Reprogramming cellular events by poly(ADP-ribose)-binding proteins

Abstract

Poly(ADP-ribosyl)ation is a posttranslational modification catalyzed by the poly(ADP-ribose) polymerases (PARPs). These enzymes covalently modify glutamic, aspartic and lysine amino acid side chains of acceptor proteins by the sequential addition of ADP-ribose (ADPr) units. The poly(ADP-ribose) (pADPr) polymers formed alter the physico-chemical characteristics of the substrate with functional consequences on its biological activities. Recently, non-covalent binding to pADPr has emerged as a key mechanism to modulate and coordinate several intracellular pathways including the DNA damage response, protein stability and cell death. In this review, we describe the basis of non-covalent binding to pADPr that has led to the emerging concept of pADPr-responsive signaling pathways. This review emphasizes the structural elements and the modular strategies developed by pADPr-binding proteins to exert a fine-tuned control of a variety of pathways. Poly(ADP-ribosyl)ation reactions are highly regulated processes, both spatially and temporally, for which at least four specialized pADPr-binding modules accommodate different pADPr structures and reprogram protein functions. In this review, we highlight the role of well-characterized and newly discovered pADPr-binding modules in a diverse set of physiological functions.

Keywords: Macro domain; PARG; PARP; PBZ; Poly(ADP-ribose); WWE.

Fig. 1

Covalent and non-covalent mechanisms of protein regulation by poly(ADP-ribosyl)ation. (A) The posttranslational modification of a protein substrate by enzymatic covalent attachment of poly(ADP-ribose) (pADPr) to specific amino acid side chains is represented. On the pADPr structure, a collection of modular protein domains non-covalently binds to pADPr through different recognition mechanisms. There are currently four pADPr-binding protein modules that have been experimentally characterized: the pADPr-binding motif (PBM); pADPr-binding zinc finger motif (PBZ); the macro domain (Macro) and the WWE domain (WWE). Experimental evidence suggests that other protein modules and sequence motifs can read this modification (see Section 3). (B) Detailed view of the covalent poly(ADP-ribosyl)ation. The proximal ADP-ribose (ADPr) is bound by an ester linkage to glutamic (Glu) and aspartic (Asp) amino acid side chains (the asterisk indicates one or two CH₂ units to represent the respective side chains of Asp or Glu) or to lysine (Lys) side chains via a ketamine linkage. The mechanism that determines selective modification of specific residues and the functional significance of this heterogeneity are not known. Additional ADP-ribose units are subsequently attached by O-glycosidic linkages to form linear or branched pADPr. Some components of the pADPr chemical structure recognized by pADPr-binding modules are shown: iso-ADPr, grey shadow, ADPr, yellow shadow.

Fig. 2

The non-covalent pADPr-binding motif (PBM). (A) The first PBM has been described by Pleschke and collaborators (2000) in a variety of DNA damage repair and checkpoint proteins. The motif is primarily composed of a hydrophobic and basic amino acid core flanked by a cluster of positively charged residues […K/R…]. Each box represents one amino acid position. (B) A refinement of the motif was proposed by Gagne et al. (2008) based on a number of PBM variations found in human proteins. The refined pADPr-binding signature confirmed the overall basic nature of the PBM but represents a minimal stand-alone version of the motif, the K/R-rich N-terminal cluster being dispensable for efficient binding. Outside the dual [KR][KR] site, there are additional preferences for hydrophobic amino acids (positions −1, +1 and +2), mostly those with alkyl side chains. The basic [KR][KR] doublet is an important requirement for the PBM since most substitutions in this region result in a substantially reduced binding affinity for pADPr.

Fig. 3

Schematic representation of human proteins harboring a PBZ, Macro domain or WWE binding module. The three protein folds currently recognized to confer high-affinity to pADPr are listed with their individual protein members. When available, 3D structure accession numbers (Protein Data Bank (PDB)) are given. The domain organization is schematized and drawn to scale according to the Uniprot database. Binding to pADPr remains to be formally demonstrated for some of the listed proteins while binding was undetectable for others. See Sections 3.3, 3.4, 3.5 for more details. FHA, forkhead-associated domain; β-Lactamase, beta-Lactamase domain; RING, RING finger; H2A, domain with similarity to histone H2A; Helicase ATP-binding, helicase superfamily 1/2 ATP-binding domain; DEAH box, DEAH box motif; Helicase C-terminal; Helicase conserved C-terminal domain; CRAL-TRIO, domain named after cellular retinaldehyde-binding protein (CRALBP) and TRIO guanine exchange factor, this domain binds lipophilic molecules; UBA, ubiquitin associated domain; UIM, ubiquitin interaction motif; HECT, homologous to E6-AP carboxyl terminus domain (has E3-ubiquitin ligase activity); Zf, zinc finger; SAM, sterile α motif domain; DDHD, domain named after the conserved residues DDHD.

Fig. 4

Schematic models of pADPr regulatory functions. (A) Protein stability can be regulated via pADPr-directed recruitment of ubiquitin-conjugating enzymes. Some protein substrates of tankyrases (TNKS1/2) (3BP2 and axin) or automodified PARP1 undergo proteasomal degradation after ubiquitylation by the WWE-containing E3 ubiquitin ligase Iduna/RNF146 or by the PBZ-containing E3 ubiquitin ligase CHFR (see Sections 3.3, 4.1 for details). (B) Neuronal cell fate after toxic stress. The excitation of glutamate receptor by N-methyl-d-aspartate (NMDA) triggers PARP activation. Non-toxic NMDA activation (left panel) induces the expression of the cell survival factor Iduna/RNF146 and its cytoplasmic accumulation. Interactions of Iduna/RNF146 with pADPr prevent apoptosis inducing factor (AIF) translocation to the nucleus and parthanatos. Excitotoxic activation of glutamate receptors (right panel) fail to induce Iduna/RNF146 expression. The accumulation of cytoplasmic pADPr promotes the release of apoptosis-inducing factor (AIF) from the mitochondria. AIF subsequently translocates to the nucleus and induces parthanatos. See Sections 3.5, 4.2 for details. (C) pADPr-dependent assembly of stress granules. Two models have been proposed (see Section 4.3 for details). In the first view, cytoplasmic ADPr and pADPr are synthesized by tankyrases and PARP12-15 upon stress exposure. This triggers the aggregation of RNA-binding proteins (RBP) to ADPr/pADPr and stress granule formation. In the second view, the nucleo-cytoplasmic trafficking of pADPr is responsible for its accumulation into the cytoplasm. By virtue of its endoglycosidic activity, PARG releases free and protein-bound pADPr following genotoxic stress and PARP activation. pADPr translocated into the cytoplasm is targeted by G3BP1 and RNA-binding proteins to initiate the aggregation of stress granules. In both views, pADPr in ribonucleoparticles acts as a scaffold for the recruitment of RNA-binding proteins. (D) pADPr plays regulatory roles in the dynamics of chromatin structure. Automodification of PARP1 and poly(ADP-ribosy)ation of histones induce chromatin relaxation. This also involves the chromatin remodeling factor CHD1L, which is recruited to specific sites by pADPr. The ATPase activity of CHD1L is stimulated by pADPr and triggers nucleosome sliding. This possibly facilitates access of the DNA repair machineries. (E) Functions of pADPr in DNA damage responses. DNA strand breaks as well as other types of altered DNA structures and DNA adducts activate PARP1. pADPr triggers the recruitment of proteins and enzymes involved in DNA damage signaling, in base excision repair (BER), non-homologous end joining (NHEJ), homologous recombination (HR) and nucleotide excision repair (NER). See Section 4.5 for details.