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Article ; Online: The function and regulation of ADP-ribosylation in the DNA damage response.

Duma, Lena / Ahel, Ivan

2023 Volume 51, Issue 3, Page(s) 995–1008

Abstract: ADP-ribosylation is a post-translational modification involved in DNA damage response (DDR). In higher organisms it is synthesised by PARP 1-3, DNA strand break sensors. Recent advances have identified serine residues as the most common targets for ADP- ... ...

Abstract	ADP-ribosylation is a post-translational modification involved in DNA damage response (DDR). In higher organisms it is synthesised by PARP 1-3, DNA strand break sensors. Recent advances have identified serine residues as the most common targets for ADP-ribosylation during DDR. To ADP-ribosylate serine, PARPs require an accessory factor, HPF1 which completes the catalytic domain. Through ADP-ribosylation, PARPs recruit a variety of factors to the break site and control their activities. However, the timely removal of ADP-ribosylation is also key for genome stability and is mostly performed by two hydrolases: PARG and ARH3. Here, we describe the key writers, readers and erasers of ADP-ribosylation and their contribution to the mounting of the DDR. We also discuss the use of PARP inhibitors in cancer therapy and the ways to tackle PARPi treatment resistance.
MeSH term(s)	ADP-Ribosylation ; DNA Damage ; Protein Processing, Post-Translational ; Hydrolases/metabolism ; Serine/metabolism
Chemical Substances	Hydrolases (EC 3.-) ; Serine (452VLY9402)
Language	English
Publishing date	2023-05-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	184237-7
ISSN	1470-8752 ; 0300-5127
ISSN (online)	1470-8752
ISSN	0300-5127
DOI	10.1042/BST20220749
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Article ; Online: Beyond protein modification: the rise of non-canonical ADP-ribosylation.

Schuller, Marion / Ahel, Ivan

The Biochemical journal

2022 Volume 479, Issue 4, Page(s) 463–477

Abstract: ADP-ribosylation has primarily been known as post-translational modification of proteins. As signalling strategy conserved in all domains of life, it modulates substrate activity, localisation, stability or interactions, thereby regulating a variety of ... ...

Abstract	ADP-ribosylation has primarily been known as post-translational modification of proteins. As signalling strategy conserved in all domains of life, it modulates substrate activity, localisation, stability or interactions, thereby regulating a variety of cellular processes and microbial pathogenicity. Yet over the last years, there is increasing evidence of non-canonical forms of ADP-ribosylation that are catalysed by certain members of the ADP-ribosyltransferase family and go beyond traditional protein ADP-ribosylation signalling. New macromolecular targets such as nucleic acids and new ADP-ribose derivatives have been established, notably extending the repertoire of ADP-ribosylation signalling. Based on the physiological relevance known so far, non-canonical ADP-ribosylation deserves its recognition next to the traditional protein ADP-ribosylation modification and which we therefore review in the following.
MeSH term(s)	ADP Ribose Transferases/chemistry ; ADP Ribose Transferases/classification ; ADP Ribose Transferases/physiology ; ADP-Ribosylation/physiology ; Adenosine Diphosphate/metabolism ; Guanosine/metabolism ; N-Glycosyl Hydrolases/physiology ; Poly(ADP-ribose) Polymerases/metabolism ; Regulatory Sequences, Ribonucleic Acid ; Signal Transduction ; Structure-Activity Relationship ; Thymidine/metabolism ; Ubiquitin/metabolism
Chemical Substances	Regulatory Sequences, Ribonucleic Acid ; Ubiquitin ; Guanosine (12133JR80S) ; Adenosine Diphosphate (61D2G4IYVH) ; ADP Ribose Transferases (EC 2.4.2.-) ; Poly(ADP-ribose) Polymerases (EC 2.4.2.30) ; N-Glycosyl Hydrolases (EC 3.2.2.-) ; ADP-ribosylarginine hydrolase (EC 3.2.2.19) ; Thymidine (VC2W18DGKR)
Language	English
Publishing date	2022-02-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2969-5
ISSN	1470-8728 ; 0006-2936 ; 0306-3275 ; 0264-6021
ISSN (online)	1470-8728
ISSN	0006-2936 ; 0306-3275 ; 0264-6021
DOI	10.1042/BCJ20210280
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Article ; Online: A Simple Method to Study ADP-Ribosylation Reversal: From Function to Drug Discovery.

Rack, Johannes Gregor Matthias / Ahel, Ivan

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2609, Page(s) 111–132

Abstract: ADP-ribosylation is an ancient modification of proteins, nucleic acids, and other biomolecules found in all kingdoms of life as well as in certain viruses. The regulation of fundamental (patho)physiological processes by ADP-ribosylation, including the ... ...

Abstract	ADP-ribosylation is an ancient modification of proteins, nucleic acids, and other biomolecules found in all kingdoms of life as well as in certain viruses. The regulation of fundamental (patho)physiological processes by ADP-ribosylation, including the cellular stress response, inflammation, and immune response to bacterial and viral pathogens, has created a strong interest into the study of modification establishment and removal to explore novel therapeutic approaches. Beyond ADP-ribosylation in humans, direct targeting of factors that alter host ADP-ribosylation signaling (e.g., viral macrodomains) or utilize ADP-ribosylation to manipulate host cell behavior (e.g., bacterial toxins) were shown to reduce virulence and disease severity. However, the realization of these therapeutic potentials is thus far hampered by the unavailability of simple, high-throughput methods to study the modification "writers" and "erasers" and screen for novel inhibitors.Here, we describe a scalable method for the measurement of (ADP-ribosyl)hydrolase activity. The assay relies on the conversion of ADP-ribose released from a modified substrate by the (ADP-ribosyl)hydrolase under investigation into AMP by the phosphodiesterase NudT5 into bioluminescence via a commercially available detection assay. Moreover, this method can be utilized to study the role of nudix- or ENPP-type phosphodiesterases in ADP-ribosylation processing and may also be adapted to investigate the activity of (ADP-ribosyl)transferases. Overall, this method is applicable for both basic biochemical characterization and screening of large drug libraries; hence, it is highly adaptable to diverse project needs.
MeSH term(s)	Humans ; ADP-Ribosylation ; Adenosine Diphosphate Ribose/chemistry ; Proteins/chemistry ; Phosphoric Diester Hydrolases/metabolism ; Hydrolases/metabolism ; Drug Discovery
Chemical Substances	Adenosine Diphosphate Ribose (20762-30-5) ; Proteins ; Phosphoric Diester Hydrolases (EC 3.1.4.-) ; Hydrolases (EC 3.-)
Language	English
Publishing date	2022-12-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2891-1_8
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Article ; Online: Detecting ADP-Ribosylation in RNA.

Munnur, Deeksha / Ahel, Ivan

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2298, Page(s) 231–243

Abstract: ADP-ribosylation is a widespread reversible chemical modification of macromolecular targets. Protein ADP-ribosylation has been widely studied and plays a vital role in the regulation of several biological processes. In recent years there has been ... ...

Abstract	ADP-ribosylation is a widespread reversible chemical modification of macromolecular targets. Protein ADP-ribosylation has been widely studied and plays a vital role in the regulation of several biological processes. In recent years there has been increasing interest in alternative ADP-ribosylation targets such as nucleic acids-DNA and RNA. Here we report different methods to detect ADP-ribosylation of RNA substrates.
MeSH term(s)	ADP-Ribosylation/genetics ; DNA/genetics ; Poly(ADP-ribose) Polymerases/genetics ; RNA/genetics
Chemical Substances	RNA (63231-63-0) ; DNA (9007-49-2) ; Poly(ADP-ribose) Polymerases (EC 2.4.2.30)
Language	English
Publishing date	2021-06-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1374-0_15
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Article ; Online: ADP-ribosylation from molecular mechanisms to therapeutic implications.

Suskiewicz, Marcin J / Prokhorova, Evgeniia / Rack, Johannes G M / Ahel, Ivan

Cell

2023 Volume 186, Issue 21, Page(s) 4475–4495

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 ... ...

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.
MeSH term(s)	Humans ; ADP-Ribosylation ; Proteins/metabolism ; DNA/metabolism ; RNA/metabolism ; Animals ; Signal Transduction ; Protein Processing, Post-Translational ; ADP Ribose Transferases/metabolism ; Poly (ADP-Ribose) Polymerase-1/metabolism
Chemical Substances	Proteins ; DNA (9007-49-2) ; RNA (63231-63-0) ; ADP Ribose Transferases (EC 2.4.2.-) ; Poly (ADP-Ribose) Polymerase-1 (EC 2.4.2.30)
Language	English
Publishing date	2023-10-11
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2023.08.030
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Zs.A 1167: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 58: Show issues

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Article ; Online: ADP-ribosylation of DNA and RNA.

Groslambert, Joséphine / Prokhorova, Evgeniia / Ahel, Ivan

DNA repair

2021 Volume 105, Page(s) 103144

Abstract: ADP-ribosylation is a chemical modification of macromolecules found across all domains of life and known to regulate a variety of cellular processes. Notably, it has a well-established role in the DNA damage response. While it was historically known as a ...

Abstract	ADP-ribosylation is a chemical modification of macromolecules found across all domains of life and known to regulate a variety of cellular processes. Notably, it has a well-established role in the DNA damage response. While it was historically known as a post-translational modification of proteins, recent studies have shown that nucleic acids can also serve as substrates of reversible ADP-ribosylation. More precisely, ADP-ribosylation of DNA bases, phosphorylated DNA ends and phosphorylated RNA ends have been reported. We will discuss these three types of modification in details. In a variety of bacterial species, including Mycobacterium tuberculosis, ADP-ribosylation of thymidine has emerged as the mode of action of a toxin-antitoxin system named DarTG, with the resultant products perceived as DNA damage by the cell. On the other hand, mammalian DNA damage sensors PARP1, PARP2 and PARP3 were shown to ADP-ribosylate phosphorylated ends of double-stranded DNA in vitro. Additionally, TRPT1 and several PARP enzymes, including PARP10, can add ADP-ribose to the 5'-phosphorylated end of single-stranded RNA in vitro, representing a novel RNA capping mechanism. Together, these discoveries have led to the emergence of a new and exciting research area, namely DNA and RNA ADP-ribosylation, that is likely to have far-reaching implications for the fields of DNA repair, replication and epigenetics.
MeSH term(s)	ADP-Ribosylation ; Animals ; Cell Cycle Proteins/metabolism ; DNA/metabolism ; DNA Damage ; DNA Repair ; Humans ; Phosphorylation ; Poly (ADP-Ribose) Polymerase-1/metabolism ; Poly(ADP-ribose) Polymerases/metabolism ; Proto-Oncogene Proteins/metabolism ; RNA/metabolism
Chemical Substances	Cell Cycle Proteins ; Proto-Oncogene Proteins ; RNA (63231-63-0) ; DNA (9007-49-2) ; PARP1 protein, human (EC 2.4.2.30) ; PARP10 protein, human (EC 2.4.2.30) ; PARP2 protein, human (EC 2.4.2.30) ; PARP3 protein, human (EC 2.4.2.30) ; Poly (ADP-Ribose) Polymerase-1 (EC 2.4.2.30) ; Poly(ADP-ribose) Polymerases (EC 2.4.2.30)
Language	English
Publishing date	2021-06-03
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2071608-4
ISSN	1568-7856 ; 1568-7864
ISSN (online)	1568-7856
ISSN	1568-7864
DOI	10.1016/j.dnarep.2021.103144
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Article ; Online: Serine ADP-ribosylation in DNA-damage response regulation.

Palazzo, Luca / Suskiewicz, Marcin J / Ahel, Ivan

Current opinion in genetics & development

2021 Volume 71, Page(s) 106–113

Abstract: PARP1 and PARP2 govern the DNA-damage response by catalysing the reversible post-translational modification ADP-ribosylation. During the repair of DNA lesions, PARP1 and PARP2 combine with an accessory factor HPF1, which is required for the modification ... ...

Abstract	PARP1 and PARP2 govern the DNA-damage response by catalysing the reversible post-translational modification ADP-ribosylation. During the repair of DNA lesions, PARP1 and PARP2 combine with an accessory factor HPF1, which is required for the modification of target proteins on serine residues. Although the physiological role of individual ADP-ribosylation sites is still unclear, serine ADP-ribosylation at damage sites leads to the recruitment of chromatin remodellers and repair factors to ensure efficient DNA repair. ADP-ribosylation signalling is tightly controlled by the coordinated activities of (ADP-ribosyl)glycohydrolases PARG and ARH3 that, by reversing the modification, guarantee proper kinetics of DNA repair and cell cycle re-entry. The recent advances in the structural and mechanistic understanding of ADP-ribosylation provide new insights into human physiopathology and cancer therapy.
MeSH term(s)	ADP-Ribosylation/genetics ; Carrier Proteins/chemistry ; Carrier Proteins/genetics ; Carrier Proteins/metabolism ; DNA/genetics ; DNA Damage/genetics ; Humans ; Nuclear Proteins/genetics ; Serine/genetics ; Serine/metabolism
Chemical Substances	Carrier Proteins ; HPF1 protein, human ; Nuclear Proteins ; Serine (452VLY9402) ; DNA (9007-49-2)
Language	English
Publishing date	2021-07-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1077312-5
ISSN	1879-0380 ; 0959-437X
ISSN (online)	1879-0380
ISSN	0959-437X
DOI	10.1016/j.gde.2021.07.005
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Article: The Making and Breaking of Serine-ADP-Ribosylation in the DNA Damage Response.

Schützenhofer, Kira / Rack, Johannes Gregor Matthias / Ahel, Ivan

Frontiers in cell and developmental biology

2021 Volume 9, Page(s) 745922

Abstract: ADP-ribosylation is a widespread posttranslational modification that is of particular therapeutic relevance due to its involvement in DNA repair. In response to DNA damage, PARP1 and 2 are the main enzymes that catalyze ADP-ribosylation at damage sites. ... ...

Abstract	ADP-ribosylation is a widespread posttranslational modification that is of particular therapeutic relevance due to its involvement in DNA repair. In response to DNA damage, PARP1 and 2 are the main enzymes that catalyze ADP-ribosylation at damage sites. Recently, serine was identified as the primary amino acid acceptor of the ADP-ribosyl moiety following DNA damage and appears to act as seed for chain elongation in this context. Serine-ADP-ribosylation strictly depends on HPF1, an auxiliary factor of PARP1/2, which facilitates this modification by completing the PARP1/2 active site. The signal is terminated by initial poly(ADP-ribose) chain degradation, primarily carried out by PARG, while another enzyme, (ADP-ribosyl)hydrolase 3 (ARH3), specifically cleaves the terminal seryl-ADP-ribosyl bond, thus completing the chain degradation initiated by PARG. This review summarizes recent findings in the field of serine-ADP-ribosylation, its mechanisms, possible functions and potential for therapeutic targeting through HPF1 and ARH3 inhibition.
Language	English
Publishing date	2021-11-15
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2021.745922
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Article ; Online: Legionella metaeffector MavL reverses ubiquitin ADP-ribosylation via a conserved arginine-specific macrodomain.

Zhang, Zhengrui / Fu, Jiaqi / Rack, Johannes Gregor Matthias / Li, Chuang / Voorneveld, Jim / Filippov, Dmitri V / Ahel, Ivan / Luo, Zhao-Qing / Das, Chittaranjan

Nature communications

2024 Volume 15, Issue 1, Page(s) 2452

Abstract: ADP-ribosylation is a reversible post-translational modification involved in various cellular activities. Removal of ADP-ribosylation requires (ADP-ribosyl)hydrolases, with macrodomain enzymes being a major family in this category. The pathogen ... ...

Abstract	ADP-ribosylation is a reversible post-translational modification involved in various cellular activities. Removal of ADP-ribosylation requires (ADP-ribosyl)hydrolases, with macrodomain enzymes being a major family in this category. The pathogen Legionella pneumophila mediates atypical ubiquitination of host targets using the SidE effector family in a process that involves ubiquitin ADP-ribosylation on arginine 42 as an obligatory step. Here, we show that the Legionella macrodomain effector MavL regulates this pathway by reversing the arginine ADP-ribosylation, likely to minimize potential detrimental effects caused by the modified ubiquitin. We determine the crystal structure of ADP-ribose-bound MavL, providing structural insights into recognition of the ADP-ribosyl group and catalytic mechanism of its removal. Further analyses reveal DUF4804 as a class of MavL-like macrodomain enzymes whose representative members show unique selectivity for mono-ADP-ribosylated arginine residue in synthetic substrates. We find such enzymes are also present in eukaryotes, as exemplified by two previously uncharacterized (ADP-ribosyl)hydrolases in Drosophila melanogaster. Crystal structures of several proteins in this class provide insights into arginine specificity and a shared mode of ADP-ribose interaction distinct from previously characterized macrodomains. Collectively, our study reveals a new regulatory layer of SidE-catalyzed ubiquitination and expands the current understanding of macrodomain enzymes.
MeSH term(s)	Animals ; Ubiquitin/metabolism ; Legionella/metabolism ; Drosophila melanogaster/metabolism ; ADP-Ribosylation ; Adenosine Diphosphate Ribose/metabolism ; Hydrolases/metabolism
Chemical Substances	Ubiquitin ; Adenosine Diphosphate Ribose (20762-30-5) ; Hydrolases (EC 3.-)
Language	English
Publishing date	2024-03-19
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-46649-2
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Article ; Online: Ubiquitylation of nucleic acids by DELTEX ubiquitin E3 ligase DTX3L

Zhu, Kang / Chatrin, Chatrin / Suskiewicz, Marcin / Aucagne, Vincent / Ahel, Dragana / Ahel, Ivan

bioRxiv

Abstract: Recent discoveries expanding the spectrum of ubiquitylation substrates to include non-proteinaceous molecules have broadened our understanding of this modification beyond conventional protein targets. However, the existence of additional types of ... ...

Abstract	Recent discoveries expanding the spectrum of ubiquitylation substrates to include non-proteinaceous molecules have broadened our understanding of this modification beyond conventional protein targets. However, the existence of additional types of substrates remains elusive. Here, we present evidence that nucleic acids can also be directly ubiquitylated. DTX3L, a member of the DELTEX family E3 ubiquitin ligases, ubiquitylates DNA and RNA in vitro and that this activity is not shared with another DELTEX family member DTX2. DTX3L shows preference for the 39-terminal adenosine over other nucleotides. In addition, we demonstrate that ubiquitylation of nucleic acids is reversible by DUBs such as USP2 and SARS-CoV-2 PLpro. Overall, our study provides evidence for reversible ubiquitylation of nucleic acids in vitro and discusses its potential functional implications.
Keywords	covid19
Language	English
Publishing date	2024-04-19
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2024.04.19.590267
Database	COVID19

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