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ADP-ribosylation

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Klaus Aktories – One of the best experts on this subject based on the ideXlab platform.

  • Strain-alleviation model of ADP-ribosylation
    Proceedings of the National Academy of Sciences of the United States of America, 2013
    Co-Authors: Thomas Jank, Klaus Aktories
    Abstract:

    ADP-ribosylation was one of the first molecular mechanisms described to be used by bacterial protprotein toxins to target eukaryotic cells. Most potent and devastating toxins belong to this group, including diphtheria toxin and Pseudomonas exotoxins A, which block protein synthesis by ADP-ribosylation of elongation factor 2. Cholera toxin from Vibrio cholerae, which causes several thousand cases of death worldwide every year, is another ADP-ribosylating toxin, of which ADP-ribosylate Gs proteins is involved in receptor signaling (1). All of these toxins modify host proteins by transferring ADP ribose from NAD+ onto specific eukaryotic target proteins, thereby altering their physiological functions. Although ADP-ribosylating toxins share only limited sequence similarity, crystal structures available from various toxins are amazingly similar (2). However, so far the precise molecular reaction by which these toxins catalyze the ADP-ribosylation of their target proteins has remained largely enigmatic. In an exciting study published in PNAS (3), Tsurumura et al. describe several crystal structures of Clostridium perfringens iota toxin, in complex with its protein substrate actin, which are obtained during different phases of the ADP-ribosylation process. The authors’ findings are groundbreaking not only for the understanding of toxin-induced ADP-ribosylation but also for comprehension of the molecular reaction induced by an increasing number of endogenous ADP ribosyltransferases.

  • Activation of phospholipase D1 by ADP-ribosylated RhoA.
    Biochemical and Biophysical Research Communications, 2003
    Co-Authors: Harald Genth, Klaus Aktories, Martina Schmidt, Ralf Gerhard, Ingo Just
    Abstract:

    Abstract Clostridium botulinum exoenzyme C3 exclusively ADP-ribosylates RhoA, B, and C to inactivate them, resulting in disaggregation of the actin filaments in intact cells. The ADP-ribose resides at Asn-41 in the effector binding region, leading to the notion that ADP-ribosylation inactivates Rho by blocking coupling of Rho to its downstream effectors. In a recombinant system, however, ADP-ribosylated Rho bound to effector proteins such as phospholipase D-1 (PLD1), Rho-kinase (ROK), and rhotekin. The ADP-ribose rather mediated binding of Rho-GDP to PLD1. ADP-ribosylation of Rho-GDP followed by GTP-γ-S loading resulted in binding but not in PLD activation. On the other hand, ADP-ribosylation of Rho previously activated by binding to GTP-γ-S resulted in full PLD activation. This finding indicates that ADP-ribosylation seems to prevent GTP-induced change to the active conformation of switch I, the prerequisite of Rho–PLD interaction. In contrast to recombinant systems, ADP-ribosylation in intact cells results in functional inactivation of Rho, indicating other mechanisms of inactivation than blocking effector coupling.

  • Glucosylation and ADP Ribosylation of Rho Proteins: Effects on Nucleotide Binding, GTPase Activity, and Effector Coupling†
    Biochemistry, 1998
    Co-Authors: Peter Sehr, Harald Genth, Ingo Just, Gili Joseph, Edgar Pick, Klaus Aktories
    Abstract:

    We studied the effects of glucosylation of RhoA, Rac1, and Cdc42 at threonine-35 and -37 by Clostridium difficile toxin B on nucleotide binding, GTPase activity, and effector coupling and compared these results with the ADP ribosylation of RhoA at asparagine-41 catalyzed by Clostridium botulinum C3 transferase. Whereas glucosylation and ADP ribosylation had no major effects on GDP release from RhoA, Rac1, and Cdc42, the rate of GTPγS release from Rho proteins was increased 3−6-fold by glucosylation. ADP ribosylation decreased the rate of GTPγS release by about 50%. Glucosylation reduced the intrinsic activities of the GTPases by 3−7-fold and completely blocked GTPase stimulation by Rho-GAP. In contrast, ADP ribosylation slightly increased GTPase activity (∼2-fold) and had no major effect on GAP stimulation of GTPase. Whereas ADP ribosylation did not affect the interaction of RhoA with the binding domain of protein kinase N, glucosylation inhibited this interaction. Glucosylation of Rac1 markedly diminishe…

Michael O. Hottiger – One of the best experts on this subject based on the ideXlab platform.

  • Uncovering the Invisible: Mono-ADP-ribosylation Moved into the Spotlight.
    Cells, 2021
    Co-Authors: Ann-katrin Hopp, Michael O. Hottiger
    Abstract:

    Adenosine diphosphate (ADP)-ribosylation is a nicotinamide adenadenineudinucleotide (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.

  • A Study into the ADP-Ribosylome of IFN-γ-Stimulated THP‑1 Human Macrophage-like Cells Identifies ARTD8/PARP14 and ARTD9/PARP9 ADP-ribosylation
    , 2019
    Co-Authors: Hideyuki Higashi, Michael O. Hottiger, Takashi Maejima, Lang Ho Lee, Yukiyoshi Yamazaki, Sasha A. Singh, Masanori Aikawa
    Abstract:

    ADP-ribosylation is a post-translational modification that, until recently, has remained elusive to study at the cellular level. Previously dependent on radioactive tracers to identify ADP-ribosylation targets, several advances in mass spectrometric workflows now permit global identification of ADP-ribosylated substrates. In this study, we capitalized on two ADP-ribosylation enrichment strategies, and multiple activation methods performed on the Orbitrap Fusion Lumos, to identify IFN-γ-induced ADP-ribosylation substrates in macrophages. The ADP-ribosyl binding protein, Af1521, was used to enrich ADP-ribosylated peptides, and the antipoly-ADP-ribosyl antibody, 10H, was used to enrich ADP-ribosylated proteins. ADP-ribosyl-specific mass spectra were further enriched by an ADP-ribose product ion triggered EThcD and HCD activation strategy, in combination with multiple acquisitions that segmented the survey scan into smaller ranges. HCD and EThcD resulted in overlapping and unique ADP-ribosyl peptide identifications, with HCD providing more peptide identifications but EThcD providing more reliable ADP-ribosyl acceptor sites. Our acquisition strategies also resulted in the first ever characterization of ADP-ribosyl on three poly-ADP-ribose polymerases, ARTD9/PARP9, ARTD10/PARP10, and ARTD8/PARP14. IFN-γ increased the ADP-ribosylation status of ARTD9/PARP9, ARTD8/PARP14, and proteins involved in RNA processes. This study therefore summarizes specific molecular pathways at the intersection of IFN-γ and ADP-ribosylation signaling pathways

  • ADP-ribose-specific chromatin-affinity purification for investigating genome-wide or locus-specific chromatin ADP-ribosylation
    Nature Protocols, 2017
    Co-Authors: Lavinia Bisceglie, Giody Bartolomei, Michael O. Hottiger
    Abstract:

    This protocol describes how to investigate genome-wide or locus-specific chromatin ADP-ribosylation using ADPr-ChAP. Protein ADP-ribosylation is a structurally heterogeneous post-translational modification (PTM) that influences the physicochemical and biological properties of the modified protein. ADP-ribosylation of chromatin changes its structural properties, thereby regulating important nuclear functions. A lack of suitable antibodies for chromatin immunoprecipitation (ChIP) has so far prevented a comprehensive analysis of DNA-associated protein ADP-ribosylation. To analyze chromatin ADP-ribosylation, we recently developed a novel ADP-ribose-specific chromatin-affinity purification (ADPr-ChAP) methodology that uses the recently identified ADP-ribose-binding domains RNF146 WWE and Af1521. In this protocol, we describe how to use this robust and versatile method for genome-wide and loci-specific localization of chromatin ADP-ribosylation. ADPr-ChAP enables bioinformatic comparisons of ADP-ribosylation with other chromatin modifications and is useful for understanding how ADP-ribosylation regulates biologically important cellular processes. ADPr-ChAP takes 1 week and requires standard skills in molecular biology and biochemistry. Although not covered in detail here, this technique can also be combined with conventional ChIP or DNA analysis to define the histone marks specifically associated with the ADP-ribosylated chromatin fractions and dissect the molecular mechanism and functional role of chromatin ADP-ribosylation.

Ingo Just – One of the best experts on this subject based on the ideXlab platform.

  • MS-based quantification of RhoA/B and RhoC ADP-ribosylation.
    Journal of chromatography. B Analytical technologies in the biomedical and life sciences, 2018
    Co-Authors: Anke Schröder, Ingo Just, Anastasia Benski, Anne Oltmanns, Astrid Rohrbeck, Andreas Pich
    Abstract:

    Abstract Mono ADP-ribosylation is a common characteristic of bacterial toxins resulting to aberrant activation or inactivation of target proteins. The C3 exoenzyme of Clostridium botulinum (C3bot) ADP-ribosylates the small GTPases RhoA, RhoB and RhoC, leading to inactivation of these important regulators and impaired down-stream signaling. Quantification of ADP-ribosylation using gel migration assays, antibodies, and radioactivity-based methods are limited. Therefore a novel LC-MS-based method to specifically determine and quantify ADP-ribosylation of Rho GTPases was established. A heavy labeled protein standard that contained ADP-ribosylation specific peptides in similar amounts in ADP ribosylated and non ADP ribosylated form was used for relative quantification in vivo. In a proof of principle experiment HT22 cells were treated with C3bot and the kinetics of RhoA/B and RhoC ADP-ribosylation were determined in vivo.

  • Activation of phospholipase D1 by ADP-ribosylated RhoA.
    Biochemical and Biophysical Research Communications, 2003
    Co-Authors: Harald Genth, Klaus Aktories, Martina Schmidt, Ralf Gerhard, Ingo Just
    Abstract:

    Abstract Clostridium botulinum exoenzyme C3 exclusively ADP-ribosylates RhoA, B, and C to inactivate them, resulting in disaggregation of the actin filaments in intact cells. The ADP-ribose resides at Asn-41 in the effector binding region, leading to the notion that ADP-ribosylation inactivates Rho by blocking coupling of Rho to its downstream effectors. In a recombinant system, however, ADP-ribosylated Rho bound to effector proteins such as phospholipase D-1 (PLD1), Rho-kinase (ROK), and rhotekin. The ADP-ribose rather mediated binding of Rho-GDP to PLD1. ADP-ribosylation of Rho-GDP followed by GTP-γ-S loading resulted in binding but not in PLD activation. On the other hand, ADP-ribosylation of Rho previously activated by binding to GTP-γ-S resulted in full PLD activation. This finding indicates that ADP-ribosylation seems to prevent GTP-induced change to the active conformation of switch I, the prerequisite of Rho–PLD interaction. In contrast to recombinant systems, ADP-ribosylation in intact cells results in functional inactivation of Rho, indicating other mechanisms of inactivation than blocking effector coupling.

  • Glucosylation and ADP Ribosylation of Rho Proteins: Effects on Nucleotide Binding, GTPase Activity, and Effector Coupling†
    Biochemistry, 1998
    Co-Authors: Peter Sehr, Harald Genth, Ingo Just, Gili Joseph, Edgar Pick, Klaus Aktories
    Abstract:

    We studied the effects of glucosylation of RhoA, Rac1, and Cdc42 at threonine-35 and -37 by Clostridium difficile toxin B on nucleotide binding, GTPase activity, and effector coupling and compared these results with the ADP ribosylation of RhoA at asparagine-41 catalyzed by Clostridium botulinum C3 transferase. Whereas glucosylation and ADP ribosylation had no major effects on GDP release from RhoA, Rac1, and Cdc42, the rate of GTPγS release from Rho proteins was increased 3−6-fold by glucosylation. ADP ribosylation decreased the rate of GTPγS release by about 50%. Glucosylation reduced the intrinsic activities of the GTPases by 3−7-fold and completely blocked GTPase stimulation by Rho-GAP. In contrast, ADP ribosylation slightly increased GTPase activity (∼2-fold) and had no major effect on GAP stimulation of GTPase. Whereas ADP ribosylation did not affect the interaction of RhoA with the binding domain of protein kinase N, glucosylation inhibited this interaction. Glucosylation of Rac1 markedly diminishe…

Bernhard Lüscher – One of the best experts on this subject based on the ideXlab platform.

  • adp ribosylation a multifaceted posttranslational modification involved in the control of cell physiology in health and disease
    Chemical Reviews, 2017
    Co-Authors: Bernhard Lüscher, Patricia Verheugd, Mareike Bütepage, Laura Eckei, Brian H Shilton, Sarah Krieg
    Abstract:

    Posttranslational modifications (PTMs) regulate protein functions and interactions. ADP-ribosylation is a PTM, in which ADP-ribosyltransferases use nicotinamide adenadenineudinucleotide (NAD+) to modify target proteins with ADP-ribose. This modification can occur as mono- or poly-ADP-ribosylation. The latter involves the synthesis of long ADP-ribose chains that have specific properties due to the nature of the polymer. ADP-ribosylation is reversed by hydrolases that cleave the glycosidic bonds either between ADP-ribose units or between the protein proximal ADP-ribose and a given amino acid side chain. Here we discuss the properties of the different enzymes associated with ADP-ribosylation and the consequences of this PTM on substrates. Furthermore, the different domains that interpret either mono- or poly-ADP-ribosylation and the implications for cellular processes are described.

  • Players in ADP-ribosylation: Readers and Erasers
    Current protein & peptide science, 2016
    Co-Authors: Patricia Verheugd, Mareike Bütepage, Laura Eckei, Bernhard Lüscher
    Abstract:

    ADP-ribosylation describes an ancient and highly conserved posttranslational modification (PTM) of proteins. Many cellular processes have been identified that are regulated by ADP-ribosylation, including DNA repair, gene transcription and signaling processes. Enzymes catalyzing ADP-ribosylation use NAD+ as a cofactor to transfer ADP-ribose to a substrate under release of nicotinamide. In mammals extracellular and intracellular enzymes have been described. ADP-ribosylation is catalyzed by ADP-ribosyltransferases (ARTs) and some Sirtuins. Extracellular and intracellular ARTs belong to the cholera toxin-like (ARTC) and the diphtheria toxin-like (ARTD) subclass, respectively. ARTDs can be further subdivided depending on their ability to either generate poly-ADP-ribose chains, or to mono-ADP-ribosylate substrates. Similar to the latter, ARTCs and Sirtuins are restricted to mono-ADP-ribosylation. Recent findings have provided information about the functional consequences of ADP-ribosylation. Analogous to other PTMs, ADP-ribosylation can exert allosteric effects on enzymes, thereby controlling their catalytic activity. Moreover, this PTM can be read by multiple protein motifs and domains mediating proteinprotein interactions. Typically these readers can distinguish between mono- and poly-ADP-ribosylation. Furthermore, with the description of proteins that can erase ADP-ribosylation, this posttranslational modification is fully reversible and thus provides an additional mechanism to transiently control protein functions and networks. In this review we will describe the most recent findings on motifs and domains that are related to ADP-ribosylation processes with a particular focus on readers and erasers. These new findings provide evidence for broad functional roles of ADP-ribosylation and a high diversity of mechanisms that contribute to the downstream consequences of this modification.

  • Expanding functions of intracellular resident mono‐ADP‐ribosylation in cell physiology
    The FEBS journal, 2013
    Co-Authors: Karla L. H. Feijs, Patricia Verheugd, Bernhard Lüscher
    Abstract:

    Poly-ADP-ribosylation functions in diverse signaling pathways, such as Wnt signaling and DNA damage repair, where its role is relatively well characterized. Contrarily, mono-ADP-ribosylation by for example ARTD10/PARP10 is much less understood. Recent developments hint at the involvement of mono-ADP-ribosylation in transcriptional regulation, the unfolded protein response, DNA repair, insulin secretion and immunity. Additionally, macrodomain-containing hydrolases, MacroD1, MacroD2 and C6orf130/TARG1, have been identified that make mono-ADP-ribosylation reversible. Complicating further progress is the lack of tools such as mono-ADP-ribose-specific antibodies. The currently known functions of mono-ADP-ribosylation are summarized here, as well as the available tools such as mass spectrometry to study this modification in vitro and in cells.

Ivan Ahel – One of the best experts on this subject based on the ideXlab platform.

  • Reversible ADP-ribosylation of RNA.
    Nucleic acids research, 2019
    Co-Authors: Deeksha Munnur, Michael S. Cohen, Edward Bartlett, Petra Mikolčević, Ilsa T. Kirby, Johannes Gregor Matthias Rack, Andreja Mikoč, Ivan Ahel
    Abstract:

    ADP-ribosylation is a reversible chemical modification catalysed by ADP-ribosyltransferases such as PARPs that utilize nicotinamide adenadenineudinucleotide (NAD+) as a cofactor to transfer monomer or polymers of ADP-ribose nucleotide onto macromolecular targets such as proteins and DNA. ADP-ribosylation plays an important role in several biological processes such as DNA repair, transcription, chromatin remodelling, host-virus interactions, cellular stress response and many more. Using biochemical methods we identify RNA as a novel target of reversible mono-ADP-ribosylation. We demonstrate that the human PARPs – PARP10, PARP11 and PARP15 as well as a highly diverged PARP homologue TRPT1, ADP-ribosylate phosphorylated ends of RNA. We further reveal that ADP-ribosylation of RNA mediated by PARP10 and TRPT1 can be efficiently reversed by several cellular ADP-ribosylhydrolases (PARG, TARG1, MACROD1, MACROD2 and ARH3), as well as by MACROD-like hydrolases from VEEV and SARS viruses. Finally, we show that TRPT1 and MACROD homologues in bacteria possess activities equivalent to the human proteins. Our data suggest that RNA ADP-ribosylation may represent a widespread and physiologically relevant form of reversible ADP-ribosylation signalling.

  • Hydrolysis of ADP-ribosylation by Macrodomains.
    Methods in molecular biology (Clifton N.J.), 2018
    Co-Authors: Melanija Posavec Marjanović, Gytis Jankevicius, Ivan Ahel
    Abstract:

    ADP-ribosylation is the process of transferring the ADP-ribose moiety from NAD+ to a substrate. While a number of proteins represent well described substrates accepting ADP-ribose modification, a recent report demonstrated biological role for DNA ADP-ribosylation as well. The conserved macrodomain fold of several known hydrolyses was found to possess de-ADP-ribosylating activity and the ability to hydrolyze (reverse) ADP-ribosylation. Here we summarize the methods that can be employed to study mono-ADP-ribosylation hydrolysis by macrodomains.

  • reversible mono adp ribosylation of dna breaks
    FEBS Journal, 2017
    Co-Authors: Deeksha Munnur, Ivan Ahel
    Abstract:

    Adenosine diphosphate (ADP)-ribosylation is a chemical modification of macromolecules that plays an important role in regulation of quintessential biological processes such as DNA repair, transcription, chromatin remodelling, stress response, apoptosis, bacterial metabolism and many others. ADP-ribosylation is carried out by ADP-ribosyltransferase proteins, such as poly (ADP-ribose) polymerases (PARPs) that transfer either monomer or polymers of ADP-ribose onto the molecular targets by using nicotinamide adenadenineudinucleotide (NAD+ ) as a cofactor. Traditionally, proteins have been described as primary targets of ADP-ribosylation; however, there has been growing evidence that DNA may be a common target as well. Here, we show using biochemical studies that PARP3, a DNA damage-activated ADP-ribosyltransferase, can mono-ADP-ribosylate double-stranded DNA ends. ADP-ribosylation of DNA mediated by PARP3 attaches a single mono-ADP-ribose moiety to the phosphate group at the terminal ends of DNA. We further show that mono ADP-ribosylation at DNA ends can be efficiently reversed by several cellular hydrolases (PARG, MACROD2, TARG1 and ARH3). This suggests that mono ADP-ribosylated DNA adducts can be efficiently removed in cells by several mechanisms.