1
|
Samgina TY, Vasileva ID, Zubarev RA, Lebedev AT. EThcD as a Unique Tool for the Top-Down De Novo Sequencing of Intact Natural Ranid Amphibian Peptides. Anal Chem 2024. [PMID: 38979842 DOI: 10.1021/acs.analchem.4c02109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
De novo sequencing of any novel peptide/protein is a difficult task. Full sequence coverage, isomeric amino acid residues, inter- and intramolecular S-S bonds, and numerous other post-translational modifications make the investigators employ various chemical modifications, providing a variety of specific fragmentation MSn patterns. The chemical processes are time-consuming, and their yields never reach 100%, while the subsequent purification often leads to the loss of minor components of the initial peptide mixture. Here, we present the advantages of the EThcD method that enables establishing the full sequence of natural intact peptides of ranid frogs in de novo top-down mode without any chemical modifications. The method provides complete sequence coverage, including the cyclic disulfide section, and reliable identification of isomeric leucine/isoleucine residues. The proposed approach demonstrated its efficiency in the analysis of peptidomes of ranid frogs from several populations of Rana arvalis, Rana temporaria, and Pelophylax esculentus complexes.
Collapse
Affiliation(s)
- Tatiana Yu Samgina
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China
- Department of Organic Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Irina D Vasileva
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China
- Department of Organic Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Roman A Zubarev
- Department of Medicinal Biochemistry and Biophysics, Division of Molecular Biometry, Karolinska Institutet, Stockholm 17177, Sweden
- Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., Moscow 117198, Russia
| | - Albert T Lebedev
- Department of Materials Science, MSU-BIT University, Shenzhen 517182, China
- Department of Organic Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Lin T, Zhang S, Tang Y, Xiao M, Li M, Gong H, Xie H, Wang Y. ART1 knockdown decreases the IL-6-induced proliferation of colorectal cancer cells. BMC Cancer 2024; 24:354. [PMID: 38504172 PMCID: PMC10953198 DOI: 10.1186/s12885-024-12120-0] [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: 11/23/2023] [Accepted: 03/13/2024] [Indexed: 03/21/2024] Open
Abstract
Colorectal cancer (CRC) is a worldwide health concern. Chronic inflammation is a risk factor for CRC, and interleukin-6 (IL-6) plays a pivotal role in this process. Arginine-specific mono-ADP-ribosyltransferase-1 (ART1) positively regulates inflammatory cytokines. ART1 knockdown reduces the level of glycoprotein 130 (gp130), a key transducer in the IL-6 signalling pathway. However, the relationship between ART1 and IL-6 and the resulting effects on IL-6-induced proliferation in CRC cells remain unclear. The aims of this study were to investigate the effects of ART1 knockdown on IL-6-induced cell proliferation in vitro and use an in vivo murine model to observe the growth of transplanted tumours. The results showed that compared with the control, ART1-sh cancer cells induced by IL-6 exhibited reduced viability, a lower rate of colony formation, less DNA synthesis, decreased protein levels of gp130, c-Myc, cyclin D1, Bcl-xL, and a reduced p-STAT3/STAT3 ratio (P < 0.05). Moreover, mice transplanted with ART1-sh CT26 cells that had high levels of IL-6 displayed tumours with smaller volumes (P < 0.05). ART1 and gp130 were colocalized in CT26, LoVo and HCT116 cells, and their expression was positively correlated in human CRC tissues. Overall, ART1 may serve as a promising regulatory factor for IL-6 signalling and a potential therapeutic target for human CRC.
Collapse
Affiliation(s)
- Ting Lin
- Department of Pathology, Molecular Medicine and Cancer Research Center, Basic Medicine College, Chongqing Medical University, Chongqing, 400016, P.R. China
| | - Shuxian Zhang
- Department of Pathology, Molecular Medicine and Cancer Research Center, Basic Medicine College, Chongqing Medical University, Chongqing, 400016, P.R. China
- Molecular Medicine Diagnostic and Testing Center, Chongqing Medical University, Chongqing, 400016, P.R. China
| | - Yi Tang
- Department of Pathology, Molecular Medicine and Cancer Research Center, Basic Medicine College, Chongqing Medical University, Chongqing, 400016, P.R. China
- Department of Pathology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P.R. China
| | - Ming Xiao
- Department of Pathology, Molecular Medicine and Cancer Research Center, Basic Medicine College, Chongqing Medical University, Chongqing, 400016, P.R. China
- Molecular Medicine Diagnostic and Testing Center, Chongqing Medical University, Chongqing, 400016, P.R. China
| | - Ming Li
- Department of Pathology, Molecular Medicine and Cancer Research Center, Basic Medicine College, Chongqing Medical University, Chongqing, 400016, P.R. China
- Department of Pathology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P.R. China
| | - Hanjuan Gong
- Department of Pathology, Molecular Medicine and Cancer Research Center, Basic Medicine College, Chongqing Medical University, Chongqing, 400016, P.R. China
| | - Hailun Xie
- Department of Pathology, Molecular Medicine and Cancer Research Center, Basic Medicine College, Chongqing Medical University, Chongqing, 400016, P.R. China
| | - Yalan Wang
- Department of Pathology, Molecular Medicine and Cancer Research Center, Basic Medicine College, Chongqing Medical University, Chongqing, 400016, P.R. China.
- Molecular Medicine Diagnostic and Testing Center, Chongqing Medical University, Chongqing, 400016, P.R. China.
- Department of Pathology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P.R. China.
| |
Collapse
|
5
|
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: 4] [Impact Index Per Article: 4.0] [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.
Collapse
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
| |
Collapse
|
6
|
Liu YT, Che Y, Qiu HL, Xia HX, Feng YZ, Deng JY, Yuan Y, Tang QZ. ADP-ribosylation: An emerging direction for disease treatment. Ageing Res Rev 2024; 94:102176. [PMID: 38141734 DOI: 10.1016/j.arr.2023.102176] [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: 09/07/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023]
Abstract
ADP-ribosylation (ADPr) is a dynamically reversible post-translational modification (PTM) driven primarily by ADP-ribosyltransferases (ADPRTs or ARTs), which have ADP-ribosyl transfer activity. ADPr modification is involved in signaling pathways, DNA damage repair, metabolism, immunity, and inflammation. In recent years, several studies have revealed that new targets or treatments for tumors, cardiovascular diseases, neuromuscular diseases and infectious diseases can be explored by regulating ADPr. Here, we review the recent research progress on ART-mediated ADP-ribosylation and the latest findings in the diagnosis and treatment of related diseases.
Collapse
Affiliation(s)
- Yu-Ting Liu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, PR China; Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan 430060, PR China
| | - Yan Che
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, PR China; Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan 430060, PR China
| | - Hong-Liang Qiu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, PR China; Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan 430060, PR China
| | - Hong-Xia Xia
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, PR China; Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan 430060, PR China
| | - Yi-Zhou Feng
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, PR China; Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan 430060, PR China
| | - Jiang-Yang Deng
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, PR China; Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan 430060, PR China
| | - Yuan Yuan
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, PR China; Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan 430060, PR China
| | - Qi-Zhu Tang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, PR China; Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan 430060, PR China.
| |
Collapse
|
7
|
Ma X, Li M, Liu Y, Zhang X, Yang X, Wang Y, Li Y, Wang J, Liu X, Yan Z, Yu X, Wu C. ARTC1-mediated VAPB ADP-ribosylation regulates calcium homeostasis. J Mol Cell Biol 2024; 15:mjad043. [PMID: 37381178 PMCID: PMC10928986 DOI: 10.1093/jmcb/mjad043] [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: 07/26/2022] [Revised: 03/28/2023] [Accepted: 06/26/2023] [Indexed: 06/30/2023] Open
Abstract
Mono-ADP-ribosylation (MARylation) is a post-translational modification that regulates a variety of biological processes, including DNA damage repair, cell proliferation, metabolism, and stress and immune responses. In mammals, MARylation is mainly catalyzed by ADP-ribosyltransferases (ARTs), which consist of two groups: ART cholera toxin-like (ARTCs) and ART diphtheria toxin-like (ARTDs, also known as PARPs). The human ARTC (hARTC) family is composed of four members: two active mono-ADP-ARTs (hARTC1 and hARTC5) and two enzymatically inactive enzymes (hARTC3 and hARTC4). In this study, we systematically examined the homology, expression, and localization pattern of the hARTC family, with a particular focus on hARTC1. Our results showed that hARTC3 interacted with hARTC1 and promoted the enzymatic activity of hARTC1 by stabilizing hARTC1. We also identified vesicle-associated membrane protein-associated protein B (VAPB) as a new target of hARTC1 and pinpointed Arg50 of VAPB as the ADP-ribosylation site. Furthermore, we demonstrated that knockdown of hARTC1 impaired intracellular calcium homeostasis, highlighting the functional importance of hARTC1-mediated VAPB Arg50 ADP-ribosylation in regulating calcium homeostasis. In summary, our study identified a new target of hARTC1 in the endoplasmic reticulum and suggested that ARTC1 plays a role in regulating calcium signaling.
Collapse
Affiliation(s)
- Xueyao Ma
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Mengyuan Li
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Yi Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Xuefang Zhang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Xiaoyun Yang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Yun Wang
- Department of Public Health, Affiliated Hospital of Hebei University, Baoding 071000, China
| | - Yipeng Li
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Jiayue Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Xiuhua Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Zhenzhen Yan
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Xiaochun Yu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Chen Wu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| |
Collapse
|
8
|
Suskiewicz MJ, Prokhorova E, Rack JGM, Ahel I. ADP-ribosylation from molecular mechanisms to therapeutic implications. Cell 2023; 186:4475-4495. [PMID: 37832523 PMCID: PMC10789625 DOI: 10.1016/j.cell.2023.08.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 10/15/2023]
Abstract
ADP-ribosylation is a ubiquitous modification of biomolecules, including proteins and nucleic acids, that regulates various cellular functions in all kingdoms of life. The recent emergence of new technologies to study ADP-ribosylation has reshaped our understanding of the molecular mechanisms that govern the establishment, removal, and recognition of this modification, as well as its impact on cellular and organismal function. These advances have also revealed the intricate involvement of ADP-ribosylation in human physiology and pathology and the enormous potential that their manipulation holds for therapy. In this review, we present the state-of-the-art findings covering the work in structural biology, biochemistry, cell biology, and clinical aspects of ADP-ribosylation.
Collapse
Affiliation(s)
| | | | - Johannes G M Rack
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK; MRC Centre of Medical Mycology, University of Exeter, Exeter, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
| |
Collapse
|
9
|
Güldenpfennig A, Hopp AK, Muskalla L, Manetsch P, Raith F, Hellweg L, Dördelmann C, Leslie Pedrioli D, Johnsson K, Superti-Furga G, Hottiger M. Absence of mitochondrial SLC25A51 enhances PARP1-dependent DNA repair by increasing nuclear NAD+ levels. Nucleic Acids Res 2023; 51:9248-9265. [PMID: 37587695 PMCID: PMC10516648 DOI: 10.1093/nar/gkad659] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023] Open
Abstract
Though the effect of the recently identified mitochondrial NAD+ transporter SLC25A51 on glucose metabolism has been described, its contribution to other NAD+-dependent processes throughout the cell such as ADP-ribosylation remains elusive. Here, we report that absence of SLC25A51 leads to increased NAD+ concentration not only in the cytoplasm and but also in the nucleus. The increase is not associated with upregulation of the salvage pathway, implying an accumulation of constitutively synthesized NAD+ in the cytoplasm and nucleus. This results in an increase of PARP1-mediated nuclear ADP-ribosylation, as well as faster repair of DNA lesions induced by different single-strand DNA damaging agents. Lastly, absence of SLC25A51 reduces both MMS/Olaparib induced PARP1 chromatin retention and the sensitivity of different breast cancer cells to PARP1 inhibition. Together these results provide evidence that SLC25A51 might be a novel target to improve PARP1 inhibitor based therapies by changing subcellular NAD+ redistribution.
Collapse
Affiliation(s)
- Anka Güldenpfennig
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Ph.D. Program, University of Zurich, 8057 Zurich, Switzerland
| | - Ann-Katrin Hopp
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland
- Research Center for Molecular Medicine (CeMM) of the Austrian Academy of Science, 1090 Vienna, Austria
| | - Lukas Muskalla
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland
- Life Science Zurich Graduate School, Cancer Biology Ph.D. Program, University of Zurich, 8057 Zurich, Switzerland
| | - Patrick Manetsch
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Ph.D. Program, University of Zurich, 8057 Zurich, Switzerland
| | - Fabio Raith
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Lars Hellweg
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Cyril Dördelmann
- Life Science Zurich Graduate School, Cancer Biology Ph.D. Program, University of Zurich, 8057 Zurich, Switzerland
- Institute of Molecular Cancer Research (IMCR), University of Zurich, 8057 Zurich, Switzerland
| | - Deena M Leslie Pedrioli
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
- Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology (EPFL) Lausanne, 1015 Lausanne, Switzerland
| | - Giulio Superti-Furga
- Research Center for Molecular Medicine (CeMM) of the Austrian Academy of Science, 1090 Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland
| |
Collapse
|
10
|
Fontana P, Buch-Larsen SC, Suyari O, Smith R, Suskiewicz MJ, Schützenhofer K, Ariza A, Rack JGM, Nielsen ML, Ahel I. Serine ADP-ribosylation in Drosophila provides insights into the evolution of reversible ADP-ribosylation signalling. Nat Commun 2023; 14:3200. [PMID: 37268618 PMCID: PMC10238386 DOI: 10.1038/s41467-023-38793-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 05/16/2023] [Indexed: 06/04/2023] Open
Abstract
In the mammalian DNA damage response, ADP-ribosylation signalling is of crucial importance to mark sites of DNA damage as well as recruit and regulate repairs factors. Specifically, the PARP1:HPF1 complex recognises damaged DNA and catalyses the formation of serine-linked ADP-ribosylation marks (mono-Ser-ADPr), which are extended into ADP-ribose polymers (poly-Ser-ADPr) by PARP1 alone. Poly-Ser-ADPr is reversed by PARG, while the terminal mono-Ser-ADPr is removed by ARH3. Despite its significance and apparent evolutionary conservation, little is known about ADP-ribosylation signalling in non-mammalian Animalia. The presence of HPF1, but absence of ARH3, in some insect genomes, including Drosophila species, raises questions regarding the existence and reversal of serine-ADP-ribosylation in these species. Here we show by quantitative proteomics that Ser-ADPr is the major form of ADP-ribosylation in the DNA damage response of Drosophila melanogaster and is dependent on the dParp1:dHpf1 complex. Moreover, our structural and biochemical investigations uncover the mechanism of mono-Ser-ADPr removal by Drosophila Parg. Collectively, our data reveal PARP:HPF1-mediated Ser-ADPr as a defining feature of the DDR in Animalia. The striking conservation within this kingdom suggests that organisms that carry only a core set of ADP-ribosyl metabolising enzymes, such as Drosophila, are valuable model organisms to study the physiological role of Ser-ADPr signalling.
Collapse
Affiliation(s)
- Pietro Fontana
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Sara C Buch-Larsen
- Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Osamu Suyari
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Rebecca Smith
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Marcin J Suskiewicz
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Centre de Biophysique Moléculaire, UPR4301 CNRS, rue Charles Sadron, CEDEX 2, F-45071, Orléans, France
| | - Kira Schützenhofer
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Antonio Ariza
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
- School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| | - Johannes Gregor Matthias Rack
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
- MRC Centre for Medical Mycology, School of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter, EX4 4QD, 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.
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
| |
Collapse
|
11
|
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.
Collapse
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.
| |
Collapse
|
12
|
Jankó L, Tóth E, Laczik M, Rauch B, Janka E, Bálint BL, Bai P. PARP2 poly(ADP-ribosyl)ates nuclear factor erythroid 2-related factor 2 (NRF2) affecting NRF2 subcellular localization. Sci Rep 2023; 13:7869. [PMID: 37188809 DOI: 10.1038/s41598-023-35076-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/12/2023] [Indexed: 05/17/2023] Open
Abstract
PARP2 is a member of the PARP enzyme family. Although, PARP2 plays role in DNA repair, it has regulatory roles in mitochondrial and lipid metabolism, it has pivotal role in bringing about the adverse effects of pharmacological PARP inhibitors. Previously, we showed that the ablation of PARP2 induces oxidative stress and, consequently, mitochondrial fragmentation. In attempt to identify the source of the reactive species we assessed the possible role of a central regulator of cellular antioxidant defense, nuclear factor erythroid 2-related factor 2 (NRF2). The silencing of PARP2 did not alter either the mRNA or the protein expression of NRF2, but changed its subcellular localization, decreasing the proportion of nuclear, active fraction of NRF2. Pharmacological inhibition of PARP2 partially restored the normal localization pattern of NRF2 and in line with that, we showed that NRF2 is PARylated that is absent in the cells in which PARP2 was silenced. Apparently, the PARylation of NRF2 by PARP2 has pivotal role in regulating the subcellular (nuclear) localization of NRF2. The silencing of PARP2 rearranged the expression of genes encoding proteins with antioxidant function, among these a subset of NRF2-dependent genes.
Collapse
Affiliation(s)
- Laura Jankó
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem Tér 1., 4032, Debrecen, Hungary
- Center of Excellence, The Hungarian Academy of Sciences, Budapest, Hungary
| | - Emese Tóth
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem Tér 1., 4032, Debrecen, Hungary
- Center of Excellence, The Hungarian Academy of Sciences, Budapest, Hungary
| | - Miklós Laczik
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary
| | - Boglárka Rauch
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem Tér 1., 4032, Debrecen, Hungary
- Center of Excellence, The Hungarian Academy of Sciences, Budapest, Hungary
| | - Eszter Janka
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary
| | - Bálint L Bálint
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary
- Department of Bioinformatics, Semmelweis University, Tűzoltó Utca 7-9., Budapest, 1094, Hungary
| | - Péter Bai
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem Tér 1., 4032, Debrecen, Hungary.
- Center of Excellence, The Hungarian Academy of Sciences, Budapest, Hungary.
- MTA-DE Lendület Laboratory of Cellular Metabolism, Debrecen, 4032, Hungary.
- Research Center for Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary.
- MTA-DE Cell Biology and Signaling Research Group ELKH, Debrecen, Hungary.
| |
Collapse
|
13
|
Ishiwata-Endo H, Kato J, Oda H, Sun J, Yu ZX, Liu C, Springer DA, Dagur P, Lizak MJ, Murphy E, Moss J. Mono-ADP-ribosyltransferase 1 ( Artc1 )-deficiency decreases tumorigenesis, increases inflammation, decreases cardiac contractility, and reduces survival. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.06.527366. [PMID: 36945646 PMCID: PMC10028742 DOI: 10.1101/2023.02.06.527366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Arginine-specific mono-ADP-ribosylation is a reversible post-translational modification; arginine-specific, cholera toxin-like mono-ADP-ribosyltransferases (ARTCs) transfer ADP-ribose from NAD + to arginine, followed by cleavage of ADP-ribose-(arginine)protein bond by ADP-ribosylarginine hydrolase 1 (ARH1), generating unmodified (arginine)protein. ARTC1 has been shown to enhance tumorigenicity as does Arh1 deficiency. In this study, Artc1 -KO and Artc1/Arh1 -double-KO mice showed decreased spontaneous tumorigenesis and increased age-dependent, multi-organ inflammation with upregulation of pro-inflammatory cytokine TNF- α . In a xenograft model using tumorigenic Arh1 -KO mouse embryonic fibroblasts (MEFs), tumorigenicity was decreased in Artc1 -KO and heterozygous recipient mice, with tumor infiltration by CD8 + T cells and macrophages, leading to necroptosis, suggesting that ARTC1 promotes the tumor microenvironment. Furthermore, Artc1/Arh1 -double-KO MEFs showed decreased tumorigenesis in nude mice, showing that tumor cells as well as tumor microenvironment require ARTC1. By echocardiography and MRI, Artc1 -KO and heterozygous mice showed male-specific, reduced myocardial contractility. Furthermore, Artc1 -KO male hearts exhibited enhanced susceptibility to myocardial ischemia-reperfusion-induced injury with increased receptor-interacting protein kinase 3 (RIP3) protein levels compared to WT mice, suggesting that ARTC1 suppresses necroptosis. Overall survival rate of Artc1 -KO was less than their Artc1 -WT counterparts, primarily due to enhanced immune response and inflammation. Thus, anti-ARTC1 agents may reduce tumorigenesis but may increase multi-organ inflammation and decrease cardiac contractility.
Collapse
|
14
|
Anagho HA, Elsborg JD, Hendriks IA, Buch-Larsen SC, Nielsen ML. Characterizing ADP-Ribosylation Sites Using Af1521 Enrichment Coupled to ETD-Based Mass Spectrometry. Methods Mol Biol 2022; 2609:251-270. [PMID: 36515840 DOI: 10.1007/978-1-0716-2891-1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
ADP-ribosylation is a posttranslational modification (PTM) that has crucial functions in a wide range of cellular processes. Although mass spectrometry (MS) in recent years has emerged as a valuable tool for profiling ADP-ribosylation on a system level, the use of conventional MS methods to profile ADP-ribosylation sites in an unbiased way remains a challenge. Here, we describe a protocol for identification of ADP-ribosylated proteins in vivo on a proteome-wide level, and localization of the amino acid side chains modified with this PTM. The method relies on the enrichment of ADP-ribosylated peptides using the Af1521 macrodomain (Karras GI, Kustatscher G, Buhecha HR, Allen MD, Pugieux C, Sait F, Bycroft M, Ladurner AG, EMBO J 24:1911-1920, 2005), followed by liquid chromatography-high-resolution tandem MS (LC-MS/MS) with electron transfer dissociation-based peptide fragmentation methods, resulting in accurate localization of ADP-ribosylation sites. This protocol explains the step-by-step enrichment and identification of ADP-ribosylated peptides from cell culture to data processing using the MaxQuant software suite.
Collapse
Affiliation(s)
- Holda A Anagho
- Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonas D Elsborg
- Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sara C Buch-Larsen
- Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael L Nielsen
- Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
15
|
Lüscher B, Ahel I, Altmeyer M, Ashworth A, Bai P, Chang P, Cohen M, Corda D, Dantzer F, Daugherty MD, Dawson TM, Dawson VL, Deindl S, Fehr AR, Feijs KLH, Filippov DV, Gagné JP, Grimaldi G, Guettler S, Hoch NC, Hottiger MO, Korn P, Kraus WL, Ladurner A, Lehtiö L, Leung AKL, Lord CJ, Mangerich A, Matic I, Matthews J, Moldovan GL, Moss J, Natoli G, Nielsen ML, Niepel M, Nolte F, Pascal J, Paschal BM, Pawłowski K, Poirier GG, Smith S, Timinszky G, Wang ZQ, Yélamos J, Yu X, Zaja R, Ziegler M. ADP-ribosyltransferases, an update on function and nomenclature. FEBS J 2022; 289:7399-7410. [PMID: 34323016 PMCID: PMC9027952 DOI: 10.1111/febs.16142] [Citation(s) in RCA: 132] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 01/13/2023]
Abstract
ADP-ribosylation, a modification of proteins, nucleic acids, and metabolites, confers broad functions, including roles in stress responses elicited, for example, by DNA damage and viral infection and is involved in intra- and extracellular signaling, chromatin and transcriptional regulation, protein biosynthesis, and cell death. ADP-ribosylation is catalyzed by ADP-ribosyltransferases (ARTs), which transfer ADP-ribose from NAD+ onto substrates. The modification, which occurs as mono- or poly-ADP-ribosylation, is reversible due to the action of different ADP-ribosylhydrolases. Importantly, inhibitors of ARTs are approved or are being developed for clinical use. Moreover, ADP-ribosylhydrolases are being assessed as therapeutic targets, foremost as antiviral drugs and for oncological indications. Due to the development of novel reagents and major technological advances that allow the study of ADP-ribosylation in unprecedented detail, an increasing number of cellular processes and pathways are being identified that are regulated by ADP-ribosylation. In addition, characterization of biochemical and structural aspects of the ARTs and their catalytic activities have expanded our understanding of this protein family. This increased knowledge requires that a common nomenclature be used to describe the relevant enzymes. Therefore, in this viewpoint, we propose an updated and broadly supported nomenclature for mammalian ARTs that will facilitate future discussions when addressing the biochemistry and biology of ADP-ribosylation. This is combined with a brief description of the main functions of mammalian ARTs to illustrate the increasing diversity of mono- and poly-ADP-ribose mediated cellular processes.
Collapse
Affiliation(s)
- Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, UK
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Switzerland
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Peter Bai
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Hungary
| | | | - Michael Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, OR, USA
| | - Daniela Corda
- Department of Biomedical Sciences, National Research Council, Rome, Italy
| | | | - Matthew D Daugherty
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Anthony R Fehr
- Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA
| | - Karla L H Feijs
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
| | | | - Jean-Philippe Gagné
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | | | - Sebastian Guettler
- Divisions of Structural Biology and Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Nicolas C Hoch
- Department of Biochemistry, University of São Paulo, Brazil
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Switzerland
| | - Patricia Korn
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
| | - W Lee Kraus
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andreas Ladurner
- Department of Physiological Chemistry, Ludwig-Maximilians-University of Munich, Planegg-Martinsried, Germany
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Christopher J Lord
- CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Ivan Matic
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster for Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Germany
| | - Jason Matthews
- Institute of Basic Medical Sciences, University of Oslo, Norway
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Joel Moss
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, Italy
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | | | - Friedrich Nolte
- Institut für Immunologie, Universitätsklinikum Hamburg-Eppendorf, Germany
| | - John Pascal
- Biochemistry and Molecular Medicine, Université de Montréal, Canada
| | - Bryce M Paschal
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guy G Poirier
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec City, QC, Canada
| | - Susan Smith
- Department of Pathology, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, NY, USA
| | - Gyula Timinszky
- Lendület Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Zhao-Qi Wang
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
- Faculty of Biological Sciences, Friedrich-Schiller University of Jena, Germany
| | - José Yélamos
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Xiaochun Yu
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Roko Zaja
- Institute of Biochemistry and Molecular Biology, RWTH Aachen University, Germany
| | | |
Collapse
|
16
|
Ishiwata-Endo H, Kato J, Yamashita S, Chea C, Koike K, Lee DY, Moss J. ARH Family of ADP-Ribose-Acceptor Hydrolases. Cells 2022; 11:3853. [PMID: 36497109 PMCID: PMC9738213 DOI: 10.3390/cells11233853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/17/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022] Open
Abstract
The ARH family of ADP-ribose-acceptor hydrolases consists of three 39-kDa members (ARH1-3), with similarities in amino acid sequence. ARH1 was identified based on its ability to cleave ADP-ribosyl-arginine synthesized by cholera toxin. Mammalian ADP-ribosyltransferases (ARTCs) mimicked the toxin reaction, with ARTC1 catalyzing the synthesis of ADP-ribosyl-arginine. ADP-ribosylation of arginine was stereospecific, with β-NAD+ as substrate and, α-anomeric ADP-ribose-arginine the reaction product. ARH1 hydrolyzed α-ADP-ribose-arginine, in addition to α-NAD+ and O-acetyl-ADP-ribose. Thus, ADP-ribose attached to oxygen-containing or nitrogen-containing functional groups was a substrate. Arh1 heterozygous and knockout (KO) mice developed tumors. Arh1-KO mice showed decreased cardiac contractility and developed myocardial fibrosis. In addition to Arh1-KO mice showed increased ADP-ribosylation of tripartite motif-containing protein 72 (TRIM72), a membrane-repair protein. ARH3 cleaved ADP-ribose from ends of the poly(ADP-ribose) (PAR) chain and released the terminal ADP-ribose attached to (serine)protein. ARH3 also hydrolyzed α-NAD+ and O-acetyl-ADP-ribose. Incubation of Arh3-KO cells with H2O2 resulted in activation of poly-ADP-ribose polymerase (PARP)-1, followed by increased nuclear PAR, increased cytoplasmic PAR, leading to release of Apoptosis Inducing Factor (AIF) from mitochondria. AIF, following nuclear translocation, stimulated endonucleases, resulting in cell death by Parthanatos. Human ARH3-deficiency is autosomal recessive, rare, and characterized by neurodegeneration and early death. Arh3-KO mice developed increased brain infarction following ischemia-reperfusion injury, which was reduced by PARP inhibitors. Similarly, PARP inhibitors improved survival of Arh3-KO cells treated with H2O2. ARH2 protein did not show activity in the in vitro assays described above for ARH1 and ARH3. ARH2 has a restricted tissue distribution, with primary involvement of cardiac and skeletal muscle. Overall, the ARH family has unique functions in biological processes and different enzymatic activities.
Collapse
Affiliation(s)
- Hiroko Ishiwata-Endo
- Laboratory of Translational Research, Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiro Kato
- Laboratory of Translational Research, Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sachiko Yamashita
- Laboratory of Translational Research, Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chanbora Chea
- Laboratory of Translational Research, Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kazushige Koike
- Laboratory of Translational Research, Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Duck-Yeon Lee
- Biochemistry Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joel Moss
- Laboratory of Translational Research, Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
17
|
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.
Collapse
|
18
|
vanLieshout TL, Stouth DW, Hartel NG, Vasam G, Ng SY, Webb EK, Rebalka IA, Mikhail AI, Graham NA, Menzies KJ, Hawke TJ, Ljubicic V. The CARM1 transcriptome and arginine methylproteome mediate skeletal muscle integrative biology. Mol Metab 2022; 64:101555. [PMID: 35872306 PMCID: PMC9379683 DOI: 10.1016/j.molmet.2022.101555] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE Coactivator-associated arginine methyltransferase 1 (CARM1) catalyzes the methylation of arginine residues on target proteins to regulate critical processes in health and disease. A mechanistic understanding of the role(s) of CARM1 in skeletal muscle biology is only gradually emerging. The purpose of this study was to elucidate the function of CARM1 in regulating the maintenance and plasticity of skeletal muscle. METHODS We used transcriptomic, methylproteomic, molecular, functional, and integrative physiological approaches to determine the specific impact of CARM1 in muscle homeostasis. RESULTS Our data defines the occurrence of arginine methylation in skeletal muscle and demonstrates that this mark occurs on par with phosphorylation and ubiquitination. CARM1 skeletal muscle-specific knockout (mKO) mice displayed altered transcriptomic and arginine methylproteomic signatures with molecular and functional outcomes confirming remodeled skeletal muscle contractile and neuromuscular junction characteristics, which presaged decreased exercise tolerance. Moreover, CARM1 regulates AMPK-PGC-1α signalling during acute conditions of activity-induced muscle plasticity. CONCLUSIONS This study uncovers the broad impact of CARM1 in the maintenance and remodelling of skeletal muscle biology.
Collapse
Affiliation(s)
| | - Derek W Stouth
- Department of Kinesiology, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Nicolas G Hartel
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, 90089, USA
| | - Goutham Vasam
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
| | - Sean Y Ng
- Department of Kinesiology, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Erin K Webb
- Department of Kinesiology, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Irena A Rebalka
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Andrew I Mikhail
- Department of Kinesiology, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Nicholas A Graham
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, 90089, USA
| | - Keir J Menzies
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, K1H 8M5, Canada; Ottawa Institute of Systems Biology and the Centre for Neuromuscular Disease, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Rd, K1H 8M5, Ottawa, Canada
| | - Thomas J Hawke
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, L8S 4L8, Canada
| | - Vladimir Ljubicic
- Department of Kinesiology, McMaster University, Hamilton, ON, L8S 4L8, Canada.
| |
Collapse
|
19
|
Stocks B, Zierath JR. Post-translational Modifications: The Signals at the Intersection of Exercise, Glucose Uptake, and Insulin Sensitivity. Endocr Rev 2022; 43:654-677. [PMID: 34730177 PMCID: PMC9277643 DOI: 10.1210/endrev/bnab038] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Indexed: 11/19/2022]
Abstract
Diabetes is a global epidemic, of which type 2 diabetes makes up the majority of cases. Nonetheless, for some individuals, type 2 diabetes is eminently preventable and treatable via lifestyle interventions. Glucose uptake into skeletal muscle increases during and in recovery from exercise, with exercise effective at controlling glucose homeostasis in individuals with type 2 diabetes. Furthermore, acute and chronic exercise sensitizes skeletal muscle to insulin. A complex network of signals converge and interact to regulate glucose metabolism and insulin sensitivity in response to exercise. Numerous forms of post-translational modifications (eg, phosphorylation, ubiquitination, acetylation, ribosylation, and more) are regulated by exercise. Here we review the current state of the art of the role of post-translational modifications in transducing exercise-induced signals to modulate glucose uptake and insulin sensitivity within skeletal muscle. Furthermore, we consider emerging evidence for noncanonical signaling in the control of glucose homeostasis and the potential for regulation by exercise. While exercise is clearly an effective intervention to reduce glycemia and improve insulin sensitivity, the insulin- and exercise-sensitive signaling networks orchestrating this biology are not fully clarified. Elucidation of the complex proteome-wide interactions between post-translational modifications and the associated functional implications will identify mechanisms by which exercise regulates glucose homeostasis and insulin sensitivity. In doing so, this knowledge should illuminate novel therapeutic targets to enhance insulin sensitivity for the clinical management of type 2 diabetes.
Collapse
Affiliation(s)
- Ben Stocks
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Juleen R Zierath
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.,Departments of Molecular Medicine and Surgery and Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
20
|
Liu L, Sandow JJ, Leslie Pedrioli DM, Samson AL, Silke N, Kratina T, Ambrose RL, Doerflinger M, Hu Z, Morrish E, Chau D, Kueh AJ, Fitzibbon C, Pellegrini M, Pearson JS, Hottiger MO, Webb AI, Lalaoui N, Silke J. Tankyrase-mediated ADP-ribosylation is a regulator of TNF-induced death. SCIENCE ADVANCES 2022; 8:eabh2332. [PMID: 35544574 PMCID: PMC9094663 DOI: 10.1126/sciadv.abh2332] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Tumor necrosis factor (TNF) is a key component of the innate immune response. Upon binding to its receptor, TNFR1, it promotes production of other cytokines via a membrane-bound complex 1 or induces cell death via a cytosolic complex 2. To understand how TNF-induced cell death is regulated, we performed mass spectrometry of complex 2 and identified tankyrase-1 as a native component that, upon a death stimulus, mediates complex 2 poly-ADP-ribosylation (PARylation). PARylation promotes recruitment of the E3 ligase RNF146, resulting in proteasomal degradation of complex 2, thereby limiting cell death. Expression of the ADP-ribose-binding/hydrolyzing severe acute respiratory syndrome coronavirus 2 macrodomain sensitizes cells to TNF-induced death via abolishing complex 2 PARylation. This suggests that disruption of ADP-ribosylation during an infection can prime a cell to retaliate with an inflammatory cell death.
Collapse
Affiliation(s)
- Lin Liu
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jarrod J. Sandow
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Deena M. Leslie Pedrioli
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zürich, Switzerland
| | - Andre L. Samson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Natasha Silke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Tobias Kratina
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Rebecca L. Ambrose
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Clayton, VIC, Australia
| | - Marcel Doerflinger
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Zhaoqing Hu
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Emma Morrish
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Diep Chau
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Andrew J. Kueh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Cheree Fitzibbon
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Marc Pellegrini
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jaclyn S. Pearson
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Michael O. Hottiger
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zürich, Switzerland
| | - Andrew I. Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Najoua Lalaoui
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
- Corresponding author. (N.L.); (J.S.)
| | - John Silke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
- Corresponding author. (N.L.); (J.S.)
| |
Collapse
|
21
|
Shu Z, Wang L, Wang J, Zhang L, Hou X, Yan H, Wang L. Integrative Analysis of Nanopore and Illumina Sequencing Reveals Alternative Splicing Complexity in Pig Longissimus Dorsi Muscle. Front Genet 2022; 13:877646. [PMID: 35480309 PMCID: PMC9035893 DOI: 10.3389/fgene.2022.877646] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing (AS) is a key step in the post-transcriptional regulation of gene expression that can affect intramuscular fat (IMF). In this study, longissimus dorsi muscles from 30 pigs in high- and low- IMF groups were used to perform Oxford Nanopore Technologies (ONT) full-length sequencing and Illumina strand-specific RNA-seq. A total of 43,688 full-length transcripts were identified, with 4,322 novel genes and 30,795 novel transcripts. Using AStalavista, a total of 14,728 AS events were detected in the longissimus dorsi muscle. About 17.79% of the genes produced splicing isoforms, in which exon skipping was the most frequent AS event. By analyzing the expression differences of mRNAs and splicing isoforms, we found that differentially expressed mRNAs with splicing isoforms could participate in skeletal muscle development and fatty acid metabolism, which might determine muscle-related traits. SERBP1, MYL1, TNNT3, and TNNT1 were identified with multiple splicing isoforms, with significant differences in expression. AS events occurring in IFI6 and GADD45G may cause significant differences in gene expression. Other AS events, such as ONT.15153.3, may regulate the function of ART1 by regulating the expression of different transcripts. Moreover, co-expression and protein-protein interaction (PPI) analysis indicated that several genes (MRPL27, AAR2, PYGM, PSMD4, SCNM1, and HNRNPDL) may be related to intramuscular fat. The splicing isoforms investigated in our research provide a reference for the study of alternative splicing regulation of intramuscular fat deposition.
Collapse
|
22
|
Hesse J, Rosse MK, Steckel B, Blank-Landeshammer B, Idel S, Reinders Y, Sickmann A, Sträter N, Schrader J. Mono-ADP-ribosylation sites of human CD73 inhibit its adenosine-generating enzymatic activity. Purinergic Signal 2021; 18:115-121. [PMID: 34961895 PMCID: PMC8850506 DOI: 10.1007/s11302-021-09832-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/24/2021] [Indexed: 12/28/2022] Open
Abstract
CD73-derived adenosine plays a major role in damage-induced tissue responses by inhibiting inflammation. Damage-associated stimuli, such as hypoxia and mechanical stress, induce the cellular release of ATP and NAD+ and upregulate the expression of the nucleotide-degrading purinergic ectoenzyme cascade, including adenosine-generating CD73. Extracellular NAD+ also serves as substrate for mono-ADP-ribosylation of cell surface proteins, which in human cells is mediated by ecto-ADP-ribosyltransferase 1 (ARTC1). Here we explored, whether human CD73 enzymatic activity is regulated by mono-ADP-ribosylation, using recombinant human CD73 in the presence of ARTC1 with etheno-labelled NAD+ as substrate. Multi-colour immunoblotting with an anti-etheno-adenosine antibody showed ARTC1-mediated transfer of ADP-ribose together with the etheno label to CD73. HPLC analysis of the enzymatic activity of in vitro-ribosylated CD73 revealed strong inhibition of adenosine generation in comparison to non-ribosylated CD73. Mass spectrometry of in vitro-ribosylated CD73 identified six ribosylation sites. 3D model analysis indicated that three of them (R328, R354, R545) can interfere with CD73 enzymatic activity. Our study identifies human CD73 as target for ARTC1-mediated mono-ADP-ribosylation, which can profoundly modulate its adenosine-generating activity. Thus, in settings with enhanced release of NAD+ as substrate for ARTC1, assessment of CD73 protein expression in human tissues may not be predictive of adenosine formation resulting in anti-inflammatory activity.
Collapse
Affiliation(s)
- Julia Hesse
- Department of Molecular Cardiology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Mona K Rosse
- Department of Molecular Cardiology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Bodo Steckel
- Department of Molecular Cardiology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | | | - Svenja Idel
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - Yvonne Reinders
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Leipzig, Germany
| | - Jürgen Schrader
- Department of Molecular Cardiology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany.
| |
Collapse
|
23
|
Leutert M, Duan Y, Winzer R, Menzel S, Tolosa E, Magnus T, Hottiger MO, Koch-Nolte F, Rissiek B. Identification of the Mouse T Cell ADP-Ribosylome Uncovers ARTC2.2 Mediated Regulation of CD73 by ADP-Ribosylation. Front Immunol 2021; 12:703719. [PMID: 34504490 PMCID: PMC8421852 DOI: 10.3389/fimmu.2021.703719] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022] Open
Abstract
Mouse T cells express the ecto-ADP-ribosyltransferase ARTC2.2, which can transfer the ADP-ribose group of extracellular nicotinamide adenine dinucleotide (NAD+) to arginine residues of various cell surface proteins thereby influencing their function. Several targets of ARTC2.2, such as P2X7, CD8a and CD25 have been identified, however a comprehensive mouse T cell surface ADP-ribosylome analysis is currently missing. Using the Af1521 macrodomain-based enrichment of ADP-ribosylated peptides and mass spectrometry, we identified 93 ADP-ribsoylated peptides corresponding to 67 distinct T cell proteins, including known targets such as CD8a and CD25 but also previously unknown targets such as CD73. We evaluated the impact of ADP-ribosylation on the capability of CD73 to generate adenosine from adenosine monophosphate. Our results show that extracellular NAD+ reduces the enzymatic activity of CD73 HEK cells co-transfected with CD73/ARTC2.2. Importantly, NAD+ significantly reduced CD73 activity on WT CD8 T cells compared to ARTC2ko CD8 T cells or WT CD8 T cells treated with an ARTC2.2-blocking nanobody. Our study provides a comprehensive list of T cell membrane proteins that serve as targets for ADP-ribosylation by ARTC2.2 and whose function may be therefore affected by ADP-ribosylation.
Collapse
Affiliation(s)
- Mario Leutert
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.,Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Yinghui Duan
- Department of Neurology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Riekje Winzer
- Institute of Immunology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Stephan Menzel
- Institute of Immunology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany.,Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Eva Tolosa
- Institute of Immunology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Tim Magnus
- Department of Neurology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Friedrich Koch-Nolte
- Institute of Immunology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Björn Rissiek
- Department of Neurology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|
24
|
Tan A, Doig CL. NAD + Degrading Enzymes, Evidence for Roles During Infection. Front Mol Biosci 2021; 8:697359. [PMID: 34485381 PMCID: PMC8415550 DOI: 10.3389/fmolb.2021.697359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022] Open
Abstract
Declines in cellular nicotinamide adenine dinucleotide (NAD) contribute to metabolic dysfunction, increase susceptibility to disease, and occur as a result of pathogenic infection. The enzymatic cleavage of NAD+ transfers ADP-ribose (ADPr) to substrate proteins generating mono-ADP-ribose (MAR), poly-ADP-ribose (PAR) or O-acetyl-ADP-ribose (OAADPr). These important post-translational modifications have roles in both immune response activation and the advancement of infection. In particular, emergent data show viral infection stimulates activation of poly (ADP-ribose) polymerase (PARP) mediated NAD+ depletion and stimulates hydrolysis of existing ADP-ribosylation modifications. These studies are important for us to better understand the value of NAD+ maintenance upon the biology of infection. This review focuses specifically upon the NAD+ utilising enzymes, discusses existing knowledge surrounding their roles in infection, their NAD+ depletion capability and their influence within pathogenic infection.
Collapse
Affiliation(s)
- Arnold Tan
- Interdisciplinary Science and Technology Centre, Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
| | - Craig L Doig
- Interdisciplinary Science and Technology Centre, Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
| |
Collapse
|
25
|
PARPs in lipid metabolism and related diseases. Prog Lipid Res 2021; 84:101117. [PMID: 34450194 DOI: 10.1016/j.plipres.2021.101117] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/10/2021] [Accepted: 08/18/2021] [Indexed: 12/28/2022]
Abstract
PARPs and tankyrases (TNKS) represent a family of 17 proteins. PARPs and tankyrases were originally identified as DNA repair factors, nevertheless, recent advances have shed light on their role in lipid metabolism. To date, PARP1, PARP2, PARP3, tankyrases, PARP9, PARP10, PARP14 were reported to have multi-pronged connections to lipid metabolism. The activity of PARP enzymes is fine-tuned by a set of cholesterol-based compounds as oxidized cholesterol derivatives, steroid hormones or bile acids. In turn, PARPs modulate several key processes of lipid homeostasis (lipotoxicity, fatty acid and steroid biosynthesis, lipoprotein homeostasis, fatty acid oxidation, etc.). PARPs are also cofactors of lipid-responsive nuclear receptors and transcription factors through which PARPs regulate lipid metabolism and lipid homeostasis. PARP activation often represents a disruptive signal to (lipid) metabolism, and PARP-dependent changes to lipid metabolism have pathophysiological role in the development of hyperlipidemia, obesity, alcoholic and non-alcoholic fatty liver disease, type II diabetes and its complications, atherosclerosis, cardiovascular aging and skin pathologies, just to name a few. In this synopsis we will review the evidence supporting the beneficial effects of pharmacological PARP inhibitors in these diseases/pathologies and propose repurposing PARP inhibitors already available for the treatment of various malignancies.
Collapse
|
26
|
Investigation of Mitochondrial ADP-Ribosylation Via Immunofluorescence. Methods Mol Biol 2021; 2276:165-171. [PMID: 34060040 DOI: 10.1007/978-1-0716-1266-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
ADP-ribosylation is a posttranslational protein modification, involved in various cellular processes, ranging from DNA-damage repair to apoptosis. While its function has been studied amply with respect to genotoxic stress-associated nuclear ADP-ribosylation, the functional relevance of mitochondrial ADP-ribosylation remains so far poorly studied. This is mainly attributed to the absence of powerful techniques able to detect the modification. However, the usage of recently developed anti-ADP-ribose-specific antibodies allows now to investigate mitochondrial ADP-ribosylation under physiological and pathophysiological conditions. In the below method, we describe in detail how to efficiently detect and quantify mitochondrial ADP-ribosylation via immunofluorescence.
Collapse
|
27
|
Lüthi SC, Howald A, Nowak K, Graage R, Bartolomei G, Neupert C, Sidler X, Leslie Pedrioli D, Hottiger MO. Establishment of a Mass-Spectrometry-Based Method for the Identification of the In Vivo Whole Blood and Plasma ADP-Ribosylomes. J Proteome Res 2021; 20:3090-3101. [PMID: 34032442 DOI: 10.1021/acs.jproteome.0c00923] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Blood and plasma proteins are heavily investigated as biomarkers for different diseases. However, the post-translational modification states of these proteins are rarely analyzed since blood contains many enzymes that rapidly remove these modifications after sampling. In contrast to the well-described role of protein ADP-ribosylation in cells and organs, its role in blood remains mostly uncharacterized. Here, we discovered that plasma phosphodiesterases and/or ADP-ribosylhydrolases rapidly demodify in vitro ADP-ribosylated proteins. Thus, to identify the in vivo whole blood and plasma ADP-ribosylomes, we established a mass-spectrometry-based workflow that was applied to blood samples collected from LPS-treated pigs (Sus scrofa domesticus), which serves as a model for human systemic inflammatory response syndrome. These analyses identified 60 ADP-ribosylated proteins, 17 of which were ADP-ribosylated plasma proteins. This new protocol provides an important step forward for the rapidly developing field of ADP-ribosylation and defines the blood and plasma ADP-ribosylomes under both healthy and disease conditions.
Collapse
Affiliation(s)
- Stephanie C Lüthi
- Department of Molecular Mechanisms of Disease, Vetsuisse Faculty and Faculty of Science, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Anna Howald
- Department of Molecular Mechanisms of Disease, Vetsuisse Faculty and Faculty of Science, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Kathrin Nowak
- Department of Molecular Mechanisms of Disease, Vetsuisse Faculty and Faculty of Science, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Robert Graage
- Department of Farm Animals, Division of Swine Medicine, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, Zurich 8057, Switzerland
| | | | | | - Xaver Sidler
- Department of Farm Animals, Division of Swine Medicine, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, Zurich 8057, Switzerland
| | - Deena Leslie Pedrioli
- Department of Molecular Mechanisms of Disease, Vetsuisse Faculty and Faculty of Science, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, Vetsuisse Faculty and Faculty of Science, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| |
Collapse
|
28
|
Buch-Larsen SC, Hendriks IA, Lodge JM, Rykær M, Furtwängler B, Shishkova E, Westphall MS, Coon JJ, Nielsen ML. Mapping Physiological ADP-Ribosylation Using Activated Ion Electron Transfer Dissociation. Cell Rep 2021; 32:108176. [PMID: 32966781 PMCID: PMC7508052 DOI: 10.1016/j.celrep.2020.108176] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/25/2020] [Accepted: 08/31/2020] [Indexed: 11/26/2022] Open
Abstract
ADP-ribosylation (ADPr) is a post-translational modification that plays pivotal roles in a wide range of cellular processes. Mass spectrometry (MS)-based analysis of ADPr under physiological conditions, without relying on genetic or chemical perturbation, has been hindered by technical limitations. Here, we describe the applicability of activated ion electron transfer dissociation (AI-ETD) for MS-based proteomics analysis of physiological ADPr using our unbiased Af1521 enrichment strategy. To benchmark AI-ETD, we profile 9,000 ADPr peptides mapping to >5,000 unique ADPr sites from a limited number of cells exposed to oxidative stress and identify 120% and 28% more ADPr peptides compared to contemporary strategies using ETD and electron-transfer higher-energy collisional dissociation (EThcD), respectively. Under physiological conditions, AI-ETD identifies 450 ADPr sites on low-abundant proteins, including in vivo cysteine modifications on poly(ADP-ribosyl)polymerase (PARP) 8 and tyrosine modifications on PARP14, hinting at specialist enzymatic functions for these enzymes. Collectively, our data provide insights into the physiological regulation of ADPr.
Collapse
Affiliation(s)
- Sara C Buch-Larsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jean M Lodge
- University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Martin Rykær
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Benjamin Furtwängler
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | | | | | - Joshua J Coon
- University of Wisconsin-Madison, Madison, WI 53706, USA
| | - 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.
| |
Collapse
|
29
|
Gasparrini M, Sorci L, Raffaelli N. Enzymology of extracellular NAD metabolism. Cell Mol Life Sci 2021; 78:3317-3331. [PMID: 33755743 PMCID: PMC8038981 DOI: 10.1007/s00018-020-03742-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/09/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023]
Abstract
Extracellular NAD represents a key signaling molecule in different physiological and pathological conditions. It exerts such function both directly, through the activation of specific purinergic receptors, or indirectly, serving as substrate of ectoenzymes, such as CD73, nucleotide pyrophosphatase/phosphodiesterase 1, CD38 and its paralog CD157, and ecto ADP ribosyltransferases. By hydrolyzing NAD, these enzymes dictate extracellular NAD availability, thus regulating its direct signaling role. In addition, they can generate from NAD smaller signaling molecules, like the immunomodulator adenosine, or they can use NAD to ADP-ribosylate various extracellular proteins and membrane receptors, with significant impact on the control of immunity, inflammatory response, tumorigenesis, and other diseases. Besides, they release from NAD several pyridine metabolites that can be taken up by the cell for the intracellular regeneration of NAD itself. The extracellular environment also hosts nicotinamide phosphoribosyltransferase and nicotinic acid phosphoribosyltransferase, which inside the cell catalyze key reactions in NAD salvaging pathways. The extracellular forms of these enzymes behave as cytokines, with pro-inflammatory functions. This review summarizes the current knowledge on the extracellular NAD metabolome and describes the major biochemical properties of the enzymes involved in extracellular NAD metabolism, focusing on the contribution of their catalytic activities to the biological function. By uncovering the controversies and gaps in their characterization, further research directions are suggested, also to better exploit the great potential of these enzymes as therapeutic targets in various human diseases.
Collapse
Affiliation(s)
- Massimiliano Gasparrini
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Leonardo Sorci
- Division of Bioinformatics and Biochemistry, Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Nadia Raffaelli
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| |
Collapse
|
30
|
Hopp AK, Hottiger MO. Uncovering the Invisible: Mono-ADP-ribosylation Moved into the Spotlight. Cells 2021; 10:680. [PMID: 33808662 PMCID: PMC8003356 DOI: 10.3390/cells10030680] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Adenosine diphosphate (ADP)-ribosylation is a nicotinamide adenine dinucleotide (NAD+)-dependent post-translational modification that is found on proteins as well as on nucleic acids. While ARTD1/PARP1-mediated poly-ADP-ribosylation has extensively been studied in the past 60 years, comparably little is known about the physiological function of mono-ADP-ribosylation and the enzymes involved in its turnover. Promising technological advances have enabled the development of innovative tools to detect NAD+ and NAD+/NADH (H for hydrogen) ratios as well as ADP-ribosylation. These tools have significantly enhanced our current understanding of how intracellular NAD dynamics contribute to the regulation of ADP-ribosylation as well as to how mono-ADP-ribosylation integrates into various cellular processes. Here, we discuss the recent technological advances, as well as associated new biological findings and concepts.
Collapse
Affiliation(s)
| | - Michael O. Hottiger
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland;
| |
Collapse
|
31
|
Menzel S, Koudelka T, Rissiek B, Haag F, Meyer-Schwesinger C, Tholey A, Koch-Nolte F. ADP-Ribosylation Regulates the Signaling Function of IFN-γ. Front Immunol 2021; 12:642545. [PMID: 33763084 PMCID: PMC7983947 DOI: 10.3389/fimmu.2021.642545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/10/2021] [Indexed: 01/22/2023] Open
Abstract
Murine T cells express the GPI-anchored ADP-ribosyltransferase 2.2 (ARTC2.2) on the cell surface. In response to T cell activation or extracellular NAD+ or ATP-mediated gating of the P2X7 ion channel ARTC2.2 is shed from the cell surface as a soluble enzyme. Shedding alters the target specificity of ARTC2.2 from cell surface proteins to secreted proteins. Here we demonstrate that shed ARTC2.2 potently ADP-ribosylates IFN-γ in addition to other cytokines. Using mass spectrometry, we identify arginine 128 as the target site of ADP-ribosylation. This residue has been implicated to play a key role in binding of IFN-γ to the interferon receptor 1 (IFNR1). Indeed, binding of IFN-γ to IFNR1 blocks ADP-ribosylation of IFN-γ. Moreover, ADP-ribosylation of IFN-γ inhibits the capacity of IFN-γ to induce STAT1 phosphorylation in macrophages and upregulation of the proteasomal subunit ß5i and the proteasomal activator PA28-α in podocytes. Our results show that ADP-ribosylation inhibits the signaling functions of IFN-γ and point to a new regulatory mechanism for controlling signaling by IFN-γ.
Collapse
Affiliation(s)
- Stephan Menzel
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tomas Koudelka
- Institute of Experimental Medicine, AG Systematic Proteome Research and Bioanalytics, Christian-Albrechts-Universität, Kiel, Germany
| | - Björn Rissiek
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Haag
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Catherine Meyer-Schwesinger
- Institute of Cellular and Integrative Physiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andreas Tholey
- Institute of Experimental Medicine, AG Systematic Proteome Research and Bioanalytics, Christian-Albrechts-Universität, Kiel, Germany
| | - Friedrich Koch-Nolte
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|
32
|
Hopp AK, Teloni F, Bisceglie L, Gondrand C, Raith F, Nowak K, Muskalla L, Howald A, Pedrioli PGA, Johnsson K, Altmeyer M, Pedrioli DML, Hottiger MO. Mitochondrial NAD + Controls Nuclear ARTD1-Induced ADP-Ribosylation. Mol Cell 2021; 81:340-354.e5. [PMID: 33450210 PMCID: PMC7837215 DOI: 10.1016/j.molcel.2020.12.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 10/30/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022]
Abstract
In addition to its role as an electron transporter, mitochondrial nicotinamide adenine dinucleotide (NAD+) is an important co-factor for enzymatic reactions, including ADP-ribosylation. Although mitochondria harbor the most intra-cellular NAD+, mitochondrial ADP-ribosylation remains poorly understood. Here we provide evidence for mitochondrial ADP-ribosylation, which was identified using various methodologies including immunofluorescence, western blot, and mass spectrometry. We show that mitochondrial ADP-ribosylation reversibly increases in response to respiratory chain inhibition. Conversely, H2O2-induced oxidative stress reciprocally induces nuclear and reduces mitochondrial ADP-ribosylation. Elevated mitochondrial ADP-ribosylation, in turn, dampens H2O2-triggered nuclear ADP-ribosylation and increases MMS-induced ARTD1 chromatin retention. Interestingly, co-treatment of cells with the mitochondrial uncoupler FCCP decreases PARP inhibitor efficacy. Together, our results suggest that mitochondrial ADP-ribosylation is a dynamic cellular process that impacts nuclear ADP-ribosylation and provide evidence for a NAD+-mediated mitochondrial-nuclear crosstalk.
Collapse
Affiliation(s)
- Ann-Katrin Hopp
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland; Life Science Zurich Graduate School, Molecular Life Science Ph.D. Program, University of Zurich, 8057 Zurich, Switzerland
| | - Federico Teloni
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland; Life Science Zurich Graduate School, Molecular Life Science Ph.D. Program, University of Zurich, 8057 Zurich, Switzerland
| | - Lavinia Bisceglie
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland; Life Science Zurich Graduate School, Molecular Life Science Ph.D. Program, University of Zurich, 8057 Zurich, Switzerland
| | - Corentin Gondrand
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Fabio Raith
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany; Faculty of Chemistry and Earth Sciences, University of Heidelberg, 69120 Heidelberg, Germany
| | - Kathrin Nowak
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland; Life Science Zurich Graduate School, Molecular Life Science Ph.D. Program, University of Zurich, 8057 Zurich, Switzerland
| | - Lukas Muskalla
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland; Life Science Zurich Graduate School, Cancer Biology Ph.D. Program, University of Zurich, 8057 Zurich
| | - Anna Howald
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland
| | - Patrick G A Pedrioli
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; PHRT-CPAC, ETH Zurich, 8093 Zurich, Switzerland
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland
| | - Deena M Leslie Pedrioli
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, 8057 Zurich, Switzerland.
| |
Collapse
|
33
|
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.
Collapse
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.)
| |
Collapse
|
34
|
Gehrig PM, Nowak K, Panse C, Leutert M, Grossmann J, Schlapbach R, Hottiger MO. Gas-Phase Fragmentation of ADP-Ribosylated Peptides: Arginine-Specific Side-Chain Losses and Their Implication in Database Searches. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:157-168. [PMID: 33140951 DOI: 10.1021/jasms.0c00040] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
ADP-ribosylation is a reversible post-translational modification of proteins that has been linked to many biological processes. The identification of ADP-ribosylated proteins and particularly of their acceptor amino acids remains a major challenge. The attachment sites of the modification are difficult to localize by mass spectrometry (MS) because of the labile nature of the linkage and the complex fragmentation pattern of the ADP-ribose in MS/MS experiments. In this study we performed a comprehensive analysis of higher-energy collisional dissociation (HCD) spectra acquired from ADP-ribosylated peptides which were modified on arginine, serine, glutamic acid, aspartic acid, tyrosine, or lysine residues. In addition to the fragmentation of the peptide backbone, various cleavages of the ADP-ribosylated amino acid side chains were investigated. We focused on gas-phase fragmentations that were specific either to ADP-ribosylated arginine or to ADP-ribosylated serine and other O-linked ADP-ribosylations. The O-glycosidic linkage between ADP-ribose and serine, glutamic acid, or aspartic acid was the major cleavage site, making localization of these modification sites difficult. In contrast, the bond between ADP-ribose and arginine was relatively stable. The main cleavage site was the inner bond of the guanidine group, which resulted in the formation of ADP-ribosylated carbodiimide and of ornithine in place of modified arginine. Taking peptide fragment ions resulting from this specific cleavage into account, a considerably larger number of peptides containing ADP-ribosylated arginine were identified in database searches. Furthermore, the presence of diagnostic ions and of losses of fragments from peptide ions allowed us, in most cases, to distinguish between ADP-ribosylated arginine and serine residues.
Collapse
Affiliation(s)
- Peter M Gehrig
- Functional Genomics Center Zurich, University of Zurich and ETH Zurich, 8057 Zurich, Switzerland
| | - Kathrin Nowak
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
- Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich, 8057 Zurich, Switzerland
| | - Christian Panse
- Functional Genomics Center Zurich, University of Zurich and ETH Zurich, 8057 Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Amphipole 1015, Lausanne, Switzerland
| | - Mario Leutert
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Jonas Grossmann
- Functional Genomics Center Zurich, University of Zurich and ETH Zurich, 8057 Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Amphipole 1015, Lausanne, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, University of Zurich and ETH Zurich, 8057 Zurich, Switzerland
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| |
Collapse
|
35
|
Insights into the Mechanism of Bovine Spermiogenesis Based on Comparative Transcriptomic Studies. Animals (Basel) 2021; 11:ani11010080. [PMID: 33466297 PMCID: PMC7824766 DOI: 10.3390/ani11010080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/26/2020] [Accepted: 12/30/2020] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Any irregularity in spermiogenesis reduces the quality of semen and may lead to male sterility in cattle and humans. Thus, we investigated the differential transcriptomics of spermatids from round spermatid to epididymal sperm and compared them with the transcriptomics of mice in the same period. We found differentially expressed genes (DEGs) involved in sperm head and tail formation, and epigenetic regulatory networks which regulated genetic material condensation, the deformation of the spermatid, and the expression of genes in it. According to the sterility report on the ART3 protein and its possible epigenetic function, we detected that it was localised outside the spermatocyte, in round and elongated spermatids. Interestingly, we observed that the ART3 protein on round and elongated spermatids was localised approximately to the lumen of seminiferous tubule. It was also localised on the head and tail part near the head in epididymal sperm, suggesting its important role in the deformation from round spermatids to sperm. Our findings provide new insights into the molecular mechanism underlying bovine spermiogenesis, thereby contributing to the improved reproductive potential of cattle and the development of strategies for the diagnosis and treatment of male infertility. Abstract To reduce subfertility caused by low semen quality and provide theoretical guidance for the eradication of human male infertility, we sequenced the bovine transcriptomes of round, elongated spermatids and epididymal sperms. The differential analysis was carried out with the reference of the mouse transcriptome, and the homology trends of gene expression to the mouse were also analysed. First, to explore the physiological mechanism of spermiogenesis that profoundly affects semen quality, homological trends of differential genes were compared during spermiogenesis in dairy cattle and mice. Next, Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment, protein–protein interaction network (PPI network), and bioinformatics analyses were performed to uncover the regulation network of acrosome formation during the transition from round to elongated spermatids. In addition, processes that regulate gene expression during spermiogenesis from elongated spermatid to epididymal sperm, such as ubiquitination, acetylation, deacetylation, and glycosylation, and the functional ART3 gene may play important roles during spermiogenesis. Therefore, its localisation in the seminiferous tubules and epididymal sperm were investigated using immunofluorescent analysis, and its structure and function were also predicted. Our findings provide a deeper understanding of the process of spermiogenesis, which involves acrosome formation, histone replacement, and the fine regulation of gene expression.
Collapse
|
36
|
Almada AE, Horwitz N, Price FD, Gonzalez AE, Ko M, Bolukbasi OV, Messemer KA, Chen S, Sinha M, Rubin LL, Wagers AJ. FOS licenses early events in stem cell activation driving skeletal muscle regeneration. Cell Rep 2021; 34:108656. [PMID: 33503437 PMCID: PMC9112118 DOI: 10.1016/j.celrep.2020.108656] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 10/14/2020] [Accepted: 12/23/2020] [Indexed: 12/25/2022] Open
Abstract
Muscle satellite cells (SCs) are a quiescent (non-proliferative) stem cell population in uninjured skeletal muscle. Although SCs have been investigated for nearly 60 years, the molecular drivers that transform quiescent SCs into the rapidly dividing (activated) stem/progenitor cells that mediate muscle repair after injury remain largely unknown. Here we identify a prominent FBJ osteosarcoma oncogene (Fos) mRNA and protein signature in recently activated SCs that is rapidly, heterogeneously, and transiently induced by muscle damage. We further reveal a requirement for FOS to efficiently initiate key stem cell functions, including cell cycle entry, proliferative expansion, and muscle regeneration, via induction of “pro-regenerative” target genes that stimulate cell migration, division, and differentiation. Disruption of one of these Fos/AP-1 targets, NAD(+)-consuming mono-ADP-ribosyl-transferase 1 (Art1), in SCs delays cell cycle entry and impedes progenitor cell expansion and muscle regeneration. This work uncovers an early-activated FOS/ART1/mono-ADP-ribosylation (MARylation) pathway that is essential for stem cell-regenerative responses. How adult stem cells are activated to repair tissues and organs after injury remains one of the greatest mysteries in regenerative biology. Almada et al. reveal a FOS-driven “pro-regenerative” transcriptional gene network, including the NAD(+)-dependent mono-ADP-ribosylating (MARylating) enzyme Art1, that drives effective muscle stem cell activation and muscle repair.
Collapse
Affiliation(s)
- Albert E Almada
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115, USA; Joslin Diabetes Center, Boston, MA 02215, USA.
| | - Naftali Horwitz
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115, USA; Joslin Diabetes Center, Boston, MA 02215, USA
| | - Feodor D Price
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Alfredo E Gonzalez
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115, USA
| | - Michelle Ko
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115, USA
| | - Ozge Vargel Bolukbasi
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Kathleen A Messemer
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115, USA
| | - Sonia Chen
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Manisha Sinha
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Joslin Diabetes Center, Boston, MA 02215, USA
| | - Lee L Rubin
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Amy J Wagers
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115, USA; Joslin Diabetes Center, Boston, MA 02215, USA.
| |
Collapse
|
37
|
Engineering Af1521 improves ADP-ribose binding and identification of ADP-ribosylated proteins. Nat Commun 2020; 11:5199. [PMID: 33060572 PMCID: PMC7566600 DOI: 10.1038/s41467-020-18981-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 09/23/2020] [Indexed: 11/09/2022] Open
Abstract
Protein ADP-ribosylation is a reversible post-translational modification that regulates important cellular functions. The identification of modified proteins has proven challenging and has mainly been achieved via enrichment methodologies. Random mutagenesis was used here to develop an engineered Af1521 ADP-ribose binding macro domain protein with 1000-fold increased affinity towards ADP-ribose. The crystal structure reveals that two point mutations K35E and Y145R form a salt bridge within the ADP-ribose binding domain. This forces the proximal ribose to rotate within the binding pocket and, as a consequence, improves engineered Af1521 ADPr-binding affinity. Its use in our proteomic ADP-ribosylome workflow increases the ADP-ribosylated protein identification rates and yields greater ADP-ribosylome coverage. Furthermore, generation of an engineered Af1521 Fc fusion protein confirms the improved detection of cellular ADP-ribosylation by immunoblot and immunofluorescence. Thus, this engineered isoform of Af1521 can also serve as a valuable tool for the analysis of cellular ADP-ribosylation under in vivo conditions.
Collapse
|
38
|
Liu X, Xie R, Yu LL, Chen SH, Yang X, Singh AK, Li H, Wu C, Yu X. AI26 inhibits the ADP-ribosylhydrolase ARH3 and suppresses DNA damage repair. J Biol Chem 2020; 295:13838-13849. [PMID: 32753484 DOI: 10.1074/jbc.ra120.012801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 08/01/2020] [Indexed: 01/21/2023] Open
Abstract
The ADP-ribosylhydrolase ARH3 plays a key role in DNA damage repair, digesting poly(ADP-ribose) and removing ADP-ribose from serine residues of the substrates. Specific inhibitors that selectively target ARH3 would be a useful tool to examine DNA damage repair, as well as a possible strategy for tumor suppression. However, efforts to date have not identified any suitable compounds. Here, we used in silico and biochemistry screening to search for ARH3 inhibitors. We discovered a small molecule compound named ARH3 inhibitor 26 (AI26) as, to our knowledge, the first ARH3 inhibitor. AI26 binds to the catalytic pocket of ARH3 and inhibits the enzymatic activity of ARH3 with an estimated IC50 of ∼2.41 μm in vitro Moreover, hydrolysis of DNA damage-induced ADP-ribosylation was clearly inhibited when cells were pretreated with AI26, leading to defects in DNA damage repair. In addition, tumor cells with DNA damage repair defects were hypersensitive to AI26 treatment, as well as combinations of AI26 and other DNA-damaging agents such as camptothecin and doxorubicin. Collectively, these results reveal not only a chemical probe to study ARH3-mediated DNA damage repair but also a chemotherapeutic strategy for tumor suppression.
Collapse
Affiliation(s)
- Xiuhua Liu
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
| | - Rong Xie
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
| | - Lily L Yu
- Westridge School, Pasadena, California, USA
| | - Shih-Hsun Chen
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Xiaoyun Yang
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
| | - Anup K Singh
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California, USA
| | - Hongzhi Li
- Drug Discovery and Structural Biology Core Facility, Beckman Research Institute, City of Hope, Duarte, California, USA
| | - Chen Wu
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, Hebei, China
| | - Xiaochun Yu
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
| |
Collapse
|
39
|
Nitika, Porter CM, Truman AW, Truttmann MC. Post-translational modifications of Hsp70 family proteins: Expanding the chaperone code. J Biol Chem 2020; 295:10689-10708. [PMID: 32518165 PMCID: PMC7397107 DOI: 10.1074/jbc.rev120.011666] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/08/2020] [Indexed: 02/01/2023] Open
Abstract
Cells must be able to cope with the challenge of folding newly synthesized proteins and refolding those that have become misfolded in the context of a crowded cytosol. One such coping mechanism that has appeared during evolution is the expression of well-conserved molecular chaperones, such as those that are part of the heat shock protein 70 (Hsp70) family of proteins that bind and fold a large proportion of the proteome. Although Hsp70 family chaperones have been extensively examined for the last 50 years, most studies have focused on regulation of Hsp70 activities by altered transcription, co-chaperone "helper" proteins, and ATP binding and hydrolysis. The rise of modern proteomics has uncovered a vast array of post-translational modifications (PTMs) on Hsp70 family proteins that include phosphorylation, acetylation, ubiquitination, AMPylation, and ADP-ribosylation. Similarly to the pattern of histone modifications, the histone code, this complex pattern of chaperone PTMs is now known as the "chaperone code." In this review, we discuss the history of the Hsp70 chaperone code, its currently understood regulation and functions, and thoughts on what the future of research into the chaperone code may entail.
Collapse
Affiliation(s)
- Nitika
- Department of Biological Sciences, University of North Carolina, Charlotte, North Carolina, USA
| | - Corey M Porter
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrew W Truman
- Department of Biological Sciences, University of North Carolina, Charlotte, North Carolina, USA
| | - Matthias C Truttmann
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
- Geriatrics Center, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
40
|
Wang C, Xiao J, Nowak K, Gunasekera K, Alippe Y, Speckman S, Yang T, Kress D, Abu-Amer Y, Hottiger MO, Mbalaviele G. PARP1 Hinders Histone H2B Occupancy at the NFATc1 Promoter to Restrain Osteoclast Differentiation. J Bone Miner Res 2020; 35:776-788. [PMID: 31793068 PMCID: PMC7465553 DOI: 10.1002/jbmr.3927] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/13/2019] [Accepted: 11/20/2019] [Indexed: 01/09/2023]
Abstract
Induction of nuclear factor of activated T cell cytoplasmic 1 (NFATc1) by macrophage colony-stimulating factor (M-CSF) and receptor activator of NF-κB ligand (RANKL) is essential for macrophage differentiation into osteoclasts (OCs), but the underlying mechanisms remain unclear. The ability of poly(ADP-ribose) polymerase 1 (PARP1) to poly-ADP-ribosylate NFATc1 in T cells prompted us to investigate the PARP1 and NFATc1 interaction during osteoclastogenesis. However, extensive studies failed to directly link PARP1 to NFATc1. A combination of transcriptomics and proteomics studies was then used to identify PARP1 targets under these conditions. These unbiased approaches in conjunction with site-directed mutagenesis studies revealed that PARP1 inhibited NFATc1 expression and OC formation by ADP-ribosylating histone H2B at serine 7 and decreasing the occupancy of this histone variant at the NFATc1 promoter. The anti-osteoclastogenic function of PARP1 was confirmed in vivo in several mouse models of PARP1 loss-of-function or gain-of-function, including a novel model in which PARP1 was conditionally ablated in myeloid cells. Thus, PARP1 ADP-ribosylates H2B to negatively regulate NFATc1 expression and OC differentiation. © 2019 American Society for Bone and Mineral Research.
Collapse
Affiliation(s)
- Chun Wang
- Division of Bone and Mineral Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Jianqiu Xiao
- Division of Bone and Mineral Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Kathrin Nowak
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Kapila Gunasekera
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Yael Alippe
- Division of Bone and Mineral Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Sheree Speckman
- Division of Bone and Mineral Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Tong Yang
- Division of Bone and Mineral Diseases, Washington University School of Medicine, St. Louis, MO, USA.,Department of Spine Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Dustin Kress
- Division of Bone and Mineral Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Yousef Abu-Amer
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO, USA.,Shriners Hospital for Children, St. Louis, MO, USA
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Gabriel Mbalaviele
- Division of Bone and Mineral Diseases, Washington University School of Medicine, St. Louis, MO, USA
| |
Collapse
|
41
|
Abstract
ADP-ribosylation is an intricate and versatile posttranslational modification involved in the regulation of a vast variety of cellular processes in all kingdoms of life. Its complexity derives from the varied range of different chemical linkages, including to several amino acid side chains as well as nucleic acids termini and bases, it can adopt. In this review, we provide an overview of the different families of (ADP-ribosyl)hydrolases. We discuss their molecular functions, physiological roles, and influence on human health and disease. Together, the accumulated data support the increasingly compelling view that (ADP-ribosyl)hydrolases are a vital element within ADP-ribosyl signaling pathways and they hold the potential for novel therapeutic approaches as well as a deeper understanding of ADP-ribosylation as a whole.
Collapse
Affiliation(s)
| | - Luca Palazzo
- Institute for the Experimental Endocrinology and Oncology, National Research Council of Italy, 80145 Naples, Italy
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| |
Collapse
|
42
|
ARH1 in Health and Disease. Cancers (Basel) 2020; 12:cancers12020479. [PMID: 32092898 PMCID: PMC7072381 DOI: 10.3390/cancers12020479] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/14/2020] [Accepted: 02/15/2020] [Indexed: 12/15/2022] Open
Abstract
Arginine-specific mono-adenosine diphosphate (ADP)-ribosylation is a nicotinamide adenine dinucleotide (NAD)+-dependent, reversible post-translational modification involving the transfer of an ADP-ribose from NAD+ by bacterial toxins and eukaryotic ADP-ribosyltransferases (ARTs) to arginine on an acceptor protein or peptide. ADP-ribosylarginine hydrolase 1 (ARH1) catalyzes the cleavage of the ADP-ribose-arginine bond, regenerating (arginine)protein. Arginine-specific mono-ADP-ribosylation catalyzed by bacterial toxins was first identified as a mechanism of disease pathogenesis. Cholera toxin ADP-ribosylates and activates the α subunit of Gαs, a guanine nucleotide-binding protein that stimulates adenylyl cyclase activity, increasing cyclic adenosine monophosphate (cAMP), and resulting in fluid and electrolyte loss. Arginine-specific mono-ADP-ribosylation in mammalian cells has potential roles in membrane repair, immunity, and cancer. In mammalian tissues, ARH1 is a cytosolic protein that is ubiquitously expressed. ARH1 deficiency increased tumorigenesis in a gender-specific manner. In the myocardium, in response to cellular injury, an arginine-specific mono-ADP-ribosylation cycle, involving ART1 and ARH1, regulated the level and cellular distribution of ADP-ribosylated tripartite motif-containing protein 72 (TRIM72). Confirmed substrates of ARH1 in vivo are Gαs and TRIM72, however, more than a thousand proteins, ADP-ribosylated on arginine, have been identified by proteomic analysis. This review summarizes the current understanding of the properties of ARH1, e.g., bacterial toxin action, myocardial membrane repair following injury, and tumorigenesis.
Collapse
|
43
|
Li M, Xu H, Wang J. Optimized functional and structural design of dual-target LMRAP, a bifunctional fusion protein with a 25-amino-acid antitumor peptide and GnRH Fc fragment. Acta Pharm Sin B 2020; 10:262-275. [PMID: 32082972 PMCID: PMC7016293 DOI: 10.1016/j.apsb.2019.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 09/19/2019] [Accepted: 09/19/2019] [Indexed: 12/13/2022] Open
Abstract
To develop fusion protein of a GnRH Fc fragment and the integrin targeting AP25 antitumor peptide for GnRH receptor-expressing cancer therapy. The LMRAP fusion protein was constructed. A transwell invasion assay was performed. The gene mRNA and protein levels of GnRHR-I, α5β1, and αvβ3 in different cancer cell lines were assessed. Cell proliferation was measured using a cell counting kit-8. An antagonist assay was performed on GnRH receptors. Anti-tumor activity was evaluated with a mouse xenograft tumor model. Immunohistochemistry (IHC) was applied to detect CD31 and CD34 expressions. Pharmacokinetic characteristics were determined with an indirect competition ELISA. The developed bifunctional fusion protein LMRAP not only inhibited HUVEC invasion, but also inhibited proliferation of GnRHR-I, α5β1, and αvβ3 high expression cancer cells. The IC50 for LMRAP in the GnRH receptor was 6.235 × 10−4 mol/L. LMRAP significantly inhibited human prostate cancer cell line 22RV1 proliferation in vivo and in vitro. LMRAP significantly inhibited CD31 and CD34 expressions. The elimination half-life of the fusion protein LMRAP was 33 h in rats. The fusion protein made of a GnRH Fc fragment and the integrin targeting AP25 peptide retained the bifunctional biological activity of GnRHR blocking, angiogenesis inhibition, prolonged half-life and good tolerance.
Collapse
Affiliation(s)
- Meng Li
- Shenyang Pharmaceutical University, Shenyang 110016, China
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 102629, China
| | - Hanmei Xu
- State Key Laboratory of Natural Medicines, Ministry of Education, the Engineering Research Center of Synthetic Polypeptide Drug Discovery and Evaluation of Jiangsu Province, Department of Marine Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Junzhi Wang
- Shenyang Pharmaceutical University, Shenyang 110016, China
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, Beijing 102629, China
- Corresponding author.
| |
Collapse
|
44
|
Stevens LA, Kato J, Kasamatsu A, Oda H, Lee DY, Moss J. The ARH and Macrodomain Families of α-ADP-ribose-acceptor Hydrolases Catalyze α-NAD + Hydrolysis. ACS Chem Biol 2019; 14:2576-2584. [PMID: 31599159 DOI: 10.1021/acschembio.9b00429] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
ADP-ribosyltransferases transfer ADP-ribose from β-NAD+ to acceptors; ADP-ribosylated acceptors are cleaved by ADP-ribosyl-acceptor hydrolases (ARHs) and proteins containing ADP-ribose-binding modules termed macrodomains. On the basis of the ADP-ribosyl-arginine hydrolase 1 (ARH1) stereospecific hydrolysis of α-ADP-ribosyl-arginine and the hypothesis that α-NAD+ is generated as a side product of β-NAD+/ NADH metabolism, we proposed that α-NAD+ was a substrate of ARHs and macrodomain proteins. Here, we report that ARH1, ARH3, and macrodomain proteins (i.e., MacroD1, MacroD2, C6orf130 (TARG1), Af1521, hydrolyzed α-NAD+ but not β-NAD+. ARH3 had the highest α-NADase specific activity. The ARH and macrodomain protein families, in stereospecific reactions, cleave ADP-ribose linkages to N- or O- containing functional groups; anomerization of α- to β-forms (e.g., α-ADP-ribosyl-arginine to β-ADP-ribose- (arginine) protein) may explain partial hydrolysis of ADP-ribosylated acceptors with an increase in content of ADP-ribosylated substrates. Af1521 and ARH3 crystal structures with bound ADP-ribose revealed similar ADP-ribose-binding pockets with the catalytic residues of the ARH and macrodomain protein families in the N-terminal helix and loop. Although the biological roles of the ARHs and macrodomain proteins differ, they share enzymatic and structural properties that may regulate metabolites such as α-NAD+.
Collapse
|
45
|
The Role of PARPs in Inflammation-and Metabolic-Related Diseases: Molecular Mechanisms and Beyond. Cells 2019; 8:cells8091047. [PMID: 31500199 PMCID: PMC6770262 DOI: 10.3390/cells8091047] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 08/27/2019] [Accepted: 09/03/2019] [Indexed: 12/18/2022] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation) is an essential post-translational modification catalyzed by poly(ADP-ribose) polymerase (PARP) enzymes. Poly(ADP-ribose) polymerase 1 (PARP1) is a well-characterized member of the PARP family. PARP1 plays a crucial role in multiple biological processes and PARP1 activation contributes to the development of various inflammatory and malignant disorders, including lung inflammatory disorders, cardiovascular disease, ovarian cancer, breast cancer, and diabetes. In this review, we will focus on the role and molecular mechanisms of PARPs enzymes in inflammation- and metabolic-related diseases. Specifically, we discuss the molecular mechanisms and signaling pathways that PARP1 is associated with in the regulation of pathogenesis. Recently, increasing evidence suggests that PARP inhibition is a promising strategy for intervention of some diseases. Thus, our in-depth understanding of the mechanism of how PARPs are activated and how their signaling downstream effecters can provide more potential therapeutic targets for the treatment of the related diseases in the future is crucial.
Collapse
|
46
|
Hopp AK, Grüter P, Hottiger MO. Regulation of Glucose Metabolism by NAD + and ADP-Ribosylation. Cells 2019; 8:cells8080890. [PMID: 31412683 PMCID: PMC6721828 DOI: 10.3390/cells8080890] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/09/2019] [Accepted: 08/11/2019] [Indexed: 12/28/2022] Open
Abstract
Cells constantly adapt their metabolic pathways to meet their energy needs and respond to nutrient availability. During the last two decades, it has become increasingly clear that NAD+, a coenzyme in redox reactions, also mediates several ubiquitous cell signaling processes. Protein ADP-ribosylation is a post-translational modification that uses NAD+ as a substrate and is best known as part of the genotoxic stress response. However, there is increasing evidence that NAD+-dependent ADP-ribosylation regulates other cellular processes, including metabolic pathways. In this review, we will describe the compartmentalized regulation of NAD+ biosynthesis, consumption, and regeneration with a particular focus on the role of ADP-ribosylation in the regulation of glucose metabolism in different cellular compartments.
Collapse
Affiliation(s)
- Ann-Katrin Hopp
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, CH-8057 Zurich, Switzerland
- Molecular Life Science Ph.D. Program, Life Science Zurich Graduate School, CH-8057 Zurich, Switzerland
| | - Patrick Grüter
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, CH-8057 Zurich, Switzerland
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease (DMMD), University of Zurich, CH-8057 Zurich, Switzerland.
| |
Collapse
|
47
|
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.
Collapse
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
| |
Collapse
|
48
|
Abstract
ADP-ribosylation (ADPr) is an ancient reversible modification of cellular macromolecules controlling major biological processes as diverse as DNA damage repair, transcriptional regulation, intracellular transport, immune and stress responses, cell survival and proliferation. Furthermore, enzymatic reactions of ADPr are central in the pathogenesis of many human diseases, including infectious conditions. By providing a review of ADPr signalling in bacterial systems, we highlight the relevance of this chemical modification in the pathogenesis of human diseases depending on host-pathogen interactions. The post-antibiotic era has raised the need to find alternative approaches to antibiotic administration, as major pathogens becoming resistant to antibiotics. An in-depth understanding of ADPr reactions provides the rationale for designing novel antimicrobial strategies for treatment of infectious diseases. In addition, the understanding of mechanisms of ADPr by bacterial virulence factors offers important hints to improve our knowledge on cellular processes regulated by eukaryotic homologous enzymes, which are often involved in the pathogenesis of human diseases.
Collapse
|
49
|
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.
Collapse
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
| |
Collapse
|
50
|
Hendriks IA, Larsen SC, Nielsen ML. An Advanced Strategy for Comprehensive Profiling of ADP-ribosylation Sites Using Mass Spectrometry-based Proteomics. Mol Cell Proteomics 2019; 18:1010-1026. [PMID: 30798302 DOI: 10.1074/mcp.tir119.001315] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/21/2019] [Indexed: 12/22/2022] Open
Abstract
ADP-ribosylation is a widespread post-translational modification (PTM) with crucial functions in many cellular processes. Here, we describe an in-depth ADP-ribosylome using our Af1521-based proteomics methodology for comprehensive profiling of ADP-ribosylation sites, by systematically assessing complementary proteolytic digestions and precursor fragmentation through application of electron-transfer higher-energy collisional dissociation (EThcD) and electron transfer dissociation (ETD), respectively. Although ETD spectra yielded higher identification scores, EThcD generally proved superior to ETD in identification and localization of ADP-ribosylation sites regardless of protease employed. Notwithstanding, the propensities of complementary proteases and fragmentation methods expanded the detectable repertoire of ADP-ribosylation to an unprecedented depth. This system-wide profiling of the ADP-ribosylome in HeLa cells subjected to DNA damage uncovered >11,000 unique ADP-ribosylated peptides mapping to >7,000 ADP-ribosylation sites, in total modifying over one-third of the human nuclear proteome and highlighting the vast scope of this PTM. High-resolution MS/MS spectra enabled identification of dozens of proteins concomitantly modified by ADP-ribosylation and phosphorylation, revealing a considerable degree of crosstalk on histones. ADP-ribosylation was confidently localized to various amino acid residue types, including less abundantly modified residues, with hundreds of ADP-ribosylation sites pinpointed on histidine, arginine, and tyrosine residues. Functional enrichment analysis suggested modification of these specific residue types is directed in a spatial manner, with tyrosine ADP-ribosylation linked to the ribosome, arginine ADP-ribosylation linked to the endoplasmic reticulum, and histidine ADP-ribosylation linked to the mitochondrion.
Collapse
Affiliation(s)
- Ivo A Hendriks
- Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Sara C Larsen
- Proteomics program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - 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..
| |
Collapse
|