Towards a structural understanding of PARP1 activation and related signalling ADP-ribosyl-transferases

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ADP-ribosylation is a post-translational modification of proteins that occurs mostly in response to cellular stress and is catalysed by members of the diverse poly-ADP-ribose (PAR) polymerase (PARP/ARTD) family. The founding member of the family, PARP1, is best recognized for its function as a sensor of DNA strand lesions, but ADP-ribosylation has been implicated in transcriptional regulation, chromatin dynamics, telomere maintenance, apoptosis and neuronal signalling. Here we summarize a number of exciting recent breakthroughs in our understanding of the structural and mechanistic aspects of how PARP1 recognizes DNA, how PARPs are regulated, how ADP-ribose modifications are set onto specific targets and how the cellular machinery recognizes this elusive post-translational modification.

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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