1
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Hao W, Jialong Z, Jiuzhi Y, Yang Y, Chongning L, Jincai L. ADP-ribosylation, a multifaceted modification: Functions and mechanisms in aging and aging-related diseases. Ageing Res Rev 2024; 98:102347. [PMID: 38815933 DOI: 10.1016/j.arr.2024.102347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 06/01/2024]
Abstract
Aging, a complex biological process, plays key roles the development of multiple disorders referred as aging-related diseases involving cardiovascular diseases, stroke, neurodegenerative diseases, cancers, lipid metabolism-related diseases. ADP-ribosylation is a reversible modification onto proteins and nucleic acids to alter their structures and/or functions. Growing evidence support the importance of ADP-ribosylation and ADP-ribosylation-associated enzymes in aging and age-related diseases. In this review, we summarized ADP-ribosylation-associated proteins including ADP-ribosyl transferases, the ADP-ribosyl hydrolyses and ADP-ribose binding domains. Furthermore, we outlined the latest knowledge about regulation of ADP-ribosylation in the pathogenesis and progression of main aging-related diseases, organism aging and cellular senescence, and we also speculated the underlying mechanisms to better disclose this novel molecular network. Moreover, we discussed current issues and provided an outlook for future research, aiming to revealing the unknown bio-properties of ADP-ribosylation, and establishing a novel therapeutic perspective in aging-related diseases and health aging via targeting ADP-ribosylation.
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Affiliation(s)
- Wu Hao
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Zhao Jialong
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Yuan Jiuzhi
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Yu Yang
- College of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Lv Chongning
- 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
| | - Lu Jincai
- 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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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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3
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Roterman I, Stapor K, Dułak D, Konieczny L. External Force Field for Protein Folding in Chaperonins-Potential Application in In Silico Protein Folding. ACS OMEGA 2024; 9:18412-18428. [PMID: 38680295 PMCID: PMC11044213 DOI: 10.1021/acsomega.4c00409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/26/2024] [Accepted: 03/29/2024] [Indexed: 05/01/2024]
Abstract
The present study discusses the influence of the TRiC chaperonin involved in the folding of the component of reovirus mu1/σ3. The TRiC chaperone is treated as a provider of a specific external force field in the fuzzy oil drop model during the structural formation of a target folded protein. The model also determines the status of the final product, which represents the structure directed by an external force field in the form of a chaperonin. This can be used for in silico folding as the process is environment-dependent. The application of the model enables the quantitative assessment of the folding dependence of an external force field, which appears to have universal application.
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Affiliation(s)
- Irena Roterman
- Department
of Bioinformatics and Telemedicine, Jagiellonian
University—Medical College, Medyczna 7, Kraków 30-688, Poland
| | - Katarzyna Stapor
- Faculty
of Automatic, Electronics and Computer Science, Department of Applied
Informatics, Silesian University of Technology, Akademicka 16, Gliwice 44-100, Poland
| | - Dawid Dułak
- ABB
Business Services Sp. z o.o, ul Żegańska 1, Warszawa 04-713, Poland
| | - Leszek Konieczny
- Chair
of Medical Biochemistry—Jagiellonian University—Medical
College, Kopernika 7, Kraków 31-034, Poland
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4
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Bashyal A, Brodbelt JS. Uncommon posttranslational modifications in proteomics: ADP-ribosylation, tyrosine nitration, and tyrosine sulfation. MASS SPECTROMETRY REVIEWS 2024; 43:289-326. [PMID: 36165040 PMCID: PMC10040477 DOI: 10.1002/mas.21811] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Posttranslational modifications (PTMs) are covalent modifications of proteins that modulate the structure and functions of proteins and regulate biological processes. The development of various mass spectrometry-based proteomics workflows has facilitated the identification of hundreds of PTMs and aided the understanding of biological significance in a high throughput manner. Improvements in sample preparation and PTM enrichment techniques, instrumentation for liquid chromatography-tandem mass spectrometry (LC-MS/MS), and advanced data analysis tools enhance the specificity and sensitivity of PTM identification. Highly prevalent PTMs like phosphorylation, glycosylation, acetylation, ubiquitinylation, and methylation are extensively studied. However, the functions and impact of less abundant PTMs are not as well understood and underscore the need for analytical methods that aim to characterize these PTMs. This review focuses on the advancement and analytical challenges associated with the characterization of three less common but biologically relevant PTMs, specifically, adenosine diphosphate-ribosylation, tyrosine sulfation, and tyrosine nitration. The advantages and disadvantages of various enrichment, separation, and MS/MS techniques utilized to identify and localize these PTMs are described.
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Affiliation(s)
- Aarti Bashyal
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA
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5
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Yang XY, Liu T, Jiang SC, Zhang ZW, Fu YF, Li ZL, Hu J, Yuan S. Antibodies against SARS-CoV-2 non-structural protein 3 cross-react with human muscle cells and neuroglial cells. Vaccine 2024; 42:1259-1267. [PMID: 38281898 DOI: 10.1016/j.vaccine.2024.01.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/23/2023] [Accepted: 01/23/2024] [Indexed: 01/30/2024]
Abstract
Coronavirus Disease 2019 (COVID-19) vaccines protect the public and limit viral spread. However, inactivated viral vaccines use the whole virus particle, which contains many non-capsid proteins that may cause adverse immune responses. A report has found that the ADP-ribose-binding domains of SARS-CoV-2 non-structural protein 3 (NSP3) and human poly(ADP-ribose) polymerase family member 14 (PARP14) share a significant degree of homology. Here, we further show that antibodies against 2019 novel SARS-like coronavirus (SARS-CoV-2) NSP3 can bind human PARP14 protein. However, when G159R + G162R mutations were introduced into NSP3, the antibody titer against human PARP14 decreased 14-fold. Antibodies against SARS-CoV-2 NSP3 can cross-react with human skeletal muscle cells and astrocytes, but not human embryonic kidney 293T cells. However, when G159R + G162R mutations were introduced into NSP3, the cross-reaction was largely inhibited. The results imply that COVID-19 patients with high antibody titers against NSP3 may have high risks of muscular and/or neurological complications. And the possible strategies to improve the safety of inactivated viral vaccines are also discussed.
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Affiliation(s)
- Xin-Yue Yang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Ting Liu
- Sichuan Kelun Pharmaceutical Comp. Ltd., Chengdu 610071, China
| | - Si-Cong Jiang
- Haisco Pharmaceutical Group Comp. Ltd., Chengdu 611138, China
| | - Zhong-Wei Zhang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu-Fan Fu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Zi-Lin Li
- Department of Cardiovascular Surgery, Xijing Hospital, Medical University of the Air Force, Xi'an 710032, China
| | - Jing Hu
- School of Medicine, Northwest University, Xi'an 710069, China
| | - Shu Yuan
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China.
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6
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Stoll GA, Nikolopoulos N, Zhai H, Zhang L, Douse CH, Modis Y. Crystal structure and biochemical activity of the macrodomain from rubella virus p150. J Virol 2024; 98:e0177723. [PMID: 38289106 PMCID: PMC10878246 DOI: 10.1128/jvi.01777-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/22/2023] [Indexed: 02/13/2024] Open
Abstract
Rubella virus encodes a nonstructural polyprotein with RNA polymerase, methyltransferase, and papain-like cysteine protease activities, along with a putative macrodomain of unknown function. Macrodomains bind ADP-ribose adducts, a post-translational modification that plays a key role in host-virus conflicts. Some macrodomains can also remove the mono-ADP-ribose adduct or degrade poly-ADP-ribose chains. Here, we report high-resolution crystal structures of the macrodomain from rubella virus nonstructural protein p150, with and without ADP-ribose binding. The overall fold is most similar to macroD-type macrodomains from various nonviral species. The specific composition and structure of the residues that coordinate ADP-ribose in the rubella virus macrodomain are most similar to those of macrodomains from alphaviruses. Isothermal calorimetry shows that the rubella virus macrodomain binds ADP-ribose in solution. Enzyme assays show that the rubella virus macrodomain can hydrolyze both mono- and poly-ADP-ribose adducts. Site-directed mutagenesis identifies Asn39 and Cys49 required for mono-ADP-ribosylhydrolase (de-MARylation) activity.IMPORTANCERubella virus remains a global health threat. Rubella infections during pregnancy can cause serious congenital pathology, for which no antiviral treatments are available. Our work demonstrates that, like alpha- and coronaviruses, rubiviruses encode a mono-ADP-ribosylhydrolase with a structurally conserved macrodomain fold to counteract MARylation by poly (ADP-ribose) polymerases (PARPs) in the host innate immune response. Our structural data will guide future efforts to develop novel antiviral therapeutics against rubella or infections with related viruses.
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Affiliation(s)
- Guido A. Stoll
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nikos Nikolopoulos
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Haoming Zhai
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Liao Zhang
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Yorgo Modis
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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7
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Saleh H, Liloglou T, Rigden DJ, Parsons JL, Grundy GJ. KH-like Domains in PARP9/DTX3L and PARP14 Coordinate Protein-Protein Interactions to Promote Cancer Cell Survival. J Mol Biol 2024; 436:168434. [PMID: 38182103 PMCID: PMC11080071 DOI: 10.1016/j.jmb.2023.168434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/12/2023] [Accepted: 12/30/2023] [Indexed: 01/07/2024]
Abstract
Certain members of the ADP-ribosyltransferase superfamily (ARTD or PARP enzymes) catalyse ADP-ribosylation in response to cellular stress, DNA damage and viral infection and are upregulated in various tumours. PARP9, its binding partner DTX3L and PARP14 protein levels are significantly correlated in head and neck squamous cell carcinoma (HNSCC) and other tumour types though a mechanism where PARP9/DTX3L regulates PARP14 post-transcriptionally. Depleting PARP9, DTX3L or PARP14 expression in HNSCC or HeLa cell lines decreases cell survival through a reduction of proliferation and an increase in apoptosis. A partial rescue of survival was achieved by expressing a PARP14 truncation containing a predicted eukaryotic type I KH domain. KH-like domains were also found in PARP9 and in DTX3L and contributed to protein-protein interactions between PARP9-DTX3L and PARP14-DTX3L. Homodimerization of DTX3L was also coordinated by a KH-like domain and was disrupted by site-specific mutation. Although, cell survival promoted by PARP14 did not require ADP-ribosyltransferase activity, interaction of DTX3L in vitro suppressed PARP14 auto-ADP-ribosylation and promoted trans-ADP-ribosylation of PARP9 and DTX3L. In summary, we characterised PARP9-DTX3L-PARP14 interactions important to pro-survival signalling in HNSCC cells, albeit in PARP14 catalytically independent fashion.
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Affiliation(s)
- Hadil Saleh
- University of Liverpool, Department of Molecular and Clinical Cancer Medicine, 6 West Derby St, Liverpool L7 8TX, UK
| | - Triantafillos Liloglou
- Edge Hill University, Faculty of Health, Social Care & Medicine, St Helens Road, Ormskirk, Lancashire L39 4QP, UK
| | - Daniel J Rigden
- University of Liverpool, Department of Biochemistry, Cell and Systems Biology, Liverpool L69 7ZB, UK
| | - Jason L Parsons
- University of Birmingham, Institute of Cancer and Genomic Sciences, IBR West, Birmingham B15 2TT, UK
| | - Gabrielle J Grundy
- University of Liverpool, Department of Molecular and Clinical Cancer Medicine, 6 West Derby St, Liverpool L7 8TX, UK.
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8
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Brooks DM, Anand S, Cohen MS. Immunomodulatory roles of PARPs: Shaping the tumor microenvironment, one ADP-ribose at a time. Curr Opin Chem Biol 2023; 77:102402. [PMID: 37801755 DOI: 10.1016/j.cbpa.2023.102402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/29/2023] [Accepted: 09/08/2023] [Indexed: 10/08/2023]
Abstract
PARPs encompass a small yet pervasive group of 17 enzymes that catalyze a post-translational modification known as ADP-ribosylation. PARP1, the founding member, has received considerable focus; however, in recent years, the spotlight has shifted to other members within the PARP family. In this opinion piece, we first discuss surprising findings that some FDA-approved PARP1 inhibitors activate innate immune signaling in cancer cells that harbor mutations in the DNA repair pathway. We then discuss hot-off-the-press genetic and pharmacological studies that reveal roles for PARP7, PARP11, and PARP14 in immune signaling in both tumor cells and tumor-associated immune cells. We conclude with thoughts on tuning PARP1-inhibitor-mediated innate immune activation and explore the unrealized potential for small molecule modulators of other PARP family members as next-generation immuno-oncology drugs.
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Affiliation(s)
- Deja M Brooks
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA; Program in Molecular and Cellular Biology, Oregon Health & Science University, Portland, OR 97239, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Sudarshan Anand
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA; Department of Cellular and Developmental Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Michael S Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA.
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9
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Đukić N, Strømland Ø, Elsborg JD, Munnur D, Zhu K, Schuller M, Chatrin C, Kar P, Duma L, Suyari O, Rack JGM, Baretić D, Crudgington DRK, Groslambert J, Fowler G, Wijngaarden S, Prokhorova E, Rehwinkel J, Schüler H, Filippov DV, Sanyal S, Ahel D, Nielsen ML, Smith R, Ahel I. PARP14 is a PARP with both ADP-ribosyl transferase and hydrolase activities. SCIENCE ADVANCES 2023; 9:eadi2687. [PMID: 37703374 PMCID: PMC10499325 DOI: 10.1126/sciadv.adi2687] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/10/2023] [Indexed: 09/15/2023]
Abstract
PARP14 is a mono-ADP-ribosyl transferase involved in the control of immunity, transcription, and DNA replication stress management. However, little is known about the ADP-ribosylation activity of PARP14, including its substrate specificity or how PARP14-dependent ADP-ribosylation is reversed. We show that PARP14 is a dual-function enzyme with both ADP-ribosyl transferase and hydrolase activity acting on both protein and nucleic acid substrates. In particular, we show that the PARP14 macrodomain 1 is an active ADP-ribosyl hydrolase. We also demonstrate hydrolytic activity for the first macrodomain of PARP9. We reveal that expression of a PARP14 mutant with the inactivated macrodomain 1 results in a marked increase in mono(ADP-ribosyl)ation of proteins in human cells, including PARP14 itself and antiviral PARP13, and displays specific cellular phenotypes. Moreover, we demonstrate that the closely related hydrolytically active macrodomain of SARS2 Nsp3, Mac1, efficiently reverses PARP14 ADP-ribosylation in vitro and in cells, supporting the evolution of viral macrodomains to counteract PARP14-mediated antiviral response.
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Affiliation(s)
- Nina Đukić
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Øyvind Strømland
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway
| | - Jonas Damgaard Elsborg
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Deeksha Munnur
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Chatrin Chatrin
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Pulak Kar
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Lena Duma
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Osamu Suyari
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Johannes Gregor Matthias Rack
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Domagoj Baretić
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | | | | | - Gerissa Fowler
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Sven Wijngaarden
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Evgeniia Prokhorova
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Herwig Schüler
- Center for Molecular Protein Science, Department of Chemistry, Lund University, 22100 Lund, Sweden
| | - Dmitri V. Filippov
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Sumana Sanyal
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Rebecca Smith
- 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
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10
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Torretta A, Chatzicharalampous C, Ebenwaldner C, Schüler H. PARP14 is a writer, reader, and eraser of mono-ADP-ribosylation. J Biol Chem 2023; 299:105096. [PMID: 37507011 PMCID: PMC10470015 DOI: 10.1016/j.jbc.2023.105096] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
PARP14/BAL2 is a large multidomain enzyme involved in signaling pathways with relevance to cancer, inflammation, and infection. Inhibition of its mono-ADP-ribosylating PARP homology domain and its three ADP-ribosyl binding macro domains has been regarded as a potential means of therapeutic intervention. Macrodomains-2 and -3 are known to stably bind to ADP-ribosylated target proteins, but the function of macrodomain-1 has remained somewhat elusive. Here, we used biochemical assays of ADP-ribosylation levels to characterize PARP14 macrodomain-1 and the homologous macrodomain-1 of PARP9. Our results show that both macrodomains display an ADP-ribosyl glycohydrolase activity that is not directed toward specific protein side chains. PARP14 macrodomain-1 is unable to degrade poly(ADP-ribose), the enzymatic product of PARP1. The F926A mutation of PARP14 and the F244A mutation of PARP9 strongly reduced ADP-ribosyl glycohydrolase activity of the respective macrodomains, suggesting mechanistic homology to the Mac1 domain of the SARS-CoV-2 Nsp3 protein. This study adds two new enzymes to the previously known six human ADP-ribosyl glycohydrolases. Our results have key implications for how PARP14 and PARP9 will be studied and how their functions will be understood.
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Affiliation(s)
- Archimede Torretta
- Department of Chemistry, Center for Molecular Protein Science (CMPS), Lund University, Lund, Sweden
| | | | - Carmen Ebenwaldner
- Department of Chemistry, Center for Molecular Protein Science (CMPS), Lund University, Lund, Sweden
| | - Herwig Schüler
- Department of Chemistry, Center for Molecular Protein Science (CMPS), Lund University, Lund, Sweden.
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11
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Dasovich M, Leung AKL. PARPs and ADP-ribosylation: Deciphering the complexity with molecular tools. Mol Cell 2023; 83:1552-1572. [PMID: 37119811 PMCID: PMC10202152 DOI: 10.1016/j.molcel.2023.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/07/2023] [Accepted: 04/05/2023] [Indexed: 05/01/2023]
Abstract
PARPs catalyze ADP-ribosylation-a post-translational modification that plays crucial roles in biological processes, including DNA repair, transcription, immune regulation, and condensate formation. ADP-ribosylation can be added to a wide range of amino acids with varying lengths and chemical structures, making it a complex and diverse modification. Despite this complexity, significant progress has been made in developing chemical biology methods to analyze ADP-ribosylated molecules and their binding proteins on a proteome-wide scale. Additionally, high-throughput assays have been developed to measure the activity of enzymes that add or remove ADP-ribosylation, leading to the development of inhibitors and new avenues for therapy. Real-time monitoring of ADP-ribosylation dynamics can be achieved using genetically encoded reporters, and next-generation detection reagents have improved the precision of immunoassays for specific forms of ADP-ribosylation. Further development and refinement of these tools will continue to advance our understanding of the functions and mechanisms of ADP-ribosylation in health and disease.
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Affiliation(s)
- Morgan Dasovich
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Molecular Biology and Genetics, Department of Oncology, and Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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12
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Badiee M, Kenet AL, Ganser LR, Paul T, Myong S, Leung AKL. Switch-like compaction of poly(ADP-ribose) upon cation binding. Proc Natl Acad Sci U S A 2023; 120:e2215068120. [PMID: 37126687 PMCID: PMC10175808 DOI: 10.1073/pnas.2215068120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 03/23/2023] [Indexed: 05/03/2023] Open
Abstract
Poly(ADP-ribose) (PAR) is a homopolymer of adenosine diphosphate ribose that is added to proteins as a posttranslational modification to regulate numerous cellular processes. PAR also serves as a scaffold for protein binding in macromolecular complexes, including biomolecular condensates. It remains unclear how PAR achieves specific molecular recognition. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) to evaluate PAR flexibility under different cation conditions. We demonstrate that, compared to RNA and DNA, PAR has a longer persistence length and undergoes a sharper transition from extended to compact states in physiologically relevant concentrations of various cations (Na+, Mg2+, Ca2+, and spermine4+). We show that the degree of PAR compaction depends on the concentration and valency of cations. Furthermore, the intrinsically disordered protein FUS also served as a macromolecular cation to compact PAR. Taken together, our study reveals the inherent stiffness of PAR molecules, which undergo switch-like compaction in response to cation binding. This study indicates that a cationic environment may drive recognition specificity of PAR.
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Affiliation(s)
- Mohsen Badiee
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD21205
| | - Adam L. Kenet
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD21205
| | - Laura R. Ganser
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218
| | - Tapas Paul
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD21218
| | - Anthony K. L. Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD21205
- Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD21205
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD21205
- Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD21205
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13
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Delgado-Rodriguez SE, Ryan AP, Daugherty MD. Recurrent Loss of Macrodomain Activity in Host Immunity and Viral Proteins. Pathogens 2023; 12:pathogens12050674. [PMID: 37242344 DOI: 10.3390/pathogens12050674] [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: 03/25/2023] [Revised: 04/29/2023] [Accepted: 04/30/2023] [Indexed: 05/28/2023] Open
Abstract
Protein post-translational modifications (PTMs) are an important battleground in the evolutionary arms races that are waged between the host innate immune system and viruses. One such PTM, ADP-ribosylation, has recently emerged as an important mediator of host antiviral immunity. Important for the host-virus conflict over this PTM is the addition of ADP-ribose by PARP proteins and removal of ADP-ribose by macrodomain-containing proteins. Interestingly, several host proteins, known as macroPARPs, contain macrodomains as well as a PARP domain, and these proteins are both important for the host antiviral immune response and evolving under very strong positive (diversifying) evolutionary selection. In addition, several viruses, including alphaviruses and coronaviruses, encode one or more macrodomains. Despite the presence of the conserved macrodomain fold, the enzymatic activity of many of these proteins has not been characterized. Here, we perform evolutionary and functional analyses to characterize the activity of macroPARP and viral macrodomains. We trace the evolutionary history of macroPARPs in metazoans and show that PARP9 and PARP14 contain a single active macrodomain, whereas PARP15 contains none. Interestingly, we also reveal several independent losses of macrodomain enzymatic activity within mammalian PARP14, including in the bat, ungulate, and carnivore lineages. Similar to macroPARPs, coronaviruses contain up to three macrodomains, with only the first displaying catalytic activity. Intriguingly, we also reveal the recurrent loss of macrodomain activity within the alphavirus group of viruses, including enzymatic loss in insect-specific alphaviruses as well as independent enzymatic losses in two human-infecting viruses. Together, our evolutionary and functional data reveal an unexpected turnover in macrodomain activity in both host antiviral proteins and viral proteins.
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Affiliation(s)
- Sofia E Delgado-Rodriguez
- Department of Molecular Biology, School of Biological Sciences, University of California-San Diego, La Jolla, CA 92093, USA
| | - Andrew P Ryan
- Department of Molecular Biology, School of Biological Sciences, University of California-San Diego, La Jolla, CA 92093, USA
| | - Matthew D Daugherty
- Department of Molecular Biology, School of Biological Sciences, University of California-San Diego, La Jolla, CA 92093, USA
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14
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IFN-Induced PARPs—Sensors of Foreign Nucleic Acids? Pathogens 2023; 12:pathogens12030457. [PMID: 36986379 PMCID: PMC10057411 DOI: 10.3390/pathogens12030457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/10/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023] Open
Abstract
Cells have developed different strategies to cope with viral infections. Key to initiating a defense response against viruses is the ability to distinguish foreign molecules from their own. One central mechanism is the perception of foreign nucleic acids by host proteins which, in turn, initiate an efficient immune response. Nucleic acid sensing pattern recognition receptors have evolved, each targeting specific features to discriminate viral from host RNA. These are complemented by several RNA-binding proteins that assist in sensing of foreign RNAs. There is increasing evidence that the interferon-inducible ADP-ribosyltransferases (ARTs; PARP9—PARP15) contribute to immune defense and attenuation of viruses. However, their activation, subsequent targets, and precise mechanisms of interference with viruses and their propagation are still largely unknown. Best known for its antiviral activities and its role as RNA sensor is PARP13. In addition, PARP9 has been recently described as sensor for viral RNA. Here we will discuss recent findings suggesting that some PARPs function in antiviral innate immunity. We expand on these findings and integrate this information into a concept that outlines how the different PARPs might function as sensors of foreign RNA. We speculate about possible consequences of RNA binding with regard to the catalytic activities of PARPs, substrate specificity and signaling, which together result in antiviral activities.
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15
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Badiee M, Kenet AL, Ganser LR, Paul T, Myong S, Leung AKL. Switch-like Compaction of Poly(ADP-ribose) Upon Cation Binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.11.531013. [PMID: 36993178 PMCID: PMC10055007 DOI: 10.1101/2023.03.11.531013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Poly(ADP-ribose) (PAR) is a homopolymer of adenosine diphosphate ribose that is added to proteins as a post-translational modification to regulate numerous cellular processes. PAR also serves as a scaffold for protein binding in macromolecular complexes, including biomolecular condensates. It remains unclear how PAR achieves specific molecular recognition. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) to evaluate PAR flexibility under different cation conditions. We demonstrate that, compared to RNA and DNA, PAR has a longer persistence length and undergoes a sharper transition from extended to compact states in physiologically relevant concentrations of various cations (Na + , Mg 2+ , Ca 2+ , and spermine). We show that the degree of PAR compaction depends on the concentration and valency of cations. Furthermore, the intrinsically disordered protein FUS also served as a macromolecular cation to compact PAR. Taken together, our study reveals the inherent stiffness of PAR molecules, which undergo switch-like compaction in response to cation binding. This study indicates that a cationic environment may drive recognition specificity of PAR. Significance Poly(ADP-ribose) (PAR) is an RNA-like homopolymer that regulates DNA repair, RNA metabolism, and biomolecular condensate formation. Dysregulation of PAR results in cancer and neurodegeneration. Although discovered in 1963, fundamental properties of this therapeutically important polymer remain largely unknown. Biophysical and structural analyses of PAR have been exceptionally challenging due to the dynamic and repetitive nature. Here, we present the first single-molecule biophysical characterization of PAR. We show that PAR is stiffer than DNA and RNA per unit length. Unlike DNA and RNA which undergoes gradual compaction, PAR exhibits an abrupt switch-like bending as a function of salt concentration and by protein binding. Our findings points to unique physical properties of PAR that may drive recognition specificity for its function.
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16
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Mono-ADP-ribosylation by PARP10 inhibits Chikungunya virus nsP2 proteolytic activity and viral replication. Cell Mol Life Sci 2023; 80:72. [PMID: 36840772 PMCID: PMC9959937 DOI: 10.1007/s00018-023-04717-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 01/28/2023] [Accepted: 01/31/2023] [Indexed: 02/26/2023]
Abstract
Replication of viruses requires interaction with host cell factors and repression of innate immunity. Recent findings suggest that a subset of intracellular mono-ADP-ribosylating PARPs, which are induced by type I interferons, possess antiviral activity. Moreover, certain RNA viruses, including Chikungunya virus (CHIKV), encode mono-ADP-ribosylhydrolases. Together, this suggests a role for mono-ADP-ribosylation (MARylation) in host-virus conflicts, but the relevant substrates have not been identified. We addressed which PARP restricts CHIKV replication and identified PARP10 and PARP12. For PARP10, this restriction was dependent on catalytic activity. Replication requires processing of the non-structural polyprotein nsP1-4 by the protease located in nsP2 and the assembly of the four individual nsP1-nsP4 into a functional replication complex. PARP10 and PARP12 inhibited the production of nsP3, indicating a defect in polyprotein processing. The nsP3 protein encodes a macrodomain with de-MARylation activity, which is essential for replication. In support for MARylation affecting polyprotein processing, de-MARylation defective CHIKV replicons revealed reduced production of nsP2 and nsP3. We hypothesized that MARylation regulates the proteolytic function of nsP2. Indeed, we found that nsP2 is MARylated by PARP10 and, as a consequence, its proteolytic activity was inhibited. NsP3-dependent de-MARylation reactivated the protease. Hence, we propose that PARP10-mediated MARylation prevents polyprotein processing and consequently virus replication. Together, our findings provide a mechanistic explanation for the role of the viral MAR hydrolase in CHIKV replication.
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17
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Murthy S, Nizi MG, Maksimainen MM, Massari S, Alaviuhkola J, Lippok BE, Vagaggini C, Sowa ST, Galera-Prat A, Ashok Y, Venkannagari H, Prunskaite-Hyyryläinen R, Dreassi E, Lüscher B, Korn P, Tabarrini O, Lehtiö L. [1,2,4]Triazolo[3,4- b]benzothiazole Scaffold as Versatile Nicotinamide Mimic Allowing Nanomolar Inhibition of Different PARP Enzymes. J Med Chem 2023; 66:1301-1320. [PMID: 36598465 PMCID: PMC9884089 DOI: 10.1021/acs.jmedchem.2c01460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We report [1,2,4]triazolo[3,4-b]benzothiazole (TBT) as a new inhibitor scaffold, which competes with nicotinamide in the binding pocket of human poly- and mono-ADP-ribosylating enzymes. The binding mode was studied through analogues and cocrystal structures with TNKS2, PARP2, PARP14, and PARP15. Based on the substitution pattern, we were able to identify 3-amino derivatives 21 (OUL243) and 27 (OUL232) as inhibitors of mono-ARTs PARP7, PARP10, PARP11, PARP12, PARP14, and PARP15 at nM potencies, with 27 being the most potent PARP10 inhibitor described to date (IC50 of 7.8 nM) and the first PARP12 inhibitor ever reported. On the contrary, hydroxy derivative 16 (OUL245) inhibits poly-ARTs with a selectivity toward PARP2. The scaffold does not possess inherent cell toxicity, and the inhibitors can enter cells and engage with the target protein. This, together with favorable ADME properties, demonstrates the potential of TBT scaffold for future drug development efforts toward selective inhibitors against specific enzymes.
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Affiliation(s)
- Sudarshan Murthy
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Maria Giulia Nizi
- Department
of Pharmaceutical Sciences, University of
Perugia, Perugia06123, Italy
| | - Mirko M. Maksimainen
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Serena Massari
- Department
of Pharmaceutical Sciences, University of
Perugia, Perugia06123, Italy
| | - Juho Alaviuhkola
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Barbara E. Lippok
- Institute
of Biochemistry and Molecular Biology, RWTH
Aachen University, Aachen52074, Germany
| | - Chiara Vagaggini
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, SienaI-53100, Italy
| | - Sven T. Sowa
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Albert Galera-Prat
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Yashwanth Ashok
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Harikanth Venkannagari
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | | | - Elena Dreassi
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, SienaI-53100, Italy
| | - Bernhard Lüscher
- Institute
of Biochemistry and Molecular Biology, RWTH
Aachen University, Aachen52074, Germany
| | - Patricia Korn
- Institute
of Biochemistry and Molecular Biology, RWTH
Aachen University, Aachen52074, Germany
| | - Oriana Tabarrini
- Department
of Pharmaceutical Sciences, University of
Perugia, Perugia06123, Italy,
| | - Lari Lehtiö
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland,
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18
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Weixler L, Ikenga NJ, Voorneveld J, Aydin G, Bolte TMHR, Momoh J, Bütepage M, Golzmann A, Lüscher B, Filippov DV, Žaja R, Feijs KLH. Protein and RNA ADP-ribosylation detection is influenced by sample preparation and reagents used. Life Sci Alliance 2022; 6:6/1/e202201455. [PMID: 36368907 PMCID: PMC9652768 DOI: 10.26508/lsa.202201455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/13/2022] Open
Abstract
The modification of substrates with ADP-ribose (ADPr) is important in, for example, antiviral immunity and cancer. Recently, several reagents were developed to detect ADP-ribosylation; however, it is unknown whether they recognise ADPr, specific amino acid-ADPr linkages, or ADPr with the surrounding protein backbone. We first optimised methods to prepare extracts containing ADPr-proteins and observe that depending on the amino acid modified, the modification is heatlabile. We tested the reactivity of available reagents with diverse ADP-ribosylated protein and RNA substrates and observed that not all reagents are equally suited for all substrates. Next, we determined cross-reactivity with adenylylated RNA, AMPylated proteins, and metabolites, including NADH, which are detected by some reagents. Lastly, we analysed ADP-ribosylation using confocal microscopy, where depending on the fixation method, either mitochondrion, nucleus, or nucleolus is stained. This study allows future work dissecting the function of ADP-ribosylation in cells, both on protein and on RNA substrates, as we optimised sample preparation methods and have defined the reagents suitable for specific methods and substrates.
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Affiliation(s)
- Lisa Weixler
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Nonso Josephat Ikenga
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Jim Voorneveld
- Leiden Institute of Chemistry, Leiden University Department of Bioorganic Synthesis, Leiden, Netherlands
| | - Gülcan Aydin
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Timo MHR Bolte
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Jeffrey Momoh
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Mareike Bütepage
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Alexandra Golzmann
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Dmitri V Filippov
- Leiden Institute of Chemistry, Leiden University Department of Bioorganic Synthesis, Leiden, Netherlands
| | - Roko Žaja
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany
| | - Karla LH Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Aachen, Germany,Correspondence: ;
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19
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Fourkiotis NK, Charalampous P, Tsika AC, Kravvariti KP, Sideras-Bisdekis C, Gallo A, Spyroulias GA. NMR study of human macroPARPs domains: 1H, 15N and 13C resonance assignment of hPARP14 macro domain 2 in the free and the ADPr bound state. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:399-406. [PMID: 36107366 PMCID: PMC9477163 DOI: 10.1007/s12104-022-10110-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
hPARP14 is a human ADP-ribosyl-transferase (ART) that belongs to the macroPARPs family, together with hPARP9 and hPARP15. It contains a tandem of three macro domains (MD) while each of them has different properties. The first one, namely MD1, has not been reported to exhibit a high binding affinity for ADP-ribose (ADPr) in contrast to the following two (MD2 and MD3). All three MDs exhibit an α/β/α sandwich-like fold as reported by the deposited crystallographic structures. MD2 and MD3 recognize mono-ADP-ribosylated (MARylated) but not poly-ADP-ribosylated (PARylated) substrates and thus they allow hPARP14 to bind its targets, which can be potentially MARylated by its catalytic domain (CD). hPARP14 participates in DNA damage repair process and immune response against viruses like SARS-CoV-2, which also harbors an MD fold. Furthermore, hPARP14 like the other two macroPARPs (hPARP9 and hPARP15), is implicated in numerous types of cancer, such as B-aggressive lymphoma and sarcoma, rendering its MDs as potential important drug targets. Herein, we report the complete NMR backbone and side chain assignment (1H, 13C, 15N) of hPARP14 MD2 in the free and ADPr bound states and the NMR chemical shift-based prediction of its secondary structure elements. This is the first reported NMR study of a hPARP macro domain, paving the way to screen by NMR chemical compounds which may alter the ability of hPARP14 to interact with its substrates affecting its function.
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Affiliation(s)
| | | | | | | | | | - Angelo Gallo
- Department of Pharmacy, University of Patras, 26504, Patras, Greece.
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20
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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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21
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Affiliation(s)
- Srivatsan Parthasarathy
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
- * E-mail:
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22
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Reversible modification of mitochondrial ADP/ATP translocases by paired Legionella effector proteins. Proc Natl Acad Sci U S A 2022; 119:e2122872119. [PMID: 35653564 DOI: 10.1073/pnas.2122872119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceMitochondria are organelles of the central metabolism that produce ATP and play fundamental roles in eukaryotic cell function and thereby become targets for pathogenic bacteria to manipulate. We found that the intracellular bacterial pathogen, Legionella pneumophila, targets mitochondrial ADP/ATP translocases (ANTs), the function of which is linked to the mitochondrial ATP synthesis. This is achieved by a pair of effector proteins, Lpg0080 and Lpg0081, which have opposing enzymatic activities as an ADP ribosyltransferase (ART) and an ADP ribosylhydrolase (ARH), respectively, coordinately regulating the chemical modification of ANTs upon infection. Our structural analyses indicate that Lpg0081 is an ARH with a noncanonical macrodomain, whose folding topology is distinct from that of the canonical macrodomain of known eukaryotic, archaeal, and bacterial proteins.
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23
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Gan Y, Sha H, Zou R, Xu M, Zhang Y, Feng J, Wu J. Research Progress on Mono-ADP-Ribosyltransferases in Human Cell Biology. Front Cell Dev Biol 2022; 10:864101. [PMID: 35652091 PMCID: PMC9149570 DOI: 10.3389/fcell.2022.864101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
ADP-ribosylation is a well-established post-translational modification that is inherently connected to diverse processes, including DNA repair, transcription, and cell signaling. The crucial roles of mono-ADP-ribosyltransferases (mono-ARTs) in biological processes have been identified in recent years by the comprehensive use of genetic engineering, chemical genetics, and proteomics. This review provides an update on current methodological advances in the study of these modifiers. Furthermore, the review provides details on the function of mono ADP-ribosylation. Several mono-ARTs have been implicated in the development of cancer, and this review discusses the role and therapeutic potential of some mono-ARTs in cancer.
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Affiliation(s)
- Yujie Gan
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
| | - Huanhuan Sha
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Renrui Zou
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
| | - Miao Xu
- Nanjing Medical University, Nanjing, China
| | - Yuan Zhang
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
| | - Jifeng Feng
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
- Nanjing Medical University, Nanjing, China
- *Correspondence: Jifeng Feng,
| | - Jianzhong Wu
- Jiangsu Cancer Hospital, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, China
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24
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Lüscher B, Verheirstraeten M, Krieg S, Korn P. Intracellular mono-ADP-ribosyltransferases at the host-virus interphase. Cell Mol Life Sci 2022; 79:288. [PMID: 35536484 PMCID: PMC9087173 DOI: 10.1007/s00018-022-04290-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/15/2022] [Accepted: 04/05/2022] [Indexed: 01/22/2023]
Abstract
The innate immune system, the primary defense mechanism of higher organisms against pathogens including viruses, senses pathogen-associated molecular patterns (PAMPs). In response to PAMPs, interferons (IFNs) are produced, allowing the host to react swiftly to viral infection. In turn the expression of IFN-stimulated genes (ISGs) is induced. Their products disseminate the antiviral response. Among the ISGs conserved in many species are those encoding mono-ADP-ribosyltransferases (mono-ARTs). This prompts the question whether, and if so how, mono-ADP-ribosylation affects viral propagation. Emerging evidence demonstrates that some mono-ADP-ribosyltransferases function as PAMP receptors and modify both host and viral proteins relevant for viral replication. Support for mono-ADP-ribosylation in virus–host interaction stems from the findings that some viruses encode mono-ADP-ribosylhydrolases, which antagonize cellular mono-ARTs. We summarize and discuss the evidence linking mono-ADP-ribosylation and the enzymes relevant to catalyze this reversible modification with the innate immune response as part of the arms race between host and viruses.
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Affiliation(s)
- Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.
| | - Maud Verheirstraeten
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Sarah Krieg
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Patricia Korn
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.
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25
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Challa S, Ryu KW, Whitaker AL, Abshier JC, Camacho CV, Kraus WL. Development and characterization of new tools for detecting poly(ADP-ribose) in vitro and in vivo. eLife 2022; 11:e72464. [PMID: 35476036 PMCID: PMC9045816 DOI: 10.7554/elife.72464] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 03/23/2022] [Indexed: 12/13/2022] Open
Abstract
ADP-ribosylation (ADPRylation) is a reversible post-translation modification resulting in the covalent attachment of ADP-ribose (ADPR) moieties on substrate proteins. Naturally occurring protein motifs and domains, including WWEs, PBZs, and macrodomains, act as 'readers' for protein-linked ADPR. Although recombinant, antibody-like ADPR detection reagents containing these readers have facilitated the detection of ADPR, they are limited in their ability to capture the dynamic nature of ADPRylation. Herein, we describe and characterize a set of poly(ADP-ribose) (PAR) Trackers (PAR-Ts)-optimized dimerization-dependent or split-protein reassembly PAR sensors in which a naturally occurring PAR binding domain, WWE, was fused to both halves of dimerization-dependent GFP (ddGFP) or split Nano Luciferase (NanoLuc), respectively. We demonstrate that these new tools allow the detection and quantification of PAR levels in extracts, living cells, and living tissues with greater sensitivity, as well as temporal and spatial precision. Importantly, these sensors detect changes in cellular ADPR levels in response to physiological cues (e.g., hormone-dependent induction of adipogenesis without DNA damage), as well as xenograft tumor tissues in living mice. Our results indicate that PAR Trackers have broad utility for detecting ADPR in many different experimental and biological systems.
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Affiliation(s)
- Sridevi Challa
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical CenterDallasUnited States
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Keun W Ryu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical CenterDallasUnited States
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Amy L Whitaker
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical CenterDallasUnited States
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical CenterDallasUnited States
- Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical CenterDallasUnited States
| | - Jonathan C Abshier
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical CenterDallasUnited States
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical CenterDallasUnited States
| | - Cristel V Camacho
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical CenterDallasUnited States
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical CenterDallasUnited States
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical CenterDallasUnited States
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical CenterDallasUnited States
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26
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O’Donoghue SI, Schafferhans A, Sikta N, Stolte C, Kaur S, Ho BK, Anderson S, Procter JB, Dallago C, Bordin N, Adcock M, Rost B. SARS-CoV-2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms. Mol Syst Biol 2021; 17:e10079. [PMID: 34519429 PMCID: PMC8438690 DOI: 10.15252/msb.202010079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 01/18/2023] Open
Abstract
We modeled 3D structures of all SARS-CoV-2 proteins, generating 2,060 models that span 69% of the viral proteome and provide details not available elsewhere. We found that ˜6% of the proteome mimicked human proteins, while ˜7% was implicated in hijacking mechanisms that reverse post-translational modifications, block host translation, and disable host defenses; a further ˜29% self-assembled into heteromeric states that provided insight into how the viral replication and translation complex forms. To make these 3D models more accessible, we devised a structural coverage map, a novel visualization method to show what is-and is not-known about the 3D structure of the viral proteome. We integrated the coverage map into an accompanying online resource (https://aquaria.ws/covid) that can be used to find and explore models corresponding to the 79 structural states identified in this work. The resulting Aquaria-COVID resource helps scientists use emerging structural data to understand the mechanisms underlying coronavirus infection and draws attention to the 31% of the viral proteome that remains structurally unknown or dark.
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MESH Headings
- Amino Acid Transport Systems, Neutral/chemistry
- Amino Acid Transport Systems, Neutral/genetics
- Amino Acid Transport Systems, Neutral/metabolism
- Angiotensin-Converting Enzyme 2/chemistry
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/metabolism
- Binding Sites
- COVID-19/genetics
- COVID-19/metabolism
- COVID-19/virology
- Computational Biology/methods
- Coronavirus Envelope Proteins/chemistry
- Coronavirus Envelope Proteins/genetics
- Coronavirus Envelope Proteins/metabolism
- Coronavirus Nucleocapsid Proteins/chemistry
- Coronavirus Nucleocapsid Proteins/genetics
- Coronavirus Nucleocapsid Proteins/metabolism
- Host-Pathogen Interactions/genetics
- Humans
- Mitochondrial Membrane Transport Proteins/chemistry
- Mitochondrial Membrane Transport Proteins/genetics
- Mitochondrial Membrane Transport Proteins/metabolism
- Mitochondrial Precursor Protein Import Complex Proteins
- Models, Molecular
- Molecular Mimicry
- Neuropilin-1/chemistry
- Neuropilin-1/genetics
- Neuropilin-1/metabolism
- Phosphoproteins/chemistry
- Phosphoproteins/genetics
- Phosphoproteins/metabolism
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Interaction Mapping/methods
- Protein Multimerization
- Protein Processing, Post-Translational
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/metabolism
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/metabolism
- Viral Matrix Proteins/chemistry
- Viral Matrix Proteins/genetics
- Viral Matrix Proteins/metabolism
- Viroporin Proteins/chemistry
- Viroporin Proteins/genetics
- Viroporin Proteins/metabolism
- Virus Replication
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Affiliation(s)
- Seán I O’Donoghue
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
- CSIRO Data61CanberraACTAustralia
- School of Biotechnology and Biomolecular Sciences (UNSW)KensingtonNSWAustralia
| | - Andrea Schafferhans
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
- Department of Bioengineering SciencesWeihenstephan‐Tr. University of Applied SciencesFreisingGermany
- Department of InformaticsBioinformatics & Computational BiologyTechnical University of MunichMunichGermany
| | - Neblina Sikta
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
| | | | - Sandeep Kaur
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
- School of Biotechnology and Biomolecular Sciences (UNSW)KensingtonNSWAustralia
| | - Bosco K Ho
- Garvan Institute of Medical ResearchDarlinghurstNSWAustralia
| | | | | | - Christian Dallago
- Department of InformaticsBioinformatics & Computational BiologyTechnical University of MunichMunichGermany
| | - Nicola Bordin
- Institute of Structural and Molecular BiologyUniversity College LondonLondonUK
| | | | - Burkhard Rost
- Department of InformaticsBioinformatics & Computational BiologyTechnical University of MunichMunichGermany
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27
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Chiu YC, Tseng MC, Hsu CH. Expanding the Substrate Specificity of Macro Domains toward 3″-Isomer of O-Acetyl-ADP-ribose. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yi-Chih Chiu
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
| | - Mei-Chun Tseng
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chun-Hua Hsu
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
- Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
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28
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Fu W, Yao H, Bütepage M, Zhao Q, Lüscher B, Li J. The search for inhibitors of macrodomains for targeting the readers and erasers of mono-ADP-ribosylation. Drug Discov Today 2021; 26:2547-2558. [PMID: 34023495 DOI: 10.1016/j.drudis.2021.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/13/2021] [Accepted: 05/14/2021] [Indexed: 01/15/2023]
Abstract
Macrodomains are evolutionarily conserved structural elements. Many macrodomains feature as binding modules of ADP-ribose, thus participating in the recognition and removal of mono- and poly-ADP-ribosylation. Macrodomains are involved in the regulation of a variety of physiological processes and represent valuable therapeutic targets. Moreover, as part of the nonstructural proteins of certain viruses, macrodomains are also pivotal for viral replication and pathogenesis. Thus, targeting viral macrodomains with inhibitors is considered to be a promising antiviral intervention. In this review, we summarize our current understanding of human and viral macrodomains that are related to mono-ADP-ribosylation, with emphasis on the search for inhibitors. The advances summarized here will be helpful for the design of macrodomain-specific agents for therapeutic and diagnostic applications.
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Affiliation(s)
- Wei Fu
- College of Chemistry, Fuzhou University, 350116 Fuzhou, China
| | - Huiqiao Yao
- College of Chemistry, Fuzhou University, 350116 Fuzhou, China
| | - Mareike Bütepage
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, 52057 Aachen, Germany
| | - Qianqian Zhao
- College of Chemistry, Fuzhou University, 350116 Fuzhou, China
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, 52057 Aachen, Germany.
| | - Jinyu Li
- College of Chemistry, Fuzhou University, 350116 Fuzhou, China.
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29
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Yang CS, Jividen K, Kamata T, Dworak N, Oostdyk L, Remlein B, Pourfarjam Y, Kim IK, Du KP, Abbas T, Sherman NE, Wotton D, Paschal BM. Androgen signaling uses a writer and a reader of ADP-ribosylation to regulate protein complex assembly. Nat Commun 2021; 12:2705. [PMID: 33976187 PMCID: PMC8113490 DOI: 10.1038/s41467-021-23055-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 04/14/2021] [Indexed: 02/03/2023] Open
Abstract
Androgen signaling through the androgen receptor (AR) directs gene expression in both normal and prostate cancer cells. Androgen regulates multiple aspects of the AR life cycle, including its localization and post-translational modification, but understanding how modifications are read and integrated with AR activity has been difficult. Here, we show that ADP-ribosylation regulates AR through a nuclear pathway mediated by Parp7. We show that Parp7 mono-ADP-ribosylates agonist-bound AR, and that ADP-ribosyl-cysteines within the N-terminal domain mediate recruitment of the E3 ligase Dtx3L/Parp9. Molecular recognition of ADP-ribosyl-cysteine is provided by tandem macrodomains in Parp9, and Dtx3L/Parp9 modulates expression of a subset of AR-regulated genes. Parp7, ADP-ribosylation of AR, and AR-Dtx3L/Parp9 complex assembly are inhibited by Olaparib, a compound used clinically to inhibit poly-ADP-ribosyltransferases Parp1/2. Our study reveals the components of an androgen signaling axis that uses a writer and reader of ADP-ribosylation to regulate protein-protein interactions and AR activity.
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Affiliation(s)
- Chun-Song Yang
- Center for Cell Signaling, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Kasey Jividen
- Center for Cell Signaling, University of Virginia, Charlottesville, VA, USA
| | - Teddy Kamata
- Center for Cell Signaling, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Natalia Dworak
- Center for Cell Signaling, University of Virginia, Charlottesville, VA, USA
| | - Luke Oostdyk
- Center for Cell Signaling, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Bartlomiej Remlein
- Center for Cell Signaling, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Yasin Pourfarjam
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - In-Kwon Kim
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Kang-Ping Du
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA, USA
| | - Tarek Abbas
- Center for Cell Signaling, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA, USA
| | - Nicholas E Sherman
- W. M. Keck Biomedical Mass Spectrometry Laboratory, University of Virginia, Charlottesville, VA, USA
| | - David Wotton
- Center for Cell Signaling, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Bryce M Paschal
- Center for Cell Signaling, University of Virginia, Charlottesville, VA, USA.
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
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30
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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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31
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Rosado MM, Pioli C. ADP-ribosylation in evasion, promotion and exacerbation of immune responses. Immunology 2021; 164:15-30. [PMID: 33783820 DOI: 10.1111/imm.13332] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/15/2021] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
ADP-ribosylation is the addition of one or more (up to some hundreds) ADP-ribose moieties to acceptor proteins. This evolutionary ancient post-translational modification (PTM) is involved in fundamental processes including DNA repair, inflammation, cell death, differentiation and proliferation, among others. ADP-ribosylation is catalysed by two major families of enzymes: the cholera toxin-like ADP-ribosyltransferases (ARTCs) and the diphtheria toxin-like ADP-ribosyltransferases (ARTDs, also known as PARPs). ARTCs sense and use extracellular NAD, which may represent a danger signal, whereas ARTDs are present in the cell nucleus and/or cytoplasm. ARTCs mono-ADP-ribosylate their substrates, whereas ARTDs, according to the specific family member, are able to mono- or poly-ADP-ribosylate target proteins or are devoid of enzymatic activity. Both mono- and poly-ADP-ribosylation are dynamic processes, as specific hydrolases are able to remove single or polymeric ADP moieties. This dynamic equilibrium between addition and degradation provides plasticity for fast adaptation, a feature being particularly relevant to immune cell functions. ADP-ribosylation regulates differentiation and functions of myeloid, T and B cells. It also regulates the expression of cytokines and chemokines, production of antibodies, isotype switch and the expression of several immune mediators. Alterations in these processes involve ADP-ribosylation in virtually any acute and chronic inflammatory/immune-mediated disease. Besides, pathogens developed mechanisms to contrast the action of ADP-ribosylating enzymes by using their own hydrolases and/or to exploit this PTM to sustain their virulence. In the present review, we summarize and discuss recent findings on the role of ADP-ribosylation in immunobiology, immune evasion/subversion by pathogens and immune-mediated diseases.
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Affiliation(s)
| | - Claudio Pioli
- Division of Health Protection Technologies, ENEA, Rome, Italy
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32
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Zha JJ, Tang Y, Wang YL. Role of mono-ADP-ribosylation histone modification (Review). Exp Ther Med 2021; 21:577. [PMID: 33850549 PMCID: PMC8027728 DOI: 10.3892/etm.2021.10009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/22/2021] [Indexed: 12/13/2022] Open
Abstract
The current knowledge regarding ADP-ribosylation modifications of histones, particularly mono-ADP-ribosylation modifications, is limited. However, recent studies have identified an increasing number of mono-ADP-ribosyltransferases and the role of mono-ADP-ribosylation has become a hot research topic. In particular, histones that are substrates of several mono-ADP-ribosyltransferases and mono-ADP-ribosylated histones were indicated to be involved in numerous physiological or pathological processes. Compared to poly-ADP-ribosylation histone modification, the use of mono-ADP-ribosylation histone modification is restricted by the limited methods for research into its function in physiological or pathological processes. The aim of the present review was to discuss the details regarding mono-ADP-ribosylation modification of histones and the currently known functions thereof, such as cell physiological and pathological processes, including tumorigenesis.
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Affiliation(s)
- Jing-Jing Zha
- Pathological Department, First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, P.R. China
| | - Yi Tang
- Department of Pathology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Ya-Lan Wang
- Department of Pathology, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, P.R. China
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33
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Challa S, Stokes MS, Kraus WL. MARTs and MARylation in the Cytosol: Biological Functions, Mechanisms of Action, and Therapeutic Potential. Cells 2021; 10:313. [PMID: 33546365 PMCID: PMC7913519 DOI: 10.3390/cells10020313] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 01/30/2021] [Accepted: 02/01/2021] [Indexed: 12/13/2022] Open
Abstract
Mono(ADP-ribosyl)ation (MARylation) is a regulatory post-translational modification of proteins that controls their functions through a variety of mechanisms. MARylation is catalyzed by mono(ADP-ribosyl) transferase (MART) enzymes, a subclass of the poly(ADP-ribosyl) polymerase (PARP) family of enzymes. Although the role of PARPs and poly(ADP-ribosyl)ation (PARylation) in cellular pathways, such as DNA repair and transcription, is well studied, the role of MARylation and MARTs (i.e., the PARP 'monoenzymes') are not well understood. Moreover, compared to PARPs, the development of MART-targeted therapeutics is in its infancy. Recent studies are beginning to shed light on the structural features, catalytic targets, and biological functions of MARTs. The development of new technologies to study MARTs have uncovered essential roles for these enzymes in the regulation of cellular processes, such as RNA metabolism, cellular transport, focal adhesion, and stress responses. These insights have increased our understanding of the biological functions of MARTs in cancers, neuronal development, and immune responses. Furthermore, several novel inhibitors of MARTs have been developed and are nearing clinical utility. In this review, we summarize the biological functions and molecular mechanisms of MARTs and MARylation, as well as recent advances in technology that have enabled detection and inhibition of their activity. We emphasize PARP-7, which is at the forefront of the MART subfamily with respect to understanding its biological roles and the development of therapeutically useful inhibitors. Collectively, the available studies reveal a growing understanding of the biochemistry, chemical biology, physiology, and pathology of MARTs.
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Affiliation(s)
- 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, TX 75390, USA;
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - MiKayla S. Stokes
- 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;
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 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, TX 75390, USA;
- Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Program in Genetics, Development, and Disease, Graduate School of Biomedical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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34
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Hammond RG, Schormann N, McPherson RL, Leung AKL, Deivanayagam CCS, Johnson MA. ADP-ribose and analogues bound to the deMARylating macrodomain from the bat coronavirus HKU4. Proc Natl Acad Sci U S A 2021; 118:e2004500118. [PMID: 33397718 PMCID: PMC7812796 DOI: 10.1073/pnas.2004500118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Macrodomains are proteins that recognize and hydrolyze ADP ribose (ADPR) modifications of intracellular proteins. Macrodomains are implicated in viral genome replication and interference with host cell immune responses. They are important to the infectious cycle of Coronaviridae and Togaviridae viruses. We describe crystal structures of the conserved macrodomain from the bat coronavirus (CoV) HKU4 in complex with ligands. The structures reveal a binding cavity that accommodates ADPR and analogs via local structural changes within the pocket. Using a radioactive assay, we present evidence of mono-ADPR (MAR) hydrolase activity. In silico analysis presents further evidence on recognition of the ADPR modification for hydrolysis. Mutational analysis of residues within the binding pocket resulted in diminished enzymatic activity and binding affinity. We conclude that the common structural features observed in the macrodomain in a bat CoV contribute to a conserved function that can be extended to other known macrodomains.
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Affiliation(s)
- Robert G Hammond
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Norbert Schormann
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Robert Lyle McPherson
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205
- Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21287
| | - Champion C S Deivanayagam
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Margaret A Johnson
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294;
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35
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Poltronieri P, Celetti A, Palazzo L. Mono(ADP-ribosyl)ation Enzymes and NAD + Metabolism: A Focus on Diseases and Therapeutic Perspectives. Cells 2021; 10:cells10010128. [PMID: 33440786 PMCID: PMC7827148 DOI: 10.3390/cells10010128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/05/2021] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
Mono(ADP-ribose) transferases and mono(ADP-ribosyl)ating sirtuins use NAD+ to perform the mono(ADP-ribosyl)ation, a simple form of post-translational modification of proteins and, in some cases, of nucleic acids. The availability of NAD+ is a limiting step and an essential requisite for NAD+ consuming enzymes. The synthesis and degradation of NAD+, as well as the transport of its key intermediates among cell compartments, play a vital role in the maintenance of optimal NAD+ levels, which are essential for the regulation of NAD+-utilizing enzymes. In this review, we provide an overview of the current knowledge of NAD+ metabolism, highlighting the functional liaison with mono(ADP-ribosyl)ating enzymes, such as the well-known ARTD10 (also named PARP10), SIRT6, and SIRT7. To this aim, we discuss the link of these enzymes with NAD+ metabolism and chronic diseases, such as cancer, degenerative disorders and aging.
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Affiliation(s)
- Palmiro Poltronieri
- Institute of Sciences of Food Productions, National Research Council of Italy, via Monteroni 7, 73100 Lecce, Italy
- Correspondence: (P.P.); (A.C.); (L.P.)
| | - Angela Celetti
- Institute for the Experimental Endocrinology and Oncology, National Research Council of Italy, Via Sergio Pansini 5, 80131 Naples, Italy
- Correspondence: (P.P.); (A.C.); (L.P.)
| | - Luca Palazzo
- Institute for the Experimental Endocrinology and Oncology, National Research Council of Italy, Via Tommaso de Amicis 95, 80145 Naples, Italy
- Correspondence: (P.P.); (A.C.); (L.P.)
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Zhao Y, Liang X, Wei L, Liu Y, Liu J, Feng H, Zheng F, Wang Y, Ma H, Wu J. RNF114 suppresses metastasis through regulation of PARP10 in cervical cancer cells. Cancer Commun (Lond) 2021; 41:187-191. [PMID: 33417305 PMCID: PMC7896744 DOI: 10.1002/cac2.12132] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/13/2020] [Accepted: 12/27/2020] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yahui Zhao
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Fudan University, Shanghai, 200438, P. R. China.,Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China
| | - Xiao Liang
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Fudan University, Shanghai, 200438, P. R. China
| | - Li Wei
- Department of Oncology, No. 971 Hospital of PLA Navy, Qingdao, Shandong, 266071, P. R. China
| | - Yao Liu
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Fudan University, Shanghai, 200438, P. R. China
| | - Juan Liu
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Fudan University, Shanghai, 200438, P. R. China
| | - Huan Feng
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Fudan University, Shanghai, 200438, P. R. China
| | - Fen Zheng
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Fudan University, Shanghai, 200438, P. R. China
| | - Ying Wang
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Fudan University, Shanghai, 200438, P. R. China
| | - Haijie Ma
- Laboratory of Cytobiology and Molecular Biology, the Affiliated Zhoushan Hospital of Wenzhou Medical University, Zhoushan, Zhejiang, 316000, P. R. China
| | - Jiaxue Wu
- State Key Laboratory of Genetic Engineering, Zhongshan Hospital and School of Life Sciences, Fudan University, Shanghai, 200438, P. R. China
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In silico family-wide profiling and 3D modelling of the poly(ADP-ribose) polymerase superfamily. Future Med Chem 2020; 12:2105-2122. [PMID: 33225737 DOI: 10.4155/fmc-2020-0274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background: Due to the conserved nature of the poly(ADP-ribose) polymerase (PARP) catalytic domain, the identification of unique residues is critical for the design of selective inhibitors. With inhibitors of the DNA-dependent PARP members already clinically approved, new efforts lie in discovering selective inhibitors for PARP5a and beyond. Targeting the noncatalytic domains, such as the macro2 and WWE domains may also provide a way to achieve selectivity. Methodology & results: This paper details the in silico profiling of x-ray crystal structures and homology models of the PARP catalytic, WWE and macro2 domains. PARP10 was the least conserved catalytic domain, with the macro2 and WWE domains possessing more unique residues than their catalytic counterparts. Conclusion: Overall, we identify unique residues to target when designing selective PARP inhibitors including HIS1610, TYR1620, ALA1627 and ARG1658 of the PARP14 catalytic domain, along with multiple unique residues across the PARP WWE and macro2 domains.
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38
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Rack JGM, Zorzini V, Zhu Z, Schuller M, Ahel D, Ahel I. Viral macrodomains: a structural and evolutionary assessment of the pharmacological potential. Open Biol 2020; 10:200237. [PMID: 33202171 PMCID: PMC7729036 DOI: 10.1098/rsob.200237] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022] Open
Abstract
Viral macrodomains possess the ability to counteract host ADP-ribosylation, a post-translational modification implicated in the creation of an antiviral environment via immune response regulation. This brought them into focus as promising therapeutic targets, albeit the close homology to some of the human macrodomains raised concerns regarding potential cross-reactivity and adverse effects for the host. Here, we evaluate the structure and function of the macrodomain of SARS-CoV-2, the causative agent of COVID-19. We show that it can antagonize ADP-ribosylation by PARP14, a cellular (ADP-ribosyl)transferase necessary for the restriction of coronaviral infections. Furthermore, our structural studies together with ligand modelling revealed the structural basis for poly(ADP-ribose) binding and hydrolysis, an emerging new aspect of viral macrodomain biology. These new insights were used in an extensive evolutionary analysis aimed at evaluating the druggability of viral macrodomains not only from the Coronaviridae but also Togaviridae and Iridoviridae genera (causing diseases such as Chikungunya and infectious spleen and kidney necrosis virus disease, respectively). We found that they contain conserved features, distinct from their human counterparts, which may be exploited during drug design.
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Affiliation(s)
| | | | | | | | | | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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39
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Žaja R, Aydin G, Lippok BE, Feederle R, Lüscher B, Feijs KLH. Comparative analysis of MACROD1, MACROD2 and TARG1 expression, localisation and interactome. Sci Rep 2020; 10:8286. [PMID: 32427867 PMCID: PMC7237415 DOI: 10.1038/s41598-020-64623-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/20/2020] [Indexed: 02/06/2023] Open
Abstract
The posttranslational modification ADP-ribosylation is involved in many cellular processes, with distinct roles for poly- and mono(ADP-ribosyl)ation (PAR- and MARylation, respectively). Reversibility of intracellular MARylation was demonstrated with the discovery of MACROD1, MACROD2 and TARG1, three macrodomain-containing enzymes capable of reversing MARylation of proteins and RNA. While the three enzymes have identical activities in vitro, their roles in cells are unclear and published data are partially contradictory, possibly due to a lack of validated reagents. We developed monoclonal antibodies to study these proteins and analysed their tissue distribution and intracellular localisation. MACROD1 is most prevalent in mitochondria of skeletal muscle, MACROD2 localises to nucleo- and cytoplasm and is found so far only in neuroblastoma cells, whereas the more ubiquitously expressed TARG1 is present in nucleoplasm, nucleolus and stress granules. Loss of MACROD1 or loss of TARG1 leads to disruption of mitochondrial or nucleolar morphology, respectively, hinting at their importance for these organelles. To start elucidating the underlying mechanisms, we have mapped their interactomes using BioID. The cellular localisation of interactors supports the mitochondrial, nucleolar and stress granule localisation of MACROD1 and TARG1, respectively. Gene ontology analysis suggests an involvement of MACROD1 and TARG1 in RNA metabolism in their respective compartments. The detailed description of the hydrolases’ expression, localisation and interactome presented here provides a solid basis for future work addressing their physiological function in more detail.
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Affiliation(s)
- R Žaja
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany.
| | - G Aydin
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany
| | - B E Lippok
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany
| | - R Feederle
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - B Lüscher
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany
| | - K L H Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany.
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40
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Classical and Deep Learning Paradigms for Detection and Validation of Key Genes of Risky Outcomes of HCV. ALGORITHMS 2020. [DOI: 10.3390/a13030073] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hepatitis C virus (HCV) is one of the most dangerous viruses worldwide. It is the foremost cause of the hepatic cirrhosis, and hepatocellular carcinoma, HCC. Detecting new key genes that play a role in the growth of HCC in HCV patients using machine learning techniques paves the way for producing accurate antivirals. In this work, there are two phases: detecting the up/downregulated genes using classical univariate and multivariate feature selection methods, and validating the retrieved list of genes using Insilico classifiers. However, the classification algorithms in the medical domain frequently suffer from a deficiency of training cases. Therefore, a deep neural network approach is proposed here to validate the significance of the retrieved genes in classifying the HCV-infected samples from the disinfected ones. The validation model is based on the artificial generation of new examples from the retrieved genes’ expressions using sparse autoencoders. Subsequently, the generated genes’ expressions data are used to train conventional classifiers. Our results in the first phase yielded a better retrieval of significant genes using Principal Component Analysis (PCA), a multivariate approach. The retrieved list of genes using PCA had a higher number of HCC biomarkers compared to the ones retrieved from the univariate methods. In the second phase, the classification accuracy can reveal the relevance of the extracted key genes in classifying the HCV-infected and disinfected samples.
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41
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Sutcu HH, Matta E, Ishchenko AA. Role of PARP-catalyzed ADP-ribosylation in the Crosstalk Between DNA Strand Breaks and Epigenetic Regulation. J Mol Biol 2019:S0022-2836(19)30719-3. [PMID: 31866292 DOI: 10.1016/j.jmb.2019.12.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/29/2019] [Accepted: 12/05/2019] [Indexed: 12/12/2022]
Abstract
Covalent linkage of ADP-ribose units to proteins catalyzed by poly(ADP-ribose) polymerases (PARPs) plays important signaling functions in a plethora of cellular processes including DNA damage response, chromatin organization, and gene transcription. Poly- and mono-ADP-ribosylation of target macromolecules are often responsible both for the initiation and for coordination of these processes in mammalian cells. Currently, the number of cellular targets for ADP-ribosylation is rapidly expanding, and the molecular mechanisms underlying the broad substrate specificity of PARPs present enormous interest. In this review, the roles of PARP-mediated modifications of protein and nucleic acids, the readers of ADP-ribosylated structures, and the origin and function of programmed DNA strand breaks in PARP activation, transcription regulation, and DNA demethylation are discussed.
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Affiliation(s)
- Haser H Sutcu
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, Villejuif, F-94805, France; Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France
| | - Elie Matta
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, Villejuif, F-94805, France; Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France
| | - Alexander A Ishchenko
- Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR 8200, Univ. Paris-Sud, Université Paris-Saclay, Villejuif, F-94805, France; Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France.
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42
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Li P, Zhen Y, Yu Y. Site-specific analysis of the Asp- and Glu-ADP-ribosylated proteome by quantitative mass spectrometry. Methods Enzymol 2019; 626:301-321. [PMID: 31606080 DOI: 10.1016/bs.mie.2019.06.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
ADP-ribosylation is a protein post-translational modification that is critically involved in a wide array of biological processes connected to cell stress responses. Enzymes known as poly-ADP-ribose polymerases (PARPs) catalyze the addition of the ADP-ribose units to amino acids with various side chain chemistries. In particular, the PARP family member PARP1 is responsible for the modification of a large number of proteins and is involved in initiation of the DNA damage response, although the mechanisms through which PARP1 functions are still incompletely understood. The analysis of protein ADP-ribosylation is challenging because PARylation is a low-abundance, labile and heterogeneous protein modification. Recently, we developed an integrative proteomic platform for the site-specific analysis of protein ADP-ribosylation on Asp and Glu residues. Herein, we describe the method, and demonstrate its utility in quantitative characterization of the human Asp- and Glu-ADP-ribosylated proteome.
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Affiliation(s)
- Peng Li
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Yuanli Zhen
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Yonghao Yu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, United States.
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43
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Di Girolamo M, Fabrizio G. Overview of the mammalian ADP-ribosyl-transferases clostridia toxin-like (ARTCs) family. Biochem Pharmacol 2019; 167:86-96. [PMID: 31283932 DOI: 10.1016/j.bcp.2019.07.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/03/2019] [Indexed: 01/22/2023]
Abstract
Mono-ADP-ribosylation is a reversible post-translational protein modification that modulates the function of proteins involved in different cellular processes, including signal transduction, protein transport, transcription, cell cycle regulation, DNA repair and apoptosis. In mammals, mono-ADP-ribosylation is mainly catalyzed by members of two different classes of enzymes: ARTCs and ARTDs. The human ARTC family is composed of four structurally related ecto-mono-ARTs, expressed at the cell surface or secreted into the extracellular compartment that are either active mono-ARTs (hARTC1, hARTC5) or inactive proteins (hARTC3, hARTC4). The human ARTD enzyme family consists of 17 multidomain proteins that can be divided on the basis of their catalytic activity into polymerases (ARTD1-6), mono-ART (ARTD7-17), and the inactive ARTD13. In recent years, ADP-ribosylation was intensively studied, and research was dominated by studies focusing on the role of this modification and its implication on various cellular processes. The aim of this review is to provide a general overview of the ARTC enzymes. In the following sections, we will report the mono-ADP-ribosylation reactions that are catalysed by the active ARTC enzymes, with a particular focus on hARTC1 that recently has been intensively studied with the discovery of new targets and functions.
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Affiliation(s)
- Maria Di Girolamo
- SoL&Pharma s.r.l. Biotechnology Research, Registered Office, Via Brasile 13, 66030 Mozzagrogna, CH, Italy.
| | - Gaia Fabrizio
- SoL&Pharma s.r.l. Biotechnology Research, Registered Office, Via Brasile 13, 66030 Mozzagrogna, CH, Italy
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44
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Grimaldi G, Catara G, Palazzo L, Corteggio A, Valente C, Corda D. PARPs and PAR as novel pharmacological targets for the treatment of stress granule-associated disorders. Biochem Pharmacol 2019; 167:64-75. [PMID: 31102582 DOI: 10.1016/j.bcp.2019.05.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022]
Abstract
Among the post-translational modifications, ADP-ribosylation has been for long time the least integrated in the scheme of the structural protein modifications affecting physiological functions. In spite of the original findings on bacterial-dependent ADP-ribosylation catalysed by toxins such as cholera and pertussis toxin, only with the discovery of the poly-ADP-ribosyl polymerase (PARP) family the field has finally expanded and the role of ADP-ribosylation has been recognised in both physiological and pathological processes, including cancer, infectious and neurodegenerative diseases. This is now a rapidly expanding field of investigation, centred on the role of the different PARPs and their substrates in various diseases, and on the potential of PARP inhibitors as novel pharmacological tools to be employed in relevant pathological context. In this review we analyse the role that members of the PARP family and poly-ADP-ribose (PAR; the product of PARP1 and PARP5a activity) play in the processes following the exposure of cells to different stresses. The cell response that arises following conditions such as heat, osmotic, oxidative stresses or viral infection relies on the formation of stress granules, which are transient cytoplasmic membrane-less structures, that include untranslated mRNA, specific proteins and PAR, this last one serving as the "collector" of all components (that bind to it in a non-covalent manner). The resulting phenotypes are cells in which translation, intracellular transport or pro-apoptotic pathways are reversibly inhibited, for the time the given stress holds. Interestingly, the formation of defective stress granules has been detected in diverse pathological conditions including neurological disorders and cancer. Analysing the molecular details of stress granule formation under these conditions offers a novel view on the pathogenesis of these diseases and, as a consequence, the possibility of identifying novel drug targets for their treatment.
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Affiliation(s)
- Giovanna Grimaldi
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy.
| | - Giuliana Catara
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy
| | - Luca Palazzo
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy
| | - Annunziata Corteggio
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy
| | - Carmen Valente
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy
| | - Daniela Corda
- Institute of Protein Biochemistry, National Research Council of Italy, Via Pietro Castellino 111, Naples 80131, Italy.
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45
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Palazzo L, Mikolčević P, Mikoč A, Ahel I. ADP-ribosylation signalling and human disease. Open Biol 2019; 9:190041. [PMID: 30991935 PMCID: PMC6501648 DOI: 10.1098/rsob.190041] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/22/2019] [Indexed: 02/06/2023] Open
Abstract
ADP-ribosylation (ADPr) is a reversible post-translational modification of proteins, which controls major cellular and biological processes, including DNA damage repair, cell proliferation and differentiation, metabolism, stress and immune responses. In order to maintain the cellular homeostasis, diverse ADP-ribosyl transferases and hydrolases are involved in the fine-tuning of ADPr systems. The control of ADPr network is vital, and dysregulation of enzymes involved in the regulation of ADPr signalling has been linked to a number of inherited and acquired human diseases, such as several neurological disorders and in cancer. Conversely, the therapeutic manipulation of ADPr has been shown to ameliorate several disorders in both human and animal models. These include cardiovascular, inflammatory, autoimmune and neurological disorders. Herein, we summarize the recent findings in the field of ADPr, which support the impact of this modification in human pathophysiology and highlight the curative potential of targeting ADPr for translational and molecular medicine.
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Affiliation(s)
- Luca Palazzo
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Petra Mikolčević
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Andreja Mikoč
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
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46
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Tsika AC, Melekis E, Tsatsouli SA, Papageorgiou N, Maté MJ, Canard B, Coutard B, Bentrop D, Spyroulias GA. Deciphering the Nucleotide and RNA Binding Selectivity of the Mayaro Virus Macro Domain. J Mol Biol 2019; 431:2283-2297. [PMID: 30998933 PMCID: PMC7094482 DOI: 10.1016/j.jmb.2019.04.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/01/2019] [Accepted: 04/08/2019] [Indexed: 12/25/2022]
Abstract
Mayaro virus (MAYV) is a member of Togaviridae family, which also includes Chikungunya virus as a notorious member. MAYV recently emerged in urban areas of the Americas, and this emergence emphasized the current paucity of knowledge about its replication cycle. The macro domain (MD) of MAYV belongs to the N-terminal region of its non-structural protein 3, part of the replication complex. Here, we report the first structural and dynamical characterization of a previously unexplored Alphavirus MD investigated through high-resolution NMR spectroscopy, along with data on its ligand selectivity and binding properties. The structural analysis of MAYV MD reveals a typical "macro" (ββαββαβαβα) fold for this polypeptide, while NMR-driven interaction studies provide in-depth insights into MAYV MD-ligand adducts. NMR data in concert with thermodynamics and biochemical studies provide convincing experimental evidence for preferential binding of adenosine diphosphate ribose (ADP-r) and adenine-rich RNAs to MAYV MD, thus shedding light on the structure-function relationship of a previously unexplored viral MD. The emerging differences with any other related MD are expected to enlighten distinct functions.
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Affiliation(s)
| | | | | | | | - Maria J Maté
- AFMB, UMR7257 CNRS/Aix Marseille Université, Marseille, CEDEX 9, France
| | - Bruno Canard
- AFMB, UMR7257 CNRS/Aix Marseille Université, Marseille, CEDEX 9, France
| | - Bruno Coutard
- UVE: Aix-Marseille Univ-IRD 190-Inserm 27-IHU Méditerranée Infection, Marseille, France.
| | - Detlef Bentrop
- Institute of Physiology II, Faculty of Medicine, University of Freiburg, D-79104 Freiburg, Germany
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47
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Abstract
ADP-ribosylation is a post-translational modification of proteins that has required the development of specific technical approaches for the full definition of its physiological roles and regulation. The identification of the enzymes and specific substrates of this reaction is an instrumental step toward these aims. Here we describe a method for the separation of ADP-ribosylated proteins based on the use of the ADP-ribose-binding macro domain of the thermophilic protein Af1521, coupled to mass spectrometry analysis for protein identification. This method foresees the coupling of the macro domain to resin, an affinity-based pull-down assay, coupled to a specificity step resulting from the clearing of cell lysates with a mutated macro domain unable to bind ADP-ribose. By this method both mono- and poly-ADP-ribosylated proteins have been identified.
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48
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Bütepage M, Krieg S, Eckei L, Li J, Rossetti G, Verheugd P, Lüscher B. Assessment of Intracellular Auto-Modification Levels of ARTD10 Using Mono-ADP-Ribose-Specific Macrodomains 2 and 3 of Murine Artd8. Methods Mol Biol 2019; 1813:41-63. [PMID: 30097860 DOI: 10.1007/978-1-4939-8588-3_4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mono-ADP-ribosylation is a posttranslational modification, which is catalyzed in cells by certain members of the ADP-ribosyltransferase diphtheria toxin-like family (ARTD) of ADP-ribosyltransferases (aka PARP enzymes). It involves the transfer of a single residue of ADP-ribose (ADPr) from the cofactor NAD+ onto substrate proteins. Although 12 of the 17 members of the ARTD family have been defined as mono-ARTDs in in vitro assays, relatively little is known about their exact cellular functions. A major challenge is the detection of mono-ADP-ribosylated (MARylated) proteins in cells as no antibodies are available that detect exclusively MARylated proteins. As an alternative to classical antibodies, the MAR-specific binding domains macro2 and macro3 of Artd8 can be utilized alone or in combination, to demonstrate intracellular auto-modification levels of ARTD10 in cells in both co-immunoprecipitation and co-localization experiments. Here we demonstrate that different macrodomain constructs of human ARTD8 and murine Artd8, alone or in combination, exert differences with regard to their interaction with ARTD10 in cells. Precisely, while the macrodomains of murine Artd8 interacted with ARTD10 in cells in a MARylation-dependent manner, the macrodomains of human ARTD8 interacted with ARTD10 independent of its catalytic activity. Moreover, we show that a combination of macro2 and macro3 of murine Artd8 was recruited more efficiently to ARTD10 during co-localization experiments compared to the single domains. Therefore, murine Artd8 macrodomain constructs can serve as a tool to evaluate intracellular ARTD10 auto-modification levels using the described methods, while the human ARTD8 macrodomains are less suited because of ADPr-independent binding to ARTD10. Protocols for co-immunoprecipitation and co-localization experiments are described in detail.
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Affiliation(s)
- Mareike Bütepage
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Aachen, Germany.
| | - Sarah Krieg
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Laura Eckei
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Jinyu Li
- College of Chemistry, Fuzhou University, Fuzhou, China
| | - Giulia Rossetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Jülich, Germany.,Jülich Supercomputing Centre, Jülich, Germany.,Department of Oncology, Hematology and Stem Cell Transplantation, Medical School, RWTH Aachen University, Aachen, Germany
| | - Patricia Verheugd
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Aachen, Germany.
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Qin W, Wu HJ, Cao LQ, Li HJ, He CX, Zhao D, Xing L, Li PQ, Jin X, Cao HL. Research Progress on PARP14 as a Drug Target. Front Pharmacol 2019; 10:172. [PMID: 30890936 PMCID: PMC6411704 DOI: 10.3389/fphar.2019.00172] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 02/11/2019] [Indexed: 12/13/2022] Open
Abstract
Poly-adenosine diphosphate-ribose polymerase (PARP) implements posttranslational mono- or poly-ADP-ribosylation modification of target proteins. Among the known 18 members in the enormous family of PARP enzymes, several investigations about PARP1, PARP2, and PARP5a/5b have been launched in the past few decades; more specifically, PARP14 is gradually emerging as a promising drug target. An intact PARP14 (also named ARTD8 or BAL2) is constructed by macro1, macro2, macro3, WWE, and the catalytic domain. PARP14 takes advantage of nicotinamide adenine dinucleotide (NAD+) as a metabolic substrate to conduct mono-ADP-ribosylation modification on target proteins, taking part in cellular responses and signaling pathways in the immune system. Therefore, PARP14 has been considered a fascinating target for treatment of tumors and allergic inflammation. More importantly, PARP14 could be a potential target for a chemosensitizer based on the theory of synthetic lethality and its unique role in homologous recombination DNA repair. This review first gives a brief introduction on several representative PARP members. Subsequently, current literatures are presented to reveal the molecular mechanisms of PARP14 as a novel drug target for cancers (e.g., diffuse large B-cell lymphoma, multiple myeloma, prostate cancer, and hepatocellular carcinoma) and allergic inflammatory. Finally, potential PARP inhibitor-associated adverse effects are discussed. The review could be a meaningful reference for innovative drug or chemosensitizer discovery targeting to PARP14.
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Affiliation(s)
- Wei Qin
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Hong-Jie Wu
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Lu-Qi Cao
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Hui-Jin Li
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Chun-Xia He
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Dong Zhao
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Lu Xing
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Peng-Quan Li
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Xi Jin
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
| | - Hui-Ling Cao
- Shaanxi Key Laboratory of Ischemic Cardiovascular Disease, Shaanxi Key Laboratory of Brain disorders, Institute of Basic and Translational Medicine, Xi'an Medical University, Xi'an, China
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ELTA: Enzymatic Labeling of Terminal ADP-Ribose. Mol Cell 2019; 73:845-856.e5. [PMID: 30712989 DOI: 10.1016/j.molcel.2018.12.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 10/22/2018] [Accepted: 12/21/2018] [Indexed: 12/14/2022]
Abstract
ADP-ribosylation refers to the addition of one or more ADP-ribose groups onto proteins. The attached ADP-ribose monomers or polymers, commonly known as poly(ADP-ribose) (PAR), modulate the activities of the modified substrates or their binding affinities to other proteins. However, progress in this area is hindered by a lack of tools to investigate this protein modification. Here, we describe a new method named ELTA (enzymatic labeling of terminal ADP-ribose) for labeling free or protein-conjugated ADP-ribose monomers and polymers at their 2'-OH termini using the enzyme OAS1 and dATP. When coupled with various dATP analogs (e.g., radioactive, fluorescent, affinity tags), ELTA can be used to explore PAR biology with techniques routinely used to investigate DNA or RNA function. We demonstrate that ELTA enables the biophysical measurements of protein binding to PAR of a defined length, detection of PAR length from proteins and cells, and enrichment of sub-femtomole amounts of ADP-ribosylated peptides from cell lysates.
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