Poly-ADP-ribose polymerase: machinery for nuclear processes

Abstract

It is becoming increasingly clear that the nuclear protein, poly-ADP-ribose polymerase 1 (PARP1), plays essential roles in the cell, including DNA repair, translation, transcription, telomere maintenance, and chromatin remodeling. Despite the exciting progress made in understanding the ubiquitous role of poly-ADP-ribose metabolism, a basic mechanism of PARP's activity regulating multiple nuclear processes is yet to be outlined. This review offers a holistic perspective on activity of PARP1, based on empirically observable phenomena. Primary attention is given to mechanisms by which PARP1 regulates a broad range of essential nuclear events, including two complementary processes (1) regulation of protein-nucleic acid interactions by means of protein shuttling and (2) utilizing poly-ADP-ribose as an anionic matrix for trapping, recruiting, and scaffolding proteins.

Keywords: Chromatin; Histones; Nucleosome; PARP1; Parg; Poly(ADP-ribose).

Figure 1. Nuclear Poly(ADP-ribose) turnover

Levels of protein pADPr reflects relative activities of the poly(ADP-ribose) polymerase (PARP) enzyme, which utilizes NAD to create pADPr-modified proteins, and the poly(ADP-Ribose) glycohydrolase (PARG) enzyme, which removes pADPr moieties. Arrowheads indicate cleavage points of poly(ADP-ribose) by PARG.

Figure 2. Two pathways of PARP1 activation

1. PARP1 is broadly distributed in chromatin as it interacts with core histones of nucleosomes. PARP1 is inactive in this state because of inhibitory effect of histone H2A. 2. Genotoxic stress –dependent PARP1 activation. N-terminal domain of PARP1 serves as a sensor of the double strand breaks and nicks in genomic DNA. Upon binding to damaged DNA, PARP1 mediates conformational changes in nucleosomes leading to disruption of interaction with histones and consequent activation of the PARP1 enzymatic reaction. 3. DNA-independent PARP1 activation. Developmental or environmental signals induce local changes in the “histone modification code” and subsequently expose N-tail of histone H4 and/or hide histone H2A. These structural changes are followed by H4-dependent PARP1 activation.

Figure 3. Model of PARP1 interaction with histone H2Av

Nucleosome with H2Av works as a high affinity site (red) for PARP1 (blue) binding with specific chromatin domains. While in complex with H2Av-nucleosome, PARP1 is catalytically inactive. Phosphorylation of H2Av disrupts its interaction with PARP1 and stimulates PARP1 activity (poly(ADP-ribosylation)). PARP1 modifies histone H1 (Aubin et al., 1983) and facilitates local chromatin relaxation and remodeling.

Figure 4. PARP1 modulates chromatin structure by “electrostatic repulsion”

Upon PARP1 activation in condensed chromatin block, this enzyme assembles poly(ADP-ribose) (pADPr), a polymer that is twice as negatively charged as the DNA molecule. Addition of pADPr to chromatin proteins likely loosens the interaction within nucleosomal arrays by electro-repulsive interactions between pADPr and DNA and removal of histones from DNA.

Figure 5. Molecular model of PAPR-1 activation by nucleosomal histones

An H2Av-bearing nucleosome has a greater affinity to PARP1 because of better surface representation of H3 and H4. Terefore, such nucleosome preferentially binds PARP1 and positions it inside promoters (Kotova et al. 2011). A neighboring H2A-nucleosome inhibits PARP1 via H2A – PARP1 interaction (Pinnola et al. 2007). Phosphorylation of H2AvSer137 increases the strength of interaction between PARP1 and H4 within H2A-nucleosome, thereby initiating pADPr production. The acetylation of H2A Lys 5 in H2A nucleosome disrupts inhibitory effect of H2A on PARP1, thus, enhance pADPr synthesis.

Figure 6. Molecular model for PARP1 dependent transcription in development

1) chromatin remodeling complexes position H2A variants-bearing nucleosomes inside promoter regions; 2) an H2A variants-bearing nucleosome has a greater affinity to PARP1 because of a better surface representation of H3 and H4; therefore, such nucleosome preferentially binds PARP1 and positions it inside promoters; 3) transcriptional factors and/or RNA Polymerase II stimulate phosphorylation of H2AvSer137, thereby activating PARP1 and initiating pADPr production; 4) pADPr induces relaxation in the nucleosome; 5) together, these modifications facilitate transcription through changes in nucleosome structure and facilitate transcription by Pol II.

Figure 7. Nuclear PARP1 facilitates ribosomal biogenesis

PARP1 becomes automodified upon each act of transcriptional start within rDNA gene and serves as a chaperoning machine during the entier cycle of ribosome maturation in nucleolus. The dynamic Poly(ADP-ribose) tree forms a network, which organizes specific nucleolar microenvironment, brings a subset of nucleolar proteins -- such as Fibrillarin and AJ1 -- to the proximity of precursor rRNA, and coordinates the order of events of rRNA processing, modification, and loading of subsets of ribosomal proteins. Depletion of PARP1 leads to removal of pADPr-binding proteins from nucleoli, which disrupts processing, modification, and folding of ribosomal RNA. PARG is required to 1) restart the system and 2) recycle protein components after completion of one cycle of ribosomal subunit synthesis.

Figure 8. A model of protein delivery to Cajal body by PARP1 shuttling

(1) PARP1 is localized in chromatin and nucleoli. (2) Upon activation, PARP1 automodifies and (3) gains the ability to bind by pADPr a number of proteins with pADPr-binding domain. (4) Whole complex consisting of automodified PARP1 and proteins seated on pADPr migrates into Cajal bodies. (5) In CB, complex is disassembled as a result of cleavage of pADPr and released proteins are recycled. PARP1, pADPr protein-complexes of chromatin and nucleolus are shown. CBm = Cajal body matrix, and Ca = Cajal body cavity.