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Suskiewicz MJ, Munnur D, Strømland Ø, Yang JC, Easton L, Chatrin C, Zhu K, Baretić D, Goffinont S, Schuller M, Wu WF, Elkins J, Ahel D, Sanyal S, Neuhaus D, Ahel I. Updated protein domain annotation of the PARP protein family sheds new light on biological function. Nucleic Acids Res 2023; 51:8217-8236. [PMID: 37326024 PMCID: PMC10450202 DOI: 10.1093/nar/gkad514] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/09/2023] [Accepted: 06/03/2023] [Indexed: 06/17/2023] Open
Abstract
AlphaFold2 and related computational tools have greatly aided studies of structural biology through their ability to accurately predict protein structures. In the present work, we explored AF2 structural models of the 17 canonical members of the human PARP protein family and supplemented this analysis with new experiments and an overview of recent published data. PARP proteins are typically involved in the modification of proteins and nucleic acids through mono or poly(ADP-ribosyl)ation, but this function can be modulated by the presence of various auxiliary protein domains. Our analysis provides a comprehensive view of the structured domains and long intrinsically disordered regions within human PARPs, offering a revised basis for understanding the function of these proteins. Among other functional insights, the study provides a model of PARP1 domain dynamics in the DNA-free and DNA-bound states and enhances the connection between ADP-ribosylation and RNA biology and between ADP-ribosylation and ubiquitin-like modifications by predicting putative RNA-binding domains and E2-related RWD domains in certain PARPs. In line with the bioinformatic analysis, we demonstrate for the first time PARP14's RNA-binding capability and RNA ADP-ribosylation activity in vitro. While our insights align with existing experimental data and are probably accurate, they need further validation through experiments.
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Affiliation(s)
| | - Deeksha Munnur
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Øyvind Strømland
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Ji-Chun Yang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Laura E Easton
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Chatrin Chatrin
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Domagoj Baretić
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | | | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Wing-Fung Wu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jonathan M Elkins
- Centre for Medicines Discovery, University of Oxford, Oxford OX3 7DQ, UK
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Sumana Sanyal
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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2
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Gan Y, Sha H, Zou R, Xu M, Zhang Y, Feng J, Wu J. Research Progress on Mono-ADP-Ribosyltransferases in Human Cell Biology. Front Cell Dev Biol 2022; 10:864101. [PMID: 35652091 PMCID: PMC9149570 DOI: 10.3389/fcell.2022.864101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
ADP-ribosylation is a well-established post-translational modification that is inherently connected to diverse processes, including DNA repair, transcription, and cell signaling. The crucial roles of mono-ADP-ribosyltransferases (mono-ARTs) in biological processes have been identified in recent years by the comprehensive use of genetic engineering, chemical genetics, and proteomics. This review provides an update on current methodological advances in the study of these modifiers. Furthermore, the review provides details on the function of mono ADP-ribosylation. Several mono-ARTs have been implicated in the development of cancer, and this review discusses the role and therapeutic potential of some mono-ARTs in cancer.
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Affiliation(s)
- Yujie Gan
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
| | - Huanhuan Sha
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Renrui Zou
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
| | - Miao Xu
- Nanjing Medical University, Nanjing, China
| | - Yuan Zhang
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Jifeng Feng
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
- *Correspondence: Jifeng Feng,
| | - Jianzhong Wu
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
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Sakari M, Tran MT, Rossjohn J, Pulliainen AT, Beddoe T, Littler DR. Crystal structures of pertussis toxin with NAD+ and analogs provide structural insights into the mechanism of its cytosolic ADP-ribosylation activity. J Biol Chem 2022; 298:101892. [PMID: 35378130 PMCID: PMC9079181 DOI: 10.1016/j.jbc.2022.101892] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 11/19/2022] Open
Abstract
Bordetella pertussis is the causative agent of whooping cough, a highly contagious respiratory disease. Pertussis toxin (PT), a major virulence factor secreted by B. pertussis, is an AB5-type protein complex topologically related to cholera toxin. The PT protein complex is internalized by host cells and follows a retrograde trafficking route to the endoplasmic reticulum, where it subsequently dissociates. The released enzymatic S1 subunit is then translocated from the endoplasmic reticulum into the cytosol and subsequently ADP-ribosylates the inhibitory alpha-subunits (Gαi) of heterotrimeric G proteins, thus promoting dysregulation of G protein–coupled receptor signaling. However, the mechanistic details of the ADP-ribosylation activity of PT are not well understood. Here, we describe crystal structures of the S1 subunit in complex with nicotinamide adenine dinucleotide (NAD+), with NAD+ hydrolysis products ADP-ribose and nicotinamide, with NAD+ analog PJ34, and with a novel NAD+ analog formed upon S1 subunit crystallization with 3-amino benzamide and NAD+, which we name benzamide amino adenine dinucleotide. These crystal structures provide unprecedented insights into pre- and post-NAD+ hydrolysis steps of the ADP-ribosyltransferase activity of PT. We propose that these data may aid in rational drug design approaches and further development of PT-specific small-molecule inhibitors.
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Affiliation(s)
- Moona Sakari
- Institute of Biomedicine, Research Unit for Infection and Immunity, University of Turku, Turku, Finland
| | - Mai T Tran
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Institute of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, Wales, United Kingdom
| | - Arto T Pulliainen
- Institute of Biomedicine, Research Unit for Infection and Immunity, University of Turku, Turku, Finland.
| | - Travis Beddoe
- Department of Animal, Plant and Soil Science and Centre for AgriBioscience, La Trobe University, Bundoora, Victoria, Australia.
| | - Dene R Littler
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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4
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Wigle TJ, Blackwell DJ, Schenkel LB, Ren Y, Church WD, Desai HJ, Swinger KK, Santospago AG, Majer CR, Lu AZ, Niepel M, Perl NR, Vasbinder MM, Keilhack H, Kuntz KW. In Vitro and Cellular Probes to Study PARP Enzyme Target Engagement. Cell Chem Biol 2021; 27:877-887.e14. [PMID: 32679093 DOI: 10.1016/j.chembiol.2020.06.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/18/2020] [Accepted: 06/15/2020] [Indexed: 02/06/2023]
Abstract
Poly(ADP-ribose) polymerase (PARP) enzymes use nicotinamide adenine dinucleotide (NAD+) to modify up to seven different amino acids with a single mono(ADP-ribose) unit (MARylation deposited by PARP monoenzymes) or branched poly(ADP-ribose) polymers (PARylation deposited by PARP polyenzymes). To enable the development of tool compounds for PARP monoenzymes and polyenzymes, we have developed active site probes for use in in vitro and cellular biophysical assays to characterize active site-directed inhibitors that compete for NAD+ binding. These assays are agnostic of the protein substrate for each PARP, overcoming a general lack of knowledge around the substrates for these enzymes. The in vitro assays use less enzyme than previously described activity assays, enabling discrimination of inhibitor potencies in the single-digit nanomolar range, and the cell-based assays can differentiate compounds with sub-nanomolar potencies and measure inhibitor residence time in live cells.
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Affiliation(s)
- Tim J Wigle
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA.
| | | | - Laurie B Schenkel
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Yue Ren
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - W David Church
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Hetvi J Desai
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Kerren K Swinger
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Andrew G Santospago
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Christina R Majer
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Alvin Z Lu
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Mario Niepel
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Nicholas R Perl
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Melissa M Vasbinder
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Heike Keilhack
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
| | - Kevin W Kuntz
- Ribon Therapeutics, 35 Cambridgepark Drive, Suite 300, Cambridge, MA 02140, USA
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5
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The Significance of Targeting Poly (ADP-Ribose) Polymerase-1 in Pancreatic Cancer for Providing a New Therapeutic Paradigm. Int J Mol Sci 2021. [PMID: 33805293 DOI: 10.3390/ijms22073509.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Genome-wide studies focusing on elucidating the effects on cancer progression have enabled the consequent identification of a distinct subpopulation of pancreatic cancer cells with unstable genomic characteristics. Based on this background, deleterious changes by poly (adenosine diphosphate (ADP)-ribose) polymerase-1 (PARP)-1 have been concentrated in oncology. One of the critical functions of PARP-1 is the response to DNA damage, which plays a pivotal role in DNA repair in cancers. PARP-1 also has widespread functions that are essential for the survival and growth of cancer cells. It regulates oxidative stress in mitochondria through the regulation of superoxide and oxidation. PARP-1 is in charge of regulating mitosis, which is a crucial role in tumorigenesis and remodels histones and chromatin enzymes related to transcriptional regulation, causing alterations in epigenetic markers and chromatin structure. Given the significance of these processes, it can be understood that these processes in cancer cells are at the frontline of the pathogenetic changes required for cancer cell survival, and these contributions can result in malignant transformation. Therefore, this review addresses the current molecular biological features for understanding the multifactorial function of PARP-1 in pancreatic cancer related to the aforementioned roles, along with the summary of recent approaches with PARP-1 inhibition in clinical studies targeting pancreatic cancer. This understanding could help to embrace the importance of targeting PARP-1 in the treatment of pancreatic cancer, which may present the potential to find out a variety of research topics that can be both challenged clinically and non-clinically.
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6
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Jeong KY, Park MH. The Significance of Targeting Poly (ADP-Ribose) Polymerase-1 in Pancreatic Cancer for Providing a New Therapeutic Paradigm. Int J Mol Sci 2021; 22:ijms22073509. [PMID: 33805293 PMCID: PMC8037971 DOI: 10.3390/ijms22073509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 12/27/2022] Open
Abstract
Genome-wide studies focusing on elucidating the effects on cancer progression have enabled the consequent identification of a distinct subpopulation of pancreatic cancer cells with unstable genomic characteristics. Based on this background, deleterious changes by poly (adenosine diphosphate (ADP)-ribose) polymerase-1 (PARP)-1 have been concentrated in oncology. One of the critical functions of PARP-1 is the response to DNA damage, which plays a pivotal role in DNA repair in cancers. PARP-1 also has widespread functions that are essential for the survival and growth of cancer cells. It regulates oxidative stress in mitochondria through the regulation of superoxide and oxidation. PARP-1 is in charge of regulating mitosis, which is a crucial role in tumorigenesis and remodels histones and chromatin enzymes related to transcriptional regulation, causing alterations in epigenetic markers and chromatin structure. Given the significance of these processes, it can be understood that these processes in cancer cells are at the frontline of the pathogenetic changes required for cancer cell survival, and these contributions can result in malignant transformation. Therefore, this review addresses the current molecular biological features for understanding the multifactorial function of PARP-1 in pancreatic cancer related to the aforementioned roles, along with the summary of recent approaches with PARP-1 inhibition in clinical studies targeting pancreatic cancer. This understanding could help to embrace the importance of targeting PARP-1 in the treatment of pancreatic cancer, which may present the potential to find out a variety of research topics that can be both challenged clinically and non-clinically.
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7
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Bioinformatic Analysis of the Nicotinamide Binding Site in Poly(ADP-Ribose) Polymerase Family Proteins. Cancers (Basel) 2021; 13:cancers13061201. [PMID: 33801950 PMCID: PMC8002165 DOI: 10.3390/cancers13061201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 12/27/2022] Open
Abstract
Simple Summary The PARP family consists of 17 proteins, and some of them are responsible for cancer cells’ viability. Much attention is therefore given to the search for chemical compounds with the ability to suppress distinct PARP family members (for example, PARP-5a and 5b). Here, we present the results of a family-wide bioinformatic analysis of an important functional region in the PARP structure and describe factors that can guide the design of highly selective compounds. Abstract The PARP family consists of 17 members with diverse functions, including those related to cancer cells’ viability. Several PARP inhibitors are of great interest as innovative anticancer drugs, but they have low selectivity towards distinct PARP family members and exert serious adverse effects. We describe a family-wide study of the nicotinamide (NA) binding site, an important functional region in the PARP structure, using comparative bioinformatic analysis and molecular modeling. Mutations in the NA site and D-loop mobility around the NA site were identified as factors that can guide the design of selective PARP inhibitors. Our findings are of particular importance for the development of novel tankyrase (PARPs 5a and 5b) inhibitors for cancer therapy.
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8
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Thorsell AG, Ekblad T, Karlberg T, Löw M, Pinto AF, Trésaugues L, Moche M, Cohen MS, Schüler H. Structural Basis for Potency and Promiscuity in Poly(ADP-ribose) Polymerase (PARP) and Tankyrase Inhibitors. J Med Chem 2016; 60:1262-1271. [PMID: 28001384 DOI: 10.1021/acs.jmedchem.6b00990] [Citation(s) in RCA: 237] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Selective inhibitors could help unveil the mechanisms by which inhibition of poly(ADP-ribose) polymerases (PARPs) elicits clinical benefits in cancer therapy. We profiled 10 clinical PARP inhibitors and commonly used research tools for their inhibition of multiple PARP enzymes. We also determined crystal structures of these compounds bound to PARP1 or PARP2. Veliparib and niraparib are selective inhibitors of PARP1 and PARP2; olaparib, rucaparib, and talazoparib are more potent inhibitors of PARP1 but are less selective. PJ34 and UPF1069 are broad PARP inhibitors; PJ34 inserts a flexible moiety into hydrophobic subpockets in various ADP-ribosyltransferases. XAV939 is a promiscuous tankyrase inhibitor and a potent inhibitor of PARP1 in vitro and in cells, whereas IWR1 and AZ-6102 are tankyrase selective. Our biochemical and structural analysis of PARP inhibitor potencies establishes a molecular basis for either selectivity or promiscuity and provides a benchmark for experimental design in assessment of PARP inhibitor effects.
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Affiliation(s)
| | | | | | | | | | | | | | - Michael S Cohen
- Program in Chemical Biology and Department of Physiology and Pharmacology, Health & Science University , Portland, Oregon 97210, United States
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9
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A comprehensive look of poly(ADP-ribose) polymerase inhibition strategies and future directions for cancer therapy. Future Med Chem 2016; 9:37-60. [PMID: 27995810 DOI: 10.4155/fmc-2016-0113] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The finding of promising drugs represents a huge challenge in cancer therapeutics, therefore it is important to seek out novel approaches and elucidate essential cellular processes in order to identify potential drug targets. Studies on DNA repair pathway suggested that an enzyme, PARP, which plays a significant role in DNA repair responses, could be targeted in cancer therapy. Hence, the efficacy of PARP inhibitors in cancer therapy has been investigated and has progressed from the laboratory to clinics, with olaparib having already been approved by the US FDA for ovarian cancer treatment. Here, we have discussed the development of PARP inhibitors, strategies to improve their selectivity and efficacy, including innovative combinational and synthetic lethality approaches to identify effective PARP inhibitors in cancer treatment.
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10
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Venkannagari H, Verheugd P, Koivunen J, Haikarainen T, Obaji E, Ashok Y, Narwal M, Pihlajaniemi T, Lüscher B, Lehtiö L. Small-Molecule Chemical Probe Rescues Cells from Mono-ADP-Ribosyltransferase ARTD10/PARP10-Induced Apoptosis and Sensitizes Cancer Cells to DNA Damage. Cell Chem Biol 2016; 23:1251-1260. [DOI: 10.1016/j.chembiol.2016.08.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 07/22/2016] [Accepted: 08/31/2016] [Indexed: 12/21/2022]
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11
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Rodas PI, Álamos-Musre AS, Álvarez FP, Escobar A, Tapia CV, Osorio E, Otero C, Calderón IL, Fuentes JA, Gil F, Paredes-Sabja D, Christodoulides M. The NarE protein of Neisseria gonorrhoeae catalyzes ADP-ribosylation of several ADP-ribose acceptors despite an N-terminal deletion. FEMS Microbiol Lett 2016; 363:fnw181. [PMID: 27465490 PMCID: PMC5812539 DOI: 10.1093/femsle/fnw181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/12/2016] [Accepted: 07/21/2016] [Indexed: 12/18/2022] Open
Abstract
The ADP-ribosylating enzymes are encoded in many pathogenic bacteria in order to affect essential functions of the host. In this study, we show that Neisseria gonorrhoeae possess a locus that corresponds to the ADP-ribosyltransferase NarE, a previously characterized enzyme in N. meningitidis The 291 bp coding sequence of gonococcal narE shares 100% identity with part of the coding sequence of the meningococcal narE gene due to a frameshift previously described, thus leading to a 49-amino-acid deletion at the N-terminus of gonococcal NarE protein. However, we found a promoter region and a GTG start codon, which allowed expression of the protein as demonstrated by RT-PCR and western blot analyses. Using a gonococcal NarE-6xHis fusion protein, we demonstrated that the gonococcal enzyme underwent auto-ADP-ribosylation but to a lower extent than meningococcal NarE. We also observed that gonoccocal NarE exhibited ADP-ribosyltransferase activity using agmatine and cell-free host proteins as ADP-ribose acceptors, but its activity was inhibited by human β-defensins. Taken together, our results showed that NarE of Neisseria gonorrhoeae is a functional enzyme that possesses key features of bacterial ADP-ribosylating enzymes.
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Affiliation(s)
- Paula I Rodas
- Center for Integrative Medicine and Innovative Sciences, Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - A Said Álamos-Musre
- Center for Integrative Medicine and Innovative Sciences, Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Francisca P Álvarez
- Center for Integrative Medicine and Innovative Sciences, Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Alejandro Escobar
- Instituto de Investigación en Ciencias Odontológicas, Facultad de Odontología, Universidad de Chile, Santiago, Chile
| | - Cecilia V Tapia
- Laboratorio Clínica Dávila, Santiago, Chile Laboratorio de Micología Médica, Programa de Microbiología y Micología, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Eduardo Osorio
- Servicio de Ginecología y Obstetricia, Clínica Dávila, Santiago, Chile
| | - Carolina Otero
- Center for Integrative Medicine and Innovative Sciences, Facultad de Medicina, Universidad Andres Bello, Santiago, Chile
| | - Iván L Calderón
- Laboratorio de Genética y Patogénesis Bacteriana, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Juan A Fuentes
- Laboratorio de Genética y Patogénesis Bacteriana, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Fernando Gil
- Laboratorio de Genética y Patogénesis Bacteriana, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Daniel Paredes-Sabja
- Microbiota-Host Interactions and Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Myron Christodoulides
- Neisseria Research Group, Molecular Microbiology, Sir Henry Wellcome Laboratories, Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, England
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12
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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: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [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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13
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Karlberg T, Klepsch M, Thorsell AG, Andersson CD, Linusson A, Schüler H. Structural basis for lack of ADP-ribosyltransferase activity in poly(ADP-ribose) polymerase-13/zinc finger antiviral protein. J Biol Chem 2015; 290:7336-44. [PMID: 25635049 PMCID: PMC4367243 DOI: 10.1074/jbc.m114.630160] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/27/2015] [Indexed: 12/15/2022] Open
Abstract
The mammalian poly(ADP-ribose) polymerase (PARP) family includes ADP-ribosyltransferases with diphtheria toxin homology (ARTD). Most members have mono-ADP-ribosyltransferase activity. PARP13/ARTD13, also called zinc finger antiviral protein, has roles in viral immunity and microRNA-mediated stress responses. PARP13 features a divergent PARP homology domain missing a PARP consensus sequence motif; the domain has enigmatic functions and apparently lacks catalytic activity. We used x-ray crystallography, molecular dynamics simulations, and biochemical analyses to investigate the structural requirements for ADP-ribosyltransferase activity in human PARP13 and two of its functional partners in stress granules: PARP12/ARTD12, and PARP15/BAL3/ARTD7. The crystal structure of the PARP homology domain of PARP13 shows obstruction of the canonical active site, precluding NAD(+) binding. Molecular dynamics simulations indicate that this closed cleft conformation is maintained in solution. Introducing consensus side chains in PARP13 did not result in 3-aminobenzamide binding, but in further closure of the site. Three-dimensional alignment of the PARP homology domains of PARP13, PARP12, and PARP15 illustrates placement of PARP13 residues that deviate from the PARP family consensus. Introducing either one of two of these side chains into the corresponding positions in PARP15 abolished PARP15 ADP-ribosyltransferase activity. Taken together, our results show that PARP13 lacks the structural requirements for ADP-ribosyltransferase activity.
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Affiliation(s)
- Tobias Karlberg
- From the Structural Genomics Consortium and the Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden and
| | - Mirjam Klepsch
- the Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden and
| | - Ann-Gerd Thorsell
- From the Structural Genomics Consortium and the Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden and
| | | | - Anna Linusson
- the Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Herwig Schüler
- From the Structural Genomics Consortium and the Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden and
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Perina D, Mikoč A, Ahel J, Ćetković H, Žaja R, Ahel I. Distribution of protein poly(ADP-ribosyl)ation systems across all domains of life. DNA Repair (Amst) 2014; 23:4-16. [PMID: 24865146 PMCID: PMC4245714 DOI: 10.1016/j.dnarep.2014.05.003] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/04/2014] [Accepted: 05/06/2014] [Indexed: 02/08/2023]
Abstract
Poly(ADP-ribosyl)ation is a post-translational modification of proteins involved in regulation of many cellular pathways. Poly(ADP-ribose) (PAR) consists of chains of repeating ADP-ribose nucleotide units and is synthesized by the family of enzymes called poly(ADP-ribose) polymerases (PARPs). This modification can be removed by the hydrolytic action of poly(ADP-ribose) glycohydrolase (PARG) and ADP-ribosylhydrolase 3 (ARH3). Hydrolytic activity of macrodomain proteins (MacroD1, MacroD2 and TARG1) is responsible for the removal of terminal ADP-ribose unit and for complete reversion of protein ADP-ribosylation. Poly(ADP-ribosyl)ation is widely utilized in eukaryotes and PARPs are present in representatives from all six major eukaryotic supergroups, with only a small number of eukaryotic species that do not possess PARP genes. The last common ancestor of all eukaryotes possessed at least five types of PARP proteins that include both mono and poly(ADP-ribosyl) transferases. Distribution of PARGs strictly follows the distribution of PARP proteins in eukaryotic species. At least one of the macrodomain proteins that hydrolyse terminal ADP-ribose is also always present. Therefore, we can presume that the last common ancestor of all eukaryotes possessed a fully functional and reversible PAR metabolism and that PAR signalling provided the conditions essential for survival of the ancestral eukaryote in its ancient environment. PARP proteins are far less prevalent in bacteria and were probably gained through horizontal gene transfer. Only eleven bacterial species possess all proteins essential for a functional PAR metabolism, although it is not known whether PAR metabolism is truly functional in bacteria. Several dsDNA viruses also possess PARP homologues, while no PARP proteins have been identified in any archaeal genome. Our analysis of the distribution of enzymes involved in PAR metabolism provides insight into the evolution of these important signalling systems, as well as providing the basis for selection of the appropriate genetic model organisms to study the physiology of the specific human PARP proteins.
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Affiliation(s)
- Dragutin Perina
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb 10002, Croatia
| | - Andreja Mikoč
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb 10002, Croatia
| | - Josip Ahel
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb 10002, Croatia
| | - Helena Ćetković
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb 10002, Croatia
| | - Roko Žaja
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb 10002, Croatia; Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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Roszak A, Lianeri M, Sowińska A, Jagodziński PP. Involvement of PARP-1 Val762Ala polymorphism in the onset of cervical cancer in caucasian women. Mol Diagn Ther 2014; 17:239-45. [PMID: 23633189 PMCID: PMC3715681 DOI: 10.1007/s40291-013-0036-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND AND OBJECTIVE Data on the Val762Ala (rs1136410) polymorphism in the poly(adenosine diphosphate [ADP]-ribose) polymerase 1 (PARP-1) gene as a risk factor for various types of cancers in different ethnicities are inconsistent. We studied this association in a Caucasian population. METHODS Using high-resolution melting curve analysis (HRM), we studied the distribution of the PARP-1 Val762Ala polymorphism in patients with cervical cancer (n = 446) and in controls (n = 491). RESULTS Logistic regression analysis adjusting for age, pregnancy, oral contraceptive use, tobacco smoking, and menopausal status demonstrated that the PARP-1 Val762Ala polymorphism was associated with an increased risk of cervical cancer. The adjusted odds ratio (OR) for patients with the Ala/Val genotype versus the Val/Val genotype was 1.381 (95 % CI = 1.025-1.859, p = 0.033), and the adjusted OR for the Ala/Ala or Ala/Val genotype versus the Val/Val genotype was 1.403 (95 % CI = 1.057-1.863, p = 0.019). The p value from the chi-square test of the trend observed for the PARP-1 Val762Ala polymorphism was statistically significant (p trend = 0.0123). Stratified analyses of the PARP-1 Val762Ala genotype distribution and cervical cancer risk showed that the age-adjusted OR of Ala/Ala or Ala/Val vs Val/Val for pregnancy was 1.388 (95 % CI = 1.027-1.877, p = 0.0328), 1.773 (95 % CI = 1.145-2.745, p = 0.0100) for contraceptive use, and 1.604 (95 % CI = 1.132-2.272, p = 0.0077) for postmenopausal women. The age-adjusted OR of Ala/Val vs Val/Val for contraceptive use was 1.769 (95 % CI = 1.114-2.809, p = 0.0154) and for postmenopausal women was 1.577 (95 % CI = 1.094-2.272, p = 0.0143). CONCLUSION Our studies suggest that the PARP-1 Val762Ala polymorphism may be a genetic risk factor for cervical cancer.
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Affiliation(s)
- Andrzej Roszak
- Department of Radiotherapy and Gynecological Oncology, Greater Poland Cancer Center Poznan, Poznan, Poland
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16
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Comparative structural analysis of the putative mono-ADP-ribosyltransferases of the ARTD/PARP family. Curr Top Microbiol Immunol 2014; 384:153-66. [PMID: 25015788 DOI: 10.1007/82_2014_417] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The existence and significance of endogenous cytosolic and nuclear mono-ADP-ribosylation has been a matter of debate. Today, evidence suggests that the human enzymes that catalyze the reaction have been rounded up. Moreover, substrate proteins and specific functions for mono-ADP-ribosyltransferases are beginning to be defined. Reader domains that specifically recognize mono-ADP-ribosylated target proteins and erasers that remove the mono-ADP-ribosyl mark have been identified. Here, we review the contribution of crystal structures to our understanding of the putative mono-ADP-ribosyltransferases with Diphtheria toxin and ARTD1/PARP1 homology.
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17
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Lindgren AEG, Karlberg T, Thorsell AG, Hesse M, Spjut S, Ekblad T, Andersson CD, Pinto AF, Weigelt J, Hottiger MO, Linusson A, Elofsson M, Schüler H. PARP inhibitor with selectivity toward ADP-ribosyltransferase ARTD3/PARP3. ACS Chem Biol 2013; 8:1698-703. [PMID: 23742272 DOI: 10.1021/cb4002014] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inhibiting ADP-ribosyl transferases with PARP-inhibitors is considered a promising strategy for the treatment of many cancers and ischemia, but most of the cellular targets are poorly characterized. Here, we describe an inhibitor of ADP-ribosyltransferase-3/poly(ADP-ribose) polymerase-3 (ARTD3), a regulator of DNA repair and mitotic progression. In vitro profiling against 12 members of the enzyme family suggests selectivity for ARTD3, and crystal structures illustrate the molecular basis for inhibitor selectivity. The compound is active in cells, where it elicits ARTD3-specific effects at submicromolar concentration. Our results show that by targeting the nicotinamide binding site, selective inhibition can be achieved among the closest relatives of the validated clinical target, ADP-ribosyltransferase-1/poly(ADP-ribose) polymerase-1.
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Affiliation(s)
| | - Tobias Karlberg
- Department of Medical Biochemistry
and Biophysics, Karolinska Institutet,
Stockholm, Sweden
| | - Ann-Gerd Thorsell
- Department of Medical Biochemistry
and Biophysics, Karolinska Institutet,
Stockholm, Sweden
| | - Mareike Hesse
- Institute
of Veterinary Biochemistry
and Molecular Biology, University of Zurich, Zurich, Switzerland
| | - Sara Spjut
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Torun Ekblad
- Department of Medical Biochemistry
and Biophysics, Karolinska Institutet,
Stockholm, Sweden
| | | | - Ana Filipa Pinto
- Department of Medical Biochemistry
and Biophysics, Karolinska Institutet,
Stockholm, Sweden
| | - Johan Weigelt
- Department of Medical Biochemistry
and Biophysics, Karolinska Institutet,
Stockholm, Sweden
| | - Michael O. Hottiger
- Institute
of Veterinary Biochemistry
and Molecular Biology, University of Zurich, Zurich, Switzerland
| | - Anna Linusson
- Department of Chemistry, Umeå University, Umeå, Sweden
| | | | - Herwig Schüler
- Department of Medical Biochemistry
and Biophysics, Karolinska Institutet,
Stockholm, Sweden
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18
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Feijs KLH, Forst AH, Verheugd P, Lüscher B. Macrodomain-containing proteins: regulating new intracellular functions of mono(ADP-ribosyl)ation. Nat Rev Mol Cell Biol 2013; 14:443-51. [PMID: 23736681 PMCID: PMC7097401 DOI: 10.1038/nrm3601] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The function and regulation of poly(ADP-ribosyl)ation is partially understood. By contrast, little is known about intracellular mono(ADP-ribosyl)ation (MARylation) by ADP-ribosyl transferases. Recent findings indicate that MARylation regulates signalling and transcription by modifying key components in these processes, and that specific macrodomain-containing proteins 'read' and 'erase' this modification. ADP-ribosylation of proteins was first described in the early 1960's, and today the function and regulation of poly(ADP-ribosyl)ation (PARylation) is partially understood. By contrast, little is known about intracellular mono(ADP-ribosyl)ation (MARylation) by ADP-ribosyl transferase (ART) enzymes, such as ARTD10. Recent findings indicate that MARylation regulates signalling and transcription by modifying key components in these processes. Emerging evidence also suggests that specific macrodomain-containing proteins, including ARTD8, macroD1, macroD2 and C6orf130, which are distinct from those affecting PARylation, interact with MARylation on target proteins to 'read' and 'erase' this modification. Thus, studying macrodomain-containing proteins is key to understanding the function and regulation of MARylation.
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Affiliation(s)
- Karla L H Feijs
- Institute of Biochemistry and Molecular Biology, Rheinisch-Westfaelische Technische Hochschule (RWTH) Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany
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19
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Scarpa ES, Fabrizio G, Di Girolamo M. A role of intracellular mono-ADP-ribosylation in cancer biology. FEBS J 2013; 280:3551-62. [PMID: 23590234 DOI: 10.1111/febs.12290] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 04/09/2013] [Indexed: 01/01/2023]
Abstract
During the development, progression and dissemination of neoplastic lesions, cancer cells can hijack normal pathways and mechanisms. This includes the control of the function of cellular proteins through reversible post-translational modifications, such as ADP-ribosylation, phosphorylation, and acetylation. In the case of mono-ADP-ribosylation and poly-ADP-ribosylation, the addition of one or several units of ADP-ribose to target proteins occurs via two families of enzymes that can generate ADP-ribosylated proteins: the diphtheria toxin-like ADP-ribosyltransferase (ARTD) family, comprising 17 different proteins that are either poly-ADP-ribosyltransferases or mono-ADP-ribosyltransferases or inactive enzymes; and the clostridial toxin-like ADP-ribosyltransferase family, with four human members, two of which are active mono-ADP-ribosyltransferases, and two of which are enzymatically inactive. In line with a central role for poly-ADP-ribose polymerase 1 in response to DNA damage, specific inhibitors of this enzyme have been developed as anticancer therapeutics and evaluated in several clinical trials. Recently, in combination with the discovery of a large number of enzymes that can catalyse mono-ADP-ribosylation, the role of this modification has been linked to human diseases, such as inflammation, diabetes, neurodegeneration, and cancer, thus revealing the need for the development of specific ARTD inhibitors. This will provide a better understanding of the roles of these enzymes in human physiology and pathology, so that they can be targeted in the future to generate new and efficacious drugs. This review summarizes our present knowledge of the ARTD enzymes that are involved in mono-ADP-ribosylation reactions and that have roles in cancer biology. In particular, the well-documented role of macro-containing ARTD8 in lymphoma and the putative role of ARTD15 in cancer are discussed.
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Affiliation(s)
- Emanuele S Scarpa
- Department of Cellular and Translational Pharmacology, Consorzio Mario Negri Sud, Santa Maria Imbaro, Chieti, Italy
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20
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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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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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22
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Hassler M, Ladurner AG. Towards a structural understanding of PARP1 activation and related signalling ADP-ribosyl-transferases. Curr Opin Struct Biol 2012; 22:721-9. [DOI: 10.1016/j.sbi.2012.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 08/30/2012] [Indexed: 11/29/2022]
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