ADP-Ribosylation, a Multifaceted Posttranslational ... - ACS Publications

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Cite This: Chem. Rev. 2018, 118, 1092−1136

ADP-Ribosylation, a Multifaceted Posttranslational Modification Involved in the Control of Cell Physiology in Health and Disease Bernhard Lüscher,*,† Mareike Bütepage,† Laura Eckei,† Sarah Krieg,† Patricia Verheugd,† and Brian H. Shilton†,‡ †

Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, 52057 Aachen, Germany Department of Biochemistry, Schulich School of Medicine & Dentistry, The University of Western Ontario, Medical Sciences Building Room 332, London, Ontario Canada N6A 5C1

‡

ABSTRACT: Posttranslational modifications (PTMs) regulate protein functions and interactions. ADP-ribosylation is a PTM, in which ADP-ribosyltransferases use nicotinamide adenine dinucleotide (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.

CONTENTS 1. Introduction 2. Historical Perspectives on the Identification of ADP-Ribosylation and Associated Enzymes 3. ADP-Ribosyltransferases 3.1. Prokaryotic and Viral ADP-Ribosyltransferases 3.2. ARTC Family of Eukaryotic ADP-Ribosyltransferases 3.3. ARTD Family of Eukaryotic ADP-Ribosyltransferases 3.3.1. Summary of Biological Functions Associated with ARTD1 and Signaling Processes Targeting ARTD1 3.3.2. PARylating ARTD Family Members beyond ARTD1: ARTD2, ARTD5, and ARTD6 3.3.3. Physiological and Disease-Associated Functions of MARylating ARTD Family Members 3.4. Sirtuins 4. Hydrolases 4.1. Poly-ADP-ribose Chain Degrading Enzymes 4.1.1. Poly-ADP-ribose Glycohydrolase PARG 4.1.2. Poly-ADP-ribose and Ser-ADP-ribose Glycohydrolase ARH3 4.2. Mono-ADP-ribosylhydrolases 4.2.1. Mono-ADP-ribosylhydrolase ARH1 4.2.2. Mono-ADP-ribosylhydrolase ARH3 4.2.3. Macrodomain Containing Mono-ADPribosylhydrolases © 2017 American Chemical Society

4.3. Nudix Hydrolases 5. Mechanism of Reaction of ADP-Ribosyltransferases 5.1. Nicotinamide Adenine Dinucleotide (NAD+) 5.2. NAD+ and ADP-Ribose Chemistry 5.3. ADP-Ribosyltransferase Mechanism 5.3.1. NAD+ Binding 5.3.2. Substrate Binding and Specificity 6. Functional Consequences of ADP-Ribosylation 6.1. Substrates of ADP-Ribosyltransferases 6.2. Domains That Recognize ADP-Ribosylation 6.2.1. Macrodomains as ADP-Ribose Binding Modules 6.2.2. PAR Binding Peptide Motif 6.2.3. Tryptophan−Tryptophan−Glutamate (WWE) Domain 6.2.4. Poly(ADP-ribose)-Binding Zinc Finger (PBZ) Domain 6.2.5. Oligonucleotide/Oligosaccharide-Binding Fold Domain 6.2.6. Additional PAR Binding Modules 6.3. Functional Role of ADP-Ribose Polymers 6.3.1. PAR Chains Are Interaction Modules for Proteins Associated with DNA Repair and Chromatin Biology

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Special Issue: Posttranslational Protein Modifications Received: March 1, 2017 Published: November 27, 2017

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DOI: 10.1021/acs.chemrev.7b00122 Chem. Rev. 2018, 118, 1092−1136

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Figure 1. Posttranslational modifications (PTMs) control protein functions. Overview of processes that control protein expression, diversity, and functions. These processes are regulated by signals that are generated by external as well as internal cues, including the interaction of growth factors and cytokines with cell membrane bound receptors and the response to intracellular stress such as DNA damage (signal). These signals control the expression of proteins by influencing gene transcription, alternative splicing (differential usage of exons of a given gene, resulting in mRNAs encoding distinct proteins), mRNA stability, and protein biosynthesis (translation). Once synthesized, proteins are regulated through PTMs that influence various aspects of protein physiology. These include stability, subcellular localization, catalytic activity, and interactions with other proteins. As a result, cells are capable of rapidly adjusting protein function by achieving the correct local concentration and activity to meet cellular needs. Note that some PTMs, including ubiquitination and ADP-ribosylation, can occur as polymers mediating specific functions. Moreover, combinations of PTMs allow the integration of multiple signals that facilitates coordination and fine-tuning of protein function across the cell and organism.

6.3.2. PAR Chains Mediate Polyubiquitination and Protein Degradation 6.3.3. PAR Chains and the Formation of Subcellular Compartments 6.3.4. Excessive PAR Production Is Toxic 6.3.5. Protein-Free PAR Chains Promote Cell Death 6.3.6. Protein-Free PAR Chains Can Regulate Signaling and Extracellular Processes 6.4. Functions Associated with Mono-ADP-ribosylation 6.4.1. ARTC-Dependent Mono-ADP-ribosylation by Eukaryotic and Bacterial Enzymes and Its Role in Stress Response and Immune Regulation 6.4.2. Consequences of Intracellular MonoADP-ribosylation 6.4.3. Mono-ADP-ribosylation of Ubiquitin 6.4.4. Intracellular Arginine Mono-ADP-ribosylation 7. Conclusions and Outlook Author Information Corresponding Author ORCID Notes Biographies Acknowledgments Abbreviations References

variants, i.e., to enable a limited number of protein-encoding genes to fulfill complex tasks. Indeed, the complexity of proteins found in any given human cell is far greater than the number of genes would indicate, with the estimates being 106 and more.1 This is the result of different processes, which include alternative splicing, alternative translational initiation, and posttranslational modifications (PTMs) that generate extensive protein product diversity with a limited number of genes (Figure 1). PTMs encompass more than 300 known modifications,1 and thus a newly synthesized protein is likely available in multiple isoforms in a given cell. In more general terms, PTMs provide mechanisms to modify proteins in response to specific cues, such as signals that control cell physiology through, for example, cell surface receptors, signals that emanate from deoxyribonucleic acid (DNA) damage, or an altered metabolic state. As a consequence, PTMs are extensively used to rapidly control the activities of proteins, allowing cells to respond quickly to many different cues and insults (Figure 1). These signaling processes and the relevant enzymes and associated proteins are frequently deregulated in human disease. PTMs can regulate signaling pathways and networks, metabolism, and gene expression in two different ways: first by altering the catalytic activity of a target protein (if the target is an enzyme) and second by modulating target interactions with other molecules. PTMs can affect enzyme activity directly by modification of active site residues, or through allosteric mechanisms. PTMs modulate molecular interactions directly by providing or blocking binding sites, or indirectly through allosteric mechanisms. Thus, PTMs can promote the binding of other macromolecules that possess a relevant interaction domain that enables it to “read” the modified protein structure (a “reader” as opposed to writers and erasers as described below). These two principal modes of regulation are not exclusive but instead are interconnected and in many cases overlapping. For example, an allosteric effect of a PTM that alters the catalytic activity of an enzyme will most likely also affect its interaction with other molecules.

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1. INTRODUCTION The analysis of the human genome has revealed roughly 21 000 genes that encode proteins. This is not too different from organisms with less complexity, including Drosophila melanogaster and Caenorhabditis elegans, two very well studied model organisms. This has resulted in the suggestion that other mechanisms might exist that increase the number of protein 1093


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Figure 2. Principles of ADP-ribosylation. (A) ADP-ribosylation is a PTM that is catalyzed by ADP-ribosyltransferases (“writers”) and removed by ADPribosylglycohydrolases (“erasers”). The modification is dependent on consumption of the cofactor nicotinamide adenine dinucleotide (NAD+). Upon release of nicotinamide (Nam) the ADP-ribose (ADPr) unit is transferred onto substrate proteins (mono-ADP-ribosylation or MARylation). Many different amino acid side chains have been described as ADPr acceptors, including acidic and basic amino acids as well as serine. Some of the writers are able to perform multiple rounds of ADP-ribosylation reactions, in an iterative process, generating ADPr polymers (PARylation). Both MARylation and PARylation have functional consequences by regulating the activity of the modified substrate and/or by affecting its interaction with other macromolecules. Because the bonds between an amino acid side chain and ADPr and between different ADPr units are distinct, different hydrolases are used to degrade poly-ADPr chains and to remove the protein proximal ADPr. The single ADPr units as well as ADPr chains that are released by the hydrolases can function in downstream signaling. (B) The structure of NAD+ and the products of the reactions are shown. The acceptor amino acid side chain executes a nucleophilic attack on the C1″ (anomeric) carbon of the nicotinamide (Nam) ribose. Linear chain elongation occurs by nucleophilic attacks of the C2″ hydroxyl of the adenine ribose on the C1″ of the next NAD+. Branching bonds are between C2″ and C1″ of the incoming ADPr (not shown).

considerations suggest that ADP-ribosylation diversified originally in the context of bacterial conflict systems, including toxin− antitoxin systems. Moreover, bacteria and viruses acquired the means to modulate host cell ADP-ribosylation, by expressing either writers or erasers of this PTM.7,8 Targeting these enzymes with small molecule inhibitors is considered to be an option for therapeutic intervention, for example as part of antiviral strategies. Thus, ADP-ribosylation is closely associated with normal and diseased cellular and organismal physiology. This review will focus on the mechanisms of how the writers and erasers of ADP-ribosylation function and on describing the consequences of ADP-ribosylation in general, highlighting specific substrates that serve as examples to illustrate the general concepts. This includes direct and allosteric mechanisms that affect catalysis and molecular interactions with downstream impacts. This information will be embedded into describing the basic characteristics of the different enzymes that write and erase ADP-ribosylation. We will briefly summarize some of the key biological properties of these enzymes. Description of writers and erasers will be brought into perspective by portraying the different reader domains that disseminate the information associated with substrate ADP-ribosylation. Knowledge about ADP-ribosylation, its consequences, and the enzymes involved has been rapidly developing and expanding, generating an increasingly larger framework of information; on this basis, it is not possible to comprehensively discuss all aspects. Thus, we

The PTM that is the subject of this review is ADP-ribosylation. This modification occurs in a process that involves the transfer of ADP-ribose (ADPr) from nicotinamide adenine dinucleotide (NAD+) onto a substrate protein and the release of nicotinamide (Nam) (Figure 2). The transfer of ADPr occurs onto amino acid side chains with a nucleophilic oxygen, nitrogen, or sulfur, resulting in N-, O-, or S-glycosidic linkage to the ribose. ADPribosylation is, similar to PTMs such as phosphorylation and ubiquitination, a reversible process. ADP-ribosylation comes in two flavors: as mono-ADP-ribosylation (MARylation) and as poly-ADP-ribosylation (PARylation). ADP-ribosyltransferases (“writers”) and ADP-ribosylglycohydrolases (“erasers”) have been described that can covalently add and remove ADPr, respectively (Figure 3). ADPr carries two negative charges at physiological pH, two ribose moieties, and an adenine ring that is capable of both hydrogen bonding and hydrophobic interactions (Figure 2); in this way modification by ADPr offers multiple means to alter the properties and functions of a substrate. This is multiplied in a poly-ADP-ribose (PAR) chain, which can be synthesized by some ADP-ribosyltransferases (ARTs) and which has rather unique properties. ADP-ribosylation has been linked to many cellular processes, including different forms of stress response and metabolism. Of particular note is that inhibitors of ARTs have recently entered clinical practice as anticancer agents,2−6 testifying to the critical functions associated with this PTM. Importantly, evolutionary 1094


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organ extracts. In 1963 a report was published that described a reaction that incorporated adenosine-triphosphate (ATP) into an acid insoluble product. This reaction was dependent on DNA, as RNA polymerase is, and was stimulated by nicotinamide mononucleotides. Because no other nucleoside triphosphates were required, it was suggested that the product might be a polymer of adenosine (polyA).10 Subsequent studies revealed that it was a polymer of ADP-ribose (ADPr) that shows similarities to RNA. Three different groups reported an activity from nuclei of mammalian cells that catalyzes the homopolymerization of ADPr units from NAD+.11−13 This was surprising as it had been argued that NAD+ functions solely as a cofactor in redox reactions where it can be regenerated. For example, in glycolysis NAD+ is reduced to NADH, which is then reoxidized in the production of ATP, which is required for most energyconsuming processes in cells. That NAD+ is indeed consumed was further suggested by the requirement of humans for vitamin B3, or niacin, which includes both Nam and nicotinic acid, as precursors for the de novo synthesis of NAD+.14−16 Because of the role of NAD+ in energy production, NAD+ is interconnected with cellular metabolism and ATP production. In this regard, the structural similarities between NAD+ and ATP are noteworthy, as both have an adenosine-diphosphate coupled to either ribose−Nam or phosphate, respectively. In parallel to the discovery of enzymes that can generate ADPr polymers from NAD+ in mammalian cell extracts, studies on the action of diphtheria toxin provided evidence that this enzyme requires NAD+. Diphtheria toxin, which is produced by Corynebacterium diphtheria, interferes with protein synthesis when added to cells.17 Cell-free protein translation systems facilitated demonstration of the requirement for NAD+ to block protein biosynthesis by diphtheria toxin.18 Subsequent studies established that diphtheria toxin transfers ADPr from NAD+ to eukaryotic elongation factor 2 (eEF2), inhibiting protein biosynthesis.19,20 Following this observation, additional bacterial toxins were identified that function as ARTs to control distinct aspects of host cell physiology and thereby contribute to the pathogenic effects of the respective bacterial infections.21−23 These findings also helped to establish that ADP-ribosylation comes in two flavors: PARylation, in which ADPr polymers are formed on substrates, and MARylation, which results in the modification of substrates by ADPr monomers. Early studies had indicated that the majority of the ART activity in mammalian cell extracts was found associated with chromatin.21,24 This was most likely due to the fact that in cell lysates the enzyme poly(ADP-ribose) synthase/poly(ADPribose) polymerase 1 (PARP1)/ART diphtheria toxin like 1 (ARTD1) (details on the nomenclature are discussed below; see Table 1 and Figure 4) is strongly activated due to the presence of damaged DNA. An important step in the analysis of ADPribosylation was the realization that it did not simply involve the formation of ADPr polymers, but that proteins themselves were modified, suggesting it to be a PTM.19,20,24,25 The more detailed analysis revealed that the PAR chains synthesized by ARTD1 are branched (Figure 2; see also Figure 11).26−29 Subsequently the gene encoding ARTD1 was cloned.30−32 An additional key finding was also the description of an activity referred to as polyADP-ribose glycohydrolase (PARG) that could hydrolyze the ribose−ribosyl O-glycosidic bonds in ADPr polymers.33 Further work led to the identification of distinct families of cellular enzymes that can ADP-ribosylate proteins in eukaryotic cells and have distinct structural and enzymatic characteristics and subcellular localization.34 Moreover, enzymes have been

Figure 3. Players in ADP-ribosylation. Depicted are the main enzyme families and protein domains mediating the transfer of ADP-ribose (ADPr) onto substrate proteins (“writers”), the removal of ADPr from substrates (“erasers”), and the interaction with ADPr or ADPribosylated substrates (“readers”). Main writers of ADP-ribosylation are the enzymes of the ART (ADP-ribosyltransferase) superfamily, characterized by structural homology of the ART domain to either diphtheria toxin (ART diphtheria toxin like, ARTD) or cholera toxin (ART cholera toxin like, ARTC). Three key amino acids are found in the active center of these enzymes, with H-Y-E or H-Y-E variants and R-S-E being characteristic for ARTDs and ARTCs, respectively. ART domains are conserved among viruses (v), prokaryotes (p) (including bacteria and archaea), and eukaryotes (e). In addition, ART activity has been ascribed to certain members of the sirtuin enzyme family. While most ARTs catalyze the transfer of a single ADPr residue (mono-ADPribosylation or MARylation), certain eukaryotic members of the ARTD subfamily as well as prokaryotic enzymes catalyze the formation of ADPr polymers (poly-ADP-ribosylation or PARylation). Macrodomains are structurally highly conserved protein domains that can serve as binding domains recognizing MARylated and/or PARylated proteins. Furthermore, they can act as enzymes catalyzing MAR removal or PAR degradation. ARH proteins comprise a second enzyme class important for MAR or PAR turnover. In addition, certain members of the Nudix family catalyze ADPr degradation via pyrophosphate hydrolysis. While PARylation in eukaryotes is recognized by a variety of reader domains, to date only macrodomains have been identified as MAR-specific reader domains. BRCT, BRCA1 C-terminal domain; FHA, forkhead-associated domain; Macro, macrodomain; OB-fold, oligonucleotide/oligosaccharide-binding fold; PEP, PAR binding peptide motif ([HKR]1-X2-X3[AIQVY]4-[KR]5-[KR]6-[AILV]7-[FILPV]8); PBZ, PAR binding zinc finger; PIN, PilT N-terminus domain; WWE, Trp-Trp-Glu domain.

indicate many excellent reviews that cover and discuss more specific aspects associated with ADP-ribosylation.

2. HISTORICAL PERSPECTIVES ON THE IDENTIFICATION OF ADP-RIBOSYLATION AND ASSOCIATED ENZYMES Identification and initial characterization of ribonucleic acid (RNA) polymerases was a hot topic in the 1950s and 1960s.9 Many studies demonstrated the synthesis of RNA in different 1095


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Table 1. Summary of the Nomenclature of ADP-Ribosyltransferases ADP-ribosyltransferase nomenclature

poly(ADP-ribosyl) polymerase nomenclature

alternative names

main activity (see text for details)

main amino acids modified (see text for details)

ARTD Family ARTD1 ARTD2 ARTD3 ARTD4 ARTD5 ARTD6 ARTD7 ARTD8 ARTD9 ARTD10 ARTD11 ARTD12 ARTD13

PARP1 PARP2 PARP3 PARP4 PARP5A PARP5B PARP15 PARP14 PARP9 PARP10 PARP11 PARP12 PARP13

ARTD14 ARTD15 ARTD17

PARP7 PARP16 PARP6

ARTC1 ARTC2

ART1 ART2.1/ART2.2 (two genes in the mouse) ART3 ART4 ART5

ARTC3 ARTC4 ARTC5

vPARP tankyrase 1 tankyrase 2 BAL3 BAL2 BAL1

ZC3HDC1 ZC3HAV1, ZAP TiPARP

PARylation (long, branched) PARylation (long, branched) MARylation MARylation PARylation (short) PARylation (short) MARylation MARylation MARylation MARylation MARylation MARylation inactive

glutamate, aspartate, serine glutamate, aspartate, serine likely acidic amino acids likely acidic amino acids likely acidic amino acids likely acidic amino acids likely acidic amino acids glutamate, aspartate C-terminal carboxylate glutamate, aspartate likely acidic amino acids likely acidic amino acids

MARylation MARylation MARylation

likely acidic amino acids likely acidic amino acids likely acidic amino acids

ARTC family ecto-ART1 MARylation ecto-ART2 MARylation (pseudogene in humans) ecto-ART3 inactive ecto-ART4 inactive ecto-ART5 MARylation

arginine arginine

arginine

toxin of Vibrio cholerae.48 Three key amino acids have been identified in the active center of these enzymes, with H-Y-E and R-S-E being characteristic for diphtheria toxin and cholera toxin, respectively. The first two amino acids are important for binding NAD+ in the active center, while the glutamate functions in catalysis. Some bacterial as well as eukaryotic ARTs have variations of the H-Y-E motif as discussed below. These two structurally defined subclasses of ARTs, together with acknowledging the biochemical activity of these enzymes as transferases, have been combined to suggest a new nomenclature, i.e., the ARTs diphtheria toxin like (ARTDs, aka PARPs) and the ARTs cholera toxin like (ARTCs, aka ecto-ARTs) families, which we will use here.34 Of note is that the ARTD family consists of enzymes that can synthesize ADPr polymers (poly-ADPr/polyADP-ribosylation or PAR/PARylation) as well as enzymes that are only able to transfer one ADPr unit (mono-ADPr/monoADP-ribosylation or MAR/MARylation). In contrast to the ARTD enzymes, all active ARTC family members MARylate their substrates and no ability to PARylate has been reported.

discovered that are able to cleave the bond between ADPr and amino acid side chains, providing evidence that this PTM is fully reversible.35

3. ADP-RIBOSYLTRANSFERASES Subsequent to the identification of ARTD1/PARP1, additionally 16 human proteins that contain a region of homology to the catalytic domain of ARTD1/PARP1 were identified.34,36,37 This largest family of ARTs with 17 members comprises the intracellular enzymes originally referred to as PARPs (Figure 4). A second family with several members (four in humans, six in mice) consists of extracellular, membrane-associated enzymes or “ecto-ARTs” (Figure 4).38,39 The third family has a single member that encodes an NAD+-dependent tRNA 2′-phosphotransferase, which will not be further discussed (see, for example, refs 40−43). Thus, in humans 22 genes exist that encode proteins with an ART domain, defining an ART superfamily. The catalytic domains of these proteins show homology to many bacterial toxins with ART activity, indicating that the enzymatically active domain is the common denominator of this class of proteins. Of note is that, in addition to these members of the ART superfamily, also two members of the sirtuin (yeast silent information regulator 2 (Sir2) like proteins) family possess ART activity. Sirtuins are best known for their activities as NAD+dependent deacylases.44,45 The study of bacterial toxins has revealed that different enzymatic activities are used by pathogens to modulate cellular factors and thus affect cell physiology.46 One of these activities is MARylation as demonstrated for various toxins, including diphtheria, pertussis, cholera, and C2 and C3 toxins.22,47 Of note for the discussion of eukaryotic enzymes is that the structural analysis of bacterial ADP-ribosylating toxins indicated two major folds for the catalytic domains. These are exemplified by the structures of diphtheria toxin of C. diphtheriae and cholera

3.1. Prokaryotic and Viral ADP-Ribosyltransferases

In general, the repertoire of genes that encode proteins associated with ADP-ribosylation correlates with the complexity of the individual organism. Thus, in contrast to eukaryotic organisms, in which typically all enzymes (readers, writers, and erasers) necessary for functional ADP-ribosylation metabolism are present, these enzymes are less prevalent in bacteria, archaea, or viruses. Thus far, only 11 bacterial species have been described to express both potential writers and erasers that would allow completion of an ADP-ribosylation cycle. In most cases the functionalities of the systems have not been demonstrated.49−53 Apart from that, several species of bacteria, archaea, and viruses appear to have single, isolated components of ADPr metabolism, including ADP-ribosyltransferases and macrodomain-containing proteins that can function as readers or erasers (Figure 3). By 1096


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Figure 4. Human ADP-ribosyltransferases of the diphtheria toxin like (ARTD) and of the cholera toxin like (ARTC) families. Schematic comparison of the domain architecture of the human ADP-ribosyltransferase proteins. MARylation and PARylation refer to the catalytic activity as mono-ADPribosyltransferases and enzymes that can synthesize poly-ADPr chains, respectively. Please note that human ARTC2 is a pseudogene. The following domains are indicated: AMD, automodification domain; ARC, ankyrin repeat cluster, can mediate protein−protein interactions; ART, ADPribosyltransferase domain; ART w/E, ADP-ribosyltransferase domain with a catalytically relevant glutamate; BRCT, BRCA1 carboxy-terminal domain, found in many DNA damage repair and cell cycle checkpoint proteins; GPI, glycosylphosphatidylinositol anchor, a PTM at the C-terminus of some proteins in the endoplasmic reticulum, typically requiring the removal of a C-terminal peptide to expose the modification site; GRD, glycine-rich domain; HPS, histidine−proline−serine region; Macro, the macrodomain is closely associated with ADPr metabolism, and some possess ADP-ribose1′-phosphatase, some possess ADP-ribosylhydrolase activity, and some interact with MARylated or PARylated substrates, while the macrodomain can serve as ADPr or O-acetyl-ADP-ribose binding module; MVP-ID, major vault particle interaction domain; NES, nuclear export sequence; PRD, PARP regulatory domain, an autoinhibitory domain for ARTD1 and suggested to be involved in branching activity; PRD-like, similarity to PRD but functionally poorly characterized; RRM, RNA-binding/recognition motif; SAM, sterile α motif, can mediate homo- or heterodimerization; SAP, SAF/ acinus/PIAS-DNA-binding domain; SP, signal peptide, required for targeting the synthesis of a protein to the endoplasmic reticulum; TMD, transmembrane domain; TR, 10 amino acid tandem repeats with the consensus sequence [GS]-E-K-N-[QW]-K-L-E-D-H; UIM, ubiquitin interaction motif; VIT, vault protein inter-α-trypsin domain, suggested to mediate protein−protein interactions; vWA, von Willebrand type A domain, suggested to mediate protein−protein interactions; WGR, domain named after a conserved central motif (W-G-R), found in some polyA polymerases; WWE, a protein−protein interaction domain named after three conserved residues (W-W-E), some interact with iso-ADP-ribose; ZF, zinc finger domain; ZF/ TPH, Ti-PARP (ARTD14) homologous zinc finger domain.

corresponding hydrolases are considered predecessors of the eukaryotic genes and proteins.7 Best characterized among the noneukaryotic ARTs are the bacterial ADP-ribosyltransferase toxins found in many different species, including human, plant, and insect pathogens. These toxins are highly substrate specific and transfer one ADPr unit typically onto a single host target, thereby contributing to bacterial pathogenesis.8,62 For example, diphtheria toxin and closely related toxins affect protein biosynthesis by specifically modifying eEF2 at position 715, a modified histidine or diphthamide residue that is critical for protein synthesis.63,64 As pointed out above, the primary diversification of the ART enzyme family occurred during the development of different bacterial conflict systems and the various eukaryotic ARTs were subsequently acquired by horizontal gene transfer.7,65 These conflict systems include toxin−antitoxin (TA) systems.66,67 TA

sequence comparisons and domain searches, some 30 bacterial strains distributed over six different phyla have been identified that have acquired genes potentially encoding ARTs.7,52 In archaea the classical ART signature has not been identified by sequence comparisons or domain searches.52 However, an ADPribosylating enzyme has been discovered in the archaeon Sulfolobus solfataricus capable of catalyzing ADPr polymerization.54 In addition, ADP-ribosylating proteins have also been identified in viruses.52,55 The presence of only a single component of the ADPr metabolism suggests that these proteins are relevant for host−pathogen interactions. Indeed, some pathogens have been described to rely on their ADP-ribosylating proteins for pathogenesis, pathogen propagation, and replication, as well as modulation of the host immune response.8,56−61 Of note is that the bacterial ARTs and thus most likely also the 1097


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skeletal muscle.73 Moreover, ARTC activity can be measured on epithelial and many immune cells.74,75 Interestingly murine Artc2.1 is expressed on T cells and macrophages and Artc2.2 is ̈ T cells expressed predominantly on T cells, in particular on naive 76−80 In contrast to the murine protein, and regulatory T cells. human ARTC2 is considered a pseudogene and the potential coding region carries premature stop codons. It is thought that ARTC1 might be the enzyme that can functionally replace ARTC2.81,82

systems act through multiple mechanisms as effectors of dormancy and persistence that allow bacteria to survive under stress conditions as well as in antiphage defense and pathogenicity.67,68 For example, during persistence bacteria have a high tolerance for antibiotics and thus understanding the underlying mechanisms is important to controlling bacterial growth. TA systems can modulate persistence because under stress conditions the antitoxin is inactivated, which leads to cell growth arrest through the action of the toxin. Reactivating the antitoxin in response to more favorable growth conditions antagonizes the toxin, and consequently cell proliferation is resumed. A recent study reported that, in the DarTG system, which is found in diverse bacterial species, the toxin (DarT) functions as a DNA modifying ART and the antitoxin (DarG), a macrodomain-containing protein, functions as a MAR hydrolase.69 Because TA systems frequently target proteins, e.g., associated with protein translation,67,68 it will be interesting to see whether proteins are also targets of ADP-ribosylating TA systems. ARTs are involved in host−pathogen interaction, as summarized above for bacterial toxins and eukaryotic host cells. Viruses also encode potential ARTs.52 A recent study has demonstrated that the Alt protein of the bacteriophage T4 possesses MARylating activity.55 It modifies and inhibits MazF, an RNase that is a component of the MazEF TA system. While all the above-mentioned prokaryotic and viral ARTs possess MARylation activity, recent findings indicate also the presence of polymer-forming ARTs in bacteria. The analysis of a Herpetosiphon aurantiacus protein with a region showing homology to the catalytic domain of ARTs revealed PARylation activity.70 Using the H. aurantiacus ART in BLAST searches reveals numerous proteins that contain an ART related domain in different bacteria and viruses (our unpublished findings). Whether these have indeed PARylation or possibly MARylation activity remains to be determined. Together, these studies provide evidence for widespread distribution of enzymes that effect and regulate ADP-ribosylation in various biological systems. Beyond the few cases that are understood at the molecular level, many more are awaiting discovery and molecular characterization. This is presaged by the sequence diversity in the ART family that makes it difficult to identify new members solely on the basis of amino acid sequence. In contrast the catalytic domains are characterized by a high level of structural conservation. Together, sequence and structural comparisons have provided the current catalogue of ART superfamily members.7,36,65

3.3. ARTD Family of Eukaryotic ADP-Ribosyltransferases

Seventeen members of the ARTD family have been identified and, in the cases that have been studied, are localized within cells (Figure 4). These are broadly expressed, although for some only mRNA data are available due to the lack of suitable reagents to study the proteins. A systematic analysis of many ARTD family members has revealed that they are located in various cellular compartments. The majority of the proteins are located in the cytosol showing distinct staining patterns (for more details see below).83 The ARTD family members are characterized by heterogeneity in the composition of recognizable protein domains. It is likely that these domains control diverse functions of ARTDs, consistent with the notion that these enzymes participate in different cellular processes. For example, some of these domains may be relevant for recognition of cellular substrates. The founding member of the ARTD family is ARTD1/ PARP1, which is the best-studied ARTD protein and thus dominates the current literature (for summaries of early findings, see refs 84−86). Several murine knockout models were developed, demonstrating that Artd1 is not essential for mouse development.87−89 At that time ARTD1 was considered the only enzyme that could synthesize PAR. However, biochemical studies using cells of the Artd1 knockout mice revealed remaining PARylation activity, which led to the identification of Artd2/ PARP2.90,91 In parallel, tankyrase-1/ARTD5 was identified and demonstrated to be capable of catalyzing PARylation.92 Subsequently, several additional family members were discovered by comparing the sequences of the catalytic domains of these proteins.36,37 This suggested that ADP-ribosylation is a more widespread modification than originally anticipated from the analysis of ARTD1. With regard to mono- versus poly-ADPribosylation, the sequences of the ARTD family catalytic domains did not allow prediction of whether a given ARTD would have PARylation activity. Characterization of ARTD10 revealed that this enzyme has MARylation activity and is unable to synthesize PAR chains.93 Structural analysis in addition to sequence comparisons suggested that the glutamate, which is found in the catalytic center of ARTD1 as well as ARTD2 and ARTD5 (the glutamate in the H-Y-E motif), does not have an equivalent in ARTD10. Expanding of this sequence/structure comparison revealed that several ARTD family members have variations of the H-Y-E motif. These studies suggested that several ARTD family members lacked the glutamate, which was considered essential for catalysis.93 This provoked the question of how these enzymes catalyze the transfer of ADPr to a substrate. ARTD10 transfers ADPr onto the side chain of glutamate, and on this basis it was postulated that ARTD10 could use substrate-assisted catalysis to modify its substrates.93 The proposed mechanism suggests two functions for the target acidic residue of a substrate. First, the acidic residue is required for catalysis in that it destabilizes the N-glycosidic bond between ribose and Nam. Second, it serves as the acceptor for ADPr. Once modified this

3.2. ARTC Family of Eukaryotic ADP-Ribosyltransferases

The ARTC (ecto-ART) family has four members in humans (ARTC1, ARTC3, ARTC4, and ARTC5) and six in mice (Artc1, Artc2.1, Artc2.2, Artc3, Artc4, and Artc5) (Figure 4). While ARTC1−ARTC4 are bound to the plasma membrane by a glycosylphosphatidylinositol anchor, ARTC5 is secreted. At least ARTC1, ARTC2, and ARTC5 have mono-ADP-ribosyltransferase activity and modify arginine side chains generating an α-Nglycosidic linkage between the guanidinium moiety of arginine and ADPr.38 It is thought that ARTC3 and ARTC4 are inactive because they lack the R-S-E motif in the active center and thus are unlikely to bind NAD+. The tissue-specific expression of the different ARTCs is based mainly on RNA data.71,72 While ARTC3 and ARTC4 are expressed broadly, ARTC1 is found predominantly in cardiac and skeletal muscle and ARTC5 is found in testis. Indeed, Artc1 was originally identified in rabbit 1098


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Figure 5. ARTD1, a sensor of DNA damage, coordinates DNA repair processes by providing poly-ADP-ribose chains that function as interaction platforms for repair and signaling proteins. Upon DNA damage, such as single-strand DNA breaks, ARTD1 interacts with the damaged DNA through its N-terminal Zn finger domains. This results in the allosteric stimulation of the catalytic activity of ARTD1. Subsequently, ARTD1 PARylates itself as well as chromatin-associated proteins, including core histones, within seconds and minutes. The PAR chains then serve to coordinate DNA repair processes. PAR chains contribute to liquid−liquid phase separation, which allows formation of subcellular, membraneless compartments. In addition, the PAR chains function as interaction platforms for proteins that contain specific reader domains, including macrodomains and WWE domains. This environment together with the recruited proteins initiates DNA repair and induces signaling that promotes cell cycle arrest and further processes associated with DNA repair. PARylated ARTD1 also interacts with the ATR−CHK1 pathway. Ataxia telangiectasia and Rad-3-related (ATR) and checkpoint kinase 1 (CHK1) function as kinases, which are activated in response to single-stranded DNA breaks. These processes are antagonized by PARG, the main enzyme that degrades PAR chains in the cell nucleus (not shown). PARG is a highly efficient enzyme, explaining the short half-life of PAR chains. Of note is that overactivation of ARTD1 results in cell death because the excessive use of NAD+ depletes cellular ATP stores (for details see the text).

activity.100 Although ADP-ribosylation is a broadly used PTM, it is likely to be less extensive than phosphorylation and ubiquitination, which are associated with more than 500 and 600 writers, respectively.101,102 With respect to the extent of ADP-ribosylation, studies are required that address in greater depth the identity of substrates and how substrate specificity is achieved (see also discussion below). In the following subsections we provide short summaries of major biological activities associated with some of the ARTD enzymes. The more mechanistic aspects that address the consequences of ADP-ribosylation on substrate function are reviewed in section 6. Here more general aspects are discussed, and we refer to many of the excellent recent reviews that provide more comprehensive overviews on the biology of specific ARTDs. 3.3.1. Summary of Biological Functions Associated with ARTD1 and Signaling Processes Targeting ARTD1. 3.3.1.1. The Role of ARTD1 in DNA Repair Is Therapeutically Relevant. ARTD1 is the most thoroughly studied member of the intracelluar ARTs. It functions in numerous processes as summarized in recent reviews.103−108 A key function is certainly its role in stress response, particularly in the control of DNA repair processes. This is manifested by increased sensitivity of Artd1 knockout animals and cells to DNA damage (Figure 5).104 Moreover, a central role of ARTD1 in DNA repair is indicated by the synthetic lethality of ARTD1 inhibition, which affects base excision repair, with defects in double-strand break repair by homologous recombination (HR). Indeed, ARTD1 inhibitors (PARPi) are clinically used to treat certain cancers (Figure

residue is no longer able to participate in catalysis, and therefore ARTs that lack the catalytic glutamate are limited to MARylation activity. The model is consistent with the observation that mutation of the catalytic glutamate in ARTD1 prevents PARylation but still allows MARylation;94 i.e., this finding suggests that the corresponding mutant of ARTD1 now uses substrate-assisted catalysis to modify proteins. The findings summarized above indicate that the ARTD family contains enzymes that can transfer multiple ADPr units in an iterative manner and thus PARylate their substrates. These include ARTD1, ARTD2, ARTD5, and ARTD6, which are referred to as polymer-forming ARTDs (pARTDs). As pointed out before, ARTD1 can synthesize branched PAR chains. Similarly, ARTD2 has also been described to generate branched PARylation,91 while ARTD5 and ARTD6 seem to produce only linear chains.95 Other family members transfer only one ADPr unit, i.e., MARylate substrates.93 These include ARTD3, ARTD4, ARTD7−ARTD12, and ARTD14−ARTD17 and are summarized as MARylating ARTDs (mARTDs). Subsequent studies supported the conclusion that ARTs without the catalytic glutamate are mARTDs.96,97 In addition, the histidine, one of the amino acids involved in NAD+ binding in the H-Y-E motif, is replaced in two ARTD family members, ARTD9 and ARTD13. From analysis of automodification activity, it was concluded that these two enzymes are catalytically inactive.93,98 Because of the altered H-Y-E motif, it was suggested that these two proteins are unable to bind NAD+, which was confirmed for ARTD13.99 On the other hand, recent evidence suggests that ARTD9, in complex with the E3 ligase Dtx3L, possesses MARylation 1099


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Figure 6. Inhibitors of ARTD1, so-called PARP inhibitors (PARPi), are synthetically lethal when combined with mutations in genes that encode for DNA repair proteins. Breast cancer genes (BRCA1 and BRCA2) encode two related proteins that are necessary for DNA double-strand break repair by homologous recombination (HR). Repair by HR is error-free. In the absence of HR, other forms of double-strand repair such as nonhomologous endjoining are used by cells. However, these repair processes are not error-free. Thus, cells with a lack of either BRCA1 or BRCA2 show enhanced mutation rates and genetic instability, defining BRCA1/BRCA2 as tumor suppressors. Inhibition of ARTD1 using a PARPi anticancer drug prevents the repair of single-strand breaks by base excision repair (BER). In cells that transit through S phase of the cell cycle, single-strand breaks progress to double-strand breaks. In the absence of BRCA1/BRCA2 this increase in double-strand breaks, which cannot be repaired error-free, is toxic to cells, and results in cell death. This is particularly relevant in tumor cells that lack checkpoints to prevent cell cycle progression in response to DNA damage. Thus, in tumor cells, inhibition of ARTD1 and the presence of BRCA mutants are synthetically lethal. Other forms of DNA damage repair defects may also be synthetically lethal with PARPi and thus relevant for therapeutic strategies for cancer patients. The arrow thickness indicates whether a process is more or less efficient or likely. Please note that the presently used PARPi’s are not specific for ARTD1 but also interfere with other ARTDs.

6).4,108−110 This is best described for tumors with homozygous deletion of either breast cancer (BRCA) gene 1 or 2, the encoded proteins are necessary for HR. More recent findings have revealed that other defects in HR are sensitive to PARPi.111 It should be noted that these PARPis are typically not specific for ARTD1 but also inhibit other ARTD family members.112 HR is a major pathway to repair double-strand DNA breaks, prevalent after DNA replication because an identical sister chromatid is available as a template for repair.113 ARTD2, which is also activated in response to DNA damage,114 cooperates with ARTD1, and the knockout of both genes in the mouse is lethal.115,116 Largely because of its contribution to stress response, ARTD1 is also considered a target for therapeutic intervention in diseases beyond cancer, including ischemiareperfusion injury after stroke and myocardial infarction, and neurodegenerative disorders such as Parkinson’s and Alzheimer’s diseases.117−120 Genetic ablation of ARTD1 as well as PARPi is protective in disease models, supporting a key role of ARTD1 in stress mechanisms associated with these diseases.109,121 3.3.1.2. ARTD1 and the Control of Chromatin and Gene Transcription. In addition to its role in stress response, another important activity of ARTD1 is in the regulation of gene transcription.105,106 ARTD1 is associated with promoters and enhancers.122 It was observed that ARTD1 participates in chromatin opening postulated to occur in response to signaling cues in Drosophila melanogaster.123 A positive role of ARTD1 and PAR formation has also been documented in the heat shock response.124 Genome-wide analysis of ARTD1 chromatin interaction shows binding to promoters that is reciprocal to histone H1 and histone H3 binding, indicating that ARTD1 functions in gene transcription.125 These and many other findings provide evidence that ARTD1 contributes to the regulation of promoter activity.126 A recent study has used the tryptophan−tryptophan−glutamate (WWE) domain of RNF146 and the macrodomain of AF1521 from Archaeoglobus f ulgidus to study chromatin associated PARylation (for more details of these domains, see below).127,128 The role of PARylation during adipocyte differentiation was addressed

using a modified chromatin immunoprecipitation procotol, referred to as ADPr-ChAP.127 It was shown previously that ARTD1 is required for PPARγ-dependent gene expression in adipocytes.129 Using ADPr-ChAP, PAR chains were detected at active promoters during differentiation of adipocytes. These findings provide evidence that catalytically active ARTD1 is important at specific promoters to stimulate gene transcription. The positive role on gene transcription in adipogenesis has recently been questioned as ARTD1-mediated PARylation was found to interfere with adipogenesis by modifying the proadipogenic transcription factor C/EBPβ, thereby inhibiting its DNA binding activity.130 At present it is not quite clear how these two sets of data interconnect. ARTD1 interacts with nucleosomes by binding to both DNA and histones, and was postulated to have linker histone H1 like functions.131 It was concluded that ARTD1 is associated with repressed chromatin but its association is less stable compared to histone H1. Thus, ARTD1 could have a structural function in organizing chromatin. Its binding is reduced upon automodification, suggesting that signal-dependent activation of catalytic activity might affect chromatin structure. Using ADPr-ChAP, a broad distribution of ARTD1-specific PARylation was measured in response to H2O2 treatment.127 The highest signals were found for repressed regions, which are associated with heterochromatic histone marks. Thus, the pattern of chromatin PARylation differs significantly when signal-dependent gene expression is compared to oxidative stress-induced DNA repair. One possibility is that two or more pools of ARTD1 exist, one of these associated with promoters, another with heterochromatic regions, that respond differently to specific signaling cues. The role of ARTD1 in chromatin structure and gene expression should be considered in the context of Artd1 knockout mice, which seems to be without consequence except when stress is applied to these animals.104 One would argue from these findings that the role of ARTD1 in the control of gene transcription is regulatory but not essential. 3.3.1.3. Posttranslational Regulation of ARTD1. The functions of ARTD1 in chromatin-associated processes imply 1100


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mARTD,93 several studies have postulated and indicated roles of these enzymes in many different cellular processes, based on functional studies and on interaction and substrate screens. The functions that have been linked to mARTDs include activities in gene transcription, stress response, and RNA metabolism. Moreover, mARTDs are involved in signaling and are targets of signaling processes.154−156 Together, these findings, still far from complete, define a number of essential functions of mARTDs that will be discussed below. As for the PARylating enzymes, several of the mARTDs are associated with chromatin and gene transcription, although the evidence is rather sketchy. ARTD8 functions as a cofactor of STAT6 (signal transducer and activator of transcription) and has been implicated in cytokine signaling, e.g., in response to IL-4 and IL-13.157,158 ARTD10 was identified as a binding partner of the oncoprotein MYC, which works as a transcriptional regulator.159,160 ARTD10 interferes with MYC-dependent transformation, but it is unclear whether this is due to its effects on the function of MYC as a transcription factor or because of effects unrelated to MYC activity. ARTD14 is another mARTD that has been connected to gene transcription. ARTD14 appears to act as a transcriptional regulator of the aryl hydrocarbon receptor, which can be stimulated by 2,3,7,8-tetrachlorodibenzop-dioxin.161,162 mARTDs have also been identified as regulators of signaling processes. ARTD10, which is localized in both the cytosol and the nucleus,163 interferes with pathways that signal through NFκB and thus is considered to be a regulator of the immune system.164 This is also consistent with ARTD10 being a substrate of caspases, including caspase-1 that is activated downstream of the inflammasome and controls the processing of the proinflammatory cytokine IL-1β, which is important for immune function.165−167 The NF-κB signaling pathway is prominently controlled by different forms of polyubiquitination. Linear, K63linked, and K11-linked polyubiquitin chains mediate protein− protein interaction to coordinate the flow of information within the pathway, while K48-linked polyubiquitin chains control protein stability of NF-κB signaling components, frequently connected to distinct phosphorylation events.168−170 ARTD10 interacts with K63-linked polyubiquitin chains and is thought to prevent the activation of the NEMO-IKKα/β complex.164 In more general terms, the NF-κB pathway provides a well-studied example in which different PTMs, including ADP-ribosylation, interact and control the activity of specific transcription factors. Various avenues of research suggest that mARTDs are associated with different forms of stress. ARTD15 has been identified as a regulator of the ER-associated unfolded protein response. ARTD15 interacts with two ER stress sensing kinases, IRE1α and PERK, and MARylates and activates their catalytic activities, supporting stress signaling.96,171,172 Several MARylating enzymes, including ARTD8, ARTD10, and SIRT6 have been implicated in the response to genotoxic stress, possibly by regulating ARTD1 (see above).154 Moreover, the expression of some mARTDs is induced upon stimulation of cells with pathogens or interferons. For example, infection of human monocytes by Borrelia burghdorferi enhances the expression of ARTD8, ARTD10, and ARTD12.173 Consistent with this finding is that these genes as well as ARTD8 and ARTD10 proteins are induced in response to interferons.174−176 These and additional findings provide evidence that MARylation is antagonizing stress induced by pathogens, which includes both bacteria and viruses.51,177

that the protein is also the target of signaling events. These emanate either from the cytosol, transmitting extracellular or intracellular cues to nuclear events, or from within the nucleus. As discussed above, damaged DNA can provide such a signal by allosteric activation of ARTD1 (Figure 5).132,133 This triggers auto-PARylation, which promotes DNA repair and subsequently negatively regulates ARTD1 activity. ARTD1 is modified by different PTMs, suggesting that it is integrated in multiple signaling pathways.134 PTMs found on ARTD1, in addition to ADP-ribosylation, include phosphorylation, acetylation, methylation, ubiquitination, and sumoylation. ERK1 and ERK2 kinases are capable of phosphorylating and activating ARTD1.135 These kinases have been associated with oxidative stress in different organs and thus are providing an extra layer of regulation of ARTD1 function.136 The phosphorylation of ARTD1 by CDK2 is involved in gene transcription.137 Recent studies provided evidence that ARTD1 is regulated by methylation. In response to oxidative stress, ARTD1 is methylated at Lys508 by Set7/9, which stimulates catalytic activity.138 Similarly, methylation at Lys528 by SMYD2 also enhances the activity of ARTD1.139 This suggests that these methyltransferases are potential drug targets for modulation of DNA repair processes, particularly because they are overexpressed in certain tumors.140 The acetylation by CBP/p300 controls the interaction of ARTD1 with p50, a member of the NF-κB family of transcription factors, but seems not to affect catalytic activity.141 Similarly, whether the sumoylation of ARTD1, which occurs in response to heat shock by PIASγ, affects its function remains to be determined.142,143 ARTD1 is polyubiquitinated with unclear functional effects.144 Finally, ARTD1 auto-PARylation is thought to modulate interaction with DNA and partner proteins.145,146 ARTD1 is also a MARylation substrate for other ARTs, including ARTD3 and SIRT6.147,148 Both have been suggested to promote the PARylation function of ARTD1 by providing an initial ADPr unit that can be further extended. In addition to ARTD1 PTMs, a large number of binding partners has been identified that are potential regulators of ARTD1 by, for example, affecting catalytic activity, substrate recognition, and/or subcellular localization.149 Together these findings suggest that many different pathways converge on ARTD1, supporting the notion that this protein is a key regulator of chromatin-associated processes. 3.3.2. PARylating ARTD Family Members beyond ARTD1: ARTD2, ARTD5, and ARTD6. In addition to ARTD1, ARTD2, ARTD5, and ARTD6 are also capable of synthesizing PAR chains.104 ARTD2 is less abundant and less active than ARTD1, but is responsible for most of the remaining PARylation activity in ARTD1 knockout cells in response to DNA damage.91 As pointed out above, ARTD2 has been described to function in DNA repair.114 Moreover, ARTD2 appears also to be involved in gene transcription.150 ARTD2 can localize to nucleoli, which seems to depend on active polymerase I transcription,151 and to centromeres.152 The relevance of the presence of ARTD2 at these locations is not fully understood. ARTD5 and ARTD6 have functions both in the nucleus and in the cytosol (see also below). They were originally identified as factors that control telomeres by interacting with the shelterin complex,153 which is also associated with ARTD1 and ARTD2. Thus, all four PAR-forming enzymes have functions associated with the control of chromatin and chromosomal integrity. 3.3.3. Physiological and Disease-Associated Functions of MARylating ARTD Family Members. The largest subgroup of the intracellular ARTDs comprises those that possess MARylating activity.154 Since the first description of an 1101


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Finally, it is worth mentioning that MARylation is associated with cancer.154 This is in part due to the fact that NAD+ is an essential cofactor in many cellular processes that directly affect cell proliferation.178,179 Thus, NAD+-consuming enzymes such as ARTs and sirtuins are obvious candidates to control basic cell physiology, including proliferation and the response to altered metabolic conditions. This has led to the suggestion that several ARTDs, in addition to ARTD1, are potential drug targets not only in cancer but also in other diseases.109,180,181 For example, ARTD8 and ARTD10 are known to modulate cell survival and apoptosis.159,166,182,183 Moreover, ARTD17 and SIRT6 have been suggested to possess tumor suppressor function.184−186 Together these examples provide evidence that mARTDs as well as SIRT4 and SIRT6 participate in the control of cell proliferation and that their deregulation can contribute to disease.

Recently, the existence of a distinct class of sirtuins, the SirTMs, has been recognized.60 This class comprises sirtuins of microbial pathogens. Unlike the mammalian sirtuins, these proteins exhibit robust ADP-ribosylation activity, suggesting that this is their primary function. The genes encoding these sirtuins are genetically coupled to genes expressing macrodomain proteins, which possess de-MARylating activity.60,202 It has been postulated that the associated ADP-ribosylation cycle is involved in stress response.60 These findings provide additional evidence for functional ADP-ribosylation mediated by sirtuin proteins. In section 4 we will discuss hydrolases of ADP-ribosylation, which are present in eukaryotes and also prominently represented in bacteria, archaea, and viruses. These erasers antagonize the writers that have been discussed above.

4. HYDROLASES

3.4. Sirtuins

4.1. Poly-ADP-ribose Chain Degrading Enzymes

Sirtuins are a class of evolutionarily conserved enzymes with seven members in humans (SIRT1−SIRT7) that function in diverse cellular processes, including transcription, aging, and longevity.187 Sirtuins are well studied for their NAD+-dependent deacetylase activity.188−190 More recently some of these enzymes have been described to also remove other lysine modifications, including crotonylation, malonylation, and succinylation.44,45 In every deacylation cycle, one NAD+ molecule is cleaved with the acyl group being transferred from lysine to ADPr, yielding the deacylated lysine, nicotinamide, and O-acyl-ADPr. These metabolites, in particular O-acetyl-ADPr, are proposed to function as second messengers. Several enzymes are capable of hydrolyzing O-acetyl-ADPr, including Nudix hydrolases, ARH3, and macrodomain-containing ADP-ribosylhydrolases such as MacroD1, MacroD2, and TARG1, which are also relevant erasers of ADP-ribosylation, as discussed below.35 Sirtuin-dependent ADP-ribosylation of substrate proteins has been initially described for yeast Sir2, before its deacetylation activity was discovered.191−193 Since then, this alternative catalytic activity has been reported for several sirtuin enzymes, including human SIRT4 and SIRT6. Because sirtuin-dependent ADP-ribosylation has been described as a slow reaction compared to deacetylation, at least in vitro, the functional relevance is being debated.194,195 Nevertheless, the MARylating activity of SIRT4 and SIRT6 is considered important in the processes summarized below. SIRT4 is a mitochondrial enzyme catalyzing MARylation of glutamate dehydrogenase (GDH), an enzyme that converts glutamate to α-ketoglutarate, a metabolite of the tricarboxylic acid cycle (or Krebs cycle). MARylation of GDH interferes with its catalytic activity, and consequently, SIRT4 negatively regulates glutamine/glutamate turnover and mitochondrial ATP synthesis, thereby affecting insulin secretion,196 cell proliferation,185 and cell cycle progression from G1 to S phase in response to genotoxic stress.184 These findings and further studies identified SIRT4 as a protein with tumor suppressor function.184,185,197−199 SIRT6-dependent MARylation is important for the maintenance of genome stability, counteracting agerelated processes such as the development of cancer. ARTD1 and KAP1 (TRIM28) have been described as relevant substrates. MARylation of ARTD1 by SIRT6 triggers ARTD1’s catalytic activity and thus promotes DNA repair.148,200 MARylation of KAP1, which is involved in DNA methylation, by SIRT6 contributes to genome stability through transcriptional silencing of transposable elements.201

The available data provide strong evidence that ADPribosylation is a fully reversible PTM. As mentioned above, PARG, a hydrolase that degrades PAR chains, was identified soon after the description of the PAR-forming ARTD1.33,203 PARG hydrolyzes efficiently the ribose−ribosyl O-glycosidic bonds between ADPr units in PAR chains.204 In addition to PARG, ADP-ribosyl-acceptor hydrolase (ARH) 3 has also been described as a PAR-degrading enzyme.205,206 Moreover, ARH3 hydrolyzes O-acetyl-ADPr, the product of the deacetylation reaction catalyzed by sirtuins.207 Thus, so far these are the two only enzymes that can degrade PAR chains (Figure 3). 4.1.1. Poly-ADP-ribose Glycohydrolase PARG. The PARG gene, which was cloned 20 years ago,208 is expressed as several alternatively spliced mRNA species, which are not identical between mouse and human.209,210 This results in at least five human PARG protein isoforms with somewhat distinct functions. Parg knockout mice, in which all isoforms are absent, show early embryonal lethality.116 Similarly, PARG is also essential in Drosophila melanogaster.211 Under specific conditions some mutant flies progress to adulthood but show a neurodegenerative phenotype. Together these findings demonstrate that the degradation of PAR chains is an essential function.212 Because ARTD1 and ARTD2, the major PAR synthesizing enzymes, are primarily localized in the nucleus, one might expect that the nuclear function of PARG is critical. However, the knockout of the longest isoform in the mouse, referred to as Parg110, which is nuclear due to an N-terminal nuclear localization sequence (NLS), has a DNA repair phenotype but is viable.213 Indeed, this nuclear Parg isoform accounts only for a small part of the overall catalytic activity, while the larger part is cytosolic.214 The cytosolic PARG isoforms are PARG102 and PARG99 in humans, which do not contain the N-terminal NLS.209 Interestingly, the human PARG55 isoform possesses an N-terminal mitochondrial targeting sequence (MTS), and indeed this protein localizes to mitochondria.215 However, PARG55 appears to be catalytically inactive and thus seems not to explain the finding that artificially generated PAR chains in mitochondria are degraded, albeit only very slowly.216 Instead, ARH3, as mentioned below, is likely the relevant enzyme. The different PARG splice variants and the use of alternative translational start codons, both in humans and in mice, have been discussed extensively elsewhere.212 The catalytic domain of PARG is a macrodomain (Figure 7),70,217,218 similar to the mono-ADP-ribosylhydrolases dis1102


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Figure 7. Macrodomain-containing proteins and domain structure. In the human genome 11 genes encode for proteins with recognizable macrodomains. In general, these macrodomains can bind to ADPr. Some function as readers for ADPr polymers (MacroH2A1.1, ALC1, ARTD9, MacroD1, TARG1); some function as readers for mono-ADP-ribosylation (ARTD8); some have catalytic activity as hydrolase for PARylation (PARG); others have catalytic activity as hydrolases for MARylation (MacroD1, MacroD2, TARG1). GDAP2 refers to ganglioside induced differentiation associated protein 2 (MacroD3). The following domains are indicated: ART, ADP-ribosyltransferase domain; CRAL-TRIO, cellular retinaldehydebinding protein−triple functional domain protein; H2A, histone fold domain of H2A, which participates in forming the core of nucleosomes; Macro, macrodomain; MTS, mitochondrial targeting sequence; NES, nuclear export sequence; NLS, nuclear localization sequence; PIP, PCNA (proliferating cell nuclear antigen) interacting peptide; RRM, RNA-binding/recognition motif; WWE, a protein−protein interaction domain named after three conserved residues (W-W-E), where some interact with iso-ADP-ribose.

cussed below. Importantly, PARG hydrolyzes ribose−ribosyl Oglycosidic bonds but does not remove the protein proximal ADPr. This bond between a ribose and an amino acid side chain is distinct from the ribose−ribose bond in PAR chains, explaining why different enzymes are required for these two reactions. Indeed, several mono-ADP-ribosylhydrolases have been discovered that remove the protein proximal ADPr.35 Evidence has been reported demonstrating that PARG has both exo- and endoglycosidase activity.204,219,220 The endoglycosidase activity seems particularly efficient on very long PAR chains.221,222 More detailed analysis of this activity indicated that the endoglycosidic cleavage ceased when polymers became less than ∼40 ADPr units long.221 Moreover, it has been argued that in branched PAR chains synthesized by ARTD1 the glycosidic bond at the branch site (2″ to 1″, Figure 2) is only very inefficiently hydrolyzed by PARG.221,223 These findings are of note because long polymers that can be generated both in vitro and in cells are branched with roughly one fork per 30−40 ADPr units.27,28,224,225 Biologically, the loss of Parg110 results in enhanced sensitivity to DNA damaging agents, similar to the loss of ARTD1.213 Thus, it appears that both the synthesis and the degradation of PAR chains are critical for efficient DNA repair. PAR chains are important for recruitment of DNA repair proteins to the sites of DNA damage, which promotes efficient repair (Figure 4).226 It is not fully understood why prolonged stability of PAR chains sensitizes cells to DNA damage. One possibility is that the local need for energy, i.e., ATP, requires the processing of PAR chains.227−229 PAR chains that are degraded to ADPr by PARG are further processed by NUDIX5 (see also below), which hydrolyzes the pyrophosphate in ADPr to generate ribose-5phosphate and AMP. NUDIX5 can transfer inorganic pyrophosphate onto AMP and thus regenerate ATP in transcription.228 It has been suggested that a comparable process might be relevant during DNA repair and provide locally essential energy equivalents for the repair process, with the pyrophosphate being generated from the use of dNTPs during the repair process.229 Interfering with PARG function, using an

inhibitor or upon knockdown of PARG, protects against certain forms of cell death,230−233 potentially because the release of PAR chains can trigger a specific form of cell death referred to as parthanatos (see section 6.3.5).234 4.1.2. Poly-ADP-ribose and Ser-ADP-ribose Glycohydrolase ARH3. The second enzyme that is capable of hydrolyzing ribose−ribosyl O-glycosidic bonds in PAR chains is ARH3.219 Unlike ARH1, ARH3 is unable to hydrolyze the Arg−ADPr bond as well as several other amino acid−ADPr bonds, which led to the suggestion that ARH3, similar to PARG, cannot fully revert ADP-ribosylation.205,235 However, this interpretation is in need of revision because most recent findings describe ARH3 as the hydrolase that cleaves the Ser−ADPr bond (personal communication of Dr. M. Hottiger, University of Zurich).236 Although many of the details have not been clarified yet, this important finding suggests that ARH3 is capable of fully reverting the activity of ARTD1 in complex with histone PARylation factor 1 (HPF1) as described in more detail below.237 ARH3 is ubiquitously expressed in human and mouse tissues and localized in the nucleus, in the cytosol, and in mitochondria.205,216,230 ARH3, which has an MTS, is as far as analyzed the only PAR-degrading enzyme in mitochondria.215,216 However, an enzyme with PAR-forming activity has not yet been found in mitochondria, and therefore the functional relevance of ARH3 in mitochondria is not clear. On the other hand, the link to Ser-ADPr hydrolysis may suggest that this PTM occurs in mitochondria, which will be interesting to address. It is worth pointing out that ARH3 is considerably less active toward PAR chains than PARG in vitro.205 On that account, it may not be surprising that Arh3 knockout mice, unlike Parg−/− animals, are healthy. In Arh3−/− mouse embryo fibroblast (MEF) cells an increase in PAR chains after DNA damage is observed, indicating that ARH3 is involved in controlling PAR stability. This is in agreement with increased susceptibility of Arh3−/− MEFs to hydrogen peroxide,230 possibly because protein-free PAR chains are more stable (for a more detailed discussion see below). These findings led to the suggestion that ARH3 is primarily important 1103


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findings that Ser-ADPr is an abundant modification.237,244,245 It will also be interesting to see whether ARH3 can release PAR chains from serines and thus produce free PAR, although the structural analysis suggests that it can only interact with a terminal ADPr.235 4.2.3. Macrodomain Containing Mono-ADP-ribosylhydrolases. Three cellular macrodomain containing enzymes, MacroD1, MacroD2, and TARG1, have been discovered that remove ADPr from MARylated substrates that were modified by ARTDs (Figure 7).246−248 All three de-MARylases contain macrodomain folds, a domain which has been implicated widely in ADPr biology.35,249 These findings are important because the identification of MacroD1, MacroD2, and TARG1 provides evidence that MARylation by ARTDs is a reversible process. This is documented by the finding that the automodification of several different mARTDs and of their substrates is reversed. For example, ARTD10 modifies acidic residues,93 and all three enzymes can remove ARTD10-mediated ADP-ribosylation; therefore, they hydrolyze the bond between Glu and Asp side chain carboxylates and the C1″ of the ADPr. Moreover, when automodified ARTD1 is de-PARylated, e.g., by PARG, the remaining MARylation can be removed by the above-mentioned de-MARylases.176,246−248 Whether MacroD1, MacroD2, and TARG1 recognize the glycosidic bond between ADPr and other amino acid side chains remains to be determined. This is relevant because many different amino acids have been described as acceptors for ADP-ribosylation in mammalian cells, including glutamate, aspartate, lysine, arginine, and serine.146,237,243,244,250−255 Protein-free PAR chains have been suggested to function in signaling (see below).234 Formally these can be generated by cleaving protein-linked PAR internal ribose−ribose bonds or by hydrolyzing the amino acid side chain−ribose bond of PAR chains. Candidates for the latter are MacroD1, MacroD2, TARG1, and ARH3. Indeed, it has been suggested that TARG1 possesses such an activity.246 However, this activity is rather weak and the physiological relevance remains to be determined.176 Whether MacroD1 and MacroD2 possess a similar activity needs to be addressed. Although analyses of MacroD1, MacroD2, and TARG1 cellular functions are only just beginning, some recent studies suggest their importance in biological processes. Homozygous, inactivating germline mutations of OARD1, the gene that encodes TARG1, have been linked to a severe neurodegenerative phenotype in children, suggesting that this enzyme fulfills a key function, possibly in neurons.246 Although the molecular consequences of the mutation were not further defined in these patients, another study suggests that de-MARylation is important. In a case report, a patient suffering from progressive neurological deterioration as well as other symptoms was diagnosed with a lysosomal storage disease. The metabolite that accumulated in this patient was glutamyl ribose-5phosphate.256,257 Such a metabolite might be expected to accumulate in lysosomes, particularly in long-lived neurons, if an enzyme were missing that cleaves the glycosidic bond in glutamyl-ADPr. In this case, the degradative pathway might involve a phosphodiesterase that removes AMP from glutamylADPr, combined with hydrolysis of the protein by lysosomal peptidases. The result of such a processing would be the accumulation of glutamyl ribose-5-phosphate in lysosomes. It is unclear whether this patient suffered from a reduction or lack of de-MARylating activity, but it is implied by the chemical structure of the metabolite. Because it is unlikely that all three

under stress conditions, which result in enhanced PAR formation. However, the observations regarding hydrolase activity toward Ser-ADPr mentioned above suggest that ARH3 most likely also functions in basal metabolism of ADPribosylation. This is supported by a recent study indicating that Ser-ADPr is significantly increased in Arh3 knockout cells (personal communications of Dr. M. Hottiger, University of Zurich). The apparent abundance of Ser-ADPr raises the question of whether ARH3 is the only hydrolase for this modification. The results summarized here describe two genes that encode the two PAR hydrolases PARG and ARH3. PARG is synthesized in several isoforms and the available data suggest that these are the major PAR-degrading enzymes, while the activity of ARH3 toward PAR is weak. These observations stem from in vitro experiments with purified enzymes and do not take into account cellular factors that might exist to control specificity and catalytic activity, aspects that will require further studies. Interestingly, ARH3 has now been shown to hydrolyze Ser-ADPr and thus has been recognized to possess an additional catalytic activity that is likely of considerable importance. 4.2. Mono-ADP-ribosylhydrolases

As mentioned above, PARG cannot hydrolyze the bond between the ribose and an amino acid side chain. On this basis, the end products of PARG activity are MARylated proteins. MARylated substrates are also produced by ARTC enzymes, which modify arginine residues, and by the majority of ARTD family members, which are unable to catalyze an iterative transfer of ADPr units to form PAR chains (Figure 3). Moreover, as mentioned above, most ADP-ribosylating bacterial toxins MARylate their substrates. Thus, to fully reverse ADP-ribosylation, additional enzymes are required. The first enzyme identified to hydrolyze MARylation was ARH1, the founding member of the ARH family.238,239 The second family member characterized, ARH3, has PAR degrading and Ser-ADPr hydrolyzing activity. For the third family member, ARH2, no enzymatic activity has been reported.72 In addition to ARH1, several proteins contain macrodomains that have also been documented as MAR hydrolases.35 4.2.1. Mono-ADP-ribosylhydrolase ARH1. ARH1, which is localized in the cytoplasm, is arginine specific and can hydrolyze substrates of ARTC enzymes as well as of argininespecific toxins.240 Consistent with the latter is that Arh1−/− mice are more sensitive to cholera toxin compared to control animals.241 Moreover, these animals develop different tumors suggesting that ARH1 has tumor suppressor function.242 Because the findings so far suggest that ARH1 is the only ADP-ribosylarginine specific hydrolase, the knockout indicates that intracellular arginine ADP-ribosylation is functionally relevant. However, the identity of intracellular NAD+:arginine ARTs remains open. ARTCs seem not to be present intracellularly, yet arginine modification is frequent, as discussed further below,243 hinting at the presence of additional arginine-specific writers. This would argue that ARH1 is not primarily involved in antagonizing pathogen-associated arginine-ADP-ribosylation but that indeed this PTM occurs inside cells and is reversible. Thus, it will be interesting to see which enzymes modify arginine residues in cells and what the functional consequences are. 4.2.2. Mono-ADP-ribosylhydrolase ARH3. The most recent findings suggest that ARH3 hydrolyzes ADP-ribose linked to serine amino acids (personal communication of Dr. M. Hottiger, University of Zurich).236 This relates to the recent 1104


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that hydrolyzes the pyrophosphate in MARylated or PARylated substrates prior to the action of PAR/MAR hydrolases. Thus, the lack of de-MARylation or the overactivation of a Nudix pyrophosphohydrolase might have been the cause of the accumulation of glutamyl ribose 5-phosphate and the associated devastating phenotype. In support of the hypothesis that Nudix proteins process ADP-ribosylated proteins is the observation that hNUDT16 (human Nudix-type motif 16) is capable of hydrolyzing both MARylation and PARylation, while several other hNUDT proteins are able to hydrolyze ADPr.273,274 More recently, hNUDT5 (aka NUDIX5) was identified as an enzyme that degrades PAR to generate ATP. Remodeling of DNA during gene transcription consumes considerable amounts of ATP. In response to progestin, chromatin remodeling and gene transcription depend on ARTD1 to generate PAR chains that are subsequently hydrolyzed by PARG. The resulting ADPr together with pyrophosphate is processed by NUDT5 to produce ATP and AMP, thereby increasing the local concentration of ATP that is required for efficient remodeling.228 Thus, Nudix hydrolases have potentially widespread activities in the control of ADPr and its further processing.

genes/proteins were inactivated, these observations indicate that MacroD1, MacroD2, and TARG1, despite having overlapping specificity in vitro, may have distinct functions and substrates in cells, not least because they occupy different subcellular locations. Several studies indicate an association of the MacroD2 gene with disease. MacroD2 was identified to confer tamoxifen resistance and estrogen-independent growth of breast cancer cells.258 Enhanced expression and amplification of MacroD2 in primary tumors correlates with poor prognosis, suggesting that MacroD2 has tumor promoting functions. Moreover, structural alterations have been linked to the MacroD2 locus in various tumors.259−263 Finally, single nucleotide polymorphisms associated with the MacroD2 locus suggest its involvement in autisticlike traits264 and in the generation of advanced glycation end products,265 which refers to products of nonenzymatic addition of glucose and other reducing sugars, such as ADPr, to proteins and other macromolecules. Importantly, recent findings have demonstrated that macrodomains of positive single-strand RNA viruses can serve as mono-ADP-ribosylhydrolases.176,266,267 Viruses and virus-mimicking constructs expressing mutant macrodomains that have impaired catalytic activity display reduced replication and virulence.57,58,266,268,269 These findings define the MAR hydrolase activity of these viral macrodomains as functionally important, further supporting the notion that MARylation is associated with regulating host−pathogen interactions. In summary, the enzymes discussed in this section have been demonstrated to hydrolyze the amino acid side chain−ADPr bond. This provides formal evidence that ADP-ribosylation is a PTM that is fully reversible. While this has been known for arginine ADP-ribosylation for many years, glutamic acid deADP-ribosylation was discovered only recently. Several important questions remain to be answered. One is whether MacroD1, MacroD2, and TARG1 are able to remove ADPr from other amino acid side chains, such as lysine and serine, which are abundantly modified.237,243 Moreover, it is not known whether these three enzymes together with ARH1 and ARH3 are the only MAR hydrolases or whether additional enzymes will be identified that are capable of de-MARylation, either with a macrodomain fold or a different catalytic motif. It will also be important to determine the relevance of consensus sequences and of targeting mechanisms in defining substrates of the different MAR hydrolases.

5. MECHANISM OF REACTION OF ADP-RIBOSYLTRANSFERASES 5.1. Nicotinamide Adenine Dinucleotide (NAD+)

NAD+ was originally identified as a factor that promotes fermentation in yeast and was referred to as “cozymase”.15,16 Subsequently its chemical structure was resolved as a nucleotide sugar phosphate (Figure 2). NAD+ is a cofactor that is central to many cellular processes, including metabolism and energy homeostasis, and is associated with many diseases.14,16 It serves in reduction−oxidation reactions and in its reduced form, NADH, is a key electron donor during oxidative phosphorylation and thus ATP production. In addition to serving in redox reactions, which was long considered the only main function of NAD+, more recent findings have defined its role in NAD+consuming processes. These include the use of NAD+ in ADPribosylation, in which ADPr is transferred to a substrate with release of Nam. A second NAD+-consuming process involves deacylation reactions on lysine side chains of histones and other proteins, e.g., during the control of chromatin and gene expression by sirtuins.44,275 NAD+ is also consumed by enzymes such as CD38 that produce cyclic ADPr, a second messenger involved in calcium signaling.276 Considering these NAD+consuming processes, synthesis becomes an important issue to balance the NAD+ pool. It involves the de novo synthesis of NAD+ from L-tryptophan and the use of Nam and nicotinic acid (vitamin B3 or niacin), either taken up from a food source or recycled from Nam released in NAD+-consuming reactions.277 A shortage of vitamin B3 and thus of NAD+ is the reason for pellagra, a potentially fatal disease with severe symptoms including dementia.278

4.3. Nudix Hydrolases

In addition to the above-described enzymes that generate ADPr, and possibly PAR, from ADP-ribosylated substrates, another class of enzymes, Nudix hydrolases, has been suggested to process ADP-ribosylation. Nudix (nucleoside diphosphate linked to a variable moiety X) proteins encompass a large family with diverse functions, some with pyrophosphohydrolase activity. They are found in all kingdoms of life and in viruses.270−272 Relevant for the discussion here, Nudix hydrolases may process ADPr or ADP-ribosylated substrates. In this respect the discussion in section 4.2.3 about the lysosomal accumulation of glutamyl ribose 5-phosphate is worth considering.256,257 Glutamyl-ADPr is expected to be generated when proteins are transported to lysosomes prior to deMARylation. Further processing of glutamyl-ADPr by phosphodiesterases, potentially Nudix pyrophosphohydrolases, would then result in glutamyl ribose 5-phosphate. Alternatively, glutamyl ribose 5-phosphate could be the product of an enzyme

5.2. NAD+ and ADP-Ribose Chemistry

The chemistry of NAD+ and ADPr provides a useful introduction to the enzymatic mechanism and characteristics of protein ADPribosylation. In aqueous solution NAD+ is subject to hydrolysis to yield Nam and ADPr. The hydrolysis of NAD+ is relatively slow and independent of pH below 6.0, where the half-life of NAD+ is approximately 6 h; increasing concentrations of hydroxide ions at higher pH values lower the half-life to 3 h at pH 8.0 and just over 20 min at pH 9.0.279 The ribose−Nam bond in NAD+ is relatively unstable for two reasons. The first is that the 1105


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Figure 8. Chemistry of NAD+ and ADPr. (A) Nonenzymatic hydrolysis of NAD+. The ribose−Nam bond is relatively unstable because the Nam is a weak base and, during the reaction, positive charge on the anomeric carbon is resonance-stabilized by the ring oxygen. The partial or full formation of an oxocarbenium ion is part of the transition state for both nonenzymatic and enzymatic hydrolyses. (B) The α- and β-furanose forms of ADPr are in equilibrium with the open chain form, which displays a reactive aldehyde. Reaction with an amine produces an initial Schiff base that could rearrange to yield the 1-amino-1-deoxyketose. (C) ADP-ribose coupled to arginine undergoes exchange between anomers. (D) Potential acyl-chain migration by glutamate-linked ADP.

aldehyde and the closed-ring α- and β-furanose anomers (Figure 8B). The aldehyde will react nonenzymatically with nucleophiles. One such reaction is with amines to form a Schiff base. The Schiff base can cyclize to yield both anomers of the furanose, producing an amine glycoside. Alternatively, the Schiff base can undergo an “Amadori rearrangement” to generate a ketone at the C2″ position and an amine at C1″ (Figure 8B). On proteins, the reaction between the ε-amino group of lysyl residues and glucose can exhibit a surprising degree of site specificity due to the microenvironment of the amine and in particular the proximity of a suitable acid−base catalyst, which can include noncovalently bound buffer components such as phosphate.287,288 The 1amino-1-deoxy-2-ketose product of the Amadori rearrangement can react further to form a wide variety of products in a multifaceted process termed the “Maillard reaction”. While these

positive charge on the anomeric carbon of the ribose can be resonance-stabilized by the ring oxygen (Figure 8A). On this basis, nucleophilic reactions at the anomeric carbon are facilitated by its propensity to adopt full or partial oxocarbenium ion character. The second reason for the instability of the ribose− Nam bond is the weak basicity of the Nam, which has a pKa of approximately 3.3. Stronger bases linked to the anomeric carbon are more stable because they are poor leaving groups.280 This is consistent with the relatively low stability of ADPr on aspartic and glutamic acid side chains while ADP-ribosylated cysteine, serine, lysine, and arginine are more stable.281−285 The ADPr produced by hydrolysis of NAD+ can undergo nonenzymatic reactions that may be relevant to studies of protein ADP-ribosylation.286 In solution, the ribose sugar is in equilibrium between open-chain forms with the reactive 1106


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residues on both the enzyme, the substrate, and accessory factors to impart specificity and efficiency to the reaction. In other words, NAD+ binding is conserved, but the catalytic machinery required to make the transfer specific for a particular substrate or chemical group is a unique feature of the individual system. This wide diversity in ADP-ribosylated groups is fundamentally different from other PTMs, in which the modifying enzymes are rather specific for groups with similar chemistry. For the ARTs, current key questions have to do with substrate specificity: what are the proteins that are ADP-ribosylated, which side chains are targeted, and what is the site specificity of the reaction? ARTs are capable of catalyzing ADP-ribosylation to chemically diverse nucleophiles in proteins, nucleic acids, and small molecules,8,69,156,244,295,296 but the efficiency and speed of the reaction are strongly dependent on the nature of the substrate and the presence of additional factors that participate in the reaction. The various ARTs bind NAD+ in a common manner that facilitates substitution at the anomeric carbon; however, it is still not clear how the actual ADPr transfer occurs and how the specificity for a particular substrate side chain is determined. 5.3.1. NAD+ Binding. When bound to an ART, NAD+ adopts a compact conformation that is different from its conformation when bound to redox enzymes. NAD+ bound to diphtheria toxin provided the first view of this unusual conformation,297 and additional toxin−NAD+ structures in the ARTD family all contain NAD+ in a similar conformation.298,299 The structurally homologous mammalian ARTD enzymes are expected to bind NAD+ in a similar manner to the toxins. The conformation of NAD+ observed in the ARTD toxins is also observed in the ARTC family, despite differences in active site residues and overall fold (Figure 9).48 One notable feature of the

reactions are relatively slow, they play a role in normal aging and also in diabetic pathologies due to elevated blood glucose concentrations.289 The Amadori product between ribose or glucose and an amine would normally cyclize to a less reactive form. However, in the case of ADPr the 5′-hydroxyl is bonded to phosphate and unable to cyclize as a furanose and therefore the Amadori product would exist in the open-chain form. On this basis, the Amadori product from reaction of ADPr could undergo rapid reversal, or it could participate in further reactions. The ARTs catalyze the cleavage of the ribosyl−Nam bond with concomitant formation of a new bond between a substrate nucleophile and the anomeric carbon of the ribose. Importantly, these enzymes can also catalyze hydrolysis of NAD+ by transferring ADPr to water rather than an amino acid side chain of a protein. Thus, ARTs will accelerate the hydrolysis of NAD+ to produce free ADPr, increasing the possibility for nonenzymatic reactions between the protein and ADPr. The rate of these reactions will be dependent on the concentration of ADPr, which in turn will depend on the concentration of NAD+ and the transferase. On this basis, a nonenzymatic reaction between ADPr and a protein could appear to depend on the presence of an ART.290 Once ADPr is enzymatically attached to a protein, there are some interesting possibilities for further nonenzymatic reactions. For example, enzymatic transfer of ADPr onto the guanidinium group of arginine occurs with inversion of configuration to produce the α-anomer, but the product gradually equilibrates between the α- and β-anomers (Figure 8C).291 Because the linkage to the guanidinium group is stable, the adduct can only be removed by an ADP-ribosylarginine glycohydrolase. One such enzyme was characterized with respect to its stereospecificity and was found to recognize only the α-anomer.292 As noted in that study, it is possible that the protein-bound ADPr is constrained and unable to undergo a change in configuration; however, observation of anomeric interconversion in free ADP-ribosylarginine raises the possibility that anomerization could be a ratedetermining factor in the enzymatic removal of arginine-linked ADPr. A second type of transformation could occur with ADPribosylated glutamic acid, as catalyzed by mammalian ARTD enzymes. In this case, the product could undergo an acyl chain migration (Figure 8D) so that the attachment equilibrates between the 1″, 2″, and 3″ hydroxyls. Indeed, there is evidence that this migration occurs with glutamyl- or aspartyl-ADPr both in vitro and in cells.293 Acyl chain migrations have been studied in the context of drug metabolism, where carboxylic acid substrates are enzymatically conjugated to glucuronic acid at the anomeric carbon. Acyl chain migration to another hydroxyl then frees the anomeric carbon which can undergo reaction with amines and subsequent Amadori rearrangement to produce drug−glucuronic acid protein adducts.294 In the case of ADP-ribosylated glutamic acid, migration of the acyl chain to the 2″ or 3″ hydroxyl would facilitate nonenzymatic reaction of the anomeric carbon with neighboring amines. Such a migration would also have implications for MAR hydrolases.

Figure 9. Active site structure and NAD+ binding by the diphtheria and cholera toxin families. (A) The catalytic domain of diphtheria toxin with bound NAD+ is shown as a representative member of the ARTD family (PDB ID 1TOX297). (B) The catalytic domain with bound NAD+ from the Clostridium botulinum C3 exoenzyme, a member of the ARTC family, is shown (PDB ID 2A9K302). (C and D) Views of the NAD+ molecule bound in the active sites of these two enzymes. In the case of the ARTD family, the active site is characterized by a conserved H-Y-E motif, whereas for the ARTC family the conserved motif is R-S-E. Despite the distant relationship between these enzymes and differences in their conserved active site residues, NAD+ is bound in a similar constrained conformation characterized by a dihedral angle about the Nam−ribose bond (N1N−C1D) of close to 0° and a very short distance between PN and N1N atoms, namely the phosphorus atom closest to the Nam ribose and the ring nitrogen of Nam.

5.3. ADP-Ribosyltransferase Mechanism

ART enzymes are present across all living systems and have evolved to catalyze ADP-ribosyl transfer onto a wide variety of nucleophiles on both proteins and nucleic acids.7 The fundamental mechanism for their activity is based on a common mode of NAD+ binding that primes it for nucleophilic transfer of ADPr, combined with “opportunistic” use of neighboring 1107


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characterized by a conserved H-Y-E sequence motif (Figure 9).34 These residues all make contact with the substrate NAD+ and mutation of any of the three to alanine drastically compromises catalytic activity. In the case of diphtheria toxin, the H-Y-E motif consists of H21, Y65, and E148. Mutation of either H21 or Y65 to alanine decreases transferase and glycohydrolase activities over 100-fold, an effect that is due primarily to loss of NAD+ binding affinity.308,309 Mutation of the catalytic glutamate, E148, to aspartate, glutamine, or serine has little if any effect on NAD+ binding, but results in a 100-fold or greater loss in ART activity.310 Furthermore, the E148S mutation in diphtheria toxin decreases glycohydrolase activity only 10-fold, while mutation to aspartate or serine actually increases glycohydrolase activity slightly.310 The catalytic glutamate is therefore different from the histidine and tyrosine residues because its primary role in catalysis seems to involve the transfer of ADPr to a substrate. This point is particularly important for the mammalian ARTD family because in several members the glutamate is not present but the enzymes are still able to catalyze mono-ADP-ribosyl transfer.93 In addition, mutation of the active-site glutamate in ARTD1 to glutamine abolishes its PAR chain forming activity, but not its mono-ADP-ribosyltransferase activity, demonstrating that the glutamate plays particular roles depending on the nature of the substrate.94 The ARTC family retains a distant structural resemblance to the ARTD enzymes, but the conserved H-Y is replaced with R-S, while the catalytic E is retained. Like the H-Y motif in the ARTD family, the R-S motif in the ARTC family promotes binding of NAD+ in a manner that primes it for cleavage of the ribose−Nam glycosidic bond (Figure 9). In both families, the catalytic glutamic acid increases the efficiency of ADP-ribosyl transfer, but is less important for NAD+glycohydrolase activity.311 To summarize, NAD+ is bound by ARTs so that the anomeric carbon is open to nucleophilic attack and at the same time the conformation of the bound NAD+ weakens the ribose−Nam bond to an extent that it is almost broken prior to the nucleophilic attack. This largely dissociative mechanism is consistent with the ability of a variety of different nucleophiles to participate in the reaction. This raises the question of how specificity in the reaction is achieved. 5.3.2. Substrate Binding and Specificity. 5.3.2.1. Interaction of ARTs with NAD+ and Substrates. There is no structure of a mammalian ART in complex with its substrate, but two bacterial ART toxin−substrate complexes have been characterized.298,311−313 These structures are remarkable because in both cases the progress of the reaction could be monitored within the crystals. The Pseudomonas aeruginosa exotoxin A catalytic domain (ETAc) was crystallized in complex with its substrate eEF2.298,312 A surprising feature of the ternary complex with a stable NAD+ analogue, β-TAD (β-methylene-thiazole-4carboxyamide-adenine dinucleotide), was that the reactive NE2 atom of the diphthamide was approximately 11 Å from C1″ of the Nam ribose.298 In the ETAc−eEF2 complex, the active site is completely open and solvent-exposed. In fact, it was demonstrated that this open active site allowed ETAc to catalyze ADPribosylation when crystals of the complex were soaked with NAD+. Therefore, the complex within the crystal was catalytically competent and somehow the 11 Å distance between the diphthamide NE2 atom and ribose C1″ was reduced without large domain movements. From these structures, it was concluded that the reaction proceeded via a fully dissociative mechanism, with active site residues, including the catalytic

ART−NAD+ conformation is that the torsion angle around the scissile N-glycosidic bond is approximately 0°, which is never observed in NAD+ molecules bound to oxidoreductases and which may correlate with lengthening and weakening of the scissile bond.300 Another feature recognized in a detailed comparison with NAD+ bound to oxidoreductases was the very short distance between PN (the phosphorus atom closest to the Nam) and the N1N atom (ring nitrogen of Nam); this distance (4.7 Å) was shorter than that observed in any of the examined oxidoreductase-bound NAD+ molecules.300 The mode of NAD+ binding by the ARTs is thought to contribute to catalysis: the C1″ atom of the Nam ribose, the site of nucleophilic attack, is solvent exposed and available for interaction with an incoming nucleophile; the Nam is buried and desolvated, which may destabilize the glycosidic bond;48 and the pyrophosphate is positioned in a manner that may stabilize the oxocarbenium ion transition state.301 As with nonenzymatic substitutions at the anomeric carbon, the formation of an oxocarbenium ion transition state is a key part of the enzymatic mechanism.303 The exact pathway taken has implications for the substrate specificity of the reaction. For a concerted, SN2 reaction, formation of a bond between the anomeric carbon and the substrate nucleophile begins in concert with cleavage of the ribose−Nam bond. Therefore, this type of reaction will proceed most efficiently if the incoming nucleophile is relatively strong compared to the leaving group. For a fully dissociative SN1 reaction, the ribose−Nam bond would be completely broken before the nucleophile attacks the oxocarbenium ion intermediate. For such a dissociative SN1 mechanism, the nature of the incoming nucleophile is less important than for a concerted SN2 reaction. The extent of the SN2 character of the reaction has been examined using kinetic isotope effects. Such experiments with diphtheria and cholera toxins, which are closely related to the mammalian ARTs, i.e., ARTDs and ARTCs, respectively, indicate that the reaction follows a “dissociative SN2” pathway, in which the ribose−Nam bond is almost completely severed before the substrate−ribose bond begins to form.304−306 A predominantly dissociative mechanism is compatible with a number of different nucleophilic substrates. The ARTs are able to catalyze ADP-ribosylation on both relatively weak nucleophiles, such as glutamic acid or the diphthamide moiety in eEF2, as well as stronger nucleophiles including the thiol in cysteine, εamino group of lysine, guanidinium in arginine, and hydroxyl groups in ADPr and serine.85 In addition, all of the ARTs exhibit NAD+-hydrolase activity, in which the nucleophile is water. Some ARTs, such as Artc2.2, are thought to function primarily as NAD+ hydrolases because they catalyze NAD+ hydrolysis at relatively high rates in addition to their ability to control cell surface receptors (see below).307 NAD+ hydrolysis by ART toxins and mammalian ART enzymes is relatively slow and likely a nonproductive side reaction. The hydrolysis reaction can be viewed as a “nonspecific” transfer of ADPr onto water, which occurs at a slow but significant rate that is maximized by binding of NAD+ to the ART and the very high concentration of water. Although NAD+ hydrolysis by these ARTs probably has no biological function, it demonstrates that these enzymes are capable of nonspecific reactions, consistent with a dissociative nature of the catalytic mechanism and the relatively open active site. The ARTD family includes diphtheria toxin and mammalian enzymes that transfer one or iteratively multiple ADPr units (MARylate and PARylate, respectively) onto substrates and are 1108


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that the analysis of in cell protein modifications, including histones, revealed that most of the serine acceptors are preceded by a lysine, providing information toward a consensus sequence for the ARTD1/HPF1 complex (for more details see below) and possibly other ARTD complexes.237,244,245,320 In light of these novel findings it is worth pointing out that in vitro ARTD1 modifies acidic residues and lysines as well.146,250,251,255,321 ARTD1 accounts for the large majority of ADP-ribosyltransferase function in cells.104 It was then not surprising that the proteome of cell lines and tissues contains a considerable amount of Glu-, Asp-, and Lys-ADPr.243 A point of discussion is whether ARTD1 is capable of modifying both acidic and basic residues as well as serines according to the new information. It will be interesting to investigate what the underlying structural and biochemical bases are for these observations. One aspect of concern is that the lysine in the KS consensus sequence, as pointed out above,244,245 might become modified by glycation as a result of ADPr migration and/ or of NAD+ hydrolysis.287−290,322,323 Moreover, if ARTD1 is the major enzyme to modify glutamates in cells, the analysis of over 800 Glu-ADPr sites might be informative.252 Several consensus sequences were derived, some containing proline, others a conserved lysine or the sequence ES. The latter is interesting because, as for the KS consensus mentioned above, two potential acceptor sites are close together. Using NAD+ analogues and analogue sensitive ARTD1−ARTD3 (see also below), many substrates were identified that possess glutamates as acceptors and that show similarities to the above-defined consensus sequences.324 The latter work was able to specify that Glu in combination with Pro or with a basic amino acid (at various positions relative to the acceptor site) correlated with ARTD1 and ARTD3 activity, respectively.324 It is important to reiterate the observation that ARTD1 changes substrate specificity when in complex with HPF1. It will now be important to compare the findings from in vitro and in cell studies to determine which substrate is modified at what site(s) in response to which condition. Together these findings reveal that acidic residues and serines are major acceptor sites in cells, to a significant part as a result of activities of ARTD family enzymes. More elaborate protocols have been developed to modify substrates, to enrich ADPribosylated peptides, and to fragment these modified peptides. It is due to these developments that we obtain more refined information about substrates and modification sites. Nevertheless, it is still of concern that the complex chemistry of ADPribosylation may confuse some of the analyses, in particular the identification of acceptor sites. Furthermore, in some protocols PAR chains are removed, e.g., by PARG, preventing distinguishing between PARylated and MARylated sites. On a positive note, these studies and findings teach us that the mass spectrometric analysis of ADP-ribosylation sites has come a long way to reach a state that allows detailed characterization of this modification with more confidence. For the further analysis of ADP-ribosylated sites, the ability to synthesize specific peptides with amino acids that carry ADPr or to appropriately modify such peptides chemically will be useful. For example, modified peptides can be applied for comparison with sites in proteins and to produce antibodies to measure such sites. Synthesizing ADPr-modified peptides has been challenging because of the nature of ADP-ribose with its numerous reactive sites. Nevertheless, the techniques to ADP-ribosylate peptides chemically is progressing and has been achieved for lysines.325−328 It will now be interesting to see the production

glutamate, stabilizing and guiding the oxocarbenium ion to react with NE2 of the diphthamide. Nonconserved residues in ETAc are important for ART activity. Scanning mutagenesis of a loop near the active site, residues 457−551, highlighted the importance of two residues: E546 and R551.312 Mutation of E546 reduced the eEF2-directed transferase activity 100−1000-fold or more depending on the nature of the change; mutation of R551 to histidine or cysteine abolished catalytic activity, whereas mutation to glutamine or lysine reduced it only slightly. On this basis, these residues are as important for catalysis as the conserved H-Y-E motif consisting of H440, Y470, and E553. For example, mutation of either the conserved E553 or the nonconserved E546 to alanine resulted in similar 600-fold reduction in transferase activity. In general, changes in E546 and R551 have much greater effects on ADPribosyl transfer to eEF2 than on glycohydrolase activity, consistent with the notion that nonconserved residues surrounding the active site have a major influence on efficiency of the reaction toward a particular substrate. In the cocrystal structure of iota toxin and its substrate actin, there was an 8 Å distance between the actin target, R177, and C1″ of the Nam ribose.311 Adoption of an alternate side chain conformation could reduce this distance to 5.6 Å; larger conformational changes seem unlikely because R177 is part of a β-sheet. Nevertheless, R177 was ADP-ribosylated when the crystals were soaked with NAD+. The iota toxin is a member of the ARTC family, and in addition to the “R-S” motif that mediates binding of NAD+, it has an “E-X-E” motif where the two glutamates correspond to E378 and E380. E380 is hydrogen bonded to the 2″-OH of the Nam ribose and occupies a similar position to the conserved glutamic acid of the ARTD family. Mutation of E380 drastically reduced both ADP-ribosyltransferase activity and glycohydrolase activity, whereas mutation of E378 affected primarily ADP-ribosyltransferase activity.311 As with ETA, the “signature” conserved catalytic elements in iota toxin function in the general activation of NAD+ that facilitates basal glycohydrolase activity while the less broadly conserved residue was critical for enhancing the efficiency of ADP-ribosyl transfer to a specific substrate. 5.3.2.2. Modified Amino Acids and Consensus Sequences. In addition to these structural and catalytic considerations, the acceptor amino acids have been of considerable interest, including whether selective consensus sequences can be derived for ARTs. Original studies had suggested that acidic amino acids are the main sites of ADP-ribosylation.314,315 However, subsequent work identified many other ADPr acceptor sites in addition to glutamate and aspartate, including lysine, arginine, cysteine, diphthamide, phosphoserine, and asparagine.34,316 The description of these different sites has been based on biochemical studies and the sensitivity of specific amino acid−ADPr linkages to certain chemical treatments. For example, the glycosidic ester bond between ADPr and an acidic amino acid is sensitive to hydroxylamine treatment,317 while the Cys−ADPr linkage is cleaved by HgCl2.286 More recently the characterization of ADPribosylated sites has profited from the development of mass spectrometry techniques. This has been a cumbersome process due to the complexity of ADPr and ADPr chains and their variable sensitivity to different fragmentation protocols as discussed in recent reviews.254,318,319 The most recent analysis led to the identification of Ser-ADPr, a modification suggested previously,284 which appears to be a prominent ADPr acceptor site of intracellular proteins in response to DNA damage and possibly other processes controlled by ARTD1.244,245 Of note is 1109


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Recent studies indicate that the activity and substrate specificity of ARTD1 are further regulated by HPF1.341 This protein is recruited to sites of DNA damage and interacts with ARTD1 to shift its activity from automodification to ADPribosylation of histones. Perhaps more remarkably, HPF1 actually alters the nature of the reaction so that the side-chain specificity for the initial ADP-ribosylation changes from glutamic acid to serine.237 Immediate questions arising are whether other hydroxylated amino acids, i.e., threonine and tyrosine, are also substrates of ARTD1/HPF1 and whether this complex catalyzes preferentially MARylation or PARylation. Moreover, can the substrate specificity of other ARTs be modified by cofactors? Additional important questions raised by this change in specificity due to HPF1 relate to the more global proteomics approaches.146,237,243,244,250−255 For example, a proteomic study using mouse liver tissue indicated that 86% of the ADPribosylation sites occur on arginine residues.243 Does this mean that the directed studies, which point toward modification predominantly of glutamate, aspartate, lysine, and cysteine,97 have failed to capture the relevant modification due to missing factors or inappropriate conditions? Or is it that arginine is overrepresented in liver because of its ability to equilibrate between anomers, which could hinder removal by enzymatic hydrolysis? Additionally, given the complicated chemistry of NAD+ and ADPr, nonenzymatic factors could play a role in the in vivo stability of the modifications as well as introducing bias through differences in sample preparation and analytical methods. In summary, despite the progress that has been made in defining and analyzing substrates and their modified amino acids, more work is required to bring together the various results that have been published. We think that this will be challenging because of the ability of ARTs to catalyze the modification of a wide variety of different groups, as deduced from in vitro reactions, the chemical sensitivity of the modification, and mass spectrometry analysis. An additional aspect that is likely contributing to some of the controversies is that ARTs possess NAD+-glycohydrolase activity, generating ADPr that can modify proteins nonenzymatically. Such glycation products can also be generated upon ADPr migration on a substrate. These processes, which may occur to various degrees in vitro and in cells, and possibly during sample preparation, are potentially resulting in a number of different products. It may well be that in cells some of these nonenzymatic events may result in biologically meaningful products. Defining which of the products are due to enzymatic versus nonenzymatic reactions and which are biologically relevant will be important to resolve. Thus, considering the complexity of these reactions, obtaining definitive answers regarding substrate specificity will be challenging.

of peptides with MARylated acidic amino acids and serines, which will most certainly be important to further define intracellular ADP-ribosylation. Despite the large number of substrates that are modified at glutamate, consensus sequences are difficult to define at present. The question arising is whether ART-mediated ADP-ribosylation occurs at well-defined sequence motifs, as seen in kinasemediated signaling.329 Alternatively, the specificity of ARTmediated ADP-ribosylation may be dictated primarily by the overall structure of the ART−substrate complex. For instance, ubiquitination relies mainly on protein−protein interaction and thus the physical presence of the substrate in close vicinity to the enzyme seems more important than the actual neighboring amino acids of an acceptor lysine.330 Once a substrate is bound by an E3 ligase different lysine residues can be modified, probably because they are simply within reach of the catalytic center. The relative contribution of consensus sequences versus the overall structure of the enzyme−substrate complex and associated domains will be important to define in order to understand the specificity of various ARTs toward particular cellular targets. 5.3.2.3. Role of Additional Factors in the Specificity of ADPRibosylation. Additional factors can affect both the activity and specificity of an ART toward a particular substrate. Cholera toxin and E. coli enterotoxins are activated by a host-supplied ADPribosylation factor (ARF).331 ARF6 is a small GTPase and ARF6GTP, but not ARF6-GDP, dramatically stimulates ADPribosylation of Gsα by the cholera toxin catalytic subunit (CTA1).332 ARF6-GTP also stimulates CT-A1 automodification and ADP-ribosyl transfer to other proteins.333 The structure of CTA1 with GTP-bound ARF6 showed that ARF6-GTP binds to CT-A1 on the side of the protein opposite the active site and effectively “opens” the active site, allosterically altering the conformation of an active site loop that facilitates binding of NAD+.334 It is still not clear how Gsα is engaged by CT-A1 such that the target arginine is ADP-ribosylated. In a mutagenesis study, residues outside of the active site were found to affect ADP-ribosylation of Gsα, but not a small molecule guanidine substrate.335 In addition, Gsα is a poor substrate for CT-A1 on its own, but ADP-ribosylation is improved in the presence of Gβγ.336 Thus, the cholera toxin catalytic subunit undergoes allosteric activation by binding ARF6-GTP, increasing its general level of ADP-ribosylation activity, but activity against its target Gsα is additionally dependent on very specific interactions with both the target and target-associated factors. It has been suggested that multiple layers of regulation also exist in the mammalian mono- and poly-ADP-ribosyltransferases. Members of the ARTD family have domains, typically Nterminal to the catalytic domain, that serve to regulate and direct catalysis. In the case of ARTD1, the catalytic domain is inhibited by a closely associated helical domain or PARP regulatory domain (PRD). The catalytic domain of ARTD1 with the PRD has considerably less catalytic activity in the presence of DNA compared to the full-length protein.337 Removal of the helical domain/PRD leads to DNA-independent poly-ADP-ribosyltransferase activity by the catalytic domain.338 For intact ARTD1, inhibition by the helical domain is relieved when DNA with a single- or double-strand break is bound by two zinc finger domains.133,339,340 Binding of broken DNA to the zinc fingers transmits an allosteric signal through the helical domain/PRD that activates the catalytic domain.132,338 This DNA-dependent activity of ARTD1 results in PARylation of ARTD1 itself (automodification) as well as substrates.

6. FUNCTIONAL CONSEQUENCES OF ADP-RIBOSYLATION In this section we summarize functional consequences of both MARylation and PARylation. This includes allosteric effects and consequences on protein−protein interactions. Moreover, we will address the role of protein-free PAR chains, which are capable of signaling. The generation of PAR chains is also tightly connected to metabolism because of the involvement of the cofactor NAD+ in many cellular processes. Therefore, the regulation of the production and the consumption of NAD+ are important parameters to control PAR production and its consequences.277 We will begin with section 6.1 describing the different approaches to identify substrates. 1110


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6.1. Substrates of ADP-Ribosyltransferases

Various approaches have been taken to identify ADP-ribosylated proteins. Many candidate proteins have been analyzed and described, with selected examples discussed in sections 6.3 and 6.4. In terms of substrate identification, recent efforts have focused on defining ADP-ribosylation substrates on the whole proteome level. Most prominent are the advances made by using mass spectrometry, which have provided a large number of potential substrates (see, for example, refs 237, 243, 252, and 255; for a database of ADP-ribosylated proteins see ADPriboDB at http://adpribodb.leunglab.org342). In combination with knockdown, knockout, and inhibitor studies, some conclusions about the relevant enzymes can be drawn. As expected from many biochemical experiments, the majority of substrates are related to ARTD1. Additional methods have been employed to define substrates of specific ARTD family members. One was to use protein arrays in combination with in vitro ADP-ribosylation assays that resulted in potential substrates of ARTD2343 as well as ARTD10 and ARTD8.344 The kinase GSK3β was one of the identified substrates of ARTD10, which was demonstrated to be inhibited reversibly upon ADP-ribosylation both in vitro and in cells.247,344 Another approach is to use NAD+ analogues that allow the subsequent analysis of the modified substrates in a complex mixture of proteins. Such analogues were designed with an alkyne group to allow click labeling.195 Indeed, potential substrates of ARTD1 and ARTD5 could be identified.345 To further expand on the substrate specificity of individual ARTs, a so-called “bump-hole” strategy was developed. This involves the use of NAD+ analogues that can only be used efficiently by ART mutants and that can be easily detected once transferred to substrates. This has been applied to different ARTD family members and allowed the identification of potential substrates.346,347 For example, a role of ARTD11 in nuclear pore complex biology and of ARTD10 and ARTD11 in RNA biology was suggested.347 A similar approach was developed with NAD+ analogues that are compatible with polymer formation.324 Using ARTD1−ARTD3 mutants capable of using these analogues revealed many nuclear proteins involved in processes such as DNA repair, transcription, and chromatin organization as predicted from previous studies. Whether these mutant ARTD enzymes possess the identical substrate specificity as the wild-type proteins will have to be demonstrated. Together the proteome-wide studies provide us with an increasing number of ADP-ribosylation substrates. The challenge for the future will be to define functional relevance of MARylation and/or PARylation on the various substrates.

Figure 10. Protein domains that function as “readers” of ADPribosylation. The different domains that have been identified as readers of PARylation (left) and MARylation (right) are shown. The specificity of the different reader domains for PAR chains are shown in Figure 11. While several domains that interact with PAR chains have been identified, thus far only macrodomains have been shown to selectively interact with mono-ADP-ribosylated proteins.

MARylation or PARylation (Figure 10). Originally macrodomains were identified as ADPr binding domains. 349 Subsequent work demonstrated that some mammalian as well as viral macrodomains are capable of binding to PAR chains, probably by binding to the accessible, terminal ADPr unit (Figure 11).351−354 This is true for MacroH2A1.1, one of only 12 human proteins, encoded by 11 genes, that possess one or several macrodomains (Figure 7).35 The interaction of MacroH2A1.1, a core histone, with PAR chains is thought to contribute to chromatin reorganization in the vicinity of regions of DNA damage.354 Similarly, ALC1 is recruited to DNA damage sites through its PAR-binding macrodomain.353,355 The macrodomain-containing ARTD9 also interacts with PAR and is proposed to participate in DNA repair.356 Other macrodomains are selective for MARylated substrates, as shown for macrodomains 2 and 3 of murine Artd8.357 These can be used to read MARylation of ARTD10 as well as its substrates.176,358 Because these two macrodomains are specific for MARylation and are unable to interact with PAR chains, they might read ADPr together with the underlying amino acid sequence, potentially providing specificity (Figure 11). Of note is that the macrodomain in PARG was only recognized when the structure of its catalytic domain was solved.70,217 Thus, it might be possible that additional macrodomains exist that have not been recognized as such. Moreover, it may be that completely different MAR reader domains have yet to be discovered. 6.2.2. PAR Binding Peptide Motif. By analyzing PAR binding proteins, a short 20 amino acid motif was identified that mediates protein−PAR interaction.359 This was further developed to yield an eight amino acid PAR-binding sequence (PEPPAR) that contains a six-residue consensus motif comprised of basic and hydrophobic amino acids (Figure 10).360 In addition to proteins that are associated with DNA-related processes such as repair, chromatin organization, and replication, this PEPPAR motif is also found in proteins involved in the control of RNA metabolism and protein biosynthesis. In fact, several hundred proteins have been reported to contain such a PEP PAR sequence.359,360 Examples are the tumor suppressor p53 and the Werner protein, which is associated with a premature aging

6.2. Domains That Recognize ADP-Ribosylation

Here we first summarize the different domains that have been found to interact with various forms of ADP-ribosylation (Figures 3 and 10). Because of the specific properties and the length of PAR chains, it was suggested early on that they could function as interaction modules for proteins and possibly other macromolecules. The ADPr reader domains and their specificity as well as the functional consequences will be discussed. 6.2.1. Macrodomains as ADP-Ribose Binding Modules. Macrodomains are the most widely distributed and versatile protein domains that interact with ADP-ribosylation and are associated with ADPr metabolism.7,35,53,249,348 Macrodomains have a conserved structure with a central six-stranded mixed βsheet, which is flanked by five α-helices.349−351 As pointed out above, some macrodomains are MAR or PAR hydrolases. Others lack enzymatic activity and function as reader modules for either 1111


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Figure 11. Specificities of ADP-ribosylation reader domains. (A) Interactions with MARylated proteins. Macrodomains that bind MARylated proteins interact with ADPr and probably also with the underlying protein sequence. Interaction with the protein itself is suggested by the observation that these macrodomains do not interact with PAR chains and thus appear to have insufficient affinity for the terminal ADPr unit only. (B) Interactions with PAR. Some macrodomains interact with ADPr and bind the terminal ADPr of PAR chains. Similarly, the BRCT domain recognizes the terminal ADPr unit; the predication is that these domains are not protein specific. The PBZ domain recognizes also the terminal ADPr, but additionally the adenosine ring of the penultimate ADPr. Thus, this interaction requires at least an ADPr dimer. Several domains, including the WWE, the FHA, and the OB-fold domains read iso-ADPr and therefore require also at least an ADPr dimer for binding. Branching of PAR chains creates an additional unique interaction surface that is specific for long chains. However, so far no domains have been described that are selective for this region of PAR chains.

disorder.361−363 The binding may depend on PAR length as shown for example for p53.364 Moreover, the presence of the PEPPAR motif in proteins associated with RNA metabolism is consistent with the reports indicating extensive regulation of RNA binding proteins by PARylation.365,366 PAR chains possess abundant possibilities to interact with positively charged as well as hydrophobic regions of proteins because of their negatively charged pyrophosphate and the hydrophobicity of the adenine ring, respectively. Thus, specific arrangements or sequences of basic and hydrophobic amino acids are well-suited to bind PAR. So far no structural information is available to further define the molecular details of this interaction and to address specificity. 6.2.3. Tryptophan−Tryptophan−Glutamate (WWE) Domain. The WWE domain, which is named after its three most conserved amino acids, was identified by sequence profile analysis and was postulated to be associated with ADPribosylation (Figure 10).367 Subsequent studies analyzed the RNF146 (aka Iduna) WWE domain (for the molecular consequences, see below), which demonstrated that this WWE domain is able to interact with PAR chains.368,369 Structural evaluation of the RNF146 WWE domain−PAR interaction defined iso-ADPr, i.e., phospho-ribose-AMP, rather than ADPr as binding site in PAR (Figure 11).368,370−372 This indicates that the WWE domain recognizes a structure that is unique for PAR chains. RNF146 is a ubiquitin E3 ligase, a family of proteins that has been noted previously to carry WWE domains.367 Indeed, several WWE domains of E3 ligases have been demonstrated to bind to PAR chains.370 The WWE domain of ARTD11 can also

bind to PAR chains, although this interaction may be different from that of the RNF146 WWE domain. Because the WWE of ARTD11 can interact with ADPr, it may therefore bind to the terminal ADPr unit in PAR. In contrast, the WWE of ARTD8 does not interact with PAR.370,372 In this regard, WWE domains have been reported to mediate protein−protein interactions independent of protein modification with PAR.373 6.2.4. Poly(ADP-ribose)-Binding Zinc Finger (PBZ) Domain. By studying the DNA damage response, which involves the synthesis of PAR chains, the PBZ domain was identified (Figure 10). This domain, with a C2H2 zinc finger motif, is found in the DNA repair protein APLF (aprataxin PNK like factor) and the checkpoint protein CHFR (checkpoint protein with FHA and RING domains), proteins associated with DNA repair.374 Functional Zn fingers of the PBZ domain are important for the interaction with PAR, which is supported by both mutational and structural studies.374−378 The PBZ domain recognizes two adjacent ADPr units by making critical interactions with the two adenine rings (Figure 11), suggesting that at least two ADPr units are required for binding. APLF contains two PBZ domains, which cooperate in binding to PAR. For both APLF and CHFR the PBZ domains are functionally relevant.374,376 A variant C2H2 zinc finger motif was identified in CHK1, which is referred to as “PAR-binding regulatory motif”.379 The kinase activity of CHK1, which mediates the activation of the ATR (ataxia-telangiectasia-related) kinase in response to single-strand DNA breaks and replication fork damage,380,381 is activated upon binding to PAR. This is 1112


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Figure 12. Poly-ADP-ribosylation, as a signal to mediate protein degradation. (A) Axin, a structural component of the WNT signaling complex, is targeted by ARTD5/6-dependent PARylation. This promotes the recruitment of the E3 ubiquitin ligase RNF146, K48-linked polyubiquitination, and subsequent proteasomal degradation of axin. This prevents β-catenin phosphorylation, which results in its stabilization and subsequent nuclear translocation and gene activation. (B) 3BP2 is an adaptor protein that is involved in signal transduction processes associated with stress response. The cellular concentration of the wild-type protein is controlled by ARTD5/6-dependent PARylation, which serves as a binding site for the WWE domain of RNF146, resulting in K48-linked polyubiquitination and proteasome-mediated degradation of 3BP2. (C) Some mutations associated with the autosomal dominant syndrome cherubism are located in the gene encoding 3BP2. These mutants affect the ankyrin-interaction domain in 3BP2 and as a consequence prevent binding to the ankyrin repeat cluster (ARC) in ARTD5. The lack of interaction with ARTD5 prevents PARylation and subsequent RNF146-mediated polyubiquitination. This results in enhanced stability of 3BP2, an increase of its protein level, and finally the activation of signaling pathways that stimulate adverse immune cell functions. In conclusion, these two examples suggest that other PARylation substrates might also become targets of the ubiquitin/proteasomal system.

DNA damage characterized by ARTD1 activation.383 Similar to the WWE domain, the OB-fold interacts with iso-ADPr, indicating that it is specific for PAR (Figures 10 and 11). The breast cancer protein 2 (BRCA2) has also been demonstrated to interact with PAR through its OB-folds.384 Of note is that these domains in BRCA2 bind ssDNA and are critical for DNA repair.385−387 This is interesting because BRCA2 mutations and inhibition of ARTD1 are synthetically lethal as mentioned above (Figure 6). 6.2.6. Additional PAR Binding Modules. Several other domains have been reported to interact with PAR chains (Figure 10). These include the BRCA1 C-terminal (BRCT) domain that contributes to recruiting BRCA1−BARD1 heterodimers to PAR

contingent on the formation of long PAR chains and reveals a novel PAR-dependent regulatory mechanism of the S phase checkpoint.379 6.2.5. Oligonucleotide/Oligosaccharide-Binding Fold Domain. Single-stranded DNA (ssDNA) arises during many processes associated with DNA metabolism, including replication and repair. Compared to double-stranded DNA, ssDNA is less stable and vulnerable to chemical and nucleolytic attacks and needs to be protected by ssDNA binding proteins (SSBs). These proteins are essential and have an oligonucleotide/oligosaccharide-binding fold domain (OB-fold) that mediates binding to ssDNA.382 A recent study has shown that the OB-fold of human SSB1 interacts with PAR and mediates its recruitment to sites of 1113


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chains at DNA damage sites.388 The forkhead-associated (FHA) domain is also involved in DNA repair processes.389 While the BRCT domain recognizes ADPr, the FHA domain reads isoADPr (Figure 11). Finally, a recent study identified the EXO1 PilT N-terminal (PIN) domain, which is linked to ribonuclease activity, as a PAR binding module.390 At present the specificity of this domain is not known.

degradation by the ubiquitin−proteasomal system (UPS).402 This study suggested that PARylation is connected to protein degradation, although it was not clear at that time whether PARylation was important only for the release of TRF1 from telomers or was also a signal for its degradation. That PARylation serves as a signal for protein ubiquitination and subsequent protein degradation is now being supported by several studies. An inhibitor of ARTD5, identified in a chemical genetic screen, interferes with the WNT signaling pathway and the activation of β-catenin-mediated transcription.403 An activated WNT signaling pathway is found in many tumors and thus is a major target in cancer therapy.404 ARTD5 exerts effects on the β-catenin regulating complex through its interaction with axin, which functions as a repressor in the complex (Figure 12A). ARTD5 PARylates axin, which results in its destabilization.403 Subsequently, it was found that the PAR chains on axin recruit RNF146 through its WWE domain.368,405 RNF146 is a RING domain E3 ligase that can promote K48-linked polyubiquitination and proteasome-dependent degradation of the substrate.406,407 The binding of RNF146 to PAR is important for catalytic activity. It results in an allosteric switch of the RING domain from an inactive into an active form.369,408 Of note is that ARTD5/6 interacts directly with RNF146, indicating that PARylation and ubiquitination are tightly coupled.408 Together, these findings provide evidence of a new mechanism to activate a ubiquitin E3 ligase. Moreover, it explains why inhibitors of ARTD5 and ARTD6 are blocking WNT signaling and are thus candidate cancer drugs.409,410 Another link between ARTD5/6-mediated PARylation and the UPS was discovered during the molecular characterization of cherubism, a rare autosomal dominant disease resulting in excessive bone resorption in the mandible as well as other phenotypes (Figure 12B,C). Mutations in the gene encoding the adaptor protein 3BP2 (aka SH3BP2, Src homology 3 domainbinding protein 2) cause the disease.411,412 3BP2 is a tyrosine kinase substrate that mediates signaling in various immune cells, one consequence being the activation of osteoclasts resulting in bone lesions. 3BP2 is stabilized because of mutations in its gene, which results in deregulated signaling and cellular stress.413−415 The large majority of mutations in 3BP2 affect the ankyrin targeting sequence, which prevents binding to the ankyrin repeat cluster (ARC) of ARTD5/6 (Figure 12C). The lack of binding precludes PARylation and subsequent RNF146-dependent polyubiquitination and proteasomal degradation.416,417 These findings provide a mechanistic explanation for the enhanced stability and signaling of mutant 3BP2 and its association with the highly activated osteoclasts and infiltrating inflammatory cells characteristic of cherubism. RNF146 has also been identified to protect neurons from cell death induced by stroke and glutamate excitotoxicity.371 It had been shown earlier that inhibition of ARTD1 activity is protective.418 Mutation of the PAR binding domain in RNF146 abolishes the protective effect, suggesting that the PAR chains generated by ARTD1 also signal through RNF146.371 Unlike the interaction with ARTD5/6 described above, which occurs in the cytosol, the association with ARTD1dependent PAR chains is linked to DNA repair. RNF146 polyubiquitinates ARTD1 and several DNA repair factors that interact with PAR chains or are PARylated and thus in close vicinity to active ARTD1.369 The PAR-ubiquitin-dependent degradation of ARTD1 might be relevant to prevent overactivation of ARTD1 and thus cellular depletion of NAD+. The suggestion that several DNA repair proteins are targets of this

6.3. Functional Role of ADP-Ribose Polymers

6.3.1. PAR Chains Are Interaction Modules for Proteins Associated with DNA Repair and Chromatin Biology. Section 6.2 discussed different domains that have been identified as reader molecules of ADP-ribosylation. The specific properties of PAR chains, including their size and the negative charge, suggested early on that they could affect protein function by steric hindrance and electrostatic perturbation. A well-studied example is the generation of PAR chains in response to DNA damage (Figure 5).108 These PAR chains are very shortlived391,392 and are used to recruit repair proteins and chromatin remodelers with the help of the above-described domains.353−355,374,375,393−395 In consequence, DNA repair processes are enhanced, which works at least in part by an increase in the local concentration of repair proteins. Whether PAR binding also stimulates the activities of most of these proteins has not been evaluated, but is an aspect that might be relevant as has been shown for CHK1, a kinase that is stimulated when interacting with PAR.379 Moreover, local effects on chromatin through the interaction of PAR with macroH2A1.1 are possible, although the mechanistic consequences are not well understood. Additional PAR-mediated effects on chromatin structure are supported by the recent suggestion that the Dtx3L/ARTD9 complex ubiquitinates histones when bound to PAR chains,100 as discussed in more detail below. pARTDs are also important for gene transcription, but the role of PAR chains is not fully understood.105,122,396 One aspect of gene transcription is the processing of RNAs. As eluded to below, ADP-ribosylation is implicated in RNA metabolism. In this respect it is worth noting that different hnRNPs, proteins involved in multiple steps of RNA processing, have been described to interact with PAR and also with ARTD1.366,397,398 In some instances the binding of either PAR or RNA was competitive.398 Thus, PAR chains contribute to the control of both DNA repair and gene transcription. As pointed out above, ARTD1 and ARTD2 produce branched PAR chains. A question arising is whether PAR chain branching is relevant for regulation of repair and transcription. It has been suggested that core histones bind better to branched compared to linear PAR;399 however, no protein motif has been identified that recognizes branch points (Figure 11) and so the mechanism of branch-point binding by core histones is not understood. As PAR chains contribute to liquid−liquid phase separation, which allows formation of subcellular, membraneless compartments (for more details see below), it is interesting to consider that branching affects the ability of PAR to form such compartments and could therefore, in this manner, influence chromatin-associated processes.400,401 6.3.2. PAR Chains Mediate Polyubiquitination and Protein Degradation. ARTD5 and ARTD6 (tankyrase 1 and tankyrase 2) are closely related PAR-synthesizing enzymes that can reside in both the nucleus and cytosol. Originally ARTD5 was identified as a protein localized at telomers.92 TRF1, a negative regulator of telomer length, is PARylated by ARTD5, which results in its release from telomers and subsequent 1114


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mechanism is less easily understood in light of the finding that RNF146 protects against DNA damage.369 Together, these studies provide several lines of evidence that PARylation can serve as a mark for UPS-dependent protein degradation. Other PTMs, including phosphorylation and hydroxylation, have been long known to provide signals for the UPS system.419−421 It is worth noting that other proteins with potentially PAR-binding domains are also E3 ligases.367,374 Thus, the interaction of PAR chains and polyubiquitination systems may be more common than initially anticipated. Indeed, recent proteomic studies identified many proteins whose degradation is controlled by ARTD5/6-dependent PARylation followed by RNF146-mediated polyubiquitination and subsequent proteasomal degradation (personal communication of Dr. S. Smith, Skirball Institute of Biomolecular Medicine, New York University). Because WWE domains recognize iso-ADPr, as far as studied, they require at least two ADPr units and will not bind to MARylated substrates (Figure 11).370 The recognition of isoADPr also means that the WWE domain can interact with PAR chains independently of the substrate that is PARylated. This raises the question about the specificity of WWE-dependent protein degradation: Is every PARylated substrate a potential target of RNF146 or other E3 ligases that can recognize PAR? This will be interesting to define. 6.3.3. PAR Chains and the Formation of Subcellular Compartments. Many subcellular compartments are not bordered by membranes. These form by liquid−liquid phase separations that depend on specific macromolecules and allow the cell to compartmentalize certain biochemical reactions.400 Examples of such liquid phase structures separated from the cytosol or the nucleoplasm include the nucleolus, nuclear pores, and stress granules.422−424 Key to these structures are nucleic acid polymers and proteins that typically possess low complexity domains (LCDs). Such proteins are frequently associated with disease, for example, because of their capacity to aggregate.425 There is increasing evidence that PAR chains can contribute to liquid phase structures. A substantial fraction of ARTD1 has been found associated with nucleoli in unstressed cells.151,426,427 One function of ARTD1 in the nucleolus is to ensure that the silent status of rDNA regions is correctly inherited.428 Moreover, the catalytic activity of ARTD1 is important to maintain the integrity of nucleoli.429 This latter finding might indicate that PAR contributes to the stability of the liquid phase structure of nucleoli.430 That PAR chains are capable of establishing liquid phase structures is shown more directly by the analysis of DNA repair processes. In response to DNA damage, PAR-dependent liquid phase separation (liquid demixing) occurs at the sites of damage.431 It was found that several proteins with LCDs, such as FUS (fused in sarcoma), EWS (Ewing sarcoma), and TAF15 (TATA box-binding protein-associated factor 15), are recruited to the sites of DNA damage. These three belong to the TET family of proteins, which are linked to many diseases.432 They interact with PAR chains through arginine−glycine−glycine-rich LCDs by electrostatic interaction and employ their serine− tyrosine−glutamine−glycine-rich LCDs to promote liquid demixing.431 FUS had been shown earlier to be recruited to DNA damage sites as well as other liquid phase structures (see below) dependent on PAR chain formation.433,434 Importantly, mutations in FUS are linked to amyotrophic lateral sclerosis and to frontotemporal dementia.435 This local organization of a liquid phase structure is thought to contribute to the DNA repair process by creation of a compartment that promotes accumulation of repair proteins, thereby enhancing their local

concentration while at the same time excluding other unwanted biochemical processes. Another structure that shows properties of a liquid phase compartment is the centrosome.436 It is of note that different pARTDs have been described to localize to centrosomes, including ARTD1 and ARTD5/6.437,438 Haploinsufficiency or lack of ARTD1 has been linked to centrosome amplification, suggesting a functional role of this enzyme in centrosome biology.439,440 These findings are consistent with the observations that inhibition of pARTDs prevents centrosome clustering.441−443 This is relevant for tumor cells because they frequently have increased numbers of centrosomes and a lack of centrosome clustering will further enhance genomic instability.444,445 Moreover, PAR formation by ARTD5 is important for centrosome function.446 NuMA (nuclear mitotic apparatus protein) has been suggested to be a functionally relevant PARylation substrate.447,448 Another substrate is Miki, and its PARylation promotes centrosome maturation.449 Collectively, these findings support the notion that PARylation is relevant for centrosome function. Whether this is due to the role of PAR chains in supporting a liquid phase compartment will be interesting to determine. An additional link between ARTDs and compartments that undergo liquid phase transitions are stress granules and P bodies.400,450 These structures participate in RNA biology, including the control of mRNA stability and translation.451 Several ARTDs can be defined as RNA binding proteins, including ARTD12, ARTD13, and ARTD14 that possess RNAbinding CCCH zinc finger domains and ARTD8 and ARTD10 that contain RRMs (Figure 4). With the exception of the inactive ARTD13, these are catalytically active mARTDs. Several of these enzymes and additionally ARTD5, a pARTD, localize to, and ADP-ribosylate components of, stress granules.452 These ARTDs are thought to participate in regulating RNA metabolism (see below). In light of the discussion in this section, they might also contribute to the formation of the liquid phase separation that underlies the structures of P bodies and stress granules. As for other nonmembranous structures, stress granule formation depends on LCD proteins,453,454 and their misregulation is disease-associated.423 In particular, FUS, mentioned above to interact with liquid phase structures involved in DNA damage repair, is capable of assembling different liquid phase structures and is also involved in stress granule formation.433 Whether MARylation, as compared to PARylation, contributes to liquid phase separation is not clear. Of note is that MARylation may function as a seed for PARylation, as has been suggested for the pair ARTD3−ARTD1.147 This, together with the presence of ARTD5 and the activation of different ARTDs upon stress,452 suggests a role for PAR chains and possibly MARylation in stress granule formation. 6.3.4. Excessive PAR Production Is Toxic. A number of experiments indicate that the overactivation of ARTD1 is toxic to cells. This can be explained in part by depletion of cellular NAD+, which is required for glycolysis and many other cellular processes. For example, oxidation of glyceraldehyde-3-phosphate to 1,3-bisphosphoglycerate, catalyzed by glyceraldehyde phosphate dehydrogenase, requires NAD+. During apoptosis, a cell death process that requires energy in the form of ATP,455 the overactivation of ARTD1 depletes NAD+ due to excessive PAR production, which in turn prevents glycolysis and ATP production.456−459 A lack of ATP could interfere with the apoptotic process and instead promote necrotic cell death, which is associated with an inflammatory response.455,460 In addition, 1115


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formed AIF−MIF complex, MIF gains nuclease activity and promotes DNA cleavage upon translocation into the nucleus.471 Together these findings suggest that PAR chains formed in response to stress promote, through an AIF−MIF complex, the degradation of nuclear DNA, resulting in programmed cell death independent of caspases. A likely consequence of the activation of nucleases and cleavage of DNA, particularly in the absence of caspase activity, is a further activation of ARTD1 and the subsequent depletion of the NAD+ pool. This is predicted to result in conditions that favor necrosis, as discussed above. Indeed, AIF has been described to induce necroptosis, a specific form of programmed necrosis.467 These analyses also provide an explanation for the beneficial effect of ARTD1 inhibitors in models of toxic insults.118 While the parthanatos model that has been developed is attractive (summarized in Figure 13), many important questions remain to be clarified. The findings are derived from a limited number of cell types, and it is unclear how broadly applicable the concept is. Moreover, definitive proof of the existence of free intracellular PAR chains is missing. Similarly, it has not been resolved how PAR chains are transported from the nuclear compartment, where they are synthesized primarily by ARTD1, into the cytosol and how this is regulated.472 Along these lines, PAR chains can also be synthesized in the cytosol by ARTD5 and ARTD6, which are under intensive study as potential drug targets in cancer.409,410 Cell death by parthanatos is inhibited by PARG. This may not be too surprising as this is a highly active enzyme that will degrade PAR chains rapidly to single ADPr units, in line with findings that PAR chains are very short-lived in cells.212,473,474 The circumstances under which PAR chains escape the complete hydrolysis by PARG are not fully understood, particularly because the endoglycosidic activity of PARG is considerably weaker than its exoglycosidic activity.220 Expression levels of PARG inversely correlate with ARTD1 and PAR-mediated cell death, which testifies to the important role of PARG in regulating PAR occurrence.466 Another enzyme that may contribute to the generation of free PAR chains is ARH3. It degrades PAR chains to ADPr units through an exoglycosidase activity but may also release PAR chains from substrates.230 With identification of the Ser-ADPr hydrolase activity of ARH3 (see above), it will be interesting to determine whether ARH3 can generate PAR chains through this hydrolase function. These findings indicate that the activities of PARG and ARH3 may be regulated to control exo- vs endoglycosidic activity. 6.3.6. Protein-Free PAR Chains Can Regulate Signaling and Extracellular Processes. The signaling activity of PAR chains was addressed in a recent study that showed extracellular PAR, but not ADPr, was capable of activating macrophages as measured by the production of cytokines.475 This was mediated by the Toll-like receptors TLR2 and TLR4. Moreover, PAR chains were rapidly internalized and sequestered in endosomes. Of note is that no cell death was induced. Evidence for extracellular PAR chains was obtained using NMR spectroscopy.476 It was concluded from this study that PAR chains are associated with the extracellular matrix during bone development, and it was suggested that PAR chains are important for the mineralization of collagen matrixes. In both studies it was speculated that extracellular PAR chains may be derived from necrotic cells; that is, necrotic cell death of osteoblasts occurs during bone formation and could be a source of PAR chains.477,478 The presence of PAR antibodies in systemic lupus erythematosus and in Alzheimer’s disease are also

ARTD1 activation has been linked to inhibition of hexokinase through direct PAR binding. PAR-mediated inhibition of hexokinase will affect glycolysis and thereby reduce energy production.461 In many situations these effects are unwanted, and indeed they are efficiently antagonized by the activation of executer caspases, including caspase-3 and caspase-7. These enzymes cleave ARTD1 and separate the N-terminal DNA binding domain from the C-terminal catalytic domain.462,463 This cleavage prevents the allosteric activation of ARTD1 by damaged DNA that is generated during apoptosis, thus decreasing catalysis and preventing exhaustion of NAD+.133,464 A lack of NAD+ also affects the integrity of mitochondria.465 To summarize, these findings indicate that the overactivation of ARTD1 needs to be blocked in many specific cellular contexts as a measure to preserve the energy status of the cell. 6.3.5. Protein-Free PAR Chains Promote Cell Death. In addition to the decisive role of ARTD1 in balancing apoptosis and necrosis, excessive activation of ARTD1 has also been suggested to induce a cell death process independent of caspases, which is referred to as parthanatos.234,466 Parthanatos has been associated with toxic insults such as ischemia-reperfusion after myocardial infarction and stroke. During parthanatos, PAR chains have been suggested to be released from their location of synthesis, e.g., at the sites of DNA damage, and transported to the cytosol where they are targeted to mitochondria (Figure 13). At

Figure 13. PAR chains promote parthanatos, a form of apoptotic cell death independent of caspases. PAR chains generated in cell nuclei upon stress such as DNA damage are suggested to be liberated and translocated into the cytosol. There they interact with mitochondria and stimulate the protease-dependent release of membrane-bound apoptosis-inducing factor (AIF). Soluble AIF can then interact with macrophage inhibitory factor (MIF), best known for its role as cytokine, and activate the nuclease activity of MIF. This results in extensive DNA fragmentation and subsequently cell death. This process is inhibited by the action of PAR chain hydrolases, in particular nuclear PARG and cytosolic ARH3.

mitochondria PAR chains function as signaling molecules. They activate apoptosis-inducing factor (AIF), a mitochondrial protein.467,468 AIF is located in the intermembrane space and more recently has also been found associated with the outer mitochondrial membrane.466,469,470 In a poorly understood process, PAR chains promote the protease-dependent release of AIF from mitochondria and its subsequent interaction with macrophage inhibitory factor (MIF) in the cytosol. In this newly 1116


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suggestive for extracellular PAR.479,480 Together, these studies point to a role of extracellular PAR chains in both physiological and pathological processes. 6.4. Functions Associated with Mono-ADP-ribosylation

6.4.1. ARTC-Dependent Mono-ADP-ribosylation by Eukaryotic and Bacterial Enzymes and Its Role in Stress Response and Immune Regulation. Extracellular ARTC enzymes modify arginine residues causing distinct changes in the chemical properties of the substrate. While arginine is positively charged at neutral pH, the addition of ADPr, which carries two negatively charged phosphates, will affect the electrostatic surface potential. This could alter substrate interactions with other proteins. As yet no mammalian readers of Arg-ADPr have been identified, although the macrodomain of AF1521 from Archaeoglobus f ulgidus can interact with proteins MARylated at arginine.243 As for other PTMs, the modification by ADPr is likely to exert allosteric effects and modulate protein−protein interactions beyond dedicated reader molecules. One example of modified protein−protein interaction that occurs in cells in response to Arg-ADPr by a bacterial toxin is actin polymerization. G-actin is MARylated by SpvB, a virulence factor of Salmonella important for intracellular replication, and by the clostridial C2 and iota toxins, all belonging to the ARTC family of ARTs.481−484 Modification of R177 interferes with actin polymerization, disrupts the cellular cytoskeleton, and can induce apoptosis.485−487 The latter has been suggested to facilitate the spread of Salmonella to neighboring cells by autophagy.483 Considering that eukaryotic ARTC enzymes are located extracellularly, an issue is the source of NAD+ as an essential cofactor of these enzymes. The serum levels of NAD+, typically below 0.5 μM, are most likely not sufficient for efficient substrate modification, as deduced from in vitro experiments.488 However, in the vicinity of stressed and dying cells that lose their membrane integrity, sufficiently high levels of NAD+ have been measured, which are in the low micromolar range (Figure 14).489,490 This suggests that extracellular NAD+, together with ATP, is a stress response mediator and acts as a danger signal.488 This appears particularly relevant in the immune system and is in agreement with the expression of Artc2 enzymes predominantly in murine T cells and macrophages and one of its major substrates, the P2X7 receptor, that functions as an ATP-gated cation channel.491 The activation of P2X7 in response to ATP, requiring a local concentration of extracellular ATP of at least 100 μM, induces the influx of Ca2+ and Na+ ions and the efflux of K+ ions, which triggers a number of molecular events that promote inflammasome activation and release of pro-inflammatory cytokines such as IL-1β.492−495 Moreover, prolonged activation of P2X7 stimulates apoptosis.496 In addition to ATP, MARylation of P2X7 at R125 by Artc2.2 on murine T cells also results in opening of the channel.497−499 Of note is that while the stimulation by ATP is transient (due to the instability of ATP in the extracellular space), the effect of MARylation results in longterm activation of the channel (Figure 14). No comparable ̈ T cells regulation has been reported for human cells. While naive are sensitive to NAD+-induced P2X7-mediated cell death, activated T cells become resistant, possibly because their P2X7 expression is lower.490,500 The extracellular NAD+ is antagonized by the ecto-NAD+-glycohydrolase CD38, which generates cyclic ADPr (cADPr) and further hydrolyzes cADPr to ADPr, thus reducing the extracellular NAD+ concentrations and inhibiting ARTC-dependent ADP-ribosylation reactions.501 Together

Figure 14. Extracellular ADP-ribosyltransferases are involved in signaling and the turnover of NAD+. On certain murine cells of the hematopoietic system Artc2 is expressed and is capable of MARylating P2X7, a ligand-gated cation channel. ADP-ribosylation results in the long-term activation of this channel, unlike the short-term stimulation by extracellular ATP. Long-term stimulation of P2X7 deregulates ion balance and promotes the influx of Ca2+ ions, promoting apoptotic cell death. Serum concentrations of NAD+ are in the submicromolar range and thus typically are not sufficient for MARylation. However, NAD+ can be released from cells under stress conditions and local concentrations are thought to be high enough for substrate modification. Several extracellular enzymes have been described that degrade extracellular NAD+, thereby participating in the control of ARTC catalytic activities. One of these enzymes is CD38, which is an NAD+-glycohydrolase/ADPr-cyclase. The latter activity generates cyclic ADPr (cADPr), a putative signaling molecule. Of note are other enzymes that degrade extracellular NAD+, including CD157 (an NAD+glycohydrolase/ADPr-cyclase), CD203 (an ectonucleotide pyrophosphatase) and CD73 (a 5′-ectonucleotidase) (not shown in the figure).

these findings suggest that, through regulation of extracellular NAD+ concentrations, T cell functions can be modulated in response to stress and danger signals. Additional substrates of Artc2 have been described. These include a number of membrane-associated proteins of T cells, such as LFA-1 and CD8. The incubation of T cells with NAD+ results in pleiotropic effects, such as reduced cytotoxicity and cell migration, supporting the notion that some of these Artc2mediated ADP-ribosylations are functionally relevant.502−505 Moreover, a recent report demonstrates that CD25 is a major Artc2 substrate.506 CD25 is expressed on regulatory T cells and mediates IL-2 signaling, which is required for their generation and function.507 Several arginines were identified in CD25 as sites of ADP-ribosylation. One of these, R35, is located in the IL2 binding surface of the receptor and prevents binding of, and thus signaling by, the cytokine.506 These results suggest that several membrane-associated proteins are ADP-ribosylated and that the MARylation has functional consequences. While progress has been made in the analysis of Artc2 on immune cells in the mouse, we still know relatively little about ARTCs on other cell types and in other tissues. As pointed out above, ARTC1 is mainly found on muscle cells.72 It is strongly up-regulated during the differentiation of myoblasts to myotubes.508 It modifies integrin α7, which together with integrin β1 forms a dimer that binds to laminin, an extracellular matrix component.509 In C2C12 myotubes, ADP-ribosylation of integrin α7 enhances the binding of integrin α7β1 to laminin.510 Of note is that ARH1, which is thus far the only known enzyme that can remove ADPr from arginine residues, is a cytosolic 1117


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modified G-actin is integrated into an actin filament, MARylation prevents the incorporation of further G-actin subunits. Thus, the barbed end of actin filaments is blocked.516,517 Because the pointed end of actin filaments will be turned over, the result of this MARylation is the complete disintegration of actin filaments, which contributes to bacterial pathogenesis. Other examples are small GTPases that are frequently targeted by bacterial toxins, including those with ART activity.518 Toxins can prevent either the activation or the inactivation of GTPases and thus manipulate signaling processes. In the case of the RhoA GTPase, MARylation occurs at N41 catalyzed by different C-type toxins.519,520 The PTM promotes strong binding to guanine nucleotide dissociation inhibitor, which prevents membrane recruitment and interferes with binding to guanine nucleotide exchange factor. This prevents the activation of RhoA.521,522 One of the consequences of inhibiting RhoA signaling is the disintegration of stress fibers and the reorganization of the actin cytoskeleton.523,524 These examples illustrate that MARylation has selective effects on protein−protein interactions. We also expect that, in addition to allosteric effects, MARylation of proteins by eukaryotic enzymes will modulate the interaction with other proteins or macromolecules. Thus far, only a few macrodomains have been identified that mediate MARylation-dependent protein−protein interactions. These are macrodomains 2 and 3 of murine Artd8, which selectively bind to MARylated substrates, including ARTD10, NEMO, and RAN.164,176,358 It seems unlikely that these domains are the only readers of MARylation. Instead, we suggest that additional domains exist that are capable of interpreting the information contained in this PTM. Several ARTDs have been associated with RNA metabolism and stress granules.365 These include ARTD1 through its many functions in gene transcription and RNA processing.105,396 In the cytosol, many proteins that are linked to ADP-ribosylation are also associated with RNA metabolism.252,255,360,452,525 This is consistent with findings that describe mARTDs as regulators of mRNA stability, silencing, and translation, observations that are mainly based on the identification of ADP-ribosylated substrates and the association of specific domains with RNA binding.365 Indeed, five mARTDs have RNA binding motifs: ARTD12, ARTD13, and ARTD14 each contain a CCCH zinc finger domain, while ARTD8 and ARTD10 carry RNA recognition motifs (RRMs) (Figure 4). Of these, ARTD13, a catalytically inactive family member with antiviral function, is so far the only ARTD with demonstrated RNA binding activity.526,527 In addition to cytosolic events, nuclear RNA processing is also affected by ADP-ribosylation. Several components of the mRNA splicing machinery have been found modified by ADPribosylation.243,252,324,345 Overall these findings indicate that mRNA splicing and processing is tightly connected to ADPribosylation. 6.4.3. Mono-ADP-ribosylation of Ubiquitin. A very recent development is the identification of ubiquitin as a substrate of MARylation. Ubiquitin is well-known for its role in cellular processes such as protein degradation and signaling through K48- and K63-linked ubiquitin polymers, respectively, that are often associated with disease.528,529 While ubiquitination contributes to the control of protein function, its own regulation has been little studied until recently.530 The finding that the Dtx3L/ARTD9 complex MARylates the C-terminus of ubiquitin provides an additional PTM that targets this key signaling protein.100 The ADP-ribosylation of the C-terminus, which is used to form isopeptide bonds between a substrate lysine and

enzyme. Indeed, initial studies suggested that ARH1 is not capable of de-MARylating integrin α7.511 This modification might be relevant to the stress response, which can be accompanied by the release of NAD+ into the extracellular space and thus might be associated with the stabilization of myofibers. Antimicrobial peptides (AMPs) are secreted by epithelial and immune cells and are important components of innate immunity.512 Some AMPs are arginine-rich proteins and were tested for modification by ARTC-dependent ADP-ribosylation. It was observed that human neutrophil peptide-1 (HNP-1) is ADP-ribosylated by ARTC1, while human β-defensin-1 was poorly modified. This modification interfered with the antimicrobial activity of HNP-1. Interestingly, ADP-ribosylated HNP-1 was found in the bronchoalveolar lavage of patients with asthma and of smokers, but not in healthy volunteers.513,514 Again, this suggests a role for ARTC-mediated ADP-ribosylation under stress conditions. The findings summarized above suggest multiple functions of extracellular ADP-ribosylation by ARTC enzymes, mainly associated with stress and inflammatory signals. It is interesting to note that arginine-specific ADP-ribosylation appears to be a modification by one ADPr unit, i.e., MARylation. Thus far, no formal evidence of arginine PARylation has been reported. Moreover, because ARTCs are ectoenzymes, one might expect that Arg-ADPr is a modification that occurs exclusively extracellularly. However, these enzymes have to pass through the ER and the Golgi and thus could modify proteins that are not located at the cell membrane but are either located within these compartments or associated with other vesicles. Indeed, it has been suggested that ARTC1 is activated in response to ER stress and MARylates the GRP78/BiP chaperone in the ER.515 It will be interesting to see whether MARylation affects the activity of GRP78/BiP, especially in light of the involvement of ADPribosylation in the ER-associated unfolded protein response pathway. 6.4.2. Consequences of Intracellular Mono-ADP-ribosylation. An increasing number of substrates that are MARylated are being described in cells, and some have been mentioned above.154 There are cases of apparent allosteric effects of MARylation on specific proteins. One example is the kinase GSK3β, which is reversibly inhibited by MARylation both in vitro and in cells.247,344 Another is the activation of the catalytic activity of ARTD1 by SIRT6-dependent MARylation.148 Here two different functions of MARylation can be envisaged. In one MARylation activates allosterically the catalytic activity of ARTD1, replacing the requirement for ARTD1 to bind to damaged DNA. Alternatively, MARylation provides the first ADPr unit on ARTD1, which can be further expanded by its automodification activity. This could be relevant if the first ADPr transfer of ARTD1 is rate-limiting to form PAR chains. Both mechanisms would explain the enhanced ARTD1 autoPARylation and the DNA repair phenotype observed.148 Moreover, SIRT4, which is localized in mitochondria, MARylates and inhibits glutamate dehydrogenase, again presumably through an allosteric mechanism.196 In many other situations MARylation by eukaryotic enzymes correlates with certain downstream effects but further studies are required to define the mechanisms of action.154 For several bacterial toxins that function as ARTs, the mechanisms of action have been elucidated. MARylation of R177 of G-actin by many different bacterial toxins prevents actin polymerization. It has been proposed that once an ADPr 1118


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finally, E3 ubiquitin ligases are responsible for the substrate specificity of ubiquitination.537 How does the activation of ubiquitin occur without E1 and E2? The findings indicate that ubiquitin is MARylated at R42, which provides an alternate mode of “activation”.536,538 In a second step, the now “activated” ubiquitin is transferred to a substrate with the help of a phosphodiesterase, linking the modified arginine of ubiquitin to a serine of the substrate through phosphoribose (Figure 16).535,538 SidE proteins are toxic when expressed in HEK293 cells, which is antagonized by SidJ, encoded by a gene that is located in the same locus as the gene for SdeA.539 Indeed, SidJ cleaves the phosphodiester bond, indicating that the ribose−phosphate linkage between ubiquitin and a substrate is reversible.540 These findings provide evidence for a novel mechanism for bacterial hijacking of the ubiquitin system, in addition to deregulating conventional ubiquitination processes because R42-ADPribosylated ubiquitin cannot be activated by the E1/E2 enzymes.538 Importantly, the SidE family effectors as well as SidJ are relevant for replication of L. pneumophila,539,541,542 indicating that this PTM is biologically relevant. 6.4.4. Intracellular Arginine Mono-ADP-ribosylation. While extracellular Arg-ADPr is firmly established, several lines of evidence suggest that this modification also occurs within cells. Arg-ADPr is reversed by ARH1, an intracellular enzyme that appears to be specific for modified arginine residues and that is conserved between different mammalian species.72,543 The presence of ARH1 argues that arginine-specific ARTs also exist in cells. This hypothesis is further supported by a recent study using mass spectrometry, which identified several hundred ADPribosylation sites in normal liver with 86% of these being on arginine.243 Because the gene ontology (GO) analysis revealed a high enrichment in mitochondrial, cytoplasmic, and nuclear proteins, it seems likely that at least part of these arginine modified substrates are intracellular proteins. The identity of the enzymes that catalyze intracellular arginine ADP-ribosylation is the next question. One possibility is that splice variants of ARTCs exist that locate to an intracellular compartment. Another is that some of the ARTD enzymes can modify arginine. One candidate is ARTD10 because mass spectrometry analysis of in vitro automodified ARTD10 or modified histones revealed aspartate, glutamate, lysine, and arginine as acceptor amino acids.253 These findings provoke a number of thoughts and questions. First, the use of inhibitors and the chemical treatment of automodified ARTD10 suggested that the ADPr is primarily linked to acidic amino acids.93 Moreover, both mammalian and viral macrodomain hydrolases remove, individually, essentially all ADPr from automodified ARTD10,176,247,267 revealing a key question that has not been resolved at present. Do transferases and hydrolases have multiple specificities with respect to the target amino acid? For the transferases, this might be possible because of the discussed open conformation and the S N 1-like (dissociative) mechanism that makes the ribose C1″ available to different nucleophiles. Less clear is the situation for the specificity of the hydrolases, which remains to be addressed.

ubiquitin, requires high NAD+ concentrations. Because of the blocked C-terminus, this MARylation interferes with ubiquitination of substrates by the conventional pathway. Interestingly, the macrodomains of ARTD9 bind to PAR, which stimulates the E3 ligase activity of Dtx3L. Thus, a model can be proposed, in which upon DNA damage PAR chains are synthesized by ARTD1 and local NAD+ levels are reduced. This results in the recruitment of the Dtx3L/ARTD9 complex to chromatin, where low NAD+ levels reduce MARylation of ubiquitin by ARTD9 and the PAR chains stimulate the E3 ligase, which can modify core histones (Figure 15). At present the consequences of this ubiquitination are not clear, but it seems feasible that it affects chromatin remodeling and DNA repair.

Figure 15. ARTD9 in complex with the E3 ligase Dtx3L couples ADPribosylation and ubiquitination. ARTD9 forms a complex with Dtx3L, an E3 ubiquitin ligase. Together with the ubiquitin activating enzyme E1, which forms a thioester linkage with the C-terminus of ubiquitin, and the ubiquitin conjugating enzyme E2, on which activated ubiquitin is transferred by trans-thioesterification, ubiquitin is ADP-ribosylated at its C-terminus. This prevents the use of ubiquitin in conventional ubiquitination reactions. This seems to be the preferred mechanism when NAD+ is high. Upon DNA damage, PAR chains are synthesized and recognized by the ARTD9 macrodomains. This together with the locally reduced NAD+ concentration prevents MARylation of ubiquitin and instead ubiquitin is used in conventional ubiquitination reactions. It is proposed that histones and other chromatin associated molecules are ubiquitinated that may affect local chromatin organization and DNA repair.

It is worth pointing out that bacterial ARTs have also been identified that MARylate ubiquitin. Pathogens target the ubiquitin system, in addition to many other proteins that fulfill regulatory activities, in many different ways to modulate host cell functions.531−533 Legionella pneumophila possesses more than 300 genes that encode proteins that manipulate host cells, including SdeA.534 This protein, one of several paralogs in the SidE effector family, ubiquitinates Rab small GTPases and the tubular endoplasmic reticulum protein, reticulon 4, independent of E1 and E2 enzymes.535,536 The E1 and E2 enzymes are used in the conventional ubiquitination process to activate ubiquitin in an ATP-dependent manner as follows: the E1 ubiquitinactivating enzyme forms a thioester linkage with the C-terminus of ubiquitin; the activated ubiquitin is transferred by transthioesterification onto the E2 ubiquitin conjugating enzyme;

7. CONCLUSIONS AND OUTLOOK It is roughly 50 years since the first description of ADPribosylation and the identification of ARTD1 and bacterial toxins that can PARylate and MARylate substrates, respectively. In the meantime, we have learned that writers and erasers of ADPribosylation developed from bacterial toxin−antitoxin systems that are used to cope with various forms of stress. It is possible that nucleic acids were the initial substrates prior to the 1119


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Figure 16. Alternative activation of ubiquitin through MARylation. SdeA of Legionella pneumophila hijacks ubiquitin through an alternative activation mode that is independent of the ubiquitin activating enzyme E1 and the ubiquitin conjugating enzyme E2. Instead, ubiquitin is activated by MARylation of arginine 42 by the ADP-ribosyltransferase (ART) domain of SdeA. Subsequently, the phosphodiesterase (PDE) domain of SdeA transfers the activated ubiquitin onto serine amino acids of substrates with release of AMP. Thereby a previously unrecognized ribose−phosphate linkage between arginine and serine is established. This is reversed by SidJ, another bacterial protein.

Figure 17. Summary of key questions that are need to be addressed, both from a mechanistic point of view and from a medical point of view.

development of protein-specific enzymes. Through horizontal gene transfer, readers and erasers were taken up by eukaryotes that allowed the generation of families of ADP-ribosyltransferases along with PAR and MAR hydrolases. Moreover, viruses have also participated in adapting writers and erasers of ADPribosylation. It is interesting to note that eukaryotes have multiple domains that read PARylation, while MARylation seems only to be seen by macrodomains. Why is this the case? We argue that the primary function of MARylation is to directly affect its substrates through allosteric mechanisms. This is true for the majority of bacterial and viral systems that have been analyzed as well as for eukaryotic MARylation. In contrast, PARylation is clearly used primarily in specific stress situations and serves as a signal to initiate cellular processes, arguably best documented for the DNA damage response. In these situations, its most prominent function is to provide an interaction surface for specific proteins, a function that is well served with the large polymers that are synthesized.

Many of the basic principles associated with the use of ADPribosylation as a PTM have been elucidated. However, there are clearly a number of questions that are being or will have to be addressed in the future (summarized in Figure 17). Some of these questions seem trivial but have remained difficult to answer because of technical challenges. For example, the sites of modification of eukaryotic ARTDs has been a matter of debate. Biochemical approaches have been used to define specificities, which are now challenged by various mass spectrometry approaches. Because of the complexity of the PTM, this has been difficult and several groups have devoted considerable effort to this problem. We do not have final answers yet, but it seems that the technologies that have been developed are finally providing reliable results. Now it will be important to define the enzymes that generate specific modifications; that is, to align individual ADP-ribosylation sites with specific enzymes. Will it be possible to define consensus sequences for individual ARTs, as we are used to for many kinases? The specificity of not only the writers but also of the erasers needs to be defined. The ability to 1120


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synthesize peptides that are ADP-ribosylated at specific positions, which is progressing, will certainly help to produce tools to clarify the specificity of the different enzymes and also help to define modified sites in cells. Finally, the consequences of the PTM on individual substrates has to be addressed and clarified. This is a considerable task as we do not have routine approaches to study individual ADP-ribosylated proteins, such as site-specific antibodies that would allow easy tracing of modified substrates. Another key task is to understand the biological functions of individual substrates and of pathways and processes in response to ADP-ribosylation. What are the effects of ADP-ribosylation on a given protein? This can be addressed in part using isolated components and studying defined properties of the substrate. However, to expand into cellular functions, the sites have to be mapped to generate appropriate mutants and tools need to be developed to visualize the modified vs the nonmodified protein under defined conditions, as pointed out above. Regarding pathways and processes, innate immunity and stress response systems seem to be the most attractive to focus on in eukaryotic cells. Because these processes are tightly associated with organismal health and disease, the development of inhibitors of the different writers and erasers, and possibly also of readers, is very attractive and has already gained considerable attention for some of the enzymes, in particular ARTD1 and ARTD5/6 (PARP inhibitors and tankyrase inhibitors, respectively). Inhibitors may also be relevant for targeting enzymes that control ADP-ribosylation reactions in prokaryotes and in viruses. Certainly the recent findings that some viral macrodomains are MAR erasers and that this function is important for viral replication implicates viral macrodomain inhibitors as virostatics. Similarly, bacterial writers and erasers of ADP-ribosylation are potentially inhibiting bacterial growth and thus might function as antibiotics. Thus, the enzymes that control ADP-ribosylation are interesting targets for intervention. Taken as a whole, the field has made strong progress in understanding the biochemistry and the biology of ADPribosylation, despite many technical obstacles that were hampering progress in the last years. Beyond understanding the details of ADP-ribosylation and the consequences on substrates, key processes that are associated with this PTM might be controllable by small molecules that affect writers and erasers and thus have the potential to be of therapeutic use.

Eisenman. He was then an assistant and associate professor at the Hannover Medical School (MHH) in Hannover, Germany, before becoming a professor at RWTH Aachen University in 2001. Dr. Lüscher’s research interests focus on the basic principle of protein function and regulation, signal transduction processes, and gene transcription associated with molecular tumor biology. Mareike Bütepage is a doctoral student at the Institute of Biochemistry and Molecular Biology at RWTH Aachen University in the laboratory of Dr. Bernhard Lüscher. She earned a B.Sc. in biology from Technical University of Braunschweig in 2011 and a M.Sc. in biomedical sciences from Hannover Medical School in 2013. Mareike Bütepage’s research interests focus on macrodomain-containing readers and erasers of intracellular mono-ADP-ribosylation. Laura Eckei is a doctoral student at the Institute of Biochemistry and Molecular Biology at the Medical School of RWTH Aachen University in the laboratory of Dr. Bernhard Lüscher. She studied biotechnology at the Aachen University of Applied Sciences in Jülich. Laura Eckei’s research interests focus on ARTD10-dependent MARylation in the control of the NF-κB signaling pathway and its involvement in liver physiology and HCC development. Sarah Krieg is a doctoral student at the Institute of Biochemistry and Molecular Biology at the Medical School of RWTH Aachen University in the laboratory of Dr. Bernhard Lüscher. She studied molecular and applied biotechnology at RWTH Aachen University. Sarah Krieg’s research interests focus on viral macrodomains and mARTDs in immunity. Patricia Verheugd is a postdoctoral fellow at the Institute of Biochemistry and Molecular Biology at the Medical School of RWTH Aachen University in the laboratory of Dr. Bernhard Lüscher. She obtained her diploma degree in biology and her doctoral degree from RWTH Aachen University and thereafter started working as a postdoctoral fellow at the department of Medical Biochemistry and Biophysics at the Karolinska Institute in Stockholm in the laboratory of Dr. H. Schüler. Dr. Verheugd’s research interests are in the function and regulation of mono-ADP-ribosylation. Brian Shilton is professor of biochemistry at The University of Western Ontario in London, Canada. He obtained his Ph.D. at Queen’s University in Kingston, Canada, which was followed by postdoctoral fellowships at the Uppsala Biomedical Centre in Sweden, the Biotechnology Research Institute in Montreal, and the Institute for Molecular Biology and Biotechnology in Crete, Greece. His main interest is in enzyme structure and mechanism with past and current projects focused on ATP-dependent transporters, redox enzymes, the Pin1 prolyl isomerase, choline acetyltransferase, serine carboxypeptidase, and ARTD10.

AUTHOR INFORMATION Corresponding Author

*Tel.: +49-241-8088850. Fax: +49-241-8082427. E-mail: [email protected].

ACKNOWLEDGMENTS We would like to thank our colleagues Ivan Ahel, Michael Hottiger, and Susan Smith for providing information prior to publication and two anonymous reviewers for their very insightful comments. We also acknowledge the Leung lab for establishing and maintaining the database of ADP-ribosylated proteins, ADPriboDB, at http://adpribodb.leunglab.org. The research in our laboratories is supported by German Reseach Foundation DFG (LU466/16-1) to B.L.; by the IZKF Aachen (O2-1-2014) of the Medical School, RWTH Aachen University, to B.L.; by the start-up program of the Excellence Initiative of the RWTH Aachen University (StUpPD_119_13) to P.V.; by the START program of the Faculty of Medicine, RWTH Aachen University (117/15), to P.V.; and by a Discovery Grant from

ORCID

Bernhard Lüscher: 0000-0002-9622-8709 Sarah Krieg: 0000-0003-1329-0185 Notes

The authors declare no competing financial interest. Biographies Bernhard Lüscher is professor of biochemistry and molecular biology and director of the Institute of Biochemistry and Molecular Biology at the Medical School of RWTH Aachen University in Aachen, Germany. He studied biochemistry at ETH Zürich, obtained a doctoral degree from the University of Lausanne, and was a postdoctoral fellow at the Fred Hutchinson Cancer Research Center in Seattle with Dr. Robert N. 1121


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PARPi PBZ PIN PRD

PARP inhibitor poly(ADP-ribose)/PAR-binding zinc finger PilT N-terminus PARP regulatory domain or helical domain in ARTD1 PTM posttranslational modification R arginine (Arg) R-ADPr arginine ADP-ribosylation reader protein that interprets a particular posttranslational modification RNA ribonucleic acid RRM RNA-recognition motif S serine (Ser) sirtuin/SIRT yeast silent information regulator 2 (Sir2) like protein SNP single nucleotide polymorphisms SSB single-stranded DNA binding protein ssDNA single-stranded DNA TA toxin−antitoxin UPS ubiquitin−proteasomal system writer enzyme that adds a particular posttranslational modification WWE tryptophan−tryptophan−glutamate domain Y tyrosine (Tyr) 3BP2 Src homology 3 domain-binding protein 2/ SH3BP2

NSERC (Natural Sciences and Engineering Research Council) Canada to B.H.S.

ABBREVIATIONS ADP adenosine-5′-diphosphate ADPr ADP-ribose AIF apoptosis-inducing factor aka also known as AMP adenosine-5′-monophosphate AMPs antimicrobial peptides APLF aprataxin PNK like factor ARF ADP-ribosylation factor ARH ADP-ribosyl-acceptor hydrolase ART ADP-ribosyltransferase ARTC ADP-ribosyltransferase of the C2/C3 toxin type ARTD ADP-ribosyltransferase of the diphtheria toxin type ATP adenosine-5′-triphosphate BRCA breast cancer gene/protein BRCT BRCA1 C-terminal domain cADPr cyclic ADP-ribose CHFR checkpoint protein with FHA and RING domain CT-A1 cholera toxin catalytic subunit D aspartate (Asp) DNA DNA E glutamate (Glu) eEF2 eukaryotic elongation factor 2 eraser enzyme that removes a particular posttranslational modification ETAc exotoxin A catalytic domain FHA forkhead-associated G glycine (Gly) GDH glutamate dehydrogenase GO gene ontology H histidine (His) HNP-1 human neutrophil peptide-1 HPF1 histone PARylation factor 1 HR homologous recombination repair K lysine (Lys) LCD low complexity domain MAR mono-ADP-ribose mARTD mono-ADP-ribosyltransferase of the diphtheria toxin type MARylated mono-ADP-ribosylated MARylation mono-ADP-ribosylation MEF mouse embryo fibroblast MIF macrophage inhibitory factor MTS mitochondrial targeting sequence NAD+ nicotinamide adenine dinucleotide Nam nicotinamide NLS nuclear localization sequence Nudix nucleoside diphosphate linked to a variable moiety X NUDT Nudix-type OB-fold oligonucleotide/oligosaccharide-binding fold PAR poly-ADP-ribose pARTD polymer-forming ADP-ribosyltransferase of the diphtheria toxin type PARG poly-ADP-ribose glycohydrolase PARylated poly-ADP-ribosylated PARylation poly-ADP-ribosylation PARP poly-ADP-ribosylpolymerase/poly(ADP-ribosyl) polymerase

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