Towards a structural understanding of PARP1 activation and related signalling ADP-ribosyl-transferases
Graphical abstract
Highlights
► PARP1 recognizes DNA strand breaks through substrate-assisted dimerization. ► PARP1 ZFIII and WGR domains link DNA break recognition to enzyme activation. ► Tankyrase-dependent PARylation regulates Wnt signalling and Cherubism syndrome.
Introduction
Cells detect and respond to environmental challenges by mounting stress responses, which are crucial for survival. A rapid stress-sensing mechanism is the ADP-ribosylation of proteins, a post-translational protein modification (PTM) that occurs primarily in response to DNA damage (rev. in [1]).
A family of poly-ADP-ribose (PAR) polymerases (PARP) catalyses these modifications, using NAD+ as a substrate (Figure 1, Figure 2). Most PARP proteins may act as mono-ADP-ribosyl-transferases, while PARP1, PARP2, PARP3, vPARP, and TNKS1/2 form complex, negatively charged ADP-ribose polymers (rev. in [2]). The best-characterized PARP, PARP1, senses DNA strand lesions [3], becomes catalytically activated and PARylates protein substrates at the damage site. Because of PARP1's function in DNA damage, there has been strong interest in PARP1 as a therapeutic target in breast and prostate cancers (see Box 1).
The diverse functional aspects and mechanisms of PAR synthesis by human PARPs have been extensively studied [1, 2, 4, 5]. Here we review recent progress in our understanding of the mechanism of PARP activation and how this elusive PTM is recognized downstream.
Section snippets
Binding mechanism and stoichiometry of PARP1–DNA break interactions
A key question in the PARP field has been to understand how PARP1 recognizes DNA lesions. DNA break recognition is mediated by a tandem repeat of N-terminal zinc-finger (ZF) domains, which are found in other DNA repair proteins (e.g. DNA ligase III) and are sufficient to recognize sequence-independent, aberrant DNA structures, including single-strand break (SSB) or double-strand break (DSB) [6]. X-ray structures of the individual ZFs bound to DNA have provided the first insight into how PARP1
Relaying the DNA binding signal to catalytic activation of PARP1
There is little insight into how PARP1 transmits the DNA-binding signal to the activation of its C-terminal catalytic domain (Figure 1a). PARP1 contains six globular domains and is thought to adopt a beads-on-a-string like architecture when not engaged in DNA or protein interactions. However, when activated by DNA lesions, PARP1 compacts, involving DNA-domain and inter-domain contacts [12]. Three domains important for PARP1 function (Figure 1e,g,h) play crucial roles in this activation.
The near
Catalytic activity and substrate specificity of PARP1 and other family members
Of the 17 human PARPs (Figure 2a), six are poly-transferases as indicated by the presence of a conserved Glu in the catalytic triad HYE [2] (Figure 1h). These include PARP1 to 3, which display nuclear localization [5], vPARP, associated with ribonucleoprotein complexes [16], and TNKS1 and TNKS2, which have roles at telomeres and in Wnt signalling [17, 18•]. The remaining PARPs (ARTD7–17) are suggested to be either mono-transferases or inactive. Mono-transferase activity has been confirmed for
Protein–protein interactions and PAR-dependent recruitment
The auto-modification region of PARP1 is required for efficient DNA repair and its BRCA1 C-terminus (BRCT) domain (Figure 1f) may directly mediate interactions with the central BRCT domain of the DNA-repair scaffolding protein XRCC1 [23]. However, a recent report showed that an isolated BRCT domain is not sufficient for XRCC1 binding [24], supporting an earlier finding that XRCC1 recruitment strictly depends on PARP1 PARylation [25].
ADP-ribosylation is the molecular basis of interaction for
Conclusion and outlook
Fifty years of research on PAR have culminated in two paradigmatic X-ray structures. First, the structure of the DNA-binding domain of PARP1 in complex with a double-stranded DNA molecule gives insight into the selectivity of PARP1 for nicks in DNA vs. undamaged DNA, providing a rationale for PARP1's highly selective and rapid recruitment to DNA damage sites. Second, the near full-length PARP1 bound to a DNA strand break sheds light on the mechanism of signal transmission from DNA damage
References and recommended reading
Papers of particular interest, published within the period of review, have been highlighted as:
• of special interest
•• of outstanding interest
Acknowledgements
We would like to thank Andrew Bowman, Gytis Jankevicius and Gyula Timinszky for helpful discussions and comments on the manuscript. M.H. was funded by DFG grant LA 2489/1-1 (to A.G.L.). We are grateful to the EMBL, the University of Munich and the DFG Excellence Cluster CIPSM for further support.
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2020, European Journal of Medicinal ChemistryCitation Excerpt :The C-terminal catalytic domain includes a tryptophan-glycine-arginine domain (WGR), an alpha helix domain (HD), and an ADP-ribose transferase domain (ART) [45]. Specifically, the WGR domain is important in DNA-dependent catalytic activation and may be the nucleic acid binding motif [46]. The HD consists of six alpha-helices with connecting linkers preventing the PARP-superfamily cofactor, b-NAD+, binding to its ART binding site.
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2018, Gynecologic OncologyCitation Excerpt :Consequently, we observed higher expression of PARP1 in olaparib treated tumors. To determine the radiosensitization in response to combined treatment of RT and olaparib in tumor tissues, we next investigated the effects of olaparib on PARP activity, by measuring PAR [poly (ADP-ribose)], which is synthesized after activation of the nuclear DNA repair enzyme PARP [37]. As anticipated, olaparib significantly decreased PAR levels in both xenograft tumors, demonstrating loss of auto-PARylation of PARP by olaparib was sufficient to inhibit PARP activity in vivo.
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2018, Journal of ProteomicsCitation Excerpt :PARP-1 contains an N-terminal DNA binding domain, an auto-modification domain and a catalytic domain [33]. Of note, DNA binding leads to a conformational alteration of PARP-1 resulting in rearrangement of the catalytic site and remarked increase in enzymatic activity [34–37]. Importantly, these PARPs are implicated in crucial DNA damage repair including base excision repair, homologous recombination, non-homologous end joining and some non-DNA repair such as chromatin modification and transcriptional regulation [34,38–40].
Coordination of DNA single strand break repair
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2017, Seminars in Cell and Developmental BiologyCitation Excerpt :PARP-1 binds damaged DNA by way of three zinc finger motifs [14]. DNA binding results in a conformational change in PARP-1 allowing realignment of the catalytic site and significant increase in enzymatic activity [9,15–17]. Once activated, it uses nicotinamide-adenine-dinucleotide (NAD+) to create PAR polymer chains, important for recruiting key members of the DNA repair machinery.
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2014, DNA RepairCitation Excerpt :Others are most likely mono-ADP-ribosyltransferases, modifying protein target sites with single ADP-ribose units. The structure, catalytic activity, and mechanism/s of activation of these enzymes has been reviewed extensively [e.g. see [1–3]], and will not be reviewed further, here. Poly(ADP-ribose) polymerase-1 (PARP-1) is the archetypal ADPRT (ADPRT1) and accounts for 80–90% of detectable poly(ADP-ribose) synthesis following DNA damage.