that bind to a variety of DNA structures to stimulate poly(ADP-ribose) synthesis activity and to mediate PARP-1 interaction with chromatin. The structural basis for interaction with DNA is unknown, which limits our understanding of PARP-1 regulation and involvement in DNA repair and transcription. Here, we have determined crystal structures for the individual Zn1 and Zn2 domains in complex with a DNA double strand break, providing the first views of PARP-1 zinc fingers bound to DNA. The Zn1-DNA and Zn2-DNA structures establish a novel, bipartite mode of sequence-independent DNA interaction that engages a continuous region of the phosphodiester backbone and the hydrophobic faces of exposed nucleotide bases. Biochemical and cell biological analysis indicate that the Zn1 and Zn2 domains perform distinct functions. The Zn2 domain exhibits high binding affinity to DNA compared with the Zn1 domain. However, the Zn1 domain is essential for DNA-dependent PARP-1 activity in vitro and in vivo, whereas the Zn2 domain is not strictly required. Structural differences between the Zn1-DNA and Zn2-DNA complexes, combined with mutational and structural analysis, indicate that a specialized region of the Zn1 domain is re-configured through the hydrophobic interaction with exposed nucleotide bases to initiate PARP-1 activation.
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Affiliation(s)
- Marie-France Langelier
- From the Department of Biochemistry and Molecular Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Jamie L. Planck
- From the Department of Biochemistry and Molecular Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Swati Roy
- From the Department of Biochemistry and Molecular Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - John M. Pascal
- From the Department of Biochemistry and Molecular Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
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Sunderland PT, Woon ECY, Dhami A, Bergin AB, Mahon MF, Wood PJ, Jones LA, Tully SR, Lloyd MD, Thompson AS, Javaid H, Martin NMB, Threadgill MD. 5-Benzamidoisoquinolin-1-ones and 5-(ω-carboxyalkyl)isoquinolin-1-ones as isoform-selective inhibitors of poly(ADP-ribose) polymerase 2 (PARP-2). J Med Chem 2011; 54:2049-59. [PMID: 21417348 DOI: 10.1021/jm1010918] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PARP-2 is a member of the poly(ADP-ribose) polymerase family, with some activities similar to those of PARP-1 but with other distinct roles. Two series of isoquinolin-1-ones were designed, synthesized, and evaluated as selective inhibitors of PARP-2, using the structures of the catalytic sites of the isoforms. A new efficient synthesis of 5-aminoisoquinolin-1-one was developed, and acylation with acyl chlorides gave 5-acylaminoisoquinolin-1-ones. By examination of isoquinolin-1-ones with carboxylates tethered to the 5-position, Heck coupling of 5-iodoisoquinolin-1-one furnished the 5-CH═CHCO(2)H compound for reduction to the 5-propanoic acid. Alkylation of 5-aminoisoquinolin-1-one under mildly basic conditions, followed by hydrolysis, gave 5-(carboxymethylamino)isoquinolin-1-one, whereas it was alkylated at 2-N with methyl propenoate and strong base. Compounds were assayed in vitro for inhibition of PARP-1 and PARP-2, using FlashPlate and solution-phase assays, respectively. The 5-benzamidoisoquinolin-1-ones were more selective for inhibition of PARP-2, whereas the 5-(ω-carboxyalkyl)isoquinolin-1-ones were less so. 5-Benzamidoisoquinolin-1-one is the most PARP-2-selective compound (IC(50(PARP-1))/IC(50(PARP-2)) = 9.3) to date, in a comparative study.
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Affiliation(s)
- Peter T Sunderland
- Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
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125
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Leung M, Rosen D, Fields S, Cesano A, Budman DR. Poly(ADP-ribose) polymerase-1 inhibition: preclinical and clinical development of synthetic lethality. Mol Med 2011; 17:854-62. [PMID: 21424107 DOI: 10.2119/molmed.2010.00240] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Accepted: 03/10/2011] [Indexed: 12/17/2022] Open
Abstract
The hereditary forms of breast cancer identified by BRCA1 and BRCA2 genes have a defect in homologous DNA repair and demonstrate a dependence on alternate DNA repair processes by base excision repair, which requires poly(ADP-ribose) polymerase 1 (PARP-1). siRNA and deletion mutations demonstrate that interference with PARP-1 function results in enhanced cell death when the malignancy has a defect in homologous recombination. These findings resulted in a plethora of agents in clinical trials that interfere with DNA repair, and these agents offer the potential of being more selective in their effects than classic chemotherapeutic drugs. An electronic search of the National Library of Medicine for published articles written in English used the terms "PARP inhibitors" and "breast cancer" to find prospective, retrospective and review articles. Additional searches were done for articles dealing with mechanism of action. A total of 152 articles dealing with breast cancer and PARP inhibition were identified. PARP inhibition not only affects nonhomologous repair, but also has several other nongenomic functions. Mutational resistance to these agents was seen in preclinical studies. To date, PARP-1 inhibitors were shown to enhance cytotoxic effects of some chemotherapy agents. This new class of agents may offer more therapeutic specificity by exploiting a DNA repair defect seen in some human tumors with initial clinical trials demonstrating antitumor activity. Although PARP inhibitors may offer a therapeutic option for selected malignancies, the long-term effects of these agents have not yet been defined.
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Affiliation(s)
- Mary Leung
- Division of Experimental Therapeutics, Monter Cancer Center and the Feinstein Institute, Hofstra University School of Medicine, Lake Success, New York, USA
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126
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The DNA-binding domain of human PARP-1 interacts with DNA single-strand breaks as a monomer through its second zinc finger. J Mol Biol 2011; 407:149-70. [PMID: 21262234 PMCID: PMC3094755 DOI: 10.1016/j.jmb.2011.01.034] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 12/16/2010] [Accepted: 01/14/2011] [Indexed: 01/10/2023]
Abstract
Poly(ADP-ribose)polymerase-1 (PARP-1) is a highly abundant chromatin-associated enzyme present in all higher eukaryotic cell nuclei, where it plays key roles in the maintenance of genomic integrity, chromatin remodeling and transcriptional control. It binds to DNA single- and double-strand breaks through an N-terminal region containing two zinc fingers, F1 and F2, following which its C-terminal catalytic domain becomes activated via an unknown mechanism, causing formation and addition of polyadenosine-ribose (PAR) to acceptor proteins including PARP-1 itself. Here, we report a biophysical and structural characterization of the F1 and F2 fingers of human PARP-1, both as independent fragments and in the context of the 24-kDa DNA-binding domain (F1 + F2). We show that the fingers are structurally independent in the absence of DNA and share a highly similar structural fold and dynamics. The F1 + F2 fragment recognizes DNA single-strand breaks as a monomer and in a single orientation. Using a combination of NMR spectroscopy and other biophysical techniques, we show that recognition is primarily achieved by F2, which binds the DNA in an essentially identical manner whether present in isolation or in the two-finger fragment. F2 interacts much more strongly with nicked or gapped DNA ligands than does F1, and we present a mutational study that suggests origins of this difference. Our data suggest that different DNA lesions are recognized by the DNA-binding domain of PARP-1 in a highly similar conformation, helping to rationalize how the full-length protein participates in multiple steps of DNA single-strand breakage and base excision repair.
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127
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Purification of human PARP-1 and PARP-1 domains from Escherichia coli for structural and biochemical analysis. Methods Mol Biol 2011; 780:209-26. [PMID: 21870263 DOI: 10.1007/978-1-61779-270-0_13] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
A general method to express and purify full-length human poly(ADP-ribose) polymerase-1 (PARP-1), individual PARP-1 domains, and groups of PARP-1 domains from Escherichia coli cells is described. The procedure allows for robust production of highly pure PARP-1 that is free of DNA contamination and well-suited for biochemical experiments and for structural and biophysical analysis. Two biochemical assays for monitoring PARP-1 automodification activity are presented that can be used to evaluate purified PARP-1, combinations of PARP-1 domains, or PARP-1 mutants.
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128
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Huambachano O, Herrera F, Rancourt A, Satoh MS. Double-stranded DNA binding domain of poly(ADP-ribose) polymerase-1 and molecular insight into the regulation of its activity. J Biol Chem 2010; 286:7149-60. [PMID: 21183686 DOI: 10.1074/jbc.m110.175190] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) modifies various proteins, including itself, with ADP-ribose polymers (automodification). Polymer synthesis is triggered by binding of its zinc finger 1 (Zn1) and 2 (Zn2) to DNA breaks and is followed by inactivation through automodification. The multiple functional domains of PARP-1 appear to regulate activation and automodification-mediated inactivation of PARP-1. However, the roles of these domains in activation-inactivation processes are not well understood. Our results suggest that Zn1, Zn2, and a domain identified in this study, the double-stranded DNA binding (DsDB) domain, are involved in DNA break-dependent activation of PARP-1. We found that binding of the DsDB domain to double-stranded DNA and DNA break recognition by Zn1 and Zn2, whose actual binding targets are likely to be single-stranded DNA, lead to the activation of PARP-1. In turn, the displacement of single- and double-stranded DNA from Zn2 and the DsDB domain caused by ADP-ribose polymer synthesis results in the dissociation of PARP-1 from DNA breaks and thus its inactivation. We also found that the WGR domain is one of the domains involved in the RNA-dependent activation of PARP-1. Furthermore, because zinc finger 3 (Zn3) has the ability to bind to single-stranded RNA, it may have an indirect role in RNA-dependent activation. PARP-1 functional domains, which are involved in oligonucleic acid binding, therefore coordinately regulate PARP-1 activity depending on the status of the neighboring oligonucleic acids. Based on these results, we proposed a model for the regulation of PARP-1 activity.
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Affiliation(s)
- Orlando Huambachano
- Laboratory of DNA Damage Responses and Bioimaging, Faculty of Medicine, Laval University Medical Centre (CHUQ), Laval University, Québec, Québec G1V 4G2, Canada
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129
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Chaitanya GV, Alexander JS, Babu PP. PARP-1 cleavage fragments: signatures of cell-death proteases in neurodegeneration. Cell Commun Signal 2010; 8:31. [PMID: 21176168 PMCID: PMC3022541 DOI: 10.1186/1478-811x-8-31] [Citation(s) in RCA: 660] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 12/22/2010] [Indexed: 11/16/2022] Open
Abstract
The normal function of poly (ADP-ribose) polymerase-1 (PARP-1) is the routine repair of DNA damage by adding poly (ADP ribose) polymers in response to a variety of cellular stresses. Recently, it has become widely appreciated that PARP-1 also participates in diverse physiological and pathological functions from cell survival to several forms of cell death and has been implicated in gene transcription, immune responses, inflammation, learning, memory, synaptic functions, angiogenesis and aging. In the CNS, PARP inhibition attenuates injury in pathologies like cerebral ischemia, trauma and excitotoxicity demonstrating a central role of PARP-1 in these pathologies. PARP-1 is also a preferred substrate for several 'suicidal' proteases and the proteolytic action of suicidal proteases (caspases, calpains, cathepsins, granzymes and matrix metalloproteinases (MMPs)) on PARP-1 produces several specific proteolytic cleavage fragments with different molecular weights. These PARP-1 signature fragments are recognized biomarkers for specific patterns of protease activity in unique cell death programs. This review focuses on specific suicidal proteases active towards PARP-1 to generate signature PARP-1 fragments that can identify key proteases and particular forms of cell death involved in pathophysiology. The roles played by some of the PARP-1 fragments and their associated binding partners in the control of different forms of cell death are also discussed.
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Affiliation(s)
- Ganta Vijay Chaitanya
- Department of Biotechnology, School of Life Sciences, University of Hyderabad, Hyderabad, India
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center-Shreveport, Louisiana-USA
| | - Jonathan S Alexander
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center-Shreveport, Louisiana-USA
| | - Phanithi Prakash Babu
- Department of Biotechnology, School of Life Sciences, University of Hyderabad, Hyderabad, India
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130
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Mégnin-Chanet F, Bollet MA, Hall J. Targeting poly(ADP-ribose) polymerase activity for cancer therapy. Cell Mol Life Sci 2010; 67:3649-62. [PMID: 20725763 PMCID: PMC2955921 DOI: 10.1007/s00018-010-0490-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 07/28/2010] [Indexed: 02/06/2023]
Abstract
Poly(ADP-ribosyl)ation is a ubiquitous protein modification found in mammalian cells that modulates many cellular responses, including DNA repair. The poly(ADP-ribose) polymerase (PARP) family catalyze the formation and addition onto proteins of negatively charged ADP-ribose polymers synthesized from NAD(+). The absence of PARP-1 and PARP-2, both of which are activated by DNA damage, results in hypersensitivity to ionizing radiation and alkylating agents. PARP inhibitors that compete with NAD(+) at the enzyme's activity site are effective chemo- and radiopotentiation agents and, in BRCA-deficient tumors, can be used as single-agent therapies acting through the principle of synthetic lethality. Through extensive drug-development programs, third-generation inhibitors have now entered clinical trials and are showing great promise. However, both PARP-1 and PARP-2 are not only involved in DNA repair but also in transcription regulation, chromatin modification, and cellular homeostasis. The impact on these processes of PARP inhibition on long-term therapeutic responses needs to be investigated.
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Affiliation(s)
- Frédérique Mégnin-Chanet
- Institut Curie, Centre de Recherche, Bât. 110–112, Centre Universitaire, 91405 Orsay, France
- INSERM, U612, Bât. 110–112, Centre Universitaire, 91405 Orsay, France
| | - Marc A. Bollet
- Département d’oncologie radiothérapique, Institut Curie, 26, rue d’Ulm, 75248 Paris cedex 05, France
| | - Janet Hall
- Institut Curie, Centre de Recherche, Bât. 110–112, Centre Universitaire, 91405 Orsay, France
- INSERM, U612, Bât. 110–112, Centre Universitaire, 91405 Orsay, France
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131
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Citarelli M, Teotia S, Lamb RS. Evolutionary history of the poly(ADP-ribose) polymerase gene family in eukaryotes. BMC Evol Biol 2010; 10:308. [PMID: 20942953 PMCID: PMC2964712 DOI: 10.1186/1471-2148-10-308] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Accepted: 10/13/2010] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The poly(ADP-ribose) polymerase (PARP) superfamily was originally identified as enzymes that catalyze the attachment of ADP-ribose subunits to target proteins using NAD+ as a substrate. The family is characterized by the catalytic site, termed the PARP signature. While these proteins can be found in a range of eukaryotes, they have been best studied in mammals. In these organisms, PARPs have key functions in DNA repair, genome integrity and epigenetic regulation. More recently it has been found that proteins within the PARP superfamily have altered catalytic sites, and have mono(ADP-ribose) transferase (mART) activity or are enzymatically inactive. These findings suggest that the PARP signature has a broader range of functions that initially predicted. In this study, we investigate the evolutionary history of PARP genes across the eukaryotes. RESULTS We identified in silico 236 PARP proteins from 77 species across five of the six eukaryotic supergroups. We performed extensive phylogenetic analyses of the identified PARPs. They are found in all eukaryotic supergroups for which sequence is available, but some individual lineages within supergroups have independently lost these genes. The PARP superfamily can be subdivided into six clades. Two of these clades were likely found in the last common eukaryotic ancestor. In addition, we have identified PARPs in organisms in which they have not previously been described. CONCLUSIONS Three main conclusions can be drawn from our study. First, the broad distribution and pattern of representation of PARP genes indicates that the ancestor of all extant eukaryotes encoded proteins of this type. Second, the ancestral PARP proteins had different functions and activities. One of these proteins was similar to human PARP1 and likely functioned in DNA damage response. The second of the ancestral PARPs had already evolved differences in its catalytic domain that suggest that these proteins may not have possessed poly(ADP-ribosyl)ation activity. Third, the diversity of the PARP superfamily is larger than previously documented, suggesting as more eukaryotic genomes become available, this gene family will grow in both number and type.
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Affiliation(s)
- Matteo Citarelli
- Plant Cellular and Molecular Biology Department, Ohio State University, 500 Aronoff Laboratory, 318 W. 12th Ave., Columbus, OH 43210 USA
| | - Sachin Teotia
- Plant Cellular and Molecular Biology Department, Ohio State University, 500 Aronoff Laboratory, 318 W. 12th Ave., Columbus, OH 43210 USA
- Molcular, Cellular and Developmental Biology Program, Ohio State University, Columbus, OH 43210 USA
| | - Rebecca S Lamb
- Plant Cellular and Molecular Biology Department, Ohio State University, 500 Aronoff Laboratory, 318 W. 12th Ave., Columbus, OH 43210 USA
- Molcular, Cellular and Developmental Biology Program, Ohio State University, Columbus, OH 43210 USA
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132
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Botta D, Jacobson MK. Identification of a regulatory segment of poly(ADP-ribose) glycohydrolase. Biochemistry 2010; 49:7674-82. [PMID: 20684510 DOI: 10.1021/bi100973m] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Coordinate regulation of PARP-1 and -2 and PARG is required for cellular responses to genotoxic stress. While PARP-1 and -2 are regulated by DNA breaks and covalent modifications, mechanisms of PARG regulation are poorly understood. We report here discovery of a PARG regulatory segment far removed linearly from residues involved in catalysis. Expression and analysis of human PARG segments identified a minimal catalytically active C-terminal PARG (hPARG59) containing a 16-residue N-terminal mitochondrial targeting sequence (MTS). Deletion analysis and site-directed mutagenesis revealed that the MTS, specifically hydrophobic residues L473 and L474, was required for PARG activity. This region of PARG was termed the "regulatory segment/MTS" (REG/MTS). The overall alpha-helical composition of hPARG59, determined by circular dichroism (CD), was unaffected by mutation of the REG/MTS leucine residues, suggesting that activity loss was not due to incorrect protein folding. REG/MTS was predicted to be in a loop conformation because the CD spectra of mutant Delta1-16 lacking the REG/MTS showed a higher alpha-helical content than hPARG59, indicating a secondary structure other than alpha-helix for this segment. Deletion of the REG/MTS from full-length hPARG111 also resulted in a complete loss of activity, indicating that all PARG isoforms are subject to regulation at this site. The presence of the REG/MTS raises the possibility that PARG activity is regulated by interactions of PARP-1 and -2 and other proteins at this site, raises interesting questions concerning mitochondrial PARG because MTS residues are often removed after transport, and offers a potentially novel site for drug targeting of PARG.
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Affiliation(s)
- Davide Botta
- Department of Pharmacology and Toxicology, College of Pharmacy and Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, USA
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133
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Krishnakumar R, Kraus WL. The PARP side of the nucleus: molecular actions, physiological outcomes, and clinical targets. Mol Cell 2010; 39:8-24. [PMID: 20603072 DOI: 10.1016/j.molcel.2010.06.017] [Citation(s) in RCA: 670] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 05/05/2010] [Accepted: 05/19/2010] [Indexed: 02/06/2023]
Abstract
The abundant nuclear enzyme PARP-1, a multifunctional regulator of chromatin structure, transcription, and genomic integrity, plays key roles in a wide variety of processes in the nucleus. Recent studies have begun to connect the molecular functions of PARP-1 to specific physiological and pathological outcomes, many of which can be altered by an expanding array of chemical inhibitors of PARP enzymatic activity.
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Affiliation(s)
- Raga Krishnakumar
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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134
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Paddock MN, Buelow BD, Takeda S, Scharenberg AM. The BRCT domain of PARP-1 is required for immunoglobulin gene conversion. PLoS Biol 2010; 8:e1000428. [PMID: 20652015 PMCID: PMC2907289 DOI: 10.1371/journal.pbio.1000428] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Accepted: 06/08/2010] [Indexed: 11/18/2022] Open
Abstract
During affinity maturation, genomic integrity is maintained through specific targeting of DNA mutations. The DNA damage sensor PARP-1 helps determine whether a DNA lesion results in faithful or mutagenic repair. Genetic variation at immunoglobulin (Ig) gene variable regions in B-cells is created through a multi-step process involving deamination of cytosine bases by activation-induced cytidine deaminase (AID) and their subsequent mutagenic repair. To protect the genome from dangerous, potentially oncogenic effects of off-target mutations, both AID activity and mutagenic repair are targeted specifically to the Ig genes. However, the mechanisms of targeting are unknown and recent data have highlighted the role of regulating mutagenic repair to limit the accumulation of somatic mutations resulting from the more widely distributed AID-induced lesions to the Ig genes. Here we investigated the role of the DNA damage sensor poly-(ADPribose)-polymerase-1 (PARP-1) in the repair of AID-induced DNA lesions. We show through sequencing of the diversifying Ig genes in PARP-1−/− DT40 B-cells that PARP-1 deficiency results in a marked reduction in gene conversion events and enhanced high-fidelity repair of AID-induced lesions at both Ig heavy and light chains. To further characterize the role of PARP-1 in the mutagenic repair of AID-induced lesions, we performed functional analyses comparing the role of engineered PARP-1 variants in high-fidelity repair of DNA damage induced by methyl methane sulfonate (MMS) and the mutagenic repair of lesions at the Ig genes induced by AID. This revealed a requirement for the previously uncharacterized BRCT domain of PARP-1 to reconstitute both gene conversion and a normal rate of somatic mutation at Ig genes, while being dispensable for the high-fidelity base excision repair. From these data we conclude that the BRCT domain of PARP-1 is required to initiate a significant proportion of the mutagenic repair specific to diversifying antibody genes. This role is distinct from the known roles of PARP-1 in high-fidelity DNA repair, suggesting that the PARP-1 BRCT domain has a specialized role in assembling mutagenic DNA repair complexes involved in antibody diversification. To produce a limitless diversity of antibodies within the constraints of a finite genome, activated B cells introduce random mutations into antibody genes through a process of targeted DNA damage and subsequent mutagenic repair. At the same time, the rest of the genome must be protected from mutagenesis to prevent off-target mutations which can lead to the development of lymphoma or leukemia. How antibody genes are specifically targeted is still largely unknown. A potential player in this process is the DNA-damage-sensing enzyme PARP-1, which recruits DNA repair enzymes to sites of damage. Using a chicken B cell lymphoma cell line because it has only a single PARP isoform and constitutively mutates its antibody genes, we compared the types of mutations accumulated in PARP-1−/− cells to wild type. We found that in cells lacking PARP-1, the major pathway of mutagenic repair was disrupted and fewer mutations than normal were introduced into their antibody genes. To identify what might be important for mutagenesis, we tested different factors for their ability to rescue this mutagenic deficiency and found a role for the BRCT (BRCA1 C-terminal) domain of PARP-1, a consensus protein domain known to be involved in directing protein-protein interactions. Our evidence suggests that PARP-1 may be interacting with another hypothetical protein via its BRCT domain that is required for the mutagenic rather than faithful repair of DNA lesions in the antibody genes.
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Affiliation(s)
- Marcia N. Paddock
- Department of Immunology, University of Washington, Seattle, Washington, United States of America
- Center for Immunity and Immunotherapies, Seattle Children's Hospital Research Institute, Seattle, Washington, United States of America
| | - Ben D. Buelow
- Department of Immunology, University of Washington, Seattle, Washington, United States of America
- Center for Immunity and Immunotherapies, Seattle Children's Hospital Research Institute, Seattle, Washington, United States of America
| | - Shunichi Takeda
- Crest Laboratory, Department of Radiation Genetics, Faculty of Medicine, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Andrew M. Scharenberg
- Department of Immunology, University of Washington, Seattle, Washington, United States of America
- Center for Immunity and Immunotherapies, Seattle Children's Hospital Research Institute, Seattle, Washington, United States of America
- * E-mail:
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135
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Perry JJP, Cotner-Gohara E, Ellenberger T, Tainer JA. Structural dynamics in DNA damage signaling and repair. Curr Opin Struct Biol 2010; 20:283-94. [PMID: 20439160 DOI: 10.1016/j.sbi.2010.03.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 03/31/2010] [Accepted: 03/31/2010] [Indexed: 10/19/2022]
Abstract
Changing macromolecular conformations and complexes are critical features of cellular networks, typified by DNA damage response pathways that are essential to life. These fluctuations enhance the specificity of macromolecular recognition and catalysis, and enable an integrated functioning of pathway components, ensuring efficiency while reducing off pathway reactions. Such dynamic complexes challenge classical detailed structural analyses, so their characterizations demand combining methods that provide detail with those that inform dynamics in solution. Small-angle X-ray scattering, electron microscopy, hydrogen-deuterium exchange and computation are complementing detailed structures from crystallography and NMR to provide comprehensive models for DNA damage searching, specificity, signaling, and repair. Here, we review new approaches and results on DNA damage responses that advance structural biology in the fourth dimension, connecting proteins to pathways.
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Affiliation(s)
- J Jefferson P Perry
- Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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136
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Langelier MF, Ruhl DD, Planck JL, Kraus WL, Pascal JM. The Zn3 domain of human poly(ADP-ribose) polymerase-1 (PARP-1) functions in both DNA-dependent poly(ADP-ribose) synthesis activity and chromatin compaction. J Biol Chem 2010; 285:18877-87. [PMID: 20388712 DOI: 10.1074/jbc.m110.105668] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
PARP-1 is involved in multiple cellular processes, including transcription, DNA repair, and apoptosis. PARP-1 attaches ADP-ribose units to target proteins, including itself as a post-translational modification that can change the biochemical properties of target proteins and mediate recruitment of proteins to sites of poly(ADP-ribose) synthesis. Independent of its catalytic activity, PARP-1 binds to chromatin and promotes compaction affecting RNA polymerase II transcription. PARP-1 has a modular structure composed of six independent domains. Two homologous zinc fingers, Zn1 and Zn2, form the DNA-binding module. Zn1-Zn2 binding to DNA breaks triggers catalytic activity. Recently, we have identified a third zinc binding domain in PARP-1, the Zn3 domain, which is essential for DNA-dependent PARP-1 activity. The crystal structure of the Zn3 domain revealed a novel zinc-ribbon fold and a homodimeric Zn3 structure that formed in the crystal lattice. Structure-guided mutagenesis was used here to investigate the roles of these two features of the Zn3 domain. Our results indicate that the zinc-ribbon fold of the Zn3 domain mediates an interdomain contact crucial to assembly of the DNA-activated conformation of PARP-1. In contrast, residues located at the Zn3 dimer interface are not required for DNA-dependent activation but rather make important contributions to the chromatin compaction activity of PARP-1. Thus, the Zn3 domain has dual roles in regulating the functions of PARP-1.
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Affiliation(s)
- Marie-France Langelier
- Department of Biochemistry and Molecular Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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137
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Abstract
Recent findings have thrust poly(ADP-ribose) polymerases (PARPs) into the limelight as potential chemotherapeutic targets. To provide a framework for understanding these recent observations, we review what is known about the structures and functions of the family of PARP enzymes, and then outline a series of questions that should be addressed to guide the rational development of PARP inhibitors as anticancer agents.
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Affiliation(s)
- Michèle Rouleau
- Laval University Medical Research Center, Laval University, Québec, Canada
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138
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Ogino H, Nakayama R, Sakamoto H, Yoshida T, Sugimura T, Masutani M. Analysis of poly(ADP-ribose) polymerase-1 (PARP1) gene alteration in human germ cell tumor cell lines. ACTA ACUST UNITED AC 2010; 197:8-15. [PMID: 20113831 DOI: 10.1016/j.cancergencyto.2009.10.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2009] [Revised: 10/17/2009] [Accepted: 10/17/2009] [Indexed: 10/19/2022]
Abstract
The poly(ADP-ribose) polymerase-1 protein (PARP-1) functions in DNA repair, maintenance of genomic stability, induction of cell death, and transcriptional regulation. We previously analyzed alterations of the PARP1 gene in 16 specimens of human germ cell tumors, and found a heterozygous sequence alteration that causes the amino acid substitution Met129Thr (M129T) in both tumor and normal tissues in a single patient. In this study, aberration of the PARP1 gene and protein was further analyzed in human germ cell tumor cell lines. We found a nonheterozygous sequence alteration that causes the amino acid substitution Glu251Lys (E251K) located at a conserved peptide stretch of PARP-1 in cell line NEC8. Sequencing of 95 samples from Japanese healthy volunteers revealed that all the samples were homozygous for the wild-type alleles at M129T and E251K. The M129T allele is thus suggested to be a rare single-nucleotide polymorphism (SNP). We observed a decrease in auto-poly(ADP-ribosyl)ation activity of PARP-1 proteins harboring M129T or E251K amino acid substitution, but the difference was not statistically significant. The levels of PARP-1 and poly(ADP-ribosyl)ation were heterogeneous among germ cell tumor cell lines. The SNPs of the PARP1 gene, as well as differences in the levels of PARP-1 and poly(ADP-ribosyl)ation of proteins, may influence germ cell tumor development and responses to chemotherapy and radiotherapy.
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Affiliation(s)
- Hideki Ogino
- Biochemistry Division, National Cancer Center Research Institute, 1-1 Tsukiji 5-chome, Chuo-ku, Tokyo, Japan
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139
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Lilyestrom W, van der Woerd MJ, Clark N, Luger K. Structural and biophysical studies of human PARP-1 in complex with damaged DNA. J Mol Biol 2010; 395:983-94. [PMID: 19962992 PMCID: PMC2864582 DOI: 10.1016/j.jmb.2009.11.062] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 11/25/2009] [Accepted: 11/29/2009] [Indexed: 12/13/2022]
Abstract
The enzyme poly(ADP-ribose) polymerase-1 (PARP-1) is a global monitor of chromatin structure and DNA damage repair. PARP-1 binds to nucleosomes and poly(ADP-ribosylates) histones and several chromatin-associated factors to expose specific DNA sequences to the cellular machinery involved in gene transcription and/or DNA damage repair. While these processes are critical to genomic stability, the molecular mechanisms of how DNA damage induces PARP-1 activation are poorly understood. We have used biochemical and thermodynamic measurements in conjunction with small-angle X-ray scattering to determine the stoichiometry, affinity, and overall structure of a human PARP-1 construct containing the entire DNA binding region, the zinc ribbon domain, and automodification domains (residues 1-486). The interaction of this PARP-1 protein construct with three different DNA damage models (DNA constructs containing a nick, a blunt end, or a 3' extension) was evaluated. Our data indicate that PARP-1 binds each DNA damage model as a monomer and with similar affinity, in all cases resulting in robust activation of the catalytic domain. Using small-angle X-ray scattering, we determined that the N-terminal half of PARP-1 behaves as an extended and flexible arrangement of individually folded domains in the absence of DNA. Upon binding DNA, PARP-1 undergoes a conformational change in the area surrounding the zinc ribbon domain. These data support a model in which PARP-1, upon binding DNA, undergoes a conformational change to become an active nuclear enzyme.
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Affiliation(s)
- Wayne Lilyestrom
- Department of Biochemistry and Molecular Biology, Colorado State University, Howard Hughes Medical Institute, Fort Collins, CO 80523, USA
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140
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Jorgensen TJ, Chen K, Chasovskikh S, Roy R, Dritschilo A, Uren A. Binding kinetics and activity of human poly(ADP-ribose) polymerase-1 on oligo-deoxyribonucleotide substrates. J Mol Recognit 2010; 22:446-52. [PMID: 19585541 DOI: 10.1002/jmr.962] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) is a mammalian enzyme that attaches long branching chains of ADP-ribose to specific nuclear proteins, including itself. Because its activity in vitro is dependent upon interaction with broken DNA, it has been postulated that PARP-1 plays an important role in DNA strand-break repair in vivo. The exact mechanism of binding to DNA and the structural determinants of binding remain to be defined, but regions of transition from single-stranded to double-strandedness may be important recognition sites. Here we employ surface plasmon resonance (SPR) to investigate this hypothesis. Oligodeoxynucleotide (ODN) substrates that mimic DNA with different degrees of single-strandedness were used for measurements of both PARP-1/DNA binding kinetics and PARP-1's enzyme activities. We found that binding correlated with activity, but was unrelated to single-strandedness of the ODN. Instead, PARP-1 binding and activity were highest on ODNs that modeled a DNA double-strand break (DSB). These results provide support for PARP-1 recognizing and binding DSBs in a manner that is independent of single-stranded features, and demonstrate the usefulness of SPR for simultaneously investigating both PARP-1 binding and PARP-1 auto-poly(ADP-ribosyl)ation activities within the same in vitro system.
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Affiliation(s)
- Timothy J Jorgensen
- Departments of Radiation Medicine, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA.
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141
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Bornhorst J, Ebert F, Hartwig A, Michalke B, Schwerdtle T. Manganese inhibits poly(ADP-ribosyl)ation in human cells: a possible mechanism behind manganese-induced toxicity? ACTA ACUST UNITED AC 2010; 12:2062-9. [DOI: 10.1039/c0em00252f] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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142
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Hoffmann MH, Trembleau S, Muller S, Steiner G. Nucleic acid-associated autoantigens: pathogenic involvement and therapeutic potential. J Autoimmun 2009; 34:J178-206. [PMID: 20031372 DOI: 10.1016/j.jaut.2009.11.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Autoimmunity to ubiquitously expressed macromolecular nucleic acid-protein complexes such as the nucleosome or the spliceosome is a characteristic feature of systemic autoimmune diseases. Disease-specificity and/or association with clinical features of some of these autoimmune responses suggest pathogenic involvement which, however, has been proven in only a few cases so far. Although the mechanisms leading to autoimmunity against nucleic acid-containing complexes are still far from being fully understood, there is increasing experimental evidence that the nucleic acid component may act as a co-stimulator or adjuvans via activation of nucleic acid-binding receptor systems such as Toll-like receptors in antigen-presenting cells. Dysregulated apoptosis and inappropriate stimulation of nucleic acid-sensing receptors may lead to loss of tolerance against the protein components of such complexes, activation of autoreactive T cells and formation of autoantibodies. This has been demonstrated to occur in systemic lupus erythematosus and seems to represent a general mechanism that may be crucial for the development of systemic autoimmune diseases. This review provides a comprehensive overview of the most thoroughly-characterized nucleic acid-associated autoantigens, describing their structure and biological function, as well as the nature and pathogenic importance of the reactivities directed against them. Furthermore, recent advances in immunotherapy such as antigen-specific approaches targeted at nucleic acid-binding antigens are discussed.
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Affiliation(s)
- Markus H Hoffmann
- Division of Rheumatology, Internal Medicine III, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria
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143
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Agarwal A, Mahfouz RZ, Sharma RK, Sarkar O, Mangrola D, Mathur PP. Potential biological role of poly (ADP-ribose) polymerase (PARP) in male gametes. Reprod Biol Endocrinol 2009; 7:143. [PMID: 19961617 PMCID: PMC2800114 DOI: 10.1186/1477-7827-7-143] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Accepted: 12/05/2009] [Indexed: 12/13/2022] Open
Abstract
Maintaining the integrity of sperm DNA is vital to reproduction and male fertility. Sperm contain a number of molecules and pathways for the repair of base excision, base mismatches and DNA strand breaks. The presence of Poly (ADP-ribose) polymerase (PARP), a DNA repair enzyme, and its homologues has recently been shown in male germ cells, specifically during stage VII of spermatogenesis. High PARP expression has been reported in mature spermatozoa and in proven fertile men. Whenever there are strand breaks in sperm DNA due to oxidative stress, chromatin remodeling or cell death, PARP is activated. However, the cleavage of PARP by caspase-3 inactivates it and inhibits PARP's DNA-repairing abilities. Therefore, cleaved PARP (cPARP) may be considered a marker of apoptosis. The presence of higher levels of cPARP in sperm of infertile men adds a new proof for the correlation between apoptosis and male infertility. This review describes the possible biological significance of PARP in mammalian cells with the focus on male reproduction. The review elaborates on the role played by PARP during spermatogenesis, sperm maturation in ejaculated spermatozoa and the potential role of PARP as new marker of sperm damage. PARP could provide new strategies to preserve fertility in cancer patients subjected to genotoxic stresses and may be a key to better male reproductive health.
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Affiliation(s)
- Ashok Agarwal
- Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Reda Z Mahfouz
- Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Rakesh K Sharma
- Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Oli Sarkar
- Department of Biochemistry and Molecular Biology, Pondicherry University, Pondicherry, India
- McGill University Health Center, Montreal, Canada
| | - Devna Mangrola
- Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Premendu P Mathur
- Department of Biochemistry and Molecular Biology, Pondicherry University, Pondicherry, India
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144
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Tao Z, Gao P, Liu HW. Identification of the ADP-ribosylation sites in the PARP-1 automodification domain: analysis and implications. J Am Chem Soc 2009; 131:14258-60. [PMID: 19764761 DOI: 10.1021/ja906135d] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) is a multimodular (domains A, B, C, D, E, and F) nuclear protein that participates in many fundamental cellular activities. Stimulated by binding to nicked DNA, PARP-1 catalyzes poly(ADP-ribosyl)ation of the acceptor proteins and itself using NAD(+) as a substrate. Early studies suggested that domain D is likely an interface for protein-protein interaction between PARP-1 and its targets and is also the primary region for automodification. However, determination of the modification sites has been complicated by the heterogeneous nature of the poly(ADP-ribose) polymer. Here we report a strategy to identify the modification sites on domain D using the PARP-1 E988Q mutant, which only catalyzes mono(ADP-ribosyl)ation. Trypsin digestion of the modified domain D followed by LC-MS/MS analysis led to the identification of three ADP-ribosylation sites in domain D (D387, E488, and E491). Our data also show, in contrast to early reports, that automodification of PARP-1 is not limited to domain D but occurs beyond this region. In addition, domain D is not essential for PARP-1 activity since PARP-1 mutant having domain D deleted is still catalytically active. Two synthetic peptides with amino acid sequences derived from the ADP-ribosylation sites of domain D were also demonstrated to act as PARP-1 substrates. The methodology and the results reported herein will facilitate future studies of PARP-1 catalysis.
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Affiliation(s)
- Zhihua Tao
- Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA
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145
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Altmeyer M, Messner S, Hassa PO, Fey M, Hottiger MO. Molecular mechanism of poly(ADP-ribosyl)ation by PARP1 and identification of lysine residues as ADP-ribose acceptor sites. Nucleic Acids Res 2009; 37:3723-38. [PMID: 19372272 PMCID: PMC2699514 DOI: 10.1093/nar/gkp229] [Citation(s) in RCA: 267] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) synthesizes poly(ADP-ribose) (PAR) using nicotinamide adenine dinucleotide (NAD) as a substrate. Despite intensive research on the cellular functions of PARP1, the molecular mechanism of PAR formation has not been comprehensively understood. In this study, we elucidate the molecular mechanisms of poly(ADP-ribosyl)ation and identify PAR acceptor sites. Generation of different chimera proteins revealed that the amino-terminal domains of PARP1, PARP2 and PARP3 cooperate tightly with their corresponding catalytic domains. The DNA-dependent interaction between the amino-terminal DNA-binding domain and the catalytic domain of PARP1 increased Vmax and decreased the Km for NAD. Furthermore, we show that glutamic acid residues in the auto-modification domain of PARP1 are not required for PAR formation. Instead, we identify individual lysine residues as acceptor sites for ADP-ribosylation. Together, our findings provide novel mechanistic insights into PAR synthesis with significant relevance for the different biological functions of PARP family members.
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Affiliation(s)
- Matthias Altmeyer
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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146
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Gagné JP, Moreel X, Gagné P, Labelle Y, Droit A, Chevalier-Paré M, Bourassa S, McDonald D, Hendzel MJ, Prigent C, Poirier GG. Proteomic investigation of phosphorylation sites in poly(ADP-ribose) polymerase-1 and poly(ADP-ribose) glycohydrolase. J Proteome Res 2009; 8:1014-29. [PMID: 19105632 DOI: 10.1021/pr800810n] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Phosphorylation is a very common post-translational modification event known to modulate a wide range of biological responses. Beyond the regulation of protein activity, the interrelation of phosphorylation with other post-translational mechanisms is responsible for the control of diverse signaling pathways. Several observations suggest that phosphorylation of poly(ADP-ribose) polymerase-1 (PARP-1) regulates its activity. There is also accumulating evidence to suggest the establishment of phosphorylation-dependent assembly of PARP-1-associated multiprotein complexes. Although it is relatively straightforward to demonstrate phosphorylation of a defined target, identification of the actual amino acids involved still represents a technical challenge for many laboratories. With the use of a combination of bioinformatics-based predictions tools for generic and kinase-specific phosphorylation sites, in vitro phosphorylation assays and mass spectrometry analysis, we investigated the phosphorylation profile of PARP-1 and poly(ADP-ribose) glycohydrolase (PARG), two major enzymes responsible for poly(ADP-ribose) turnover. Mass spectrometry analysis revealed the phosphorylation of several serine/threonine residues within important regulatory domains and motifs of both enzymes. With the use of in vivo microirradiation-induced DNA damage, we show that altered phosphorylation at specific sites can modify the dynamics of assembly and disassembly of PARP-1 at sites of DNA damage. By documenting and annotating a collection of known and newly identified phosphorylation sites, this targeted proteomics study significantly advances our understanding of the roles of phosphorylation in the regulation of PARP-1 and PARG.
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Affiliation(s)
- Jean-Philippe Gagné
- Laval University Medical Research Center, Laval University, G1V4G2, Quebec, Canada
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147
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Tao Z, Gao P, Hoffman DW, Liu HW. Domain C of human poly(ADP-ribose) polymerase-1 is important for enzyme activity and contains a novel zinc-ribbon motif. Biochemistry 2008; 47:5804-13. [PMID: 18452307 DOI: 10.1021/bi800018a] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) is a multimodular nuclear protein that participates in many fundamental cellular activities. Stimulated by binding to nicked DNA, PARP-1 catalyzes poly(ADP-ribosyl)ation of the acceptor proteins using NAD (+) as a substrate. In this work, NMR methods were used to determine the solution structure of human PARP-1 protein. Domain C was found to contain a zinc-binding motif of three antiparallel beta-strands with four conserved cysteines positioned to coordinate the metal ligand, in addition to a helical region. The zinc-binding motif is structurally reminiscent of the "zinc-ribbon" fold, but with a novel spacing between the conserved cysteines (CX2CX12CX 9C). Domain C alone does not appear to bind to DNA. Interestingly, domain C is essential for PARP-1 activity, since a mixture containing nicked DNA and the PARP-1 ABDEF domains has only basal enzymatic activity, while the addition of domain C to the mixture initiated NAD (+) hydrolysis and the formation of poly(ADP-ribose), as detected by an NMR-based assay and autoradiography. The structural model for domain C in solution provides an important framework for further studies aimed at improving our understanding of how the various domains within the complex PARP-1 enzyme play their respective roles in regulating the enzyme activity when cells are under conditions of genotoxic stress.
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Affiliation(s)
- Zhihua Tao
- Division of Medicinal Chemistry, College of Pharmacy, Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA
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148
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Kraus WL. Transcriptional control by PARP-1: chromatin modulation, enhancer-binding, coregulation, and insulation. Curr Opin Cell Biol 2008; 20:294-302. [PMID: 18450439 DOI: 10.1016/j.ceb.2008.03.006] [Citation(s) in RCA: 342] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 03/11/2008] [Accepted: 03/11/2008] [Indexed: 10/22/2022]
Abstract
The regulation of gene expression requires a wide array of protein factors that can modulate chromatin structure, act at enhancers, function as transcriptional coregulators, or regulate insulator function. Poly(ADP-ribose) polymerase-1 (PARP-1), an abundant and ubiquitous nuclear enzyme that catalyzes the NAD(+)-dependent addition of ADP-ribose polymers on a variety of nuclear proteins, has been implicated in all of these functions. Recent biochemical, genomic, proteomic, and cell-based studies have highlighted the role of PARP-1 in each of these processes and provided new insights about the molecular mechanisms governing PARP-1-dependent regulation of gene expression. In addition, these studies have demonstrated how PARP-1 functions as an integral part of cellular signaling pathways that culminate in gene-regulatory outcomes.
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Affiliation(s)
- W Lee Kraus
- Department of Molecular Biology and Genetics, Cornell University, 465 Biotechnology Building, Ithaca, NY 14853, United States.
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149
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Stable depletion of poly (ADP-ribose) polymerase-1 reduces in vivo melanoma growth and increases chemosensitivity. Eur J Cancer 2008; 44:1302-14. [PMID: 18440222 DOI: 10.1016/j.ejca.2008.03.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Revised: 03/19/2008] [Accepted: 03/20/2008] [Indexed: 11/22/2022]
Abstract
Poly(ADP-ribose) polymerase (PARP)-1, which plays a key role in DNA repair, inflammation and transcription, has recently been shown to be involved in angiogenesis. The aim of this study was to investigate PARP-1 role in melanoma aggressiveness and chemoresistance in vivo using clones stably silenced for PARP-1 expression. Whilst the growth characteristics of PARP-1-deficient melanoma cells were comparable to those of PARP-1-proficient cells in vitro, their tumourigenic potential in vivo was significantly compromised. In fact, mice challenged intra-muscle with PARP-1-deficient cells showed a delayed development of measurable tumour nodules, which were also significantly reduced in size with respect to those of mice inoculated with PARP-1-proficient cells. Moreover, animals challenged intra-cranially with PARP-1-deficient cells, a model that mimics CNS localisation of melanoma, showed an increased survival. Immunohistochemical analyses of PARP-1-depleted melanoma grafts indicated a reduced expression of the angiogenesis marker PECAM-1/CD31 and of the pro-inflammatory mediators TNF-alpha and GITR. Notably, PARP-1-silenced melanoma was extremely sensitive to temozolomide, an anticancer agent used for the treatment of metastatic melanoma. These results provide novel evidence for a direct role of PARP-1 in tumour aggressiveness and chemoresistance.
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Yélamos J, Schreiber V, Dantzer F. Toward specific functions of poly(ADP-ribose) polymerase-2. Trends Mol Med 2008; 14:169-78. [PMID: 18353725 DOI: 10.1016/j.molmed.2008.02.003] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Revised: 02/12/2008] [Accepted: 02/13/2008] [Indexed: 12/31/2022]
Abstract
Poly(ADP-ribose) polymerase-2 (PARP-2) belongs to a family of enzymes that catalyze poly(ADP-ribosyl)ation of proteins. PARP-1 and PARP-2 are so far the only PARP enzymes whose catalytic activity has been shown to be induced by DNA-strand breaks, providing strong support for key shared functions in the cellular response to DNA damage. Accordingly, clinical trials for cancer, using PARP inhibitors that target the conserved catalytic domain of PARP proteins, are now ongoing. However, recent data suggest unique functions for PARP-2 in specific processes, such as genome surveillance, spermatogenesis, adipogenesis and T cell development. Understanding these physiological roles might provide invaluable clues to the rational development and exploitation of specific PARP-2 inhibitor drugs in a clinical setting and the design of new therapeutic approaches in different pathophysiological conditions.
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Affiliation(s)
- José Yélamos
- Department of Immunology, IMIM-Hospital del Mar, Barcelona Biomedical Research Park, Barcelona, Spain.
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