351
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Ryu KW, Kim DS, Kraus WL. New facets in the regulation of gene expression by ADP-ribosylation and poly(ADP-ribose) polymerases. Chem Rev 2015; 115:2453-81. [PMID: 25575290 PMCID: PMC4378458 DOI: 10.1021/cr5004248] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Indexed: 12/11/2022]
Affiliation(s)
- Keun Woo Ryu
- Laboratory of Signaling and Gene
Regulation, Cecil H. and Ida Green
Center for Reproductive Biology Sciences, Division of Basic Research, Department
of Obstetrics and Gynecology, and Graduate School of Biomedical Sciences, Program
in Genetics and Development, University
of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Dae-Seok Kim
- Laboratory of Signaling and Gene
Regulation, Cecil H. and Ida Green
Center for Reproductive Biology Sciences, Division of Basic Research, Department
of Obstetrics and Gynecology, and Graduate School of Biomedical Sciences, Program
in Genetics and Development, University
of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
| | - W. Lee Kraus
- Laboratory of Signaling and Gene
Regulation, Cecil H. and Ida Green
Center for Reproductive Biology Sciences, Division of Basic Research, Department
of Obstetrics and Gynecology, and Graduate School of Biomedical Sciences, Program
in Genetics and Development, University
of Texas Southwestern Medical Center, Dallas, Texas 75390, United States
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352
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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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353
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Abstract
The development of poly (adenosine diphosphate [ADP]) ribose polymerase (PARP) inhibitors (PARPi) has progressed greatly over the last few years and has shown encouraging results in the BRCA1/2 mutation–related cancers. This article attempts to summarize the rationale and theory behind PARPi, the clinical trials already reported, as well as ongoing studies designed to determine the role of PARPi in patients with and without germline mutations of BRCA genes. Future plans for PARPi both as monotherapy and in combination with standard cytotoxics, other biological agents, and as radiosensitizers are also covered. The widening scope of PARPi adds another important targeted agent to the growing list of molecular inhibitors; future and ongoing trials will identify the most effective role for PARPi, including for patients other than BRCA germline mutation carriers.
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Affiliation(s)
- Sarah Benafif
- Mount Vernon Cancer Centre, Northwood, Middlesex, UK
| | - Marcia Hall
- Mount Vernon Cancer Centre, Northwood, Middlesex, UK
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354
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Hottiger MO. Nuclear ADP-Ribosylation and Its Role in Chromatin Plasticity, Cell Differentiation, and Epigenetics. Annu Rev Biochem 2015; 84:227-63. [PMID: 25747399 DOI: 10.1146/annurev-biochem-060614-034506] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein ADP-ribosylation is an ancient posttranslational modification with high biochemical complexity. It alters the function of modified proteins or provides a scaffold for the recruitment of other proteins and thus regulates several cellular processes. ADP-ribosylation is governed by ADP-ribosyltransferases and a subclass of sirtuins (writers), is sensed by proteins that contain binding modules (readers) that recognize specific parts of the ADP-ribosyl posttranslational modification, and is removed by ADP-ribosylhydrolases (erasers). The large amount of experimental data generated and technical progress made in the last decade have significantly advanced our knowledge of the function of ADP-ribosylation at the molecular level. This review summarizes the current knowledge of nuclear ADP-ribosylation reactions and their role in chromatin plasticity, cell differentiation, and epigenetics and discusses current progress and future perspectives.
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Affiliation(s)
- Michael O Hottiger
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, 8057 Zurich, Switzerland;
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355
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Gagné JP, Ethier C, Defoy D, Bourassa S, Langelier MF, Riccio AA, Pascal JM, Moon KM, Foster LJ, Ning Z, Figeys D, Droit A, Poirier GG. Quantitative site-specific ADP-ribosylation profiling of DNA-dependent PARPs. DNA Repair (Amst) 2015; 30:68-79. [PMID: 25800440 DOI: 10.1016/j.dnarep.2015.02.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/04/2015] [Indexed: 12/13/2022]
Abstract
An important feature of poly(ADP-ribose) polymerases (PARPs) is their ability to readily undergo automodification upon activation. Although a growing number of substrates were found to be poly(ADP-ribosyl)ated, including histones and several DNA damage response factors, PARPs themselves are still considered as the main acceptors of poly(ADP-ribose). By monitoring spectral counts of specific hydroxamic acid signatures generated after the conversion of the ADP-ribose modification onto peptides by hydroxylamine hydrolysis, we undertook a thorough mass spectrometry mapping of the glutamate and aspartate ADP-ribosylation sites onto automodified PARP-1, PARP-2 and PARP-3. Thousands of hydroxamic acid-conjugated peptides were identified with high confidence and ranked based on their spectral count. This semi-quantitative approach allowed us to locate the preferentially targeted residues in DNA-dependent PARPs. In contrast to what has been reported in the literature, automodification of PARP-1 is not predominantly targeted towards its BRCT domain. Our results show that interdomain linker regions that connect the BRCT to the WGR module and the WGR to the PRD domain undergo prominent ADP-ribosylation during PARP-1 automodification. We also found that PARP-1 efficiently automodifies the D-loop structure within its own catalytic fold. Interestingly, additional major ADP-ribosylation sites were identified in functional domains of PARP-1, including all three zinc fingers. Similar to PARP-1, specific residues located within the catalytic sites of PARP-2 and PARP-3 are major targets of automodification following their DNA-dependent activation. Together our results suggest that poly(ADP-ribosyl)ation hot spots make a dominant contribution to the overall automodification process.
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Affiliation(s)
- Jean-Philippe Gagné
- Centre de recherche du CHU de Québec - Pavillon CHUL, Faculté de Médecine, Université Laval, Québec, Canada
| | - Chantal Ethier
- Centre de recherche du CHU de Québec - Pavillon CHUL, Faculté de Médecine, Université Laval, Québec, Canada
| | - Daniel Defoy
- Plateforme Protéomique du Centre de Recherche du CHU de Québec - Pavillon CHUL, Faculté de Médecine, Université Laval, Québec, Canada
| | - Sylvie Bourassa
- Plateforme Protéomique du Centre de Recherche du CHU de Québec - Pavillon CHUL, Faculté de Médecine, Université Laval, Québec, Canada
| | - Marie-France Langelier
- Department of Biochemistry & Molecular Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, USA
| | - Amanda A Riccio
- Department of Biochemistry & Molecular Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, USA
| | - John M Pascal
- Department of Biochemistry & Molecular Biology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, USA
| | - Kyung-Mee Moon
- Department of Biochemistry and Molecular Biology, University of British Columbia, Centre for High-Throughput Biology, Vancouver, British Columbia, Canada
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, University of British Columbia, Centre for High-Throughput Biology, Vancouver, British Columbia, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Arnaud Droit
- Plateforme Protéomique du Centre de Recherche du CHU de Québec - Pavillon CHUL, Faculté de Médecine, Université Laval, Québec, Canada
| | - Guy G Poirier
- Centre de recherche du CHU de Québec - Pavillon CHUL, Faculté de Médecine, Université Laval, Québec, Canada.
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356
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Meyer-Ficca ML, Ihara M, Bader JJ, Leu NA, Beneke S, Meyer RG. Spermatid head elongation with normal nuclear shaping requires ADP-ribosyltransferase PARP11 (ARTD11) in mice. Biol Reprod 2015; 92:80. [PMID: 25673562 DOI: 10.1095/biolreprod.114.123661] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Sperm are highly differentiated cells characterized by their species-specific nuclear shapes and extremely condensed chromatin. Abnormal head shapes represent a form of teratozoospermia that can impair fertilization capacity. This study shows that poly(ADP-ribose) polymerase-11 (ARTD11/PARP11), a member of the ADP-ribosyltransferase (ARTD) family, is expressed preferentially in spermatids undergoing nuclear condensation and differentiation. Deletion of the Parp11 gene results in teratozoospermia and male infertility in mice due to the formation of abnormally shaped fertilization-incompetent sperm, despite normal testis weights and sperm counts. At the subcellular level, PARP11-deficient elongating spermatids reveal structural defects in the nuclear envelope and chromatin detachment associated with abnormal nuclear shaping, suggesting functional relevance of PARP11 for nuclear envelope stability and nuclear reorganization during spermiogenesis. In vitro, PARP11 exhibits mono(ADP-ribosyl)ation activity with the ability to ADP-ribosylate itself. In transfected somatic cells, PARP11 colocalizes with nuclear pore components, such as NUP153. Amino acids Y77, Q86, and R95 in the N-terminal WWE domain, as well as presence of the catalytic domain, are essential for colocalization of PARP11 with the nuclear envelope, but catalytic activity of the protein is not required for colocalization with NUP153. This study demonstrates that PARP11 is a novel enzyme important for proper sperm head shaping and identifies it as a potential factor involved in idiopathic mammalian teratozoospermia.
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Affiliation(s)
- Mirella L Meyer-Ficca
- Department of Animal Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah Agricultural Experimental Station, Utah State University, Logan, Utah Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Motomasa Ihara
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jessica J Bader
- Department of Animal Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah Agricultural Experimental Station, Utah State University, Logan, Utah Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - N Adrian Leu
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sascha Beneke
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Ralph G Meyer
- Department of Animal Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah Agricultural Experimental Station, Utah State University, Logan, Utah Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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357
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A human tRNA synthetase is a potent PARP1-activating effector target for resveratrol. Nature 2014; 519:370-3. [PMID: 25533949 PMCID: PMC4368482 DOI: 10.1038/nature14028] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 11/03/2014] [Indexed: 12/18/2022]
Abstract
Resveratrol is reported to extend lifespan and provide cardio-neuro-protective, anti-diabetic, and anti-cancer effects by initiating a stress response that induces survival genes. Because human tyrosyl transfer-RNA (tRNA) synthetase (TyrRS) translocates to the nucleus under stress conditions, we considered the possibility that the tyrosine-like phenolic ring of resveratrol might fit into the active site pocket to effect a nuclear role. Here we present a 2.1 Å co-crystal structure of resveratrol bound to the active site of TyrRS. Resveratrol nullifies the catalytic activity and redirects TyrRS to a nuclear function, stimulating NAD(+)-dependent auto-poly-ADP-ribosylation of poly(ADP-ribose) polymerase 1 (PARP1). Downstream activation of key stress signalling pathways are causally connected to TyrRS-PARP1-NAD(+) collaboration. This collaboration is also demonstrated in the mouse, and is specifically blocked in vivo by a resveratrol-displacing tyrosyl adenylate analogue. In contrast to functionally diverse tRNA synthetase catalytic nulls created by alternative splicing events that ablate active sites, here a non-spliced TyrRS catalytic null reveals a new PARP1- and NAD(+)-dependent dimension to the physiological mechanism of resveratrol.
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358
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Vivelo CA, Leung AKL. Proteomics approaches to identify mono-(ADP-ribosyl)ated and poly(ADP-ribosyl)ated proteins. Proteomics 2014; 15:203-17. [PMID: 25263235 DOI: 10.1002/pmic.201400217] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 08/17/2014] [Accepted: 09/24/2014] [Indexed: 12/18/2022]
Abstract
ADP-ribosylation refers to the addition of one or more ADP-ribose units onto protein substrates and this protein modification has been implicated in various cellular processes including DNA damage repair, RNA metabolism, transcription, and cell cycle regulation. This review focuses on a compilation of large-scale proteomics studies that identify ADP-ribosylated proteins and their associated proteins by MS using a variety of enrichment strategies. Some methods, such as the use of a poly(ADP-ribose)-specific antibody and boronate affinity chromatography and NAD(+) analogues, have been employed for decades while others, such as the use of protein microarrays and recombinant proteins that bind ADP-ribose moieties (such as macrodomains), have only recently been developed. The advantages and disadvantages of each method and whether these methods are specific for identifying mono(ADP-ribosyl)ated and poly(ADP-ribosyl)ated proteins will be discussed. Lastly, since poly(ADP-ribose) is heterogeneous in length, it has been difficult to attain a mass signature associated with the modification sites. Several strategies on how to reduce polymer chain length heterogeneity for site identification will be reviewed.
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Affiliation(s)
- Christina A Vivelo
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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359
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Lehmann M, Pirinen E, Mirsaidi A, Kunze FA, Richards PJ, Auwerx J, Hottiger MO. ARTD1-induced poly-ADP-ribose formation enhances PPARγ ligand binding and co-factor exchange. Nucleic Acids Res 2014; 43:129-42. [PMID: 25452336 PMCID: PMC4288160 DOI: 10.1093/nar/gku1260] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
PPARγ-dependent gene expression during adipogenesis is facilitated by ADP-ribosyltransferase D-type 1 (ARTD1; PARP1)-catalyzed poly-ADP-ribose (PAR) formation. Adipogenesis is accompanied by a dynamic modulation of the chromatin landscape at PPARγ target genes by ligand-dependent co-factor exchange. However, how endogenous PPARγ ligands, which have a low affinity for the receptor and are present at low levels in the cell, can induce sufficient co-factor exchange is unknown. Moreover, the significance of PAR formation in PPARγ-regulated adipose tissue function is also unknown. Here, we show that inhibition of PAR formation in mice on a high-fat diet reduces weight gain and cell size of adipocytes, as well as PPARγ target gene expression in white adipose tissue. Mechanistically, topoisomerase II activity induces ARTD1 recruitment to PPARγ target genes, and ARTD1 automodification enhances ligand binding to PPARγ, thus promoting sufficient transcriptional co-factor exchange in adipocytes. Thus, ARTD1-mediated PAR formation during adipogenesis is necessary to adequately convey the low signal of endogenous PPARγ ligand to effective gene expression. These results uncover a new regulatory mechanism of ARTD1-induced ADP-ribosylation and highlight its importance for nuclear factor-regulated gene expression.
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Affiliation(s)
- Mareike Lehmann
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, 8057 Zurich, Switzerland Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich, 8057 Zurich, Switzerland
| | - Eija Pirinen
- Laboratory of Integrative and Systems Physiology, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, Biocenter Kuopio, University of Eastern Finland, Kuopio, Finland
| | - Ali Mirsaidi
- Competence Centre for Applied Biotechnology and Molecular Medicine, University of Zurich, 8057 Zurich, Switzerland Zurich Centre for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland
| | - Friedrich A Kunze
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, 8057 Zurich, Switzerland Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich, 8057 Zurich, Switzerland
| | - Peter J Richards
- Competence Centre for Applied Biotechnology and Molecular Medicine, University of Zurich, 8057 Zurich, Switzerland Zurich Centre for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative and Systems Physiology, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Michael O Hottiger
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, 8057 Zurich, Switzerland Competence Centre for Applied Biotechnology and Molecular Medicine, University of Zurich, 8057 Zurich, Switzerland Zurich Centre for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland
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