ADP-ribosylation from molecular mechanisms to therapeutic implications

Abstract

ADP-ribosylation is a ubiquitous modification of biomolecules, including proteins and nucleic acids, that regulates various cellular functions in all kingdoms of life. The recent emergence of new technologies to study ADP-ribosylation has reshaped our understanding of the molecular mechanisms that govern the establishment, removal, and recognition of this modification, as well as its impact on cellular and organismal function. These advances have also revealed the intricate involvement of ADP-ribosylation in human physiology and pathology and the enormous potential that their manipulation holds for therapy. In this review, we present the state-of-the-art findings covering the work in structural biology, biochemistry, cell biology, and clinical aspects of ADP-ribosylation.

Figure 1

The ADP-ribosylation reaction (A) Simplified mechanism of the ADP-ribosylation reaction. Nucleophilic attack of a suitable nucleophilic acceptor group (Nu) in a substrate on the C1″ atom of NAD⁺ is indicated with the blue curly arrow. Following the addition of the initial ADP-ribose moiety to the substrate, the ADP-ribosylation reaction can be repeated with either the 2′ or 2″ hydroxyl group of the initial ADP-ribose serving as a nucleophilic acceptor for linear or branched chain elongation, respectively. (B) Regulation of ADP-ribosylation by writers and erasers and its recognition by readers. The ADP-ribosylation reaction that stops at the initiation stage produces mono(ADP-ribosyl)ation or MARylation, while the initiation followed by repeated rounds of elongation generates poly(ADP-ribosyl)ation (PARylation). Initiation and elongation stages can be associated with distinct sets of writers, erasers, and readers.

Figure 2

(ADP-ribosyl)transferases (ARTs) and domain organization of PARPs (A) Examples of the ART domain from cholera and diphtheria toxin-like families (ARTC and ARTD, respectively) are provided showing conserved features (a central β sheet, a conserved catalytic glutamate residue, a similar conformation of the bound NAD⁺ donor) as well as structural divergence. PDB entries used for the figure, PDB: 1XTC, 1TOX, and 6BHV. (B) Domain composition of all human PARP proteins based on both experimental studies and computational predictions, including AlphaFold 2 models. PARPs are grouped into evolutionary clades. Parts of “split” domains that are consecutive in structure but not in sequence are connected with a dashed line. Zn1–3, zinc-finger domains 1–3; BRCT, BRCA1 C terminus; WGR, tryptophane-glycine-arginine; HD, helical domain; ART, (ADP-ribosyl)transferase; CAT, catalytic domain; VIT, vault protein inter-alpha-trypsin; vWA, von Willebrand factor type A; ITIHL, inter-alpha-trypsin heavy chain-like; MVPID, MVP-interacting domain; CCCH, cysteine-cysteine-cysteine-histidine zinc finger; WWE, tryptophane-tryptophane-glutamate; KH, ribonucleoprotein K homology; RRM, RNA-recognition motif; UIM, ubiquitin-interacting motif; NZAP, N-terminal domain of zinc-finger antiviral protein; ARC, ankyrin repeat cluster; SAM, sterile-alpha motif; RWD, RING-fingers, WD proteins, and DEXDc-like helicases; C4, four-cysteine zinc finger; HE, helical extension; TM, transmembrane helix.

Figure 3

Mechanisms and structures of writers, erasers, and readers of ADP-ribosylation (A) The structural model of the active site of PARP1 during the catalysis of PAR chain elongation. The donor NAD⁺ and a fragment of the acceptor ADP-ribose molecule are shown according to the PDB entries, PDB: 6BHV and 1A26. Residues implicated in catalysis as well as donor and acceptor binding are shown. (B) The mechanism of serine ADP-ribosylation catalysis by the composite active site built by PARP1 and HPF1. Possible movement of electrons during the reaction is indicated with blue curly arrows. For figure clarity, NAD⁺ is not shown in correct stereochemistry (see Figure 1A). (C) Structures of (ADP-ribosyl)hydrolases from the macrodomain (PARG and MacroD2) and ARH (ARH3) families. Co-crystallized substrates are shown. PDB entries used for the figure, PDB: 4L2H, 4IQY, and 7AKS. (D) Scheme showing the specificity of various reader domains for their cognate MAR and PAR signals (left) and structures of two representative reader domains co-crystallized with their ligands (right). PDB entries used for the figure, PDB: 2BFQ and 4QPL.

Figure 4

Molecular and cellular functions of ADP-ribosylation (A) Selective summary of localization and function of ADP-ribosylation writers in a eukaryotic cell. The figure does not provide a comprehensive list of known localizations, particularly for PARPs that have been detected in multiple cellular compartments. The enzymes capable of PARylation are shown in orange, the enzymes with MARylation but not PARylation activity are shown in purple, and enzymes for which no ADP-ribosylation activity has been identified are shown in gray. (B) Simplified scheme of PARP1-dependent regulation of DNA repair. PARP1 recognizes a DNA break, becomes activated, and catalyzes both MARylation and PARylation on PARP1 itself and other proteins, including histones. HPF1 is involved in the initial attachment of ADP-ribose to a protein but not in PAR chain elongation. Deposited MAR and PAR signals trigger chromatin decondensation, recruitment of chromatin remodelers and DNA repair factors, and dissociation of some proteins, including PARP1 itself and possibly histones or nucleosomes. (C) Implication of tankyrase-dependent degradation of proteins in cellular signaling illustrated using a representative substrate, AXIN. Tankyrases exist as noncovalent polymers (filaments), which might provide multivalency for recognizing polymeric substrates such as AXIN. Following tankyrase-mediated substrate PARylation, the PAR signals on the substrate are recognized by the PAR-directed ubiquitin E3 ligase RNF146, which catalyzes substrate ubiquitylation, triggering its subsequent proteasomal degradation.