PARP-1 mechanism for coupling DNA damage detection to poly(ADP-ribose) synthesis

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Poly(ADP-ribose) polymerase 1 (PARP-1) regulates gene transcription, cell death signaling, and DNA repair through production of the posttranslational modification poly(ADP-ribose). During the cellular response to genotoxic stress PARP-1 rapidly associates with DNA damage, which robustly stimulates poly(ADP-ribose) production over a low basal level of PARP-1 activity. DNA damage-dependent PARP-1 activity is central to understanding PARP-1 biological function, but structural insights into the mechanisms underlying this mode of regulation have remained elusive, in part due to the highly modular six-domain architecture of PARP-1. Recent structural studies have illustrated how PARP-1 uses specialized zinc fingers to detect DNA breaks through sequence-independent interaction with exposed nucleotide bases, a common feature of damaged and abnormal DNA structures. The mechanism of coupling DNA damage detection to elevated poly(ADP-ribose) production has been elucidated based on a crystal structure of the essential domains of PARP-1 in complex with a DNA strand break. The multiple domains of PARP-1 collapse onto damaged DNA, forming a network of interdomain contacts that introduce destabilizing alterations in the catalytic domain leading to an enhanced rate of poly(ADP-ribose) production.

Highlights

► PARP-1 zinc finger domains recognize exposed nucleotide bases as a DNA damage signal. ► The modular domain architecture of PARP-1 collapses onto DNA damage as a monomer. ► Interdomain communication is critical to PARP-1 activation in response to DNA damage. ► A destabilized PARP-1 catalytic domain has increased poly(ADP-ribosyl)ation activity.

Introduction

Poly(ADP-ribose) is a reversible posttranslational modification synthesized from NAD+ by poly(ADP-ribose) polymerases (PARPs), most commonly in response to cellular stress signals such as DNA damage. The most abundant PARP enzyme in cells, PARP-1 creates long and branched poly(ADP-ribose) covalently attached onto target proteins involved in gene transcription, DNA damage repair, and cell death signaling (reviewed in [1]). Owing to PARP-1 involvement in DNA damage repair, inhibitors of PARP-1 are being actively pursued for the treatment of cancer (reviewed in [2]). The primary target for PARP-1 mediated poly(ADP-ribosyl)ation is PARP-1 itself, an activity termed automodification. Several other nuclear targets are modified by PARP-1 (reviewed in [3]); however the mechanism for PARP-1 substrate selection is not well understood. PARP-1 catalytic activity is chiefly regulated through its interaction with DNA damage. Binding to DNA strand breaks elevates the PAR synthesis activity of PARP-1 over 500-fold above basal levels of DNA-independent activity. DNA-dependent PARP-1 automodification is an immediate and robust cellular response to DNA damage that contributes to the recruitment of DNA repair and chromatin remodeling factors to sites of DNA breaks [4, 5, 6, 7]. Recent structural studies highlighted in this article have begun to establish the physical basis for PARP-1 structure-specific detection of DNA breaks, and the mechanism for DNA damage-dependent activation of PARP-1 catalytic activity.

Section snippets

PARP-1 ‘beads-on-a-string’ architecture

PARP-1 has a modular architecture with DNA binding, catalytic, and regulatory functions distributed among six independently folded domains (Figure 1a). Structures of each of the individual domains of PARP-1 in the absence of DNA have been determined (Figure 1b) [8•, 9•, 10•, 11, 12] (RIKEN, Structural Genomics Consortium). Located at the PARP-1 N-terminus, two homologous zinc finger domains, Zn1 and Zn2, recognize particular DNA structures, rather than specific DNA sequences [8•, 13•, 14, 15, 16

DNA damage detection by PARP-like zinc fingers

The structure of a PARP-like DNA binding zinc finger was first determined for the homologous N-terminal zinc finger domain of DNA ligase III [42], where it serves a nick sensing function [43, 44]. The structural basis for DNA strand break detection has recently come from crystal structures of the human PARP-1 zinc fingers in complex with different models of DNA damage. The individual zinc fingers of human PARP-1, Zn1 and Zn2 were each crystallized in complex with DNA double strand breaks [13].

DNA damage-induced PARP-1 interdomain communication

The crystal structure of PARP-1 essential domains (Zn1, Zn3, WGR-CAT) bound to a DNA double-strand break has provided the first views of how the multiple domains of PARP-1 assemble on DNA to form the active enzyme (Figure 3a) [41••]. This study has taken advantage of the fact that the Zn2 and BRCT domains are not required for DNA-dependent activity on double-strand breaks [13•, 41••, 45] and that PARP-1 activity can be reconstituted by mixing the isolated Zn1, Zn3 and WGR-CAT fragments with DNA

Coupling DNA damage detection to catalytic activity

Upon binding to a DNA break, PARP-1 domains collapse together and establish interdomain contacts that collectively distort the structure of HD when compared to HD structures determined for isolated CAT domains [41••]. The most prominent change in HD structure occurs near the interface with WGR, in the region surrounding αC (Figure 3a). In CAT structures determined in the absence of DNA and regulatory domains, αC forms an interface with αF and αB and contributes Leu698 and Leu701 to the

Remaining questions and challenges

The modular domain architecture has challenged structural analysis of PARP-1, but the divide and conquer approach has provided key insights into PARP-1 mechanism of action that are consistent with biochemical analysis of the full-length protein. Nonetheless, a structure of full-length PARP-1 bound to DNA damage will build on our understanding of how the domains of PARP-1 assemble and communicate. For example, the BRCT domain is not strictly required for DNA damage-dependent activity, but its

Conclusion

The structural biology of poly(ADP-ribose) signaling has made important advances over the past several years. In addition to the structures highlighted in this review, we have recently seen the first structures of poly(ADP-ribose) glycohydrolase (PARG) enzymes that reverse the modification [53••, 54•, 55•], protein modules that recognize the modification (WWE [56, 57] and PBZ [58, 59, 60, 61]), catalytic domains from additional PARP family enzymes [30, 32, 34], and the regulatory ankyrin

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

Research in the Pascal laboratory is supported by the NIH (GM087282) and the American Cancer Society (RSG0918301DMC).

References (64)

  • T.D. Penning et al.

    Optimization of phenyl-substituted benzimidazole carboxamide poly(ADP-ribose) polymerase inhibitors: identification of (S)-2-(2-fluoro-4-(pyrrolidin-2-yl)phenyl)-1H-benzimidazole-4-carboxamide (A-966492), a highly potent and efficacious inhibitor

    J Med Chem

    (2010)
  • E. Wahlberg et al.

    Family-wide chemical profiling and structural analysis of PARP and tankyrase inhibitors

    Nat Biotechnol

    (2012)
  • C.A. Kirby et al.

    Structure of human tankyrase 1 in complex with small-molecule inhibitors PJ34 and XAV939

    Acta Crystallogr Sect F Struct Biol Cryst Commun

    (2012)
  • Z.B. Mackey et al.

    DNA ligase III is recruited to DNA strand breaks by a zinc finger motif homologous to that of poly(ADP-ribose) polymerase, Identification of two functionally distinct DNA binding regions within DNA ligase III

    J Biol Chem

    (1999)
  • M.Y. Kim et al.

    NAD+-dependent modulation of chromatin structure and transcription by nucleosome binding properties of PARP-1

    Cell

    (2004)
  • W. Lilyestrom et al.

    Structural and biophysical studies of human PARP-1 in complex with damaged DNA

    J Mol Biol

    (2010)
  • T.M. Kauppinen et al.

    Direct phosphorylation and regulation of poly(ADP-ribose) polymerase-1 by extracellular signal-regulated kinases 1/2

    Proc Natl Acad Sci USA

    (2006)
  • A. Pinnola et al.

    Nucleosomal core histones mediate dynamic regulation of poly (ADP-Ribose) polymerase 1 protein binding to chromatin and induction of its enzymatic activity

    J Biol Chem

    (2007)
  • D. Slade et al.

    The structure and catalytic mechanism of a poly(ADP-ribose) glycohydrolase

    Nature

    (2011)
  • M.S. Dunstan et al.

    Structure and mechanism of a canonical poly(ADP-ribose) glycohydrolase

    Nat Commun

    (2012)
  • I.K. Kim et al.

    Structure of mammalian poly(ADP-ribose) glycohydrolase reveals a flexible tyrosine clasp as a substrate-binding element

    Nat Struct Mol Biol

    (2012)
  • S. Eustermann et al.

    Solution structures of the two PBZ domains from human APLF and their interaction with poly(ADP-ribose)

    Nat Struct Mol Biol

    (2010)
  • M. Rouleau et al.

    PARP inhibition: PARP1 and beyond

    Nat Rev Cancer

    (2010)
  • P.O. Hassa et al.

    The diverse biological roles of mammalian PARPS, a small but powerful family of poly-ADP-ribose polymerases

    Front Biosci

    (2008)
  • A.J. Gottschalk et al.

    Poly(ADP-ribosyl)ation directs recruitment and activation of an ATP-dependent chromatin remodeler

    Proc Natl Acad Sci USA

    (2009)
  • G. Timinszky et al.

    A macrodomain-containing histone rearranges chromatin upon sensing PARP1 activation

    Nat Struct Mol Biol

    (2009)
  • D. Ahel et al.

    Poly(ADP-ribose)-dependent regulation of DNA repair by the chromatin remodeling enzyme ALC1

    Science

    (2009)
  • M.F. Langelier et al.

    A third zinc-binding domain of human poly(ADP-ribose) polymerase-1 coordinates DNA-dependent enzyme activation

    J Biol Chem

    (2008)
  • P.A. Loeffler et al.

    Structural studies of the PARP-1 BRCT domain

    BMC Struct Biol

    (2011)
  • A. Ruf et al.

    Structure of the catalytic fragment of poly(ADP-ribose) polymerase from chicken

    Proc Natl Acad Sci USA

    (1996)
  • M.F. Langelier et al.

    Crystal structures of poly(ADP-ribose) polymerase-1 (PARP-1) zinc fingers bound to DNA: structural and functional insights into DNA-dependent PARP-1 activity

    J Biol Chem

    (2011)
  • I. Lonskaya et al.

    Regulation of poly(ADP-ribose) polymerase-1 by DNA structure-specific binding

    J Biol Chem

    (2005)
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