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Article ; Online: Hydrolysis of ADP-Ribosylation by Macrodomains.

Posavec Marjanovic, Melanija / Jankevicius, Gytis / Ahel, Ivan

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

2018 Volume 1813, Page(s) 215–223

Abstract: ADP-ribosylation is the process of transferring the ADP-ribose moiety from ... ...

Abstract	ADP-ribosylation is the process of transferring the ADP-ribose moiety from NAD
MeSH term(s)	ADP Ribose Transferases/chemistry ; ADP Ribose Transferases/genetics ; ADP-Ribosylation ; Adenosine Diphosphate Ribose/chemistry ; Hydrolysis ; Models, Molecular ; Molecular Biology/methods ; NAD/chemistry ; NAD/genetics ; Protein Domains ; Protein Processing, Post-Translational ; Proteins/chemistry ; Proteins/genetics
Chemical Substances	Proteins ; NAD (0U46U6E8UK) ; Adenosine Diphosphate Ribose (20762-30-5) ; ADP Ribose Transferases (EC 2.4.2.-)
Language	English
Publishing date	2018-08-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-8588-3_14
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Article: Streptomyces coelicolor macrodomain hydrolase SCO6735 cleaves thymidine-linked ADP-ribosylation of DNA

Hloušek-Kasun, Andrea / Mikolčević, Petra / Rack, Johannes Gregor Matthias / Tromans-Coia, Callum / Schuller, Marion / Jankevicius, Gytis / Matković, Marija / Bertoša, Branimir / Ahel, Ivan / Mikoč, Andreja

Computational and Structural Biotechnology Journal. 2022, v. 20

2022

Abstract: ADP-ribosylation is an ancient, highly conserved, and reversible covalent modification critical for a variety of endogenous processes in both prokaryotes and eukaryotes. ADP-ribosylation targets proteins, nucleic acids, and small molecules (including ... ...

Abstract	ADP-ribosylation is an ancient, highly conserved, and reversible covalent modification critical for a variety of endogenous processes in both prokaryotes and eukaryotes. ADP-ribosylation targets proteins, nucleic acids, and small molecules (including antibiotics). ADP-ribosylation signalling involves enzymes that add ADP-ribose to the target molecule, the (ADP-ribosyl)transferases; and those that remove it, the (ADP-ribosyl)hydrolases. Recently, the toxin/antitoxin pair DarT/DarG composed of a DNA ADP-ribosylating toxin, DarT, and (ADP-ribosyl)hydrolase antitoxin, DarG, was described. DarT modifies thymidine in single-stranded DNA in a sequence-specific manner while DarG reverses this modification, thereby rescuing cells from DarT toxicity. We studied the DarG homologue SCO6735 which is highly conserved in all Streptomyces species and known to be associated with antibiotic production in the bacterium S. coelicolor. SCO6735 shares a high structural similarity with the bacterial DarG and human TARG1. Like DarG and TARG1, SCO6735 can also readily reverse thymidine-linked ADP-ribosylation catalysed by DarT in vitro and in cells. SCO6735 active site analysis including molecular dynamic simulations of its complex with ADP-ribosylated thymidine suggests a novel catalytic mechanism of DNA-(ADP-ribose) hydrolysis. Moreover, a comparison of SCO6735 structure with ALC1-like homologues revealed an evolutionarily conserved feature characteristic for this subclass of macrodomain hydrolases.
Keywords	Streptomyces coelicolor ; active sites ; antibiotics ; antitoxins ; bacteria ; biotechnology ; eukaryotic cells ; humans ; hydrolases ; hydrolysis ; prokaryotic cells ; single-stranded DNA ; thymidine ; toxicity ; toxins ; transferases
Language	English
Size	p. 4337-4350.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2022.08.002
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Article ; Online: DNA ADP-Ribosylation Stalls Replication and Is Reversed by RecF-Mediated Homologous Recombination and Nucleotide Excision Repair.

Lawarée, Emeline / Jankevicius, Gytis / Cooper, Charles / Ahel, Ivan / Uphoff, Stephan / Tang, Christoph M

Cell reports

2020 Volume 30, Issue 5, Page(s) 1373–1384.e4

Abstract: ADP-ribosylation of proteins is crucial for fundamental cellular processes. Despite increasing examples of DNA ADP-ribosylation, the impact of this modification on DNA metabolism and cell physiology is unknown. Here, we show that the DarTG toxin- ... ...

Abstract	ADP-ribosylation of proteins is crucial for fundamental cellular processes. Despite increasing examples of DNA ADP-ribosylation, the impact of this modification on DNA metabolism and cell physiology is unknown. Here, we show that the DarTG toxin-antitoxin system from enteropathogenic Escherichia coli (EPEC) catalyzes reversible ADP-ribosylation of single-stranded DNA (ssDNA). The DarT toxin recognizes specific sequence motifs. EPEC DarG abrogates DarT toxicity by two distinct mechanisms: removal of DNA ADP-ribose (ADPr) groups and DarT sequestration. Furthermore, we investigate how cells recognize and deal with DNA ADP-ribosylation. We demonstrate that DNA ADPr stalls replication and is perceived as DNA damage. Removal of ADPr from DNA requires the sequential activity of two DNA repair pathways, with RecF-mediated homologous recombination likely to transfer ADP-ribosylation from single- to double-stranded DNA (dsDNA) and subsequent nucleotide excision repair eliminating the lesion. Our work demonstrates that these DNA repair pathways prevent the genotoxic effects of DNA ADP-ribosylation.
MeSH term(s)	ADP-Ribosylation ; Adenosine Diphosphate Ribose/metabolism ; DNA Repair ; DNA Replication ; DNA, Bacterial/metabolism ; DNA-Binding Proteins/metabolism ; Enteropathogenic Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Homologous Recombination ; Microbial Viability ; Models, Biological ; SOS Response, Genetics
Chemical Substances	DNA, Bacterial ; DNA-Binding Proteins ; Escherichia coli Proteins ; recF protein, E coli ; Adenosine Diphosphate Ribose (20762-30-5)
Language	English
Publishing date	2020-02-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2020.01.014
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Article ; Online: The Toxin-Antitoxin System DarTG Catalyzes Reversible ADP-Ribosylation of DNA.

Jankevicius, Gytis / Ariza, Antonio / Ahel, Marijan / Ahel, Ivan

Molecular cell

2016 Volume 64, Issue 6, Page(s) 1109–1116

Abstract: The discovery and study of toxin-antitoxin (TA) systems helps us advance our understanding of the strategies prokaryotes employ to regulate cellular processes related to the general stress response, such as defense against phages, growth control, biofilm ...

Abstract	The discovery and study of toxin-antitoxin (TA) systems helps us advance our understanding of the strategies prokaryotes employ to regulate cellular processes related to the general stress response, such as defense against phages, growth control, biofilm formation, persistence, and programmed cell death. Here we identify and characterize a TA system found in various bacteria, including the global pathogen Mycobacterium tuberculosis. The toxin of the system (DarT) is a domain of unknown function (DUF) 4433, and the antitoxin (DarG) a macrodomain protein. We demonstrate that DarT is an enzyme that specifically modifies thymidines on single-stranded DNA in a sequence-specific manner by a nucleotide-type modification called ADP-ribosylation. We also show that this modification can be removed by DarG. Our results provide an example of reversible DNA ADP-ribosylation, and we anticipate potential therapeutic benefits by targeting this enzyme-enzyme TA system in bacterial pathogens such as M. tuberculosis.
MeSH term(s)	ADP Ribose Transferases/antagonists & inhibitors ; ADP Ribose Transferases/chemistry ; ADP Ribose Transferases/genetics ; ADP Ribose Transferases/metabolism ; Adenosine Diphosphate/metabolism ; Amino Acid Motifs ; Antitoxins/chemistry ; Antitoxins/genetics ; Antitoxins/metabolism ; Bacterial Toxins/antagonists & inhibitors ; Bacterial Toxins/chemistry ; Bacterial Toxins/genetics ; Bacterial Toxins/metabolism ; Binding Sites ; Cloning, Molecular ; Crystallography, X-Ray ; DNA, Single-Stranded/chemistry ; DNA, Single-Stranded/genetics ; DNA, Single-Stranded/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Gene Expression ; Models, Molecular ; Mycobacterium tuberculosis/genetics ; Mycobacterium tuberculosis/metabolism ; Mycobacterium tuberculosis/pathogenicity ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Structure, Secondary ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Substrate Specificity ; Thymidine/metabolism
Chemical Substances	Antitoxins ; Bacterial Toxins ; DNA, Single-Stranded ; Recombinant Proteins ; Adenosine Diphosphate (61D2G4IYVH) ; ADP Ribose Transferases (EC 2.4.2.-) ; Thymidine (VC2W18DGKR)
Language	English
Publishing date	2016-12-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2016.11.014
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Article: The Toxin-Antitoxin System DarTG Catalyzes Reversible ADP-Ribosylation of DNA

Jankevicius, Gytis / Antonio Ariza / Ivan Ahel / Marijan Ahel

Molecular cell. 2016 Dec. 15, v. 64, no. 6

2016

Abstract	The discovery and study of toxin-antitoxin (TA) systems helps us advance our understanding of the strategies prokaryotes employ to regulate cellular processes related to the general stress response, such as defense against phages, growth control, biofilm formation, persistence, and programmed cell death. Here we identify and characterize a TA system found in various bacteria, including the global pathogen Mycobacterium tuberculosis. The toxin of the system (DarT) is a domain of unknown function (DUF) 4433, and the antitoxin (DarG) a macrodomain protein. We demonstrate that DarT is an enzyme that specifically modifies thymidines on single-stranded DNA in a sequence-specific manner by a nucleotide-type modification called ADP-ribosylation. We also show that this modification can be removed by DarG. Our results provide an example of reversible DNA ADP-ribosylation, and we anticipate potential therapeutic benefits by targeting this enzyme-enzyme TA system in bacterial pathogens such as M. tuberculosis.
Keywords	antitoxins ; apoptosis ; bacteria ; bacteriophages ; biofilm ; Mycobacterium tuberculosis ; pathogens ; prokaryotic cells ; single-stranded DNA ; stress response
Language	English
Dates of publication	2016-1215
Size	p. 1109-1116.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2016.11.014
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Article ; Online: Structural basis of NINJ1-mediated plasma membrane rupture in cell death.

Degen, Morris / Santos, José Carlos / Pluhackova, Kristyna / Cebrero, Gonzalo / Ramos, Saray / Jankevicius, Gytis / Hartenian, Ella / Guillerm, Undina / Mari, Stefania A / Kohl, Bastian / Müller, Daniel J / Schanda, Paul / Maier, Timm / Perez, Camilo / Sieben, Christian / Broz, Petr / Hiller, Sebastian

Nature

2023 Volume 618, Issue 7967, Page(s) 1065–1071

Abstract: Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture as the defining terminal ... ...

Abstract	Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture as the defining terminal event
MeSH term(s)	Animals ; Humans ; Mice ; Cell Adhesion Molecules, Neuronal/chemistry ; Cell Adhesion Molecules, Neuronal/genetics ; Cell Adhesion Molecules, Neuronal/metabolism ; Cell Adhesion Molecules, Neuronal/ultrastructure ; Cell Membrane/metabolism ; Cell Membrane/pathology ; Cell Membrane/ultrastructure ; Cryoelectron Microscopy ; Nerve Growth Factors/chemistry ; Nerve Growth Factors/genetics ; Nerve Growth Factors/metabolism ; Nerve Growth Factors/ultrastructure ; Mutagenesis, Site-Directed ; Biopolymers/chemistry ; Biopolymers/genetics ; Biopolymers/metabolism ; Cell Death
Chemical Substances	Cell Adhesion Molecules, Neuronal ; Nerve Growth Factors ; NINJ1 protein, human ; Ninj1 protein, mouse ; Biopolymers
Language	English
Publishing date	2023-05-17
Publishing country	England
Document type	Journal Article
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-023-05991-z
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Article ; Online: Viral Macrodomains: Unique Mediators of Viral Replication and Pathogenesis.

Fehr, Anthony R / Jankevicius, Gytis / Ahel, Ivan / Perlman, Stanley

Trends in microbiology

2017 Volume 26, Issue 7, Page(s) 598–610

Abstract: Viruses from the Coronaviridae, Togaviridae, and Hepeviridae families all contain genes that encode a conserved protein domain, called a macrodomain; however, the role of this domain during infection has remained enigmatic. The recent discovery that ... ...

Abstract	Viruses from the Coronaviridae, Togaviridae, and Hepeviridae families all contain genes that encode a conserved protein domain, called a macrodomain; however, the role of this domain during infection has remained enigmatic. The recent discovery that mammalian macrodomain proteins enzymatically remove ADP-ribose, a common post-translation modification, from proteins has led to an outburst of studies describing both the enzymatic activity and function of viral macrodomains. These new studies have defined these domains as de-ADP-ribosylating enzymes, which indicates that these viruses have evolved to counteract antiviral ADP-ribosylation, likely mediated by poly-ADP-ribose polymerases (PARPs). Here, we comprehensively review this rapidly expanding field, describing the structures and enzymatic activities of viral macrodomains, and discussing their roles in viral replication and pathogenesis.
MeSH term(s)	Adenosine Diphosphate Ribose/metabolism ; Coronaviridae/genetics ; Coronaviridae/pathogenicity ; Hepevirus/genetics ; Hepevirus/pathogenicity ; Histones ; Poly(ADP-ribose) Polymerases ; Protein Domains ; Protein Processing, Post-Translational ; Togaviridae/genetics ; Togaviridae/pathogenicity ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/metabolism ; Virus Replication ; Viruses/enzymology ; Viruses/genetics ; Viruses/pathogenicity
Chemical Substances	Histones ; Viral Nonstructural Proteins ; macroH2A histone ; Adenosine Diphosphate Ribose (20762-30-5) ; Poly(ADP-ribose) Polymerases (EC 2.4.2.30)
Keywords	covid19
Language	English
Publishing date	2017-12-21
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1158963-2
ISSN	1878-4380 ; 0966-842X
ISSN (online)	1878-4380
ISSN	0966-842X
DOI	10.1016/j.tim.2017.11.011
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Article: Viral Macrodomains: Unique Mediators of Viral Replication and Pathogenesis

Fehr, Anthony R / Jankevicius, Gytis / Ahel, Ivan / Perlman, Stanley

Trends in microbiology. 2018 July, v. 26

2018

Abstract	Viruses from the Coronaviridae, Togaviridae, and Hepeviridae families all contain genes that encode a conserved protein domain, called a macrodomain; however, the role of this domain during infection has remained enigmatic. The recent discovery that mammalian macrodomain proteins enzymatically remove ADP-ribose, a common post-translation modification, from proteins has led to an outburst of studies describing both the enzymatic activity and function of viral macrodomains. These new studies have defined these domains as de-ADP-ribosylating enzymes, which indicates that these viruses have evolved to counteract antiviral ADP-ribosylation, likely mediated by poly-ADP-ribose polymerases (PARPs). Here, we comprehensively review this rapidly expanding field, describing the structures and enzymatic activities of viral macrodomains, and discussing their roles in viral replication and pathogenesis.
Keywords	Coronaviridae ; Hepeviridae ; Togaviridae ; enzyme activity ; enzymes ; genes ; mammals ; pathogenesis ; post-translational modification ; protein domains ; proteins ; translation (genetics) ; virus replication ; viruses ; covid19
Language	English
Dates of publication	2018-07
Size	p. 598-610.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1158963-2
ISSN	1878-4380 ; 0966-842X
ISSN (online)	1878-4380
ISSN	0966-842X
DOI	10.1016/j.tim.2017.11.011
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Article ; Online: Structures and Mechanisms of Enzymes Employed in the Synthesis and Degradation of PARP-Dependent Protein ADP-Ribosylation.

Barkauskaite, Eva / Jankevicius, Gytis / Ahel, Ivan

Molecular cell

2015 Volume 58, Issue 6, Page(s) 935–946

Abstract: The poly(ADP-ribose) polymerases (PARPs) are a major family of enzymes capable of modifying proteins by ADP-ribosylation. Due to the large size and diversity of this family, PARPs affect almost every aspect of cellular life and have fundamental roles in ... ...

Abstract	The poly(ADP-ribose) polymerases (PARPs) are a major family of enzymes capable of modifying proteins by ADP-ribosylation. Due to the large size and diversity of this family, PARPs affect almost every aspect of cellular life and have fundamental roles in DNA repair, transcription, heat shock and cytoplasmic stress responses, cell division, protein degradation, and much more. In the past decade, our understanding of the PARP enzymatic mechanism and activation, as well as regulation of ADP-ribosylation signals by the readers and erasers of protein ADP-ribosylation, has been significantly advanced by the emergence of new structural data, reviewed herein, which allow for better understanding of the biological roles of this widespread post-translational modification.
MeSH term(s)	Catalytic Domain ; Glycoside Hydrolases/chemistry ; Glycoside Hydrolases/metabolism ; Humans ; Models, Molecular ; Molecular Structure ; Poly Adenosine Diphosphate Ribose/chemistry ; Poly Adenosine Diphosphate Ribose/metabolism ; Poly(ADP-ribose) Polymerases/chemistry ; Poly(ADP-ribose) Polymerases/metabolism ; Protein Binding ; Protein Structure, Tertiary ; Thiolester Hydrolases/chemistry ; Thiolester Hydrolases/metabolism
Chemical Substances	Poly Adenosine Diphosphate Ribose (26656-46-2) ; Poly(ADP-ribose) Polymerases (EC 2.4.2.30) ; OARD1 protein, human (EC 3.1.2.-) ; Thiolester Hydrolases (EC 3.1.2.-) ; Glycoside Hydrolases (EC 3.2.1.-) ; poly ADP-ribose glycohydrolase (EC 3.2.1.143)
Language	English
Publishing date	2015-06-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2015.05.007
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Article: Streptomyces coelicolor

Computational and structural biotechnology journal

2022 Volume 20, Page(s) 4337–4350

Abstract	ADP-ribosylation is an ancient, highly conserved, and reversible covalent modification critical for a variety of endogenous processes in both prokaryotes and eukaryotes. ADP-ribosylation targets proteins, nucleic acids, and small molecules (including antibiotics). ADP-ribosylation signalling involves enzymes that add ADP-ribose to the target molecule, the (ADP-ribosyl)transferases; and those that remove it, the (ADP-ribosyl)hydrolases. Recently, the toxin/antitoxin pair DarT/DarG composed of a DNA ADP-ribosylating toxin, DarT, and (ADP-ribosyl)hydrolase antitoxin, DarG, was described. DarT modifies thymidine in single-stranded DNA in a sequence-specific manner while DarG reverses this modification, thereby rescuing cells from DarT toxicity. We studied the DarG homologue SCO6735 which is highly conserved in all
Language	English
Publishing date	2022-08-08
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2022.08.002
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