Functional aspects of PARylation in induced and programmed DNA repair processes: Preserving genome integrity and modulating physiological events

Abstract

To cope with the devastating insults constantly inflicted to their genome by intrinsic and extrinsic DNA damaging sources, cells have evolved a sophisticated network of interconnected DNA caretaking mechanisms that will detect, signal and repair the lesions. Among the underlying molecular mechanisms that regulate these events, PARylation catalyzed by Poly(ADP-ribose) polymerases (PARPs), appears as one of the earliest post-translational modification at the site of the lesion that is known to elicit recruitment and regulation of many DNA damage response proteins.

In this review we discuss how the complex PAR molecule operates in stress-induced DNA damage signaling and genome maintenance but also in various physiological settings initiated by developmentally programmed DNA breakage. To illustrate the latter, particular emphasis will be placed on the emerging contribution of PARPs to B cell receptor assembly and diversification.

Introduction

The chemical stability of the genome is permanently challenged by both intracellular (byproducts of normal metabolism) and extracellular toxic stresses (ionizing radiations, chemical agents). If not repaired or incorrectly repaired, the lesions can result in mutations and chromosomal aberrations, diseases and cell death (Friedberg et al., 2006, Hoeijmakers, 2001a, Hoeijmakers, 2001b, Jackson and Bartek, 2009). To protect their genome against the deleterious consequences of these lesions, mammalian organisms have developed sophisticated cellular networks to detect the DNA damage, signal its presence and stimulate the appropriate repair pathway (Ciccia and Elledge, 2010).

In the last decade, several reports have highlighted the major contribution of post-translational modifications such as phosphorylation, sumoylation and acetylation in controlling these three events (Polo and Jackson, 2011). Recently, PARylation has emerged as an additional key regulator as highlighted throughout this review.

PARylation is the process whereby a linear or multibranched polymer of ADP-ribose units (termed PAR for poly(ADP-ribose)) that is catalyzed by Poly(ADP-ribose) polymerases (PARPs) is covalently attached to Glu, Lys or Asp residues of acceptor proteins (heteromodification) or onto PARP itself (automodification) (Hakme et al., 2008, Hottiger et al., 2010, Krishnakumar and Kraus, 2010). Among the 17 members of the PARP family, so far only PARP1, PARP2 and PARP3 have been found to be induced by DNA strand breaks and characterized for their role in cellular response to DNA damage (reviewed in (De Vos et al., 2012)). Although it requires further investigation, it seems likely from recent studies that the telomere associated PARP Tankyrase 1 (PARP5) also plays an important role in genome maintenance (De Vos et al., 2012, Dregalla et al., 2010, White et al., 2009).

The extent of the PARylation response to DNA damage largely depends on the nature and amount of DNA breaks produced. In response to low levels of DNA lesions, PARP activity favors repair and survival. In the presence of extensive DNA injury as observed during ischemia/reperfusion and inflammatory conditions, the massive production of PAR ultimately causes cell-death via at least two distinct mechanisms: energy-failure induced necrosis or apoptosis-inducing factor (AIF) dependent apoptosis (Luo and Kraus, 2012). A tight regulation of PARylation homeostasis is therefore of critical importance for efficient repair when cells are exposed to sub-lethal doses of DNA damage. As such, the transient and highly dynamic nature of PAR is regulated by its rapid reversal by the activity of the poly(ADP-ribose) glycohydrolase PARG and presumably also the ADP-ribosylarginine hydrolase ARH3 (Davidovic et al., 2001, Oka et al., 2006).

Determination of the structural properties of PARP1, PARP2, PARP3 and PARG together with the phenotyping of the gene knockout animals have been instrumental in revealing the key functions of these proteins in response to genotoxic stress (reviewed in (Hottiger et al., 2010, Krishnakumar and Kraus, 2010, Schreiber et al., 2006, Yelamos et al., 2008)) (Table 1).

PAR is now recognized as a central post-translational protein modification that coordinates the building of repair complexes at damage sites with the timely controlled dissociation of the repair factors. Furthermore, through its multiple functions in response to DNA damage, the PAR synthesized by PARP1 and PARP2 also operates in diverse biological events induced by programmed DNA breakage either to generate immune-receptor diversity or healthy gametes for sexual reproduction and likely also to facilitate viral integration.

In this review, we develop the above mentioned properties of PARylation in stress conditions. More particularly, we describe how the DNA-damage induced PARylation and its homeostasis regulate the diverse repair events, and we highlight the biological significance of this response particularly to programmed DNA strand breaks produced during physiological processes. Special emphasis is given to the participation of PARylation in the mechanisms driving the assembly and the diversification of the antibody repertoire.