1
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Wu H, Lu A, Yuan J, Yu Y, Lv C, Lu J. Mono-ADP-ribosylation, a MARylationmultifaced modification of protein, DNA and RNA: characterizations, functions and mechanisms. Cell Death Discov 2024; 10:226. [PMID: 38734665 PMCID: PMC11088682 DOI: 10.1038/s41420-024-01994-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
The functional alterations of proteins and nucleic acids mainly rely on their modifications. ADP-ribosylation is a NAD+-dependent modification of proteins and, in some cases, of nucleic acids. This modification is broadly categorized as Mono(ADP-ribosyl)ation (MARylation) or poly(ADP-ribosyl)ation (PARylation). MARylation catalyzed by mono(ADP-ribosyl) transferases (MARTs) is more common in cells and the number of MARTs is much larger than poly(ADP-ribosyl) transferases. Unlike PARylation is well-characterized, research on MARylation is at the starting stage. However, growing evidence demonstrate the cellular functions of MARylation, supporting its potential roles in human health and diseases. In this review, we outlined MARylation-associated proteins including MARTs, the ADP-ribosyl hydrolyses and ADP-ribose binding domains. We summarized up-to-date findings about MARylation onto newly identified substrates including protein, DNA and RNA, and focused on the functions of these reactions in pathophysiological conditions as well as speculated the potential mechanisms. Furthermore, new strategies of MARylation detection and the current state of MARTs inhibitors were discussed. We also provided an outlook for future study, aiming to revealing the unknown biological properties of MARylation and its relevant mechanisms, and establish a novel therapeutic perspective in human diseases.
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Affiliation(s)
- Hao Wu
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Anqi Lu
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Jiuzhi Yuan
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Yang Yu
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Chongning Lv
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
- Liaoning Provincial Key Laboratory of TCM Resources Conservation and Development, Shenyang Pharmaceutical University, Shenyang, China
| | - Jincai Lu
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China.
- Liaoning Provincial Key Laboratory of TCM Resources Conservation and Development, Shenyang Pharmaceutical University, Shenyang, China.
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2
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Wondisford AR, Lee J, Lu R, Schuller M, Groslambert J, Bhargava R, Schamus-Haynes S, Cespedes LC, Opresko PL, Pickett HA, Min J, Ahel I, O'Sullivan RJ. Deregulated DNA ADP-ribosylation impairs telomere replication. Nat Struct Mol Biol 2024; 31:791-800. [PMID: 38714889 PMCID: PMC11102865 DOI: 10.1038/s41594-024-01279-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 03/18/2024] [Indexed: 05/21/2024]
Abstract
The recognition that DNA can be ADP ribosylated provides an unexpected regulatory level of how ADP-ribosylation contributes to genome stability, epigenetics and immunity. Yet, it remains unknown whether DNA ADP-ribosylation (DNA-ADPr) promotes genome stability and how it is regulated. Here, we show that telomeres are subject to DNA-ADPr catalyzed by PARP1 and removed by TARG1. Mechanistically, we show that DNA-ADPr is coupled to lagging telomere DNA strand synthesis, forming at single-stranded DNA present at unligated Okazaki fragments and on the 3' single-stranded telomere overhang. Persistent DNA-linked ADPr, due to TARG1 deficiency, eventually leads to telomere shortening. Furthermore, using the bacterial DNA ADP-ribosyl-transferase toxin to modify DNA at telomeres directly, we demonstrate that unhydrolyzed DNA-linked ADP-ribose compromises telomere replication and telomere integrity. Thus, by identifying telomeres as chromosomal targets of PARP1 and TARG1-regulated DNA-ADPr, whose deregulation compromises telomere replication and integrity, our study highlights and establishes the critical importance of controlling DNA-ADPr turnover for sustained genome stability.
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Affiliation(s)
- Anne R Wondisford
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Junyeop Lee
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Robert Lu
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales, Australia
| | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Ragini Bhargava
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sandra Schamus-Haynes
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Leyneir C Cespedes
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Patricia L Opresko
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales, Australia
| | - Jaewon Min
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Roderick J O'Sullivan
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.
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3
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Doksani Y, Lottersberger F. The risky business of ADP-ribosylating telomeric DNA. Nat Struct Mol Biol 2024; 31:737-738. [PMID: 38714888 DOI: 10.1038/s41594-024-01285-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Affiliation(s)
- Ylli Doksani
- IFOM ETS - The AIRC Institute of Molecular Oncology, Milan, Italy.
| | - Francisca Lottersberger
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden.
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4
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Melikishvili M, Fried MG, Fondufe-Mittendorf YN. Cooperative nucleic acid binding by Poly ADP-ribose polymerase 1. Sci Rep 2024; 14:7530. [PMID: 38553566 PMCID: PMC10980755 DOI: 10.1038/s41598-024-58076-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/25/2024] [Indexed: 04/02/2024] Open
Abstract
Poly (ADP)-ribose polymerase 1 (PARP1) is an abundant nuclear protein well-known for its role in DNA repair yet also participates in DNA replication, transcription, and co-transcriptional splicing, where DNA is undamaged. Thus, binding to undamaged regions in DNA and RNA is likely a part of PARP1's normal repertoire. Here we describe analyses of PARP1 binding to two short single-stranded DNAs, a single-stranded RNA, and a double stranded DNA. The investigations involved comparing the wild-type (WT) full-length enzyme with mutants lacking the catalytic domain (∆CAT) or zinc fingers 1 and 2 (∆Zn1∆Zn2). All three protein types exhibited monomeric characteristics in solution and formed saturated 2:1 complexes with single-stranded T20 and U20 oligonucleotides. These complexes formed without accumulation of 1:1 intermediates, a pattern suggestive of positive binding cooperativity. The retention of binding activities by ∆CAT and ∆Zn1∆Zn2 enzymes suggests that neither the catalytic domain nor zinc fingers 1 and 2 are indispensable for cooperative binding. In contrast, when a double stranded 19mer DNA was tested, WT PARP1 formed a 4:1 complex while the ∆Zn1Zn2 mutant binding saturated at 1:1 stoichiometry. These deviations from the 2:1 pattern observed with T20 and U20 oligonucleotides show that PARP's binding mechanism can be influenced by the secondary structure of the nucleic acid. Our studies show that PARP1:nucleic acid interactions are strongly dependent on the nucleic acid type and properties, perhaps reflecting PARP1's ability to respond differently to different nucleic acid ligands in cells. These findings lay a platform for understanding how the functionally versatile PARP1 recognizes diverse oligonucleotides within the realms of chromatin and RNA biology.
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Affiliation(s)
- Manana Melikishvili
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - Michael G Fried
- Center for Structural Biology, Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA.
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5
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Abstract
Biomolecular condensates are reversible compartments that form through a process called phase separation. Post-translational modifications like ADP-ribosylation can nucleate the formation of these condensates by accelerating the self-association of proteins. Poly(ADP-ribose) (PAR) chains are remarkably transient modifications with turnover rates on the order of minutes, yet they can be required for the formation of granules in response to oxidative stress, DNA damage, and other stimuli. Moreover, accumulation of PAR is linked with adverse phase transitions in neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. In this review, we provide a primer on how PAR is synthesized and regulated, the diverse structures and chemistries of ADP-ribosylation modifications, and protein-PAR interactions. We review substantial progress in recent efforts to determine the molecular mechanism of PAR-mediated phase separation, and we further delineate how inhibitors of PAR polymerases may be effective treatments for neurodegenerative pathologies. Finally, we highlight the need for rigorous biochemical interrogation of ADP-ribosylation in vivo and in vitro to clarify the exact pathway from PARylation to condensate formation.
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Affiliation(s)
- Kevin Rhine
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Hana M Odeh
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - James Shorter
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Sua Myong
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Physics Frontier Center (Center for the Physics of Living Cells), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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6
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Duma L, Ahel I. The function and regulation of ADP-ribosylation in the DNA damage response. Biochem Soc Trans 2023; 51:995-1008. [PMID: 37171085 PMCID: PMC10317172 DOI: 10.1042/bst20220749] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023]
Abstract
ADP-ribosylation is a post-translational modification involved in DNA damage response (DDR). In higher organisms it is synthesised by PARP 1-3, DNA strand break sensors. Recent advances have identified serine residues as the most common targets for ADP-ribosylation during DDR. To ADP-ribosylate serine, PARPs require an accessory factor, HPF1 which completes the catalytic domain. Through ADP-ribosylation, PARPs recruit a variety of factors to the break site and control their activities. However, the timely removal of ADP-ribosylation is also key for genome stability and is mostly performed by two hydrolases: PARG and ARH3. Here, we describe the key writers, readers and erasers of ADP-ribosylation and their contribution to the mounting of the DDR. We also discuss the use of PARP inhibitors in cancer therapy and the ways to tackle PARPi treatment resistance.
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Affiliation(s)
- Lena Duma
- Sir William Dunn School of Pathology, University of Oxford, Oxford, U.K
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, U.K
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7
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Poly(ADP-ribose) in Condensates: The PARtnership of Phase Separation and Site-Specific Interactions. Int J Mol Sci 2022; 23:ijms232214075. [PMID: 36430551 PMCID: PMC9694962 DOI: 10.3390/ijms232214075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022] Open
Abstract
Biomolecular condensates are nonmembrane cellular compartments whose formation in many cases involves phase separation (PS). Despite much research interest in this mechanism of macromolecular self-organization, the concept of PS as applied to a live cell faces certain challenges. In this review, we discuss a basic model of PS and the role of site-specific interactions and percolation in cellular PS-related events. Using a multivalent poly(ADP-ribose) molecule as an example, which has high PS-driving potential due to its structural features, we consider how site-specific interactions and network formation are involved in the formation of phase-separated cellular condensates.
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8
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Musheev MU, Schomacher L, Basu A, Han D, Krebs L, Scholz C, Niehrs C. Mammalian N1-adenosine PARylation is a reversible DNA modification. Nat Commun 2022; 13:6138. [PMID: 36253381 PMCID: PMC9576699 DOI: 10.1038/s41467-022-33731-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022] Open
Abstract
Poly-ADP-ribosylation (PARylation) is regarded as a protein-specific modification. However, some PARPs were recently shown to modify DNA termini in vitro. Here, we use ultrasensitive mass spectrometry (LC-MS/MS), anti-PAR antibodies, and anti-PAR reagents to show that mammalian DNA is physiologically PARylated and to different levels in primary tissues. Inhibition of PAR glycohydrolase (PARG) increases DNA PARylation, supporting that the modification is reversible. DNA PARylation requires PARP1 and in vitro PARP1 PARylates single-stranded DNA, while PARG reverts the modification. DNA PARylation occurs at the N1-position of adenosine residues to form N1-Poly(ADP-ribosyl)-deoxyadenosine. Through partial hydrolysis of mammalian gDNA we identify PAR-DNA via the diagnostic deamination product N1-ribosyl-deoxyinosine to occur in vivo. The discovery of N1-adenosine PARylation as a DNA modification establishes the conceptual and methodological framework to elucidate its biological relevance and extends the role of PARP enzymes.
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Affiliation(s)
- Michael U. Musheev
- grid.424631.60000 0004 1794 1771Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Lars Schomacher
- grid.424631.60000 0004 1794 1771Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Amitava Basu
- grid.424631.60000 0004 1794 1771Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Dandan Han
- grid.424631.60000 0004 1794 1771Institute of Molecular Biology (IMB), 55128 Mainz, Germany ,Present Address: STEMCELL Technologies Germany GmbH, 50933 Cologne, Germany
| | - Laura Krebs
- grid.424631.60000 0004 1794 1771Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Carola Scholz
- grid.424631.60000 0004 1794 1771Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Christof Niehrs
- grid.424631.60000 0004 1794 1771Institute of Molecular Biology (IMB), 55128 Mainz, Germany ,grid.509524.fDivision of Molecular Embryology, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
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9
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Revisiting PARP2 and PARP1 trapping through quantitative live-cell imaging. Biochem Soc Trans 2022; 50:1169-1177. [PMID: 35959996 DOI: 10.1042/bst20220366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/15/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022]
Abstract
Poly (ADP-ribose) polymerase-1 (PARP1) and 2 (PARP2) are two DNA damage-induced poly (ADP-ribose) (PAR) polymerases in cells and are the targets of PARP inhibitors used for cancer therapy. Strand breaks recruit and activate PARP1 and 2, which rapidly generate PAR from NAD+. PAR promotes the recruitment of other repair factors, relaxes chromatin, and has a role in DNA repair, transcription regulation, and RNA biology. Four PARP1/2 dual inhibitors are currently used to treat BRCA-deficient breast, ovarian, prostate, and pancreatic cancers. In addition to blocking the enzymatic activity of PARP1 and 2, clinical PARP inhibitors extend the appearance of PARP1 and PARP2 on chromatin after damage, termed trapping. Loss of PARP1 confers resistance to PARP inhibitors, suggesting an essential role of trapping in cancer therapy. Yet, whether the persistent PARP1 and 2 foci at the DNA damage sites are caused by the retention of the same molecules or by the continual exchange of different molecules remains unknown. Here, we discuss recent results from quantitative live-cell imaging studies focusing on PARP1 and PARP2's distinct DNA substrate specificities and modes of recruitment and trapping with implications for cancer therapy and on-target toxicities of PARP inhibitors.
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10
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Li P, Lei Y, Qi J, Liu W, Yao K. Functional roles of ADP-ribosylation writers, readers and erasers. Front Cell Dev Biol 2022; 10:941356. [PMID: 36035988 PMCID: PMC9404506 DOI: 10.3389/fcell.2022.941356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
ADP-ribosylation is a reversible post-translational modification (PTM) tightly regulated by the dynamic interplay between its writers, readers and erasers. As an intricate and versatile PTM, ADP-ribosylation plays critical roles in various physiological and pathological processes. In this review, we discuss the major players involved in the ADP-ribosylation cycle, which may facilitate the investigation of the ADP-ribosylation function and contribute to the understanding and treatment of ADP-ribosylation associated disease.
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11
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Schuller M, Ahel I. Beyond protein modification: the rise of non-canonical ADP-ribosylation. Biochem J 2022; 479:463-477. [PMID: 35175282 PMCID: PMC8883491 DOI: 10.1042/bcj20210280] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/18/2022] [Accepted: 01/21/2022] [Indexed: 12/22/2022]
Abstract
ADP-ribosylation has primarily been known as post-translational modification of proteins. As signalling strategy conserved in all domains of life, it modulates substrate activity, localisation, stability or interactions, thereby regulating a variety of cellular processes and microbial pathogenicity. Yet over the last years, there is increasing evidence of non-canonical forms of ADP-ribosylation that are catalysed by certain members of the ADP-ribosyltransferase family and go beyond traditional protein ADP-ribosylation signalling. New macromolecular targets such as nucleic acids and new ADP-ribose derivatives have been established, notably extending the repertoire of ADP-ribosylation signalling. Based on the physiological relevance known so far, non-canonical ADP-ribosylation deserves its recognition next to the traditional protein ADP-ribosylation modification and which we therefore review in the following.
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Affiliation(s)
- Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, U.K
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, U.K
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12
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In vitro reconstitution of an efficient nucleotide excision repair system using mesophilic enzymes from Deinococcus radiodurans. Commun Biol 2022; 5:127. [PMID: 35149830 PMCID: PMC8837605 DOI: 10.1038/s42003-022-03064-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/18/2022] [Indexed: 11/08/2022] Open
Abstract
Nucleotide excision repair (NER) is a universal and versatile DNA repair pathway, capable of removing a very wide range of lesions, including UV-induced pyrimidine dimers and bulky adducts. In bacteria, NER involves the sequential action of the UvrA, UvrB and UvrC proteins to release a short 12- or 13-nucleotide DNA fragment containing the damaged site. Although bacterial NER has been the focus of numerous studies over the past 40 years, a number of key questions remain unanswered regarding the mechanisms underlying DNA damage recognition by UvrA, the handoff to UvrB and the site-specific incision by UvrC. In the present study, we have successfully reconstituted in vitro a robust NER system using the UvrABC proteins from the radiation resistant bacterium, Deinococcus radiodurans. We have investigated the influence of various parameters, including temperature, salt, protein and ATP concentrations, protein purity and metal cations, on the dual incision by UvrABC, so as to find the optimal conditions for the efficient release of the short lesion-containing oligonucleotide. This newly developed assay relying on the use of an original, doubly-labelled DNA substrate has allowed us to probe the kinetics of repair on different DNA substrates and to determine the order and precise sites of incisions on the 5′ and 3′ sides of the lesion. This new assay thus constitutes a valuable tool to further decipher the NER pathway in bacteria. Reconstitution of D radiodurans nucleotide excision repair provides insights into the kinetics of repair on different DNA substrates and determines the order and precise sites of incisions on the 5’ and 3’ sides of the lesion.
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13
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Sha H, Gan Y, Zou R, Wu J, Feng J. Research Advances in the Role of the Poly ADP Ribose Polymerase Family in Cancer. Front Oncol 2022; 11:790967. [PMID: 34976832 PMCID: PMC8716401 DOI: 10.3389/fonc.2021.790967] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/24/2021] [Indexed: 12/27/2022] Open
Abstract
Poly ADP ribose polymerases (PARPs) catalyze the modification of acceptor proteins, DNA, or RNA with ADP-ribose, which plays an important role in maintaining genomic stability and regulating signaling pathways. The rapid development of PARP1/2 inhibitors for the treatment of ovarian and breast cancers has advanced research on other PARP family members for the treatment of cancer. This paper reviews the role of PARP family members (except PARP1/2 and tankyrases) in cancer and the underlying regulatory mechanisms, which will establish a molecular basis for the clinical application of PARPs in the future.
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Affiliation(s)
- Huanhuan Sha
- Department of Chemotherapy, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yujie Gan
- Department of Chemotherapy, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Renrui Zou
- Department of Chemotherapy, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jianzhong Wu
- Research Center of Clinical Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jifeng Feng
- Department of Chemotherapy, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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14
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Alemasova EE, Naumenko KN, Sukhanova MV, Lavrik OI. Role of YB-1 in Regulation of Poly(ADP-Ribosylation) Catalyzed by Poly(ADP-Ribose) Polymerases. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S32-S0. [PMID: 35501985 DOI: 10.1134/s0006297922140048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/14/2021] [Accepted: 09/17/2021] [Indexed: 06/14/2023]
Abstract
Poly(ADP-ribosyl)ation is a post-translational modification of proteins that performs an essential regulatory function in the cellular response to DNA damage. The key enzyme synthesizing poly(ADP-ribose) (PAR) in the cells is poly(ADP-ribose) polymerase 1 (PARP1). Understanding the mechanisms of the PARP1 activity regulation within the cells is necessary for development of the PARP1-targeted antitumor therapy. This review is devoted to the studies of the role of the RNA-binding protein YB-1 in the PARP1-catalyzed PARylation. The mechanisms of PARP1 activity stimulation by YB-1 protein can possibly be extended to other RNA-binding proteins involved in the maintenance of the genome stability.
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Affiliation(s)
- Elizaveta E Alemasova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Konstantin N Naumenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Maria V Sukhanova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia
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15
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Wallace SR, Chihab LY, Yamasaki M, Yoshinaga BT, Torres YM, Rideaux D, Javed Z, Turumella S, Zhang M, Lawton DR, Fuller AA, Carter-O’Connell I. Rapid Analysis of ADP-Ribosylation Dynamics and Site-Specificity Using TLC-MALDI. ACS Chem Biol 2021; 16:2137-2143. [PMID: 34647721 PMCID: PMC8609518 DOI: 10.1021/acschembio.1c00542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Poly(ADP-ribose)
polymerases, PARPs, transfer ADP-ribose onto target
proteins from nicotinamide adenine dinucleotide (NAD+).
Current mass spectrometric analytical methods require proteolysis
of target proteins, limiting the study of dynamic ADP-ribosylation
on contiguous proteins. Herein, we present a matrix-assisted laser
desorption/ionization time-of-flight (MALDI-TOF) method that facilitates
multisite analysis of ADP-ribosylation. We observe divergent ADP-ribosylation
dynamics for the catalytic domains of PARPs 14 and 15, with PARP15
modifying more sites on itself (+3–4 ADP-ribose) than the closely
related PARP14 protein (+1–2 ADP-ribose)—despite similar
numbers of potential modification sites. We identify, for the first
time, a minimal peptide fragment (18 amino-acids) that is preferentially
modified by PARP14. Finally, we demonstrate through mutagenesis and
chemical treatment with hydroxylamine that PARPs 14/15 prefer acidic
residues. Our results highlight the utility of MALDI-TOF in the analysis
of PARP target modifications and in elucidating the biochemical mechanism
governing PARP target selection.
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Affiliation(s)
- Sean R. Wallace
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Leila Y. Chihab
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Miles Yamasaki
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Braden T. Yoshinaga
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Yazmin M. Torres
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Damon Rideaux
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Zeeshan Javed
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Soumya Turumella
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Michelle Zhang
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Dylan R. Lawton
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Amelia A. Fuller
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
| | - Ian Carter-O’Connell
- Santa Clara University, Department of Chemistry and Biochemistry, Santa Clara, California 95053, United States
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16
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HPF1 dynamically controls the PARP1/2 balance between initiating and elongating ADP-ribose modifications. Nat Commun 2021; 12:6675. [PMID: 34795260 PMCID: PMC8602370 DOI: 10.1038/s41467-021-27043-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [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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17
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Tromans-Coia C, Sanchi A, Moeller GK, Timinszky G, Lopes M, Ahel I. TARG1 protects against toxic DNA ADP-ribosylation. Nucleic Acids Res 2021; 49:10477-10492. [PMID: 34508355 PMCID: PMC8501950 DOI: 10.1093/nar/gkab771] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/16/2021] [Accepted: 09/09/2021] [Indexed: 01/15/2023] Open
Abstract
ADP-ribosylation is a modification that targets a variety of macromolecules and regulates a diverse array of important cellular processes. ADP-ribosylation is catalysed by ADP-ribosyltransferases and reversed by ADP-ribosylhydrolases. Recently, an ADP-ribosyltransferase toxin termed 'DarT' from bacteria, which is distantly related to human PARPs, was shown to modify thymidine in single-stranded DNA in a sequence specific manner. The antitoxin of DarT is the macrodomain containing ADP-ribosylhydrolase DarG, which shares striking structural homology with the human ADP-ribosylhydrolase TARG1. Here, we show that TARG1, like DarG, can reverse thymidine-linked DNA ADP-ribosylation. We find that TARG1-deficient human cells are extremely sensitive to DNA ADP-ribosylation. Furthermore, we also demonstrate the first detection of reversible ADP-ribosylation on genomic DNA in vivo from human cells. Collectively, our results elucidate the impact of DNA ADP-ribosylation in human cells and provides a molecular toolkit for future studies into this largely unknown facet of ADP-ribosylation.
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Affiliation(s)
- Callum Tromans-Coia
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Andrea Sanchi
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Giuliana K Moeller
- Department of Physiological Chemistry, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Gyula Timinszky
- Lendület Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), 6276 Szeged, Hungary
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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18
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Groslambert J, Prokhorova E, Ahel I. ADP-ribosylation of DNA and RNA. DNA Repair (Amst) 2021; 105:103144. [PMID: 34116477 PMCID: PMC8385414 DOI: 10.1016/j.dnarep.2021.103144] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 12/22/2022]
Abstract
ADP-ribosylation is a chemical modification of macromolecules found across all domains of life and known to regulate a variety of cellular processes. Notably, it has a well-established role in the DNA damage response. While it was historically known as a post-translational modification of proteins, recent studies have shown that nucleic acids can also serve as substrates of reversible ADP-ribosylation. More precisely, ADP-ribosylation of DNA bases, phosphorylated DNA ends and phosphorylated RNA ends have been reported. We will discuss these three types of modification in details. In a variety of bacterial species, including Mycobacterium tuberculosis, ADP-ribosylation of thymidine has emerged as the mode of action of a toxin-antitoxin system named DarTG, with the resultant products perceived as DNA damage by the cell. On the other hand, mammalian DNA damage sensors PARP1, PARP2 and PARP3 were shown to ADP-ribosylate phosphorylated ends of double-stranded DNA in vitro. Additionally, TRPT1 and several PARP enzymes, including PARP10, can add ADP-ribose to the 5'-phosphorylated end of single-stranded RNA in vitro, representing a novel RNA capping mechanism. Together, these discoveries have led to the emergence of a new and exciting research area, namely DNA and RNA ADP-ribosylation, that is likely to have far-reaching implications for the fields of DNA repair, replication and epigenetics.
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Affiliation(s)
- Joséphine Groslambert
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Evgeniia Prokhorova
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom.
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19
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Schuller M, Butler RE, Ariza A, Tromans-Coia C, Jankevicius G, Claridge TDW, Kendall SL, Goh S, Stewart GR, Ahel I. Molecular basis for DarT ADP-ribosylation of a DNA base. Nature 2021; 596:597-602. [PMID: 34408320 DOI: 10.1038/s41586-021-03825-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 07/15/2021] [Indexed: 02/07/2023]
Abstract
ADP-ribosyltransferases use NAD+ to catalyse substrate ADP-ribosylation1, and thereby regulate cellular pathways or contribute to toxin-mediated pathogenicity of bacteria2-4. Reversible ADP-ribosylation has traditionally been considered a protein-specific modification5, but recent in vitro studies have suggested nucleic acids as targets6-9. Here we present evidence that specific, reversible ADP-ribosylation of DNA on thymidine bases occurs in cellulo through the DarT-DarG toxin-antitoxin system, which is found in a variety of bacteria (including global pathogens such as Mycobacterium tuberculosis, enteropathogenic Escherichia coli and Pseudomonas aeruginosa)10. We report the structure of DarT, which identifies this protein as a diverged member of the PARP family. We provide a set of high-resolution structures of this enzyme in ligand-free and pre- and post-reaction states, which reveals a specialized mechanism of catalysis that includes a key active-site arginine that extends the canonical ADP-ribosyltransferase toolkit. Comparison with PARP-HPF1, a well-established DNA repair protein ADP-ribosylation complex, offers insights into how the DarT class of ADP-ribosyltransferases evolved into specific DNA-modifying enzymes. Together, our structural and mechanistic data provide details of this PARP family member and contribute to a fundamental understanding of the ADP-ribosylation of nucleic acids. We also show that thymine-linked ADP-ribose DNA adducts reversed by DarG antitoxin (functioning as a noncanonical DNA repair factor) are used not only for targeted DNA damage to induce toxicity, but also as a signalling strategy for cellular processes. Using M. tuberculosis as an exemplar, we show that DarT-DarG regulates growth by ADP-ribosylation of DNA at the origin of chromosome replication.
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Affiliation(s)
- Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rachel E Butler
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Antonio Ariza
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Gytis Jankevicius
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Biozentrum, University of Basel, Basel, Switzerland
| | - Tim D W Claridge
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Sharon L Kendall
- Centre for Emerging, Endemic and Exotic Disease, Pathology and Population Sciences, The Royal Veterinary College, Hatfield, UK
| | - Shan Goh
- Centre for Emerging, Endemic and Exotic Disease, Pathology and Population Sciences, The Royal Veterinary College, Hatfield, UK
| | - Graham R Stewart
- Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK.
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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20
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Fijen C, Rothenberg E. The evolving complexity of DNA damage foci: RNA, condensates and chromatin in DNA double-strand break repair. DNA Repair (Amst) 2021; 105:103170. [PMID: 34256335 DOI: 10.1016/j.dnarep.2021.103170] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 06/08/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023]
Abstract
Formation of biomolecular condensates is increasingly recognized as a mechanism employed by cells to deal with stress and to optimize enzymatic reactions. Recent studies have characterized several DNA repair foci as phase-separated condensates, behaving like liquid droplets. Concomitantly, the apparent importance of long non-coding RNAs and RNA-binding proteins for the repair of double-strand breaks has raised many questions about their exact contribution to the repair process. Here we discuss how RNA molecules can participate in condensate formation and how RNA-binding proteins can act as molecular scaffolds. We furthermore summarize our current knowledge about how properties of condensates can influence the choice of repair pathway (homologous recombination or non-homologous end joining) and identify the open questions in this field of emerging importance.
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Affiliation(s)
- Carel Fijen
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, USA.
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, USA.
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21
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van Beek L, McClay É, Patel S, Schimpl M, Spagnolo L, Maia de Oliveira T. PARP Power: A Structural Perspective on PARP1, PARP2, and PARP3 in DNA Damage Repair and Nucleosome Remodelling. Int J Mol Sci 2021; 22:ijms22105112. [PMID: 34066057 PMCID: PMC8150716 DOI: 10.3390/ijms22105112] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 12/30/2022] Open
Abstract
Poly (ADP-ribose) polymerases (PARP) 1-3 are well-known multi-domain enzymes, catalysing the covalent modification of proteins, DNA, and themselves. They attach mono- or poly-ADP-ribose to targets using NAD+ as a substrate. Poly-ADP-ribosylation (PARylation) is central to the important functions of PARP enzymes in the DNA damage response and nucleosome remodelling. Activation of PARP happens through DNA binding via zinc fingers and/or the WGR domain. Modulation of their activity using PARP inhibitors occupying the NAD+ binding site has proven successful in cancer therapies. For decades, studies set out to elucidate their full-length molecular structure and activation mechanism. In the last five years, significant advances have progressed the structural and functional understanding of PARP1-3, such as understanding allosteric activation via inter-domain contacts, how PARP senses damaged DNA in the crowded nucleus, and the complementary role of histone PARylation factor 1 in modulating the active site of PARP. Here, we review these advances together with the versatility of PARP domains involved in DNA binding, the targets and shape of PARylation and the role of PARPs in nucleosome remodelling.
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Affiliation(s)
- Lotte van Beek
- Structure and Biophysics, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK; (L.v.B.); (M.S.)
| | - Éilís McClay
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Garscube Campus, University of Glasgow, Glasgow G61 1QQ, UK;
| | - Saleha Patel
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK;
| | - Marianne Schimpl
- Structure and Biophysics, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK; (L.v.B.); (M.S.)
| | - Laura Spagnolo
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Garscube Campus, University of Glasgow, Glasgow G61 1QQ, UK;
- Correspondence: (L.S.); (T.M.d.O.)
| | - Taiana Maia de Oliveira
- Structure and Biophysics, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK; (L.v.B.); (M.S.)
- Correspondence: (L.S.); (T.M.d.O.)
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22
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Weixler L, Schäringer K, Momoh J, Lüscher B, Feijs KLH, Žaja R. ADP-ribosylation of RNA and DNA: from in vitro characterization to in vivo function. Nucleic Acids Res 2021; 49:3634-3650. [PMID: 33693930 PMCID: PMC8053099 DOI: 10.1093/nar/gkab136] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
The functionality of DNA, RNA and proteins is altered dynamically in response to physiological and pathological cues, partly achieved by their modification. While the modification of proteins with ADP-ribose has been well studied, nucleic acids were only recently identified as substrates for ADP-ribosylation by mammalian enzymes. RNA and DNA can be ADP-ribosylated by specific ADP-ribosyltransferases such as PARP1-3, PARP10 and tRNA 2'-phosphotransferase (TRPT1). Evidence suggests that these enzymes display different preferences towards different oligonucleotides. These reactions are reversed by ADP-ribosylhydrolases of the macrodomain and ARH families, such as MACROD1, TARG1, PARG, ARH1 and ARH3. Most findings derive from in vitro experiments using recombinant components, leaving the relevance of this modification in cells unclear. In this Survey and Summary, we provide an overview of the enzymes that ADP-ribosylate nucleic acids, the reversing hydrolases, and the substrates' requirements. Drawing on data available for other organisms, such as pierisin1 from cabbage butterflies and the bacterial toxin-antitoxin system DarT-DarG, we discuss possible functions for nucleic acid ADP-ribosylation in mammals. Hypothesized roles for nucleic acid ADP-ribosylation include functions in DNA damage repair, in antiviral immunity or as non-conventional RNA cap. Lastly, we assess various methods potentially suitable for future studies of nucleic acid ADP-ribosylation.
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Affiliation(s)
- Lisa Weixler
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| | - Katja Schäringer
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| | - Jeffrey Momoh
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| | - Karla L H Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
| | - Roko Žaja
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, Aachen, Germany
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23
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Rapid Detection and Signaling of DNA Damage by PARP-1. Trends Biochem Sci 2021; 46:744-757. [PMID: 33674152 DOI: 10.1016/j.tibs.2021.01.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/14/2021] [Accepted: 01/29/2021] [Indexed: 12/16/2022]
Abstract
Poly(ADP-ribosyl) polymerase-1 (PARP-1) is an abundant ADP-ribosyl transferase that regulates various biological processes. PARP-1 is widely recognized as a first-line responder molecule in DNA damage response (DDR). Here, we review the full cycle of detecting DNA damage by PARP-1, PARP-1 activation upon DNA binding, and PARP-1 release from a DNA break. We also discuss the allosteric consequence upon binding of PARP inhibitors (PARPi) and the opportunity to tune its release from a DNA break. It is now possible to harness this new understanding to design novel PARPi for treating diseases where cell toxicity caused by PARP-1 'trapping' on DNA is either the desired consequence or entirely counterproductive.
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24
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Eleazer R, Fondufe‐Mittendorf YN. The multifaceted role of PARP1 in RNA biogenesis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1617. [PMID: 32656996 PMCID: PMC7856298 DOI: 10.1002/wrna.1617] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/11/2020] [Accepted: 06/17/2020] [Indexed: 12/31/2022]
Abstract
Poly(ADP-ribose) polymerases (PARPs) are abundant nuclear proteins that synthesize ADP ribose polymers (pADPr) and catalyze the addition of (p)ADPr to target biomolecules. PARP1, the most abundant and well-studied PARP, is a multifunctional enzyme that participates in numerous critical cellular processes. A considerable amount of PARP research has focused on PARP1's role in DNA damage. However, an increasing body of evidence outlines more routine roles for PARP and PARylation in nearly every step of RNA biogenesis and metabolism. PARP1's involvement in these RNA processes is pleiotropic and has been ascribed to PARP1's unique flexible domain structures. PARP1 domains are modular self-arranged enabling it to recognize structurally diverse substrates and to act simultaneously through multiple discrete mechanisms. These mechanisms include direct PARP1-protein binding, PARP1-nucleic acid binding, covalent PARylation of target molecules, covalent autoPARylation, and induction of noncovalent interactions with PAR molecules. A combination of these mechanisms has been implicated in PARP1's context-specific regulation of RNA biogenesis and metabolism. We examine the mechanisms of PARP1 regulation in transcription initiation, elongation and termination, co-transcriptional splicing, RNA export, and post-transcriptional RNA processing. Finally, we consider promising new investigative avenues for PARP1 involvement in these processes with an emphasis on PARP1 regulation of subcellular condensates. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Rebekah Eleazer
- Department of Molecular and Cellular Biochemistry and Markey Cancer CenterUniversity of KentuckyLexingtonKentuckyUSA
| | - Yvonne N. Fondufe‐Mittendorf
- Department of Molecular and Cellular Biochemistry and Markey Cancer CenterUniversity of KentuckyLexingtonKentuckyUSA
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25
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Abstract
Adenosine diphosphate (ADP)-ribosylation is a unique post-translational modification that regulates many biological processes, such as DNA damage repair. During DNA repair, ADP-ribosylation needs to be reversed by ADP-ribosylhydrolases. A group of ADP-ribosylhydrolases have a catalytic domain, namely the macrodomain, which is conserved in evolution from prokaryotes to humans. Not all macrodomains remove ADP-ribosylation. One set of macrodomains loses enzymatic activity and only binds to ADP-ribose (ADPR). Here, we summarize the biological functions of these macrodomains in DNA damage repair and compare the structure of enzymatically active and inactive macrodomains. Moreover, small molecular inhibitors have been developed that target macrodomains to suppress DNA damage repair and tumor growth. Macrodomain proteins are also expressed in pathogens, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, these domains may not be directly involved in DNA damage repair in the hosts or pathogens. Instead, they play key roles in pathogen replication. Thus, by targeting macrodomains it may be possible to treat pathogen-induced diseases, such as coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Lily Yu
- Westridge School, Pasadena, California 91105, USA
| | - Xiuhua Liu
- Institute of Life Science and Green Development, College of Life Science, Hebei University, Baoding 071002, China.
| | - Xiaochun Yu
- School of Life Sciences, Westlake University, Hangzhou 310024, China.
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26
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Taipakova S, Kuanbay A, Saint-Pierre C, Gasparutto D, Baiken Y, Groisman R, Ishchenko AA, Saparbaev M, Bissenbaev AK. The Arabidopsis thaliana Poly(ADP-Ribose) Polymerases 1 and 2 Modify DNA by ADP-Ribosylating Terminal Phosphate Residues. Front Cell Dev Biol 2020; 8:606596. [PMID: 33324653 PMCID: PMC7726343 DOI: 10.3389/fcell.2020.606596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/22/2020] [Indexed: 12/20/2022] Open
Abstract
Proteins from the poly(ADP-ribose) polymerase (PARP) family, such as PARP1 and PARP2, use NAD+ as a substrate to catalyze the synthesis of polymeric chains consisting of ADP-ribose units covalently attached to an acceptor molecule. PARP1 and PARP2 are viewed as DNA damage sensors that, upon binding to strand breaks, poly(ADP-ribosyl)ate themselves and nuclear acceptor proteins. The flowering plant Arabidopsis thaliana contains three genes encoding homologs of mammalian PARPs: atPARP1, atPARP2, and atPARP3. Both atPARP1 and atPARP2 contain poly(ADP-ribosyl)ating activity; however, it is unknown whether they could covalently modify DNA by ADP-ribosylating the strand break termini. Here, we report that similar to their mammalian counterparts, the plant atPARP1 and atPARP2 proteins ADP-ribosylate 5′-terminal phosphate residues in duplex DNA oligonucleotides and plasmid containing at least two closely spaced DNA strand breaks. AtPARP1 preferentially catalyzes covalent attachment of ADP-ribose units to the ends of recessed DNA duplexes containing 5′-phosphate, whereas atPARP2 preferentially ADP-ribosylates the nicked and gapped DNA duplexes containing the terminal 5′-phosphate. Similar to their mammalian counterparts, the plant PARP-catalyzed DNA ADP-ribosylation is particularly sensitive to the distance that separates two strand breaks in the same DNA molecule, 1.5 and 1 or 2 turns of helix for atPARP1 and atPARP2, respectively. PAR glycohydrolase (PARG) restored native DNA structure by hydrolyzing the PAR–DNA adducts generated by atPARPs. Biochemical and mass spectrometry analyses of the PAR–DNA adducts showed that atPARPs utilize phosphorylated DNA termini as an alternative to protein acceptor residues to catalyze PAR chain synthesis via phosphodiester bond formation between C1′ of ADP-ribose and a phosphate residue of the terminal nucleotide in DNA fragment. Taken together, these data establish the presence of a new type of DNA-modifying activity in Arabidopsis PARPs, suggesting a possible role of DNA ADP-ribosylation in DNA damage signaling and repair of terrestrial plants.
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Affiliation(s)
- Sabira Taipakova
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Aigerim Kuanbay
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Groupe «Mechanisms of DNA Repair and Carcinogenesis», Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Saclay, Villejuif, France
| | | | - Didier Gasparutto
- CEA, CNRS, IRIG/SyMMES-UMR 5819/CREAB, Université Grenoble Alpes, Grenoble, France
| | - Yeldar Baiken
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.,School of Engineering and Digital Sciences, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Regina Groisman
- Groupe «Mechanisms of DNA Repair and Carcinogenesis», Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Saclay, Villejuif, France
| | - Alexander A Ishchenko
- Groupe «Mechanisms of DNA Repair and Carcinogenesis», Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Saclay, Villejuif, France
| | - Murat Saparbaev
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Groupe «Mechanisms of DNA Repair and Carcinogenesis», Equipe Labellisée LIGUE 2016, CNRS UMR 9019, Université Paris-Saclay, Villejuif, France
| | - Amangeldy K Bissenbaev
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
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27
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Harrision D, Gravells P, Thompson R, Bryant HE. Poly(ADP-Ribose) Glycohydrolase (PARG) vs. Poly(ADP-Ribose) Polymerase (PARP) - Function in Genome Maintenance and Relevance of Inhibitors for Anti-cancer Therapy. Front Mol Biosci 2020; 7:191. [PMID: 33005627 PMCID: PMC7485115 DOI: 10.3389/fmolb.2020.00191] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/20/2020] [Indexed: 12/21/2022] Open
Abstract
Poly(ADP-ribose) polymerases (PARPs) are a family of enzymes that catalyze the addition of poly(ADP-ribose) (PAR) subunits onto themselves and other acceptor proteins. PARPs are known to function in a large range of cellular processes including DNA repair, DNA replication, transcription and modulation of chromatin structure. Inhibition of PARP holds great potential for therapy, especially in cancer. Several PARP1/2/3 inhibitors (PARPi) have had success in treating ovarian, breast and prostate tumors harboring defects in the homologous recombination (HR) DNA repair pathway, especially BRCA1/2 mutated tumors. However, treatment is limited to specific sub-groups of patients and resistance can occur, limiting the use of PARPi. Poly(ADP-ribose) glycohydrolase (PARG) reverses the action of PARP enzymes, hydrolysing the ribose-ribose bonds present in poly(ADP-ribose). Like PARPs, PARG is involved in DNA replication and repair and PARG depleted/inhibited cells show increased sensitivity to DNA damaging agents. They also display an accumulation of perturbed replication intermediates which can lead to synthetic lethality in certain contexts. In addition, PARG is thought to play an important role in preventing the accumulation of cytoplasmic PAR and therefore parthanatos, a caspase-independent PAR-mediated type of cell death. In contrast to PARP, the therapeutic potential of PARG has been largely ignored. However, several recent papers have demonstrated the exciting possibilities that inhibitors of this enzyme may have for cancer treatment, both as single agents and in combination with cytotoxic drugs and radiotherapy. This article discusses what is known about the functions of PARP and PARG and the potential future implications of pharmacological inhibition in anti-cancer therapy.
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Affiliation(s)
- Daniel Harrision
- Academic Unit of Molecular Oncology, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Polly Gravells
- Academic Unit of Molecular Oncology, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Ruth Thompson
- Academic Unit of Molecular Oncology, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Helen E Bryant
- Academic Unit of Molecular Oncology, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
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28
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Kulikova VA, Nikiforov AA. Role of NUDIX Hydrolases in NAD and ADP-Ribose Metabolism in Mammals. BIOCHEMISTRY. BIOKHIMIIA 2020; 85:883-894. [PMID: 33045949 DOI: 10.1134/s0006297920080040] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/21/2020] [Accepted: 06/22/2020] [Indexed: 12/20/2022]
Abstract
Proteins of the NUDIX hydrolase (NUDT) superfamily that cleave organic pyrophosphates are found in all classes of organisms, from archaea and bacteria to higher eukaryotes. In mammals, NUDTs exhibit a wide range of functions and are characterized by different substrate specificity and intracellular localization. They control the concentration of various metabolites in the cell, including key regulatory molecules such as nicotinamide adenine dinucleotide (NAD), ADP-ribose, and their derivatives. In this review, we discuss the role of NUDT proteins in the metabolism of NAD and ADP-ribose in human and animal cells.
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Affiliation(s)
- V A Kulikova
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia.
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, 194064, Russia
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Saint Petersburg, 194223, Russia
| | - A A Nikiforov
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, 194064, Russia
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29
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Cambronne XA, Kraus WL. Location, Location, Location: Compartmentalization of NAD + Synthesis and Functions in Mammalian Cells. Trends Biochem Sci 2020; 45:858-873. [PMID: 32595066 DOI: 10.1016/j.tibs.2020.05.010] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/06/2020] [Accepted: 05/19/2020] [Indexed: 02/07/2023]
Abstract
The numerous biological roles of NAD+ are organized and coordinated via its compartmentalization within cells. The spatial and temporal partitioning of this intermediary metabolite is intrinsic to understanding the impact of NAD+ on cellular signaling and metabolism. We review evidence supporting the compartmentalization of steady-state NAD+ levels in cells, as well as how the modulation of NAD+ synthesis dynamically regulates signaling by controlling subcellular NAD+ concentrations. We further discuss potential benefits to the cell of compartmentalizing NAD+, and methods for measuring subcellular NAD+ levels.
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Affiliation(s)
- Xiaolu A Cambronne
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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30
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Kosova AA, Kutuzov MM, Evdokimov AN, Ilina ES, Belousova EA, Romanenko SA, Trifonov VA, Khodyreva SN, Lavrik OI. Poly(ADP-ribosyl)ation and DNA repair synthesis in the extracts of naked mole rat, mouse, and human cells. Aging (Albany NY) 2020; 11:2852-2873. [PMID: 31085801 PMCID: PMC6535076 DOI: 10.18632/aging.101959] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/03/2019] [Indexed: 12/16/2022]
Abstract
DNA repair capacity in cells of naked mole rat (Hgl), a species known for its longevity and resistance to cancer, is still poorly characterized. Here, using the whole-cell extracts (WCEs) of Hgl, mouse and human cells, we studied the interrelation between DNA synthesis on the substrates of base excision repair and the activity of poly(ADP-ribose) polymerases (PARPs) responsible for the transfer of the ADP-ribose moieties onto different targets. The level of PAR synthesis was more than ten-fold higher in human WCE as compared to rodent WCEs, while the efficiency of DNA synthesis was comparable. Under conditions of PAR synthesis, the efficiency of DNA synthesis was only slightly enhanced in all extracts and in mouse WCEs unusual products of the primer elongation were detected. The results obtained with WCEs, recombinant proteins and recently found ability of PARPs to attach the ADP-ribose moieties to DNA allowed us to attribute these products to primer mono(ADP-ribosyl)ation (MARylation) at the 5ʹ-terminal phosphate by PARP3 during the DNA synthesis. PARP1/PARP2 can then transfer the ADP-ribose moieties onto initial ADP-ribose. Our results suggest that MARylation/PARylation of DNA in the extracts depends on the ratios between PARPs and can be controlled by DNA-binding proteins.
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Affiliation(s)
- Anastasiya A Kosova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Mikhail M Kutuzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexei N Evdokimov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Ekaterina S Ilina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Ekaterina A Belousova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| | - Svetlana A Romanenko
- Novosibirsk State University, Novosibirsk 630090, Russia.,Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Vladimir A Trifonov
- Novosibirsk State University, Novosibirsk 630090, Russia.,Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Svetlana N Khodyreva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
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31
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Krüger A, Bürkle A, Hauser K, Mangerich A. Real-time monitoring of PARP1-dependent PARylation by ATR-FTIR spectroscopy. Nat Commun 2020; 11:2174. [PMID: 32358582 PMCID: PMC7195430 DOI: 10.1038/s41467-020-15858-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 03/27/2020] [Indexed: 12/20/2022] Open
Abstract
Poly-ADP-ribosylation (PARylation) is a fully reversible post-translational modification with key roles in cellular physiology. Due to the multi-domain structure of poly(ADP-ribose) polymerase-1 (PARP1) and the highly dynamic nature of the PARylation reaction, studies on the biochemical mechanism and structural dynamics remain challenging. Here, we report label-free, time-resolved monitoring of PARP1-dependent PARylation using ATR-FTIR spectroscopy. This includes PARP1 activation by binding to DNA strand break models, NAD+ substrate binding, PAR formation, and dissociation of automodified PARP1 from DNA. Analyses of PARP1 activation at different DNA models demonstrate a strong positive correlation of PARylation and PARP1 dissociation, with the strongest effects observed for DNA nicks and 3’ phosphorylated ends. Moreover, by examining dynamic structural changes of PARP1, we reveal changes in the secondary structure of PARP1 induced by NAD+ and PARP inhibitor binding. In summary, this approach enables holistic and dynamic insights into PARP1-dependent PARylation with molecular and temporal resolution. The mechanism of PARP1-dependent poly-ADP-ribosylation in response to DNA damage is still under debate. Here, the authors use ATR-FTIR spectroscopy to provide time-resolved insights into the molecular details of this process under near physiological conditions.
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Affiliation(s)
- Annika Krüger
- Department of Biology, University of Konstanz, Konstanz, 78464, Germany.,Department of Chemistry, University of Konstanz, Konstanz, 78464, Germany
| | - Alexander Bürkle
- Department of Biology, University of Konstanz, Konstanz, 78464, Germany
| | - Karin Hauser
- Department of Chemistry, University of Konstanz, Konstanz, 78464, Germany.
| | - Aswin Mangerich
- Department of Biology, University of Konstanz, Konstanz, 78464, Germany.
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32
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Abstract
ADP-ribosylation is an intricate and versatile posttranslational modification involved in the regulation of a vast variety of cellular processes in all kingdoms of life. Its complexity derives from the varied range of different chemical linkages, including to several amino acid side chains as well as nucleic acids termini and bases, it can adopt. In this review, we provide an overview of the different families of (ADP-ribosyl)hydrolases. We discuss their molecular functions, physiological roles, and influence on human health and disease. Together, the accumulated data support the increasingly compelling view that (ADP-ribosyl)hydrolases are a vital element within ADP-ribosyl signaling pathways and they hold the potential for novel therapeutic approaches as well as a deeper understanding of ADP-ribosylation as a whole.
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Affiliation(s)
| | - Luca Palazzo
- Institute for the Experimental Endocrinology and Oncology, National Research Council of Italy, 80145 Naples, Italy
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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33
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Matta E, Kiribayeva A, Khassenov B, Matkarimov BT, Ishchenko AA. Insight into DNA substrate specificity of PARP1-catalysed DNA poly(ADP-ribosyl)ation. Sci Rep 2020; 10:3699. [PMID: 32111879 PMCID: PMC7048826 DOI: 10.1038/s41598-020-60631-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/14/2020] [Indexed: 11/09/2022] Open
Abstract
DNA-dependent poly(ADP-ribose) polymerases (PARPs) PARP1, PARP2 and PARP3 act as DNA break sensors signalling DNA damage. Upon detecting DNA damage, these PARPs use nicotine adenine dinucleotide as a substrate to synthesise a monomer or polymer of ADP-ribose (MAR or PAR, respectively) covalently attached to the acceptor residue of target proteins. Recently, it was demonstrated that PARP1–3 proteins can directly ADP-ribosylate DNA breaks by attaching MAR and PAR moieties to terminal phosphates. Nevertheless, little is still known about the mechanisms governing substrate recognition and specificity of PARP1, which accounts for most of cellular PARylation activity. Here, we characterised PARP1-mediated DNA PARylation of DNA duplexes containing various types of breaks at different positions. The 3′-terminal phosphate residue at double-strand DNA break ends served as a major acceptor site for PARP1-catalysed PARylation depending on the orientation and distance between DNA strand breaks in a single DNA molecule. A preference for ADP-ribosylation of DNA molecules containing 3′-terminal phosphate over PARP1 auto-ADP-ribosylation was observed, and a model of DNA modification by PARP1 was proposed. Similar results were obtained with purified recombinant PARP1 and HeLa cell-free extracts. Thus, the biological effects of PARP-mediated ADP-ribosylation may strongly depend on the configuration of complex DNA strand breaks.
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Affiliation(s)
- Elie Matta
- Laboratoire «Intégrité du Génome et Cancers» CNRS, UMR9019, Université Paris-Saclay, F-94805, Villejuif, France.,Gustave Roussy, Université Paris-Saclay, F-94805, Villejuif, France
| | - Assel Kiribayeva
- National Center for Biotechnology, Nur-Sultan, 010000, Kazakhstan.,L.N. Gumilyov Eurasian National University, Nur-Sultan, 010000, Kazakhstan
| | | | - Bakhyt T Matkarimov
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, 010000, Kazakhstan
| | - Alexander A Ishchenko
- Laboratoire «Intégrité du Génome et Cancers» CNRS, UMR9019, Université Paris-Saclay, F-94805, Villejuif, France. .,Gustave Roussy, Université Paris-Saclay, F-94805, Villejuif, France.
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34
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Kim DS, Challa S, Jones A, Kraus WL. PARPs and ADP-ribosylation in RNA biology: from RNA expression and processing to protein translation and proteostasis. Genes Dev 2020; 34:302-320. [PMID: 32029452 PMCID: PMC7050490 DOI: 10.1101/gad.334433.119] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this review, Kim et al. discuss the importance of PARP family members and ADPRylation in gene regulation, mRNA processing, and protein abundance. ADP-ribosylation (ADPRylation) is a posttranslational modification of proteins discovered nearly six decades ago, but many important questions remain regarding its molecular functions and biological roles, as well as the activity of the ADP-ribose (ADPR) transferase enzymes (PARP family members) that catalyze it. Growing evidence indicates that PARP-mediated ADPRylation events are key regulators of the protein biosynthetic pathway, leading from rDNA transcription and ribosome biogenesis to mRNA synthesis, processing, and translation. In this review we describe the role of PARP proteins and ADPRylation in all facets of this pathway. PARP-1 and its enzymatic activity are key regulators of rDNA transcription, which is a critical step in ribosome biogenesis. An emerging role of PARPs in alternative splicing of mRNAs, as well as direct ADPRylation of mRNAs, highlight the role of PARP members in RNA processing. Furthermore, PARP activity, stimulated by cellular stresses, such as viral infections and ER stress, leads to the regulation of mRNA stability and protein synthesis through posttranscriptional mechanisms. Dysregulation of PARP activity in these processes can promote disease states. Collectively, these results highlight the importance of PARP family members and ADPRylation in gene regulation, mRNA processing, and protein abundance. Future studies in these areas will yield new insights into the fundamental mechanisms and a broader utility for PARP-targeted therapeutic agents.
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Affiliation(s)
- Dae-Seok Kim
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Sridevi Challa
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Aarin Jones
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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35
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van
der Heden van
Noort GJ. Chemical Tools to Study Protein ADP-Ribosylation. ACS OMEGA 2020; 5:1743-1751. [PMID: 32039309 PMCID: PMC7003193 DOI: 10.1021/acsomega.9b03591] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/08/2020] [Indexed: 05/03/2023]
Abstract
Post-translational modification of substrate proteins plays crucial roles in the regulation of their activity, cellular localization, and ability to be recognized by other proteins. One of those modifications involves the installment of adenosine-diphosphate-ribose (ADPr) onto nucleophilic side-chain groups of amino acid residues. This highly dynamic process is regulated by ADP-ribosyl transferases (ARTs) that install the ADPr-molecules on selected proteins and poly(ADP-ribosyl) glycohydrolases (PARGs) and (ADP-ribosyl)hydrolases (ARHs) that trim down and remove ADPr-chains. In this mini-review, the most recent advances in the chemical synthesis of ADPr-conjugates, poly-ADP-ribose, ADPr-peptides, and -proteins, and other tools to investigate ADPr-biology are discussed.
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36
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Lawarée E, Jankevicius G, Cooper C, Ahel I, Uphoff S, Tang CM. DNA ADP-Ribosylation Stalls Replication and Is Reversed by RecF-Mediated Homologous Recombination and Nucleotide Excision Repair. Cell Rep 2020; 30:1373-1384.e4. [PMID: 32023456 PMCID: PMC7003065 DOI: 10.1016/j.celrep.2020.01.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/16/2019] [Accepted: 01/02/2020] [Indexed: 01/08/2023] Open
Abstract
ADP-ribosylation of proteins is crucial for fundamental cellular processes. Despite increasing examples of DNA ADP-ribosylation, the impact of this modification on DNA metabolism and cell physiology is unknown. Here, we show that the DarTG toxin-antitoxin system from enteropathogenic Escherichia coli (EPEC) catalyzes reversible ADP-ribosylation of single-stranded DNA (ssDNA). The DarT toxin recognizes specific sequence motifs. EPEC DarG abrogates DarT toxicity by two distinct mechanisms: removal of DNA ADP-ribose (ADPr) groups and DarT sequestration. Furthermore, we investigate how cells recognize and deal with DNA ADP-ribosylation. We demonstrate that DNA ADPr stalls replication and is perceived as DNA damage. Removal of ADPr from DNA requires the sequential activity of two DNA repair pathways, with RecF-mediated homologous recombination likely to transfer ADP-ribosylation from single- to double-stranded DNA (dsDNA) and subsequent nucleotide excision repair eliminating the lesion. Our work demonstrates that these DNA repair pathways prevent the genotoxic effects of DNA ADP-ribosylation.
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Affiliation(s)
- Emeline Lawarée
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Gytis Jankevicius
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Charles Cooper
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
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37
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Design, Synthesis and Molecular Modeling Study of Conjugates of ADP and Morpholino Nucleosides as A Novel Class of Inhibitors of PARP-1, PARP-2 and PARP-3. Int J Mol Sci 2019; 21:ijms21010214. [PMID: 31892271 PMCID: PMC6982223 DOI: 10.3390/ijms21010214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 12/12/2022] Open
Abstract
We report on the design, synthesis and molecular modeling study of conjugates of adenosine diphosphate (ADP) and morpholino nucleosides as potential selective inhibitors of poly(ADP-ribose)polymerases-1, 2 and 3. Sixteen dinucleoside pyrophosphates containing natural heterocyclic bases as well as 5-haloganeted pyrimidines, and mimicking a main substrate of these enzymes, nicotinamide adenine dinucleotide (NAD+)-molecule, have been synthesized in a high yield. Morpholino nucleosides have been tethered to the β-phosphate of ADP via a phosphoester or phosphoramide bond. Screening of the inhibiting properties of these derivatives on the autopoly(ADP-ribosyl)ation of PARP-1 and PARP-2 has shown that the effect depends upon the type of nucleobase as well as on the linkage between ADP and morpholino nucleoside. The 5-iodination of uracil and the introduction of the P–N bond in NAD+-mimetics have shown to increase inhibition properties. Structural modeling suggested that the P–N bond can stabilize the pyrophosphate group in active conformation due to the formation of an intramolecular hydrogen bond. The most active NAD+ analog against PARP-1 contained 5-iodouracil 2ʹ-aminomethylmorpholino nucleoside with IC50 126 ± 6 μM, while in the case of PARP-2 it was adenine 2ʹ-aminomethylmorpholino nucleoside (IC50 63 ± 10 μM). In silico analysis revealed that thymine and uracil-based NAD+ analogs were recognized as the NAD+-analog that targets the nicotinamide binding site. On the contrary, the adenine 2ʹ-aminomethylmorpholino nucleoside-based NAD+ analogs were predicted to identify as PAR-analogs that target the acceptor binding site of PARP-2, representing a novel molecular mechanism for selective PARP inhibition. This discovery opens a new avenue for the rational design of PARP-1/2 specific inhibitors.
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38
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Putri JF, Bhargava P, Dhanjal JK, Yaguchi T, Sundar D, Kaul SC, Wadhwa R. Mortaparib, a novel dual inhibitor of mortalin and PARP1, is a potential drug candidate for ovarian and cervical cancers. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:499. [PMID: 31856867 PMCID: PMC6923857 DOI: 10.1186/s13046-019-1500-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023]
Abstract
Background Mortalin is enriched in a large variety of cancers and has been shown to contribute to proliferation and migration of cancer cells in multiple ways. It has been shown to bind to p53 protein in cell cytoplasm and nucleus causing inactivation of its tumor suppressor activity in cancer cells. Several other activities of mortalin including mitochondrial biogenesis, ATP production, chaperoning, anti-apoptosis contribute to pro-proliferative and migration characteristics of cancer cells. Mortalin-compromised cancer cells have been shown to undergo apoptosis in in vitro and in vivo implying that it could be a potential target for cancer therapy. Methods We implemented a screening of a chemical library for compounds with potential to abrogate cancer cell specific mortalin-p53 interactions, and identified a new compound (named it as Mortaparib) that caused nuclear enrichment of p53 and shift in mortalin from perinuclear (typical of cancer cells) to pancytoplasmic (typical of normal cells). Biochemical and molecular assays were used to demonstrate the effect of Mortaparib on mortalin, p53 and PARP1 activities. Results Molecular homology search revealed that Mortaparib is a novel compound that showed strong cytotoxicity to ovarian, cervical and breast cancer cells. Bioinformatics analysis revealed that although Mortaparib could interact with mortalin, its binding with p53 interaction site was not stable. Instead, it caused transcriptional repression of mortalin leading to activation of p53 and growth arrest/apoptosis of cancer cells. By extensive computational and experimental analyses, we demonstrate that Mortaparib is a dual inhibitor of mortalin and PARP1. It targets mortalin, PARP1 and mortalin-PARP1 interactions leading to inactivation of PARP1 that triggers growth arrest/apoptosis signaling. Consistent with the role of mortalin and PARP1 in cancer cell migration, metastasis and angiogenesis, Mortaparib-treated cells showed inhibition of these phenotypes. In vivo tumor suppression assays showed that Mortaparib is a potent tumor suppressor small molecule and awaits clinical trials. Conclusion These findings report (i) the discovery of Mortaparib as a first dual inhibitor of mortalin and PARP1 (both frequently enriched in cancers), (ii) its molecular mechanism of action, and (iii) in vitro and in vivo tumor suppressor activity that emphasize its potential as an anticancer drug.
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Affiliation(s)
- Jayarani F Putri
- DBT-AIST International Laboratory for Advanced Biomedicine [DAILAB], DAICENTER, National Institute of Advanced Industrial Science and Technology [AIST], Central 5-41, Higashi 1-1-1, Tsukuba, Ibaraki, 305 8565, Japan
| | - Priyanshu Bhargava
- DBT-AIST International Laboratory for Advanced Biomedicine [DAILAB], DAICENTER, National Institute of Advanced Industrial Science and Technology [AIST], Central 5-41, Higashi 1-1-1, Tsukuba, Ibaraki, 305 8565, Japan
| | - Jaspreet Kaur Dhanjal
- DBT-AIST International Laboratory for Advanced Biomedicine [DAILAB], DAICENTER, National Institute of Advanced Industrial Science and Technology [AIST], Central 5-41, Higashi 1-1-1, Tsukuba, Ibaraki, 305 8565, Japan.,DAILAB, Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology [IIT] Delhi, New Delhi, Hauz Khas, 110 016, India
| | - Tomoko Yaguchi
- DBT-AIST International Laboratory for Advanced Biomedicine [DAILAB], DAICENTER, National Institute of Advanced Industrial Science and Technology [AIST], Central 5-41, Higashi 1-1-1, Tsukuba, Ibaraki, 305 8565, Japan
| | - Durai Sundar
- DAILAB, Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology [IIT] Delhi, New Delhi, Hauz Khas, 110 016, India
| | - Sunil C Kaul
- DBT-AIST International Laboratory for Advanced Biomedicine [DAILAB], DAICENTER, National Institute of Advanced Industrial Science and Technology [AIST], Central 5-41, Higashi 1-1-1, Tsukuba, Ibaraki, 305 8565, Japan.
| | - Renu Wadhwa
- DBT-AIST International Laboratory for Advanced Biomedicine [DAILAB], DAICENTER, National Institute of Advanced Industrial Science and Technology [AIST], Central 5-41, Higashi 1-1-1, Tsukuba, Ibaraki, 305 8565, Japan.
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39
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Hoch NC, Polo LM. ADP-ribosylation: from molecular mechanisms to human disease. Genet Mol Biol 2019; 43:e20190075. [PMID: 31930280 PMCID: PMC7198025 DOI: 10.1590/1678-4685-gmb-2019-0075] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/04/2019] [Indexed: 12/23/2022] Open
Abstract
Post-translational modification of proteins by ADP-ribosylation, catalysed by
poly (ADP-ribose) polymerases (PARPs) using NAD+ as a substrate,
plays central roles in DNA damage signalling and repair, modulates a range of
cellular signalling cascades and initiates programmed cell death by parthanatos.
Here, we present mechanistic aspects of ADP-ribose modification, PARP activation
and the cellular functions of ADP-ribose signalling, and discuss how this
knowledge is uncovering therapeutic avenues for the treatment of increasingly
prevalent human diseases such as cancer, ischaemic damage and
neurodegeneration.
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Affiliation(s)
- Nicolas C Hoch
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Luis M Polo
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK.,Institute of Histology and Embryology of Mendoza - CONICET, Mendoza, Argentina
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40
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Alemasova EE, Lavrik OI. Poly(ADP-ribosyl)ation by PARP1: reaction mechanism and regulatory proteins. Nucleic Acids Res 2019; 47:3811-3827. [PMID: 30799503 PMCID: PMC6486540 DOI: 10.1093/nar/gkz120] [Citation(s) in RCA: 268] [Impact Index Per Article: 53.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 02/04/2019] [Accepted: 02/14/2019] [Indexed: 12/18/2022] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation) is posttranslational modification of proteins by linear or branched chains of ADP-ribose units, originating from NAD+. The central enzyme for PAR production in cells and the main target of poly(ADP-ribosyl)ation during DNA damage is poly(ADP-ribose) polymerase 1 (PARP1). PARP1 ability to function as a catalytic and acceptor protein simultaneously made a considerable contribution to accumulation of contradictory data. This topic is directly related to other questions, such as the stoichiometry of PARP1 molecules in auto-modification reaction, direction of the chain growth during PAR elongation and functional coupling of PARP1 with PARylation targets. Besides DNA damage necessary for the folding of catalytically active PARP1, other mechanisms appear to be required for the relevant intensity and specificity of PARylation reaction. Indeed, in recent years, PARP research has been enriched by the discovery of novel PARP1 interaction partners modulating its enzymatic activity. Understanding the details of PARP1 catalytic mechanism and its regulation is especially important in light of PARP-targeted therapy and may significantly aid to PARP inhibitors drug design. In this review we summarize old and up-to-date literature to clarify several points concerning PARylation mechanism and discuss different ways for regulation of PAR synthesis by accessory proteins reported thus far.
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Affiliation(s)
- Elizaveta E Alemasova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
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41
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Fischbach A, Krüger A, Hampp S, Assmann G, Rank L, Hufnagel M, Stöckl MT, Fischer JMF, Veith S, Rossatti P, Ganz M, Ferrando-May E, Hartwig A, Hauser K, Wiesmüller L, Bürkle A, Mangerich A. The C-terminal domain of p53 orchestrates the interplay between non-covalent and covalent poly(ADP-ribosyl)ation of p53 by PARP1. Nucleic Acids Res 2019; 46:804-822. [PMID: 29216372 PMCID: PMC5778597 DOI: 10.1093/nar/gkx1205] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 11/22/2017] [Indexed: 01/25/2023] Open
Abstract
The post-translational modification poly(ADP-ribosyl)ation (PARylation) plays key roles in genome maintenance and transcription. Both non-covalent poly(ADP-ribose) binding and covalent PARylation control protein functions, however, it is unknown how the two modes of modification crosstalk mechanistically. Employing the tumor suppressor p53 as a model substrate, this study provides detailed insights into the interplay between non-covalent and covalent PARylation and unravels its functional significance in the regulation of p53. We reveal that the multifunctional C-terminal domain (CTD) of p53 acts as the central hub in the PARylation-dependent regulation of p53. Specifically, p53 bound to auto-PARylated PARP1 via highly specific non–covalent PAR-CTD interaction, which conveyed target specificity for its covalent PARylation by PARP1. Strikingly, fusing the p53-CTD to a protein that is normally not PARylated, renders this a target for covalent PARylation as well. Functional studies revealed that the p53–PAR interaction had substantial implications on molecular and cellular levels. Thus, PAR significantly influenced the complex p53–DNA binding properties and controlled p53 functions, with major implications on the p53-dependent interactome, transcription, and replication-associated recombination. Remarkably, this mechanism potentially also applies to other PARylation targets, since a bioinformatics analysis revealed that CTD-like regions are highly enriched in the PARylated proteome.
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Affiliation(s)
- Arthur Fischbach
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Annika Krüger
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany.,Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Stephanie Hampp
- Department of Obstetrics and Gynaecology, University of Ulm, 89075 Ulm, Germany
| | - Greta Assmann
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Lisa Rank
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Matthias Hufnagel
- Department of Food Chemistry and Toxicology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Martin T Stöckl
- Bioimaging Center, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Jan M F Fischer
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Sebastian Veith
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany.,Research Training Group 1331, University of Konstanz, 78457 Konstanz, Germany
| | - Pascal Rossatti
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Magdalena Ganz
- Bioimaging Center, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Elisa Ferrando-May
- Bioimaging Center, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Andrea Hartwig
- Department of Food Chemistry and Toxicology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Karin Hauser
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynaecology, University of Ulm, 89075 Ulm, Germany
| | - Alexander Bürkle
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Aswin Mangerich
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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42
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Zarkovic G, Belousova EA, Talhaoui I, Saint-Pierre C, Kutuzov MM, Matkarimov BT, Biard D, Gasparutto D, Lavrik OI, Ishchenko AA. Characterization of DNA ADP-ribosyltransferase activities of PARP2 and PARP3: new insights into DNA ADP-ribosylation. Nucleic Acids Res 2019; 46:2417-2431. [PMID: 29361132 PMCID: PMC5861426 DOI: 10.1093/nar/gkx1318] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/28/2017] [Indexed: 12/22/2022] Open
Abstract
Poly(ADP-ribose) polymerases (PARPs) act as DNA break sensors and catalyze the synthesis of polymers of ADP-ribose (PAR) covalently attached to acceptor proteins at DNA damage sites. It has been demonstrated that both mammalian PARP1 and PARP2 PARylate double-strand break termini in DNA oligonucleotide duplexes in vitro. Here, we show that mammalian PARP2 and PARP3 can PARylate and mono(ADP-ribosyl)ate (MARylate), respectively, 5′- and 3′-terminal phosphate residues at double- and single-strand break termini of a DNA molecule containing multiple strand breaks. PARP3-catalyzed DNA MARylation can be considered a new type of reversible post-replicative DNA modification. According to DNA substrate specificity of PARP3 and PARP2, we propose a putative mechanistic model of PARP-catalyzed strand break–oriented ADP-ribosylation of DNA termini. Notably, PARP-mediated DNA ADP-ribosylation can be more effective than PARPs’ auto-ADP-ribosylation depending on the DNA substrates and reaction conditions used. Finally, we show an effective PARP3- or PARP2-catalyzed ADP-ribosylation of high-molecular-weight (∼3-kb) DNA molecules, PARP-mediated DNA PARylation in cell-free extracts and a persisting signal of anti-PAR antibodies in a serially purified genomic DNA from bleomycin-treated poly(ADP-ribose) glycohydrolase-depleted HeLa cells. These results suggest that certain types of complex DNA breaks can be effectively ADP-ribosylated by PARPs in cellular response to DNA damage.
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Affiliation(s)
- Gabriella Zarkovic
- Laboratoire «Stabilité Génétique et Oncogenèse» CNRS, UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, F-94805 Villejuif, France.,Gustave Roussy, Université Paris-Saclay, F-94805 Villejuif, France
| | - Ekaterina A Belousova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Av. 8, Novosibirsk 630090, Russia
| | - Ibtissam Talhaoui
- Laboratoire «Stabilité Génétique et Oncogenèse» CNRS, UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, F-94805 Villejuif, France.,Gustave Roussy, Université Paris-Saclay, F-94805 Villejuif, France
| | - Christine Saint-Pierre
- Université Grenoble Alpes, CEA, CNRS, INAC/SyMMES-UMR5819/CREAB, F-38000 Grenoble, France
| | - Mikhail M Kutuzov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Av. 8, Novosibirsk 630090, Russia
| | - Bakhyt T Matkarimov
- National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Denis Biard
- CEA, Institut de Biologie François Jacob, SEPIA, Team Cellular Engineering and Human Syndromes, Université Paris-Saclay, F-92265 Fontenay-aux-Roses, France
| | - Didier Gasparutto
- Université Grenoble Alpes, CEA, CNRS, INAC/SyMMES-UMR5819/CREAB, F-38000 Grenoble, France
| | - Olga I Lavrik
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Av. 8, Novosibirsk 630090, Russia.,Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Alexander A Ishchenko
- Laboratoire «Stabilité Génétique et Oncogenèse» CNRS, UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, F-94805 Villejuif, France.,Gustave Roussy, Université Paris-Saclay, F-94805 Villejuif, France
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43
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Munnur D, Bartlett E, Mikolčević P, Kirby IT, Matthias Rack JG, Mikoč A, Cohen MS, Ahel I. Reversible ADP-ribosylation of RNA. Nucleic Acids Res 2019; 47:5658-5669. [PMID: 31216043 PMCID: PMC6582358 DOI: 10.1093/nar/gkz305] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 04/10/2019] [Accepted: 04/23/2019] [Indexed: 12/17/2022] Open
Abstract
ADP-ribosylation is a reversible chemical modification catalysed by ADP-ribosyltransferases such as PARPs that utilize nicotinamide adenine dinucleotide (NAD+) as a cofactor to transfer monomer or polymers of ADP-ribose nucleotide onto macromolecular targets such as proteins and DNA. ADP-ribosylation plays an important role in several biological processes such as DNA repair, transcription, chromatin remodelling, host-virus interactions, cellular stress response and many more. Using biochemical methods we identify RNA as a novel target of reversible mono-ADP-ribosylation. We demonstrate that the human PARPs - PARP10, PARP11 and PARP15 as well as a highly diverged PARP homologue TRPT1, ADP-ribosylate phosphorylated ends of RNA. We further reveal that ADP-ribosylation of RNA mediated by PARP10 and TRPT1 can be efficiently reversed by several cellular ADP-ribosylhydrolases (PARG, TARG1, MACROD1, MACROD2 and ARH3), as well as by MACROD-like hydrolases from VEEV and SARS viruses. Finally, we show that TRPT1 and MACROD homologues in bacteria possess activities equivalent to the human proteins. Our data suggest that RNA ADP-ribosylation may represent a widespread and physiologically relevant form of reversible ADP-ribosylation signalling.
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Affiliation(s)
- Deeksha Munnur
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Edward Bartlett
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Petra Mikolčević
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ilsa T Kirby
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97239, USA
| | | | - Andreja Mikoč
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Michael S Cohen
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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44
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Abstract
ADP-ribosylation (ADPr) is an ancient reversible modification of cellular macromolecules controlling major biological processes as diverse as DNA damage repair, transcriptional regulation, intracellular transport, immune and stress responses, cell survival and proliferation. Furthermore, enzymatic reactions of ADPr are central in the pathogenesis of many human diseases, including infectious conditions. By providing a review of ADPr signalling in bacterial systems, we highlight the relevance of this chemical modification in the pathogenesis of human diseases depending on host-pathogen interactions. The post-antibiotic era has raised the need to find alternative approaches to antibiotic administration, as major pathogens becoming resistant to antibiotics. An in-depth understanding of ADPr reactions provides the rationale for designing novel antimicrobial strategies for treatment of infectious diseases. In addition, the understanding of mechanisms of ADPr by bacterial virulence factors offers important hints to improve our knowledge on cellular processes regulated by eukaryotic homologous enzymes, which are often involved in the pathogenesis of human diseases.
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45
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O'Sullivan J, Tedim Ferreira M, Gagné JP, Sharma AK, Hendzel MJ, Masson JY, Poirier GG. Emerging roles of eraser enzymes in the dynamic control of protein ADP-ribosylation. Nat Commun 2019; 10:1182. [PMID: 30862789 PMCID: PMC6414514 DOI: 10.1038/s41467-019-08859-x] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 02/02/2019] [Indexed: 12/21/2022] Open
Abstract
Protein ADP-ribosylation is essential for the regulation of several cellular pathways, enabling dynamic responses to diverse pathophysiological conditions. It is modulated through a dynamic interplay between ADP-ribose readers, writers and erasers. While ADP-ribose synthesis has been studied and reviewed extensively, ADP-ribose processing by erasing enzymes has received comparably less attention. However, major progress in the mass spectrometric identification of ADP-ribosylated residues and the biochemical characterization of ADP-ribose erasers has substantially expanded our knowledge of ADP-ribosylation dynamics. Herein, we describe recent insights into the biology of ADP-ribose erasers and discuss the intricately orchestrated cellular processes to switch off ADP-ribose-dependent mechanisms. ADP-ribose erasing enzymes are increasingly recognized as critical regulators of protein ADP-ribosylation dynamics in living systems. Here, the authors review recent advances in the discovery and characterization of ADP-ribose erasers and discuss their role within the cellular ADP-ribosylation machinery.
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Affiliation(s)
- Julia O'Sullivan
- Genome Stability Laboratory, Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, HDQ Pavilion, Oncology Division, Québec, G1R 2J6, Canada.,Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, G1V 0A6, Canada
| | - Maria Tedim Ferreira
- Genome Stability Laboratory, Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, HDQ Pavilion, Oncology Division, Québec, G1R 2J6, Canada.,Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, G1V 0A6, Canada.,Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, CHUL Pavilion, Oncology division, Québec, G1V 4G2, Canada
| | - Jean-Philippe Gagné
- Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, G1V 0A6, Canada.,Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, CHUL Pavilion, Oncology division, Québec, G1V 4G2, Canada
| | - Ajit K Sharma
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, T6G 1Z2, Canada
| | - Michael J Hendzel
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, T6G 1Z2, Canada.,Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, T6G 2H7, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, HDQ Pavilion, Oncology Division, Québec, G1R 2J6, Canada.,Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, G1V 0A6, Canada.,Centre de Recherche sur le Cancer de l'Université Laval, Québec, G1R 3S3, Canada
| | - Guy G Poirier
- Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, G1V 0A6, Canada. .,Centre de Recherche du Centre Hospitalier Universitaire de Québec-Université Laval, CHUL Pavilion, Oncology division, Québec, G1V 4G2, Canada. .,Centre de Recherche sur le Cancer de l'Université Laval, Québec, G1R 3S3, Canada.
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46
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Kassab MA, Yu X. The role of dePARylation in DNA damage repair and cancer suppression. DNA Repair (Amst) 2019; 76:20-29. [PMID: 30807923 DOI: 10.1016/j.dnarep.2019.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/03/2019] [Indexed: 12/19/2022]
Abstract
Poly(ADP-ribosyl)ation (PARylation) is a reversible post-translational modification regulating various biological pathways including DNA damage repair (DDR). Rapid turnover of PARylation is critically important for an optimal DNA damage response and maintaining genomic stability. Recent studies show that PARylation is tightly regulated by a group of enzymes that can erase the ADP-ribose (ADPR) groups from target proteins. The aim of this review is to present a comprehensive understanding of dePARylation enzymes, their substrates and roles in DDR. Special attention will be laid on the role of these proteins in the development of cancer and their feasibility in anticancer therapeutics.
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Affiliation(s)
- Muzaffer Ahmad Kassab
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010, USA
| | - Xiaochun Yu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010, USA.
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47
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Multiple Roles for Mono- and Poly(ADP-Ribose) in Regulating Stress Responses. Trends Genet 2018; 35:159-172. [PMID: 30595401 DOI: 10.1016/j.tig.2018.12.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 01/27/2023]
Abstract
Although stress-induced synthesis of mono(ADP-ribose) (mADPr) and poly(ADP-ribose) (pADPr) conjugates by pADPr polymerase (PARP) enzymes has been studied extensively, the removal and degradation of pADPr, as well as the fate of ADPr metabolites, have received less attention. The observations that stress-induced pADPr undergoes rapid turnover, and that deficiencies in ADPr degradation phenocopy loss of pADPr synthesis, suggest that ADPr degradation is fundamentally important to the cellular stress response. Recent work has identified several distinct families of pADPr hydrolases that can degrade pADPr to release pADPr or mADPr into the cytoplasm. Further, many stress-response proteins contain ADPr-binding domains that can interact with these metabolites. We discuss how pADPr metabolites generated during pADPr degradation can function as signaling intermediates in processes such as inflammation, apoptosis, and DNA damage responses. These studies highlight that the full cycle of ADPr metabolism, including both synthesis and degradation, is necessary for responses to genotoxic stress.
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48
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Poly(ADP-Ribose) Polymerases in Host-Pathogen Interactions, Inflammation, and Immunity. Microbiol Mol Biol Rev 2018; 83:83/1/e00038-18. [PMID: 30567936 DOI: 10.1128/mmbr.00038-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The literature review presented here details recent research involving members of the poly(ADP-ribose) polymerase (PARP) family of proteins. Among the 17 recognized members of the family, the human enzyme PARP1 is the most extensively studied, resulting in a number of known biological and metabolic roles. This review is focused on the roles played by PARP enzymes in host-pathogen interactions and in diseases with an associated inflammatory response. In mammalian cells, several PARPs have specific roles in the antiviral response; this is perhaps best illustrated by PARP13, also termed the zinc finger antiviral protein (ZAP). Plant stress responses and immunity are also regulated by poly(ADP-ribosyl)ation. PARPs promote inflammatory responses by stimulating proinflammatory signal transduction pathways that lead to the expression of cytokines and cell adhesion molecules. Hence, PARP inhibitors show promise in the treatment of inflammatory disorders and conditions with an inflammatory component, such as diabetes, arthritis, and stroke. These functions are correlated with the biophysical characteristics of PARP family enzymes. This work is important in providing a comprehensive understanding of the molecular basis of pathogenesis and host responses, as well as in the identification of inhibitors. This is important because the identification of inhibitors has been shown to be effective in arresting the progression of disease.
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49
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Palazzo L, Ahel I. PARPs in genome stability and signal transduction: implications for cancer therapy. Biochem Soc Trans 2018; 46:1681-1695. [PMID: 30420415 PMCID: PMC6299239 DOI: 10.1042/bst20180418] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/15/2018] [Accepted: 09/21/2018] [Indexed: 01/03/2023]
Abstract
The poly(ADP-ribose) polymerase (PARP) superfamily of enzymes catalyses the ADP-ribosylation (ADPr) of target proteins by using nicotinamide adenine dinucleotide (NAD+) as a donor. ADPr reactions occur either in the form of attachment of a single ADP-ribose nucleotide unit on target proteins or in the form of ADP-ribose chains, with the latter called poly(ADP-ribosyl)ation. PARPs regulate many cellular processes, including the maintenance of genome stability and signal transduction. In this review, we focus on the PARP family members that possess the ability to modify proteins by poly(ADP-ribosyl)ation, namely PARP1, PARP2, Tankyrase-1, and Tankyrase-2. Here, we detail the cellular functions of PARP1 and PARP2 in the regulation of DNA damage response and describe the function of Tankyrases in Wnt-mediated signal transduction. Furthermore, we discuss how the understanding of these pathways has provided some major breakthroughs in the treatment of human cancer.
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Affiliation(s)
- Luca Palazzo
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, U.K.
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50
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Bartlett E, Bonfiglio JJ, Prokhorova E, Colby T, Zobel F, Ahel I, Matic I. Interplay of Histone Marks with Serine ADP-Ribosylation. Cell Rep 2018; 24:3488-3502.e5. [PMID: 30257210 PMCID: PMC6172693 DOI: 10.1016/j.celrep.2018.08.092] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/29/2018] [Accepted: 08/30/2018] [Indexed: 02/07/2023] Open
Abstract
Serine ADP-ribosylation (Ser-ADPr) is a recently discovered protein modification that is catalyzed by PARP1 and PARP2 when in complex with the eponymous histone PARylation factor 1 (HPF1). In addition to numerous other targets, core histone tails are primary acceptors of Ser-ADPr in the DNA damage response. Here, we show that specific canonical histone marks interfere with Ser-ADPr of neighboring residues and vice versa. Most notably, acetylation, but not methylation of H3K9, is mutually exclusive with ADPr of H3S10 in vitro and in vivo. We also broaden the O-linked ADPr spectrum by providing evidence for tyrosine ADPr on HPF1 and other proteins. Finally, we facilitate wider investigations into the interplay of histone marks with Ser-ADPr by introducing a simple approach for profiling posttranslationally modified peptides. Our findings implicate Ser-ADPr as a dynamic addition to the complex interplay of modifications that shape the histone code.
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Affiliation(s)
- Edward Bartlett
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Juan José Bonfiglio
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9b, Cologne 50931, Germany
| | - Evgeniia Prokhorova
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Thomas Colby
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9b, Cologne 50931, Germany
| | - Florian Zobel
- 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.
| | - Ivan Matic
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9b, Cologne 50931, Germany.
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