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Kamaletdinova T, Zong W, Urbánek P, Wang S, Sannai M, Grigaravičius P, Sun W, Fanaei-Kahrani Z, Mangerich A, Hottiger MO, Li T, Wang ZQ. Poly(ADP-Ribose) Polymerase-1 Lacking Enzymatic Activity Is Not Compatible with Mouse Development. Cells 2023; 12:2078. [PMID: 37626888 PMCID: PMC10453916 DOI: 10.3390/cells12162078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Poly(ADP-ribose) polymerase-1 (PARP1) binds DNA lesions to catalyse poly(ADP-ribosyl)ation (PARylation) using NAD+ as a substrate. PARP1 plays multiple roles in cellular activities, including DNA repair, transcription, cell death, and chromatin remodelling. However, whether these functions are governed by the enzymatic activity or scaffolding function of PARP1 remains elusive. In this study, we inactivated in mice the enzymatic activity of PARP1 by truncating its C-terminus that is essential for ART catalysis (PARP1ΔC/ΔC, designated as PARP1-ΔC). The mutation caused embryonic lethality between embryonic day E8.5 and E13.5, in stark contrast to PARP1 complete knockout (PARP1-/-) mice, which are viable. Embryonic stem (ES) cell lines can be derived from PARP1ΔC/ΔC blastocysts, and these mutant ES cells can differentiate into all three germ layers, yet, with a high degree of cystic structures, indicating defects in epithelial cells. Intriguingly, PARP1-ΔC protein is expressed at very low levels compared to its full-length counterpart, suggesting a selective advantage for cell survival. Noticeably, PARP2 is particularly elevated and permanently present at the chromatin in PARP1-ΔC cells, indicating an engagement of PARP2 by non-enzymatic PARP1 protein at the chromatin. Surprisingly, the introduction of PARP1-ΔC mutation in adult mice did not impair their viability; yet, these mutant mice are hypersensitive to alkylating agents, similar to PARP1-/- mutant mice. Our study demonstrates that the catalytically inactive mutant of PARP1 causes the developmental block, plausibly involving PARP2 trapping.
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Affiliation(s)
- Tatiana Kamaletdinova
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany; (T.K.); (P.U.); (M.S.); (P.G.); (Z.F.-K.)
| | - Wen Zong
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (W.Z.); (S.W.); (W.S.); (T.L.)
| | - Pavel Urbánek
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany; (T.K.); (P.U.); (M.S.); (P.G.); (Z.F.-K.)
| | - Sijia Wang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (W.Z.); (S.W.); (W.S.); (T.L.)
| | - Mara Sannai
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany; (T.K.); (P.U.); (M.S.); (P.G.); (Z.F.-K.)
| | - Paulius Grigaravičius
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany; (T.K.); (P.U.); (M.S.); (P.G.); (Z.F.-K.)
| | - Wenli Sun
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (W.Z.); (S.W.); (W.S.); (T.L.)
| | - Zahra Fanaei-Kahrani
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany; (T.K.); (P.U.); (M.S.); (P.G.); (Z.F.-K.)
| | - Aswin Mangerich
- Molecular Toxicology, Department of Biology, University of Konstanz, 78464 Konstanz, Germany;
- Nutritional Toxicology, Institute of Nutritional Science, University of Potsdam, 14469 Potsdam, Germany
| | - Michael O. Hottiger
- Department of Molecular Mechanisms of Disease, University of Zürich, 8057 Zürich, Switzerland;
| | - Tangliang Li
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (W.Z.); (S.W.); (W.S.); (T.L.)
| | - Zhao-Qi Wang
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), 07745 Jena, Germany; (T.K.); (P.U.); (M.S.); (P.G.); (Z.F.-K.)
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China; (W.Z.); (S.W.); (W.S.); (T.L.)
- Faculty of Biological Sciences, Friedrich Schiller University of Jena, 07743 Jena, Germany
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2
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Langelier MF, Billur R, Sverzhinsky A, Black BE, Pascal JM. HPF1 dynamically controls the PARP1/2 balance between initiating and elongating ADP-ribose modifications. Nat Commun 2021; 12:6675. [PMID: 34795260 DOI: 10.1038/s41467-021-27043-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/29/2021] [Indexed: 11/21/2022] Open
Abstract
PARP1 and PARP2 produce poly(ADP-ribose) in response to DNA breaks. HPF1 regulates PARP1/2 catalytic output, most notably permitting serine modification with ADP-ribose. However, PARP1 is substantially more abundant in cells than HPF1, challenging whether HPF1 can pervasively modulate PARP1. Here, we show biochemically that HPF1 efficiently regulates PARP1/2 catalytic output at sub-stoichiometric ratios matching their relative cellular abundances. HPF1 rapidly associates/dissociates from multiple PARP1 molecules, initiating serine modification before modification initiates on glutamate/aspartate, and accelerating initiation to be more comparable to elongation reactions forming poly(ADP-ribose). This “hit and run” mechanism ensures HPF1 contributions to PARP1/2 during initiation do not persist and interfere with PAR chain elongation. We provide structural insights into HPF1/PARP1 assembled on a DNA break, and assess HPF1 impact on PARP1 retention on DNA. Our data support the prevalence of serine-ADP-ribose modification in cells and the efficiency of serine-ADP-ribose modification required for an acute DNA damage response. HPF1 controls the ADP-ribosylation activity of PARP1/2 in response to DNA breaks. Here, the authors show that HPF1 regulates the balance between ADP-ribose initiation and elongation through a dynamic interaction that accelerates the initiation rate on serine residues.
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3
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Ooi SK, Sato S, Tomomori-Sato C, Zhang Y, Wen Z, Banks CAS, Washburn MP, Unruh JR, Florens L, Conaway RC, Conaway JW. Multiple roles for PARP1 in ALC1-dependent nucleosome remodeling. Proc Natl Acad Sci U S A 2021; 118:e2107277118. [PMID: 34465625 DOI: 10.1073/pnas.2107277118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The SNF2 family ATPase Amplified in Liver Cancer 1 (ALC1) is the only chromatin remodeling enzyme with a poly(ADP-ribose) (PAR) binding macrodomain. ALC1 functions together with poly(ADP-ribose) polymerase PARP1 to remodel nucleosomes. Activation of ALC1 cryptic ATPase activity and the subsequent nucleosome remodeling requires binding of its macrodomain to PAR chains synthesized by PARP1 and NAD+ A key question is whether PARP1 has a role(s) in ALC1-dependent nucleosome remodeling beyond simply synthesizing the PAR chains needed to activate the ALC1 ATPase. Here, we identify PARP1 separation-of-function mutants that activate ALC1 ATPase but do not support nucleosome remodeling by ALC1. Investigation of these mutants has revealed multiple functions for PARP1 in ALC1-dependent nucleosome remodeling and provides insights into its multifaceted role in chromatin remodeling.
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4
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Spiegel JO, Van Houten B, Durrant JD. PARP1: Structural insights and pharmacological targets for inhibition. DNA Repair (Amst) 2021; 103:103125. [PMID: 33940558 PMCID: PMC8206044 DOI: 10.1016/j.dnarep.2021.103125] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/24/2021] [Accepted: 04/09/2021] [Indexed: 12/25/2022]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1, also known as ADPRT1) is a multifunctional human ADP-ribosyltransferase. It plays a role in multiple DNA repair pathways, including the base excision repair (BER), non-homologous end joining (NHEJ), homologous recombination (HR), and Okazaki-fragment processing pathways. In response to DNA strand breaks, PARP1 covalently attaches ADP-ribose moieties to arginine, glutamate, aspartate, cysteine, lysine, and serine acceptor sites on both itself and other proteins. This signal recruits DNA repair proteins to the site of DNA damage. PARP1 binding to these sites enhances ADP-ribosylation via allosteric communication between the distant DNA binding and catalytic domains. In this review, we provide a general overview of PARP1 and emphasize novel potential approaches for pharmacological inhibition. Clinical PARP1 inhibitors bind the catalytic pocket, where they directly interfere with ADP-ribosylation. Some inhibitors may further enhance potency by "trapping" PARP1 on DNA via an allosteric mechanism, though this proposed mode of action remains controversial. PARP1 inhibitors are used clinically to treat some cancers, but resistance is common, so novel pharmacological approaches are urgently needed. One approach may be to design novel small molecules that bind at inter-domain interfaces that are essential for PARP1 allostery. To illustrate these points, this review also includes instructive videos showing PARP1 structures and mechanisms.
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Affiliation(s)
- Jacob O Spiegel
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Bennett Van Houten
- UPMC-Hillman Cancer Center, Pittsburgh, PA, 15232, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Jacob D Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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Rudolph J, Roberts G, Muthurajan UM, Luger K. HPF1 and nucleosomes mediate a dramatic switch in activity of PARP1 from polymerase to hydrolase. eLife 2021; 10:65773. [PMID: 33683197 PMCID: PMC8012059 DOI: 10.7554/elife.65773] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/07/2021] [Indexed: 12/13/2022] Open
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) is an important player in the response to DNA damage. Recently, Histone PARylation Factor (HPF1) was shown to be a critical modulator of the activity of PARP1 by facilitating PARylation of histones and redirecting the target amino acid specificity from acidic to serine residues. Here, we investigate the mechanism and specific consequences of HPF1-mediated PARylation using nucleosomes as both activators and substrates for PARP1. HPF1 provides that catalytic base Glu284 to substantially redirect PARylation by PARP1 such that the histones in nucleosomes become the primary recipients of PAR chains. Surprisingly, HPF1 partitions most of the reaction product to free ADP-ribose (ADPR), resulting in much shorter PAR chains compared to reactions in the absence of HPF1. This HPF1-mediated switch from polymerase to hydrolase has important implications for the PARP1-mediated response to DNA damage and raises interesting new questions about the role of intracellular ADPR and depletion of NAD+.
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Affiliation(s)
- Johannes Rudolph
- Department of Biochemistry, University of Colorado Boulder, Boulder, United States
| | - Genevieve Roberts
- Department of Biochemistry, University of Colorado Boulder, Boulder, United States
| | - Uma M Muthurajan
- Department of Biochemistry, University of Colorado Boulder, Boulder, United States
| | - Karolin Luger
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, United States
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Kamaletdinova T, Fanaei-Kahrani Z, Wang ZQ. The Enigmatic Function of PARP1: From PARylation Activity to PAR Readers. Cells. 2019;8:1625. [PMID: 31842403 PMCID: PMC6953017 DOI: 10.3390/cells8121625] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 12/16/2022] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation) is catalysed by poly(ADP-ribose) polymerases (PARPs, also known as ARTDs) and then rapidly removed by degrading enzymes. Poly(ADP-ribose) (PAR) is produced from PARylation and provides a delicate and spatiotemporal interaction scaffold for numerous target proteins. The PARylation system, consisting of PAR synthesizers and erasers and PAR itself and readers, plays diverse roles in the DNA damage response (DDR), DNA repair, transcription, replication, chromatin remodeling, metabolism, and cell death. Despite great efforts by scientists in biochemistry, cell and molecular biology, genetics, and pharmacology over the last five decades, the biology of PARPs and PARylation remains enigmatic. In this review, we summarize the current understanding of the biological function of PARP1 (ARTD1), the founding member of the PARP family, focusing on the inter-dependent or -independent nature of different functional domains of the PARP1 protein. We also discuss the readers of PAR, whose function may transduce signals and coordinate the cellular processes, which has recently emerged as a new research avenue for PARP biology. We aim to provide some perspective on how future research might disentangle the biology of PARylation by dissecting the structural and functional relationship of PARP1, a major effector of the PARPs family.
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Chen HD, Chen CH, Wang YT, Guo N, Tian YN, Huan XJ, Song SS, He JX, Miao ZH. Increased PARP1-DNA binding due to autoPARylation inhibition of PARP1 on DNA rather than PARP1-DNA trapping is correlated with PARP1 inhibitor's cytotoxicity. Int J Cancer 2019; 145:714-727. [PMID: 30675909 DOI: 10.1002/ijc.32131] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/26/2018] [Accepted: 01/10/2019] [Indexed: 12/27/2022]
Abstract
PARP1 inhibitors (PARPis) are used clinically during cancer therapy and are thought to exert their cytotoxicity through PARP1 polymerase inhibition and PARP1-DNA trapping. Here, we showed no significant correlation between PARP1-DNA trapping and cytotoxicity induced by PARPis. We complemented PARP1-knockout sublines with wild-type PARP1 and 11 mutants with different point mutations that affect the polymerase activity. When examining the PARPi talazoparib, the induced cytotoxicity was highly significantly correlated with cellular PARP1 polymerase activity, but not with its PARP1-DNA trapping or polymerase inhibition. Similarly, talazoparib's PARP1-DNA trapping revealed significant correlation with the polymerase activity rather than its inhibition. Differently, however, when evaluating purified wild-type and mutated PARP1, we identified an almost linear relationship between PARPis' inhibiting PARP1 dissociation from DNA and their cytotoxicity in 17 cancer cell lines. In contrast, no significant correlation existed between PARP1 polymerase inhibition in the histone-based systems and the cytotoxicity. After careful comparisons on different methods and detection targets, we conclude that the PARPi-mediated increase in PARP1-DNA binding by inhibiting autoPARylation of PARP1 on DNA rather than in PARP1-DNA trapping is correlated with PARPi's cytotoxicity. Accordingly, we established a new PARPi screening model that more closely predicts cytotoxicity.
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Affiliation(s)
- Hua-Dong Chen
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chuan-Huizi Chen
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Ting Wang
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ne Guo
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Nan Tian
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xia-Juan Huan
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shan-Shan Song
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jin-Xue He
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ze-Hong Miao
- Division of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
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8
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Rank L, Veith S, Gwosch EC, Demgenski J, Ganz M, Jongmans MC, Vogel C, Fischbach A, Buerger S, Fischer JMF, Zubel T, Stier A, Renner C, Schmalz M, Beneke S, Groettrup M, Kuiper RP, Bürkle A, Ferrando-May E, Mangerich A. Analyzing structure-function relationships of artificial and cancer-associated PARP1 variants by reconstituting TALEN-generated HeLa PARP1 knock-out cells. Nucleic Acids Res 2016; 44:10386-10405. [PMID: 27694308 PMCID: PMC5137445 DOI: 10.1093/nar/gkw859] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 09/05/2016] [Accepted: 09/16/2016] [Indexed: 12/17/2022] Open
Abstract
Genotoxic stress activates PARP1, resulting in the post-translational modification of proteins with poly(ADP-ribose) (PAR). We genetically deleted PARP1 in one of the most widely used human cell systems, i.e. HeLa cells, via TALEN-mediated gene targeting. After comprehensive characterization of these cells during genotoxic stress, we analyzed structure–function relationships of PARP1 by reconstituting PARP1 KO cells with a series of PARP1 variants. Firstly, we verified that the PARP1\E988K mutant exhibits mono-ADP-ribosylation activity and we demonstrate that the PARP1\L713F mutant is constitutively active in cells. Secondly, both mutants exhibit distinct recruitment kinetics to sites of laser-induced DNA damage, which can potentially be attributed to non-covalent PARP1–PAR interaction via several PAR binding motifs. Thirdly, both mutants had distinct functional consequences in cellular patho-physiology, i.e. PARP1\L713F expression triggered apoptosis, whereas PARP1\E988K reconstitution caused a DNA-damage-induced G2 arrest. Importantly, both effects could be rescued by PARP inhibitor treatment, indicating distinct cellular consequences of constitutive PARylation and mono(ADP-ribosyl)ation. Finally, we demonstrate that the cancer-associated PARP1 SNP variant (V762A) as well as a newly identified inherited PARP1 mutation (F304L\V762A) present in a patient with pediatric colorectal carcinoma exhibit altered biochemical and cellular properties, thereby potentially supporting human carcinogenesis. Together, we establish a novel cellular model for PARylation research, by revealing strong structure–function relationships of natural and artificial PARP1 variants.
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Affiliation(s)
- Lisa Rank
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Sebastian Veith
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.,Research Training Group 1331, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Eva C Gwosch
- Bioimaging Center, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.,Konstanz Research School Chemical Biology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Janine Demgenski
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Magdalena Ganz
- Bioimaging Center, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.,Konstanz Research School Chemical Biology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Marjolijn C Jongmans
- Department of Human Genetics, Radboud University Medical Center Nijmegen, Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands.,Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherland
| | - Christopher Vogel
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Arthur Fischbach
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.,Konstanz Research School Chemical Biology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Stefanie Buerger
- FlowKon FACS Facility, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Jan M F Fischer
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.,Konstanz Research School Chemical Biology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Tabea Zubel
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.,Konstanz Research School Chemical Biology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Anna Stier
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Christina Renner
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Michael Schmalz
- Center of Applied Photonics, Department of Physics, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Sascha Beneke
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.,Ecotoxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Marcus Groettrup
- FlowKon FACS Facility, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.,Immunology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Roland P Kuiper
- Department of Human Genetics, Radboud University Medical Center Nijmegen, Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Elisa Ferrando-May
- Bioimaging Center, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Aswin Mangerich
- Molecular Toxicology Group, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
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9
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Dawicki-McKenna JM, Langelier MF, DeNizio JE, Riccio AA, Cao CD, Karch KR, McCauley M, Steffen JD, Black BE, Pascal JM. PARP-1 Activation Requires Local Unfolding of an Autoinhibitory Domain. Mol Cell 2015; 60:755-768. [PMID: 26626480 PMCID: PMC4712911 DOI: 10.1016/j.molcel.2015.10.013] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 07/31/2015] [Accepted: 10/06/2015] [Indexed: 12/11/2022]
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) creates the posttranslational modification PAR from substrate NAD(+) to regulate multiple cellular processes. DNA breaks sharply elevate PARP-1 catalytic activity to mount a cell survival repair response, whereas persistent PARP-1 hyperactivation during severe genotoxic stress is associated with cell death. The mechanism for tight control of the robust catalytic potential of PARP-1 remains unclear. By monitoring PARP-1 dynamics using hydrogen/deuterium exchange-mass spectrometry (HXMS), we unexpectedly find that a specific portion of the helical subdomain (HD) of the catalytic domain rapidly unfolds when PARP-1 encounters a DNA break. Together with biochemical and crystallographic analysis of HD deletion mutants, we show that the HD is an autoinhibitory domain that blocks productive NAD(+) binding. Our molecular model explains how PARP-1 DNA damage detection leads to local unfolding of the HD that relieves autoinhibition, and has important implications for the design of PARP inhibitors.
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Affiliation(s)
- Jennine M Dawicki-McKenna
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6059, USA
| | - Marie-France Langelier
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107-5544, USA
| | - Jamie E DeNizio
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6059, USA; Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6059, USA
| | - Amanda A Riccio
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107-5544, USA
| | - Connie D Cao
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6059, USA
| | - Kelly R Karch
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6059, USA; Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6059, USA
| | - Michael McCauley
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107-5544, USA
| | - Jamin D Steffen
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107-5544, USA
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6059, USA; Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6059, USA.
| | - John M Pascal
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107-5544, USA.
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10
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Barkauskaite E, Jankevicius G, Ahel I. Structures and Mechanisms of Enzymes Employed in the Synthesis and Degradation of PARP-Dependent Protein ADP-Ribosylation. Mol Cell 2015; 58:935-46. [PMID: 26091342 DOI: 10.1016/j.molcel.2015.05.007] [Citation(s) in RCA: 186] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The poly(ADP-ribose) polymerases (PARPs) are a major family of enzymes capable of modifying proteins by ADP-ribosylation. Due to the large size and diversity of this family, PARPs affect almost every aspect of cellular life and have fundamental roles in DNA repair, transcription, heat shock and cytoplasmic stress responses, cell division, protein degradation, and much more. In the past decade, our understanding of the PARP enzymatic mechanism and activation, as well as regulation of ADP-ribosylation signals by the readers and erasers of protein ADP-ribosylation, has been significantly advanced by the emergence of new structural data, reviewed herein, which allow for better understanding of the biological roles of this widespread post-translational modification.
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Affiliation(s)
- Eva Barkauskaite
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
| | - Gytis Jankevicius
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK.
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11
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Shen Y, Aoyagi-Scharber M, Wang B. Trapping Poly(ADP-Ribose) Polymerase. J Pharmacol Exp Ther 2015; 353:446-57. [DOI: 10.1124/jpet.114.222448] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/09/2015] [Indexed: 12/16/2022] Open
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Mansoorabadi SO, Wu M, Tao Z, Gao P, Pingali SV, Guo L, Liu HW. Conformational activation of poly(ADP-ribose) polymerase-1 upon DNA binding revealed by small-angle X-ray scattering. Biochemistry 2014; 53:1779-88. [PMID: 24588584 PMCID: PMC3971956 DOI: 10.1021/bi401439n] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) is a nuclear protein that plays key roles in several fundamental cellular processes. PARP-1 catalyzes the polymerization of nicotinamide adenine dinucleotide on itself and other acceptor proteins, forming long branched poly(ADP-ribose) polymers. The catalytic activity of PARP-1 is stimulated upon binding to damaged DNA, but how this signal is transmitted from the N-terminal DNA binding domain to the C-terminal catalytic domain in the context of the full-length enzyme is unknown. In this paper, small-angle X-ray scattering experiments and molecular dynamics simulations were used to gain insight into the conformational changes that occur during the catalytic activation of PARP-1 by an 8-mer DNA ligand. The data are consistent with a model in which binding of the DNA ligand establishes interdomain interactions between the DNA binding and catalytic domains, which induces an allosteric change in the active site that promotes catalysis. Moreover, the PARP-1-8-mer complex is seen to adopt a conformation that is poised to recruit DNA repair factors to the site of DNA damage. This study provides the first structural information about the DNA-induced conformational activation of full-length PARP-1.
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Affiliation(s)
- Steven O Mansoorabadi
- Division of Medicinal Chemistry, College of Pharmacy, Department of Chemistry, and Institute of Cellular and Molecular Biology, The University of Texas at Austin , Austin, Texas 78712, United States
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13
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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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Affiliation(s)
- Mohit Narwal
- Pharmaceutical
Sciences, Department of Biosciences, Abo Akademi University, FI-20520 Turku, Finland
| | - Harikanth Venkannagari
- Pharmaceutical
Sciences, Department of Biosciences, Abo Akademi University, FI-20520 Turku, Finland
| | - Lari Lehtiö
- Pharmaceutical
Sciences, Department of Biosciences, Abo Akademi University, FI-20520 Turku, Finland
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15
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Lehtiö L, Collins R, van den Berg S, Johansson A, Dahlgren LG, Hammarström M, Helleday T, Holmberg-Schiavone L, Karlberg T, Weigelt J. Zinc binding catalytic domain of human tankyrase 1. J Mol Biol 2008; 379:136-45. [PMID: 18436240 DOI: 10.1016/j.jmb.2008.03.058] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 03/20/2008] [Accepted: 03/25/2008] [Indexed: 12/31/2022]
Abstract
Tankyrases are recently discovered proteins implicated in many important functions in the cell including telomere homeostasis and mitosis. Tankyrase modulates the activity of target proteins through poly(ADP-ribosyl)ation, and here we report the structure of the catalytic poly(ADP-ribose) polymerase (PARP) domain of human tankyrase 1. This is the first structure of a PARP domain from the tankyrase subfamily. The present structure reveals that tankyrases contain a short zinc-binding motif, which has not been predicted. Tankyrase activity contributes to telomere elongation observed in various cancer cells and tankyrase inhibition has been suggested as a potential route for cancer therapy. In comparison with other PARPs, significant structural differences are observed in the regions lining the substrate-binding site of tankyrase 1. These findings will be of great value to facilitate structure-based design of selective PARP inhibitors, in general, and tankyrase inhibitors, in particular.
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Affiliation(s)
- Lari Lehtiö
- Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden
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16
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Yu W, Ginjala V, Pant V, Chernukhin I, Whitehead J, Docquier F, Farrar D, Tavoosidana G, Mukhopadhyay R, Kanduri C, Oshimura M, Feinberg AP, Lobanenkov V, Klenova E, Ohlsson R. Poly(ADP-ribosyl)ation regulates CTCF-dependent chromatin insulation. Nat Genet 2004; 36:1105-10. [PMID: 15361875 DOI: 10.1038/ng1426] [Citation(s) in RCA: 208] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2004] [Accepted: 08/06/2004] [Indexed: 01/22/2023]
Abstract
Chromatin insulators demarcate expression domains by blocking the cis effects of enhancers or silencers in a position-dependent manner. We show that the chromatin insulator protein CTCF carries a post-translational modification: poly(ADP-ribosyl)ation. Chromatin immunoprecipitation analysis showed that a poly(ADP-ribosyl)ation mark, which exclusively segregates with the maternal allele of the insulator domain in the H19 imprinting control region, requires the bases that are essential for interaction with CTCF. Chromatin immunoprecipitation-on-chip analysis documented that the link between CTCF and poly(ADP-ribosyl)ation extended to more than 140 mouse CTCF target sites. An insulator trap assay showed that the insulator function of most of these CTCF target sites is sensitive to 3-aminobenzamide, an inhibitor of poly(ADP-ribose) polymerase activity. We suggest that poly(ADP-ribosyl)ation imparts chromatin insulator properties to CTCF at both imprinted and nonimprinted loci, which has implications for the regulation of expression domains and their demise in pathological lesions.
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Affiliation(s)
- Wenqiang Yu
- Department of Development & Genetics, Evolution Biology Centre, Uppsala University, Norbyvägen 18A, S-752 36 Uppsala, Sweden
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17
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Beneke S, Alvarez-Gonzalez R, Bürkle A. Comparative characterisation of poly(ADP-ribose) polymerase-1 from two mammalian species with different life span. Exp Gerontol 2000; 35:989-1002. [PMID: 11121685 DOI: 10.1016/s0531-5565(00)00134-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
DNA damage induced in higher eukaryotes by alkylating agents, oxidants or ionising radiation triggers the synthesis of protein-conjugated poly(ADP-ribose) catalysed by poly(ADP-ribose) polymerase-1 (PARP-1). Previously, cellular poly(ADP-ribosyl)ation capacity has been shown to correlate positively with the life span of mammalian species [Proc. Natl. Acad. Sci. USA 89 (1992) 11,759-11,763]. Here, we have tested whether this correlation results from differences in kinetic parameters of the enzymatic activity of PARP-1. We therefore compared recombinant enzymes, expressed in a baculovirus system, from rat and man as two mammalian species with extremely divergent life span. In standard activity assays performed in the presence of histones as poly(ADP-ribose) acceptors both enzymes showed saturation kinetics with [NAD(+)]. The kinetic parameters (k(cat), k(m) and k(cat)/k(m)) of the two enzymes were not significantly different. However, in assays assessing the auto-poly(ADP-ribosyl)ation reaction, both enzymes displayed second-order kinetics with respect to [PARP-1], and up to two-fold higher specific activity was observed for human versus rat PARP-1. We conclude that the correlation of poly(ADP-ribosyl)ation capacity with life span is not reflected in the kinetic parameters, but that subtle differences in primary structure of PARP-1 from mammalian species of different longevity may control the extent of the automodification reaction.
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Affiliation(s)
- S Beneke
- Abteilung Tumorvirologie, Deutsches Krebsforschungszentrum, Heidelberg, Germany
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18
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De Murcia G, Dantzer F, Trucco C, Rolli V, Oliver FJ, Niedergang C, Ménissier-de Murcia J. Poly(ADP-Ribose) Polymerase Is Required for Maintenance of Genomic Integrity During Base Excision Repair. DNA Repair (Amst) 1998. [DOI: 10.1007/978-3-642-48770-5_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Abstract
Recent molecular techniques have made it feasible to simulate evolutionary processes and apply in vitro selection to evolve enzymes with novel properties that may have potential benefits for medical and industrial applications. The characterization of such mutants has also provided new insights into how molecular structure determines enzyme function.
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Affiliation(s)
- A Skandalis
- The Joseph Gottstein Memorial Cancer Research Laboratory, Department of Pathology, University of Washington School of Medicine, Box 357705, Seattle, WA 98195-7705, USA
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20
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Affiliation(s)
- S L Oei
- Institut für Biochemie, Freie Universität Berlin, Germany
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Trucco C, Flatter E, Fribourg S, de Murcia G, Ménissier-de Murcia J. Mutations in the amino-terminal domain of the human poly(ADP-ribose) polymerase that affect its catalytic activity but not its DNA binding capacity. FEBS Lett 1996; 399:313-6. [PMID: 8985170 DOI: 10.1016/s0014-5793(96)01347-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Poly-ADP ribosylation of nuclear proteins is activated when poly(ADP-ribose) polymerase (PARP), a nuclear zinc-finger enzyme, binds to single-strand DNA breaks. To understand how the signal emerging from its DNA-binding domain (DBD) bound to such breaks is transduced to its catalytic domain, the structure-function relationship of the DBD was investigated. We have used mutagenesis by the polymerase chain reaction (PCR) to generate a random library of PARP mutants. In this work, we describe the identification of catalytically inactive mutants bearing single point mutations, located outside the two zinc fingers in the DBD, that have conserved their full capacity to bind DNA. The results obtained demonstrate that the DNA-dependent activation of PARP requires not only a capacity to bind DNA but also a number of crucial residues to maintain a conformation of the domain necessary to transfer an 'activation signal' to the catalytic domain.
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Affiliation(s)
- C Trucco
- Ecole Supérieure de Biotechnologie de Strasbourg, UPR A9003 du CNRS, Illkirch-Graffenstaden, France
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