Model systems for the study of the role of PADPRP in essential biological processes

Purification and characterization of poly(ADP-ribosyl)ated DNA replication/repair complexes

PARP-1, the best studied isoform and most abundantly expressed member of the PARP family of 18 proteins, catalyzes the poly(ADP-ribosyl)ation (PARylation) of various nuclear proteins and play key roles in DNA repair, genome maintenance, DNA replication, recombination, apoptosis, gene expression, and regulation of chromatin function. PARylation modulates the functions of target proteins, mainly PARP-1 itself. A multifunctional enzyme, PARP-1 has been localized within DNA replication, repair, recombination, and transcription complexes, and modifies and regulates the functions of specific components of these complexes. PARylation can regulate the activities of replicative enzymes, such as DNA polymerases α, δ, and ε, topo I and II, primase, RPA, and PCNA in isolated enzymes or within DNA replication complexes (DNA synthesome). PARP-1 and PARylation may (1) play dual roles in nuclear processes, depending on the levels of the substrate NAD and the presence of PARP-activating DNA breaks, (2) recruit acceptor proteins to certain sites or complexes through direct association or through binding to PAR and PAR-binding proteins, and (3) alters the nucleosomal structure of DNA by PARylation of nucleosomal proteins, such as histone H1 to destabilize higher order chromatin structures and promote access of DNA repair and replication enzymes as well as transcription factors to these sites. Here, we describe biochemical approaches that have been utilized in our laboratory for the purification and characterization of PARylated DNA replicative complexes. These methods can be modified for the purification of complexes involved in other nuclear processes. This chapter also briefly discusses current methods by which new PARylated complexes are being identified and studied. Identification, evaluation, and characterization of new complexes could aid in the elucidation of the molecular mechanisms by which PARylation and PARP mediates its pleiotropic roles in various nuclear processes.

Purification and cDNA cloning of maize Poly(ADP)-ribose polymerase

Poly(ADP)-ribose polymerase (PADPRP) has been purified to apparent homogeneity from suspension cultures of the maize (Zea mays) callus line. The purified enzyme is a single polypeptide of approximately 115 kD, which appears to dimerize through an S-S linkage. The catalytic properties of the maize enzyme are very similar to those of its animal counterpart. The amino acid sequences of three tryptic peptides were obtained by microsequencing. Antibodies raised against peptides from maize PADPRP cross-reacted specifically with the maize enzyme but not with the enzyme from human cells, and vice versa. We have also characterized a 3.45-kb expressed-sequence-tag clone that contains a full-length cDNA for maize PADPRP. An open reading frame of 2943 bp within this clone encodes a protein of 980 amino acids. The deduced amino acid sequence of the maize PADPRP shows 40% to 42% identity and about 50% similarity to the known vertebrate PADPRP sequences. All important features of the modular structure of the PADPRP molecule, such as two zinc fingers, a putative nuclear localization signal, the automodification domain, and the NAD+-binding domain, are conserved in the maize enzyme. Northern-blot analysis indicated that the cDNA probe hybridizes to a message of about 4 kb.

Alterations in human lymphocyte DNA caused by sulfur mustard can be mitigated by selective inhibitors of poly(ADP-ribose) polymerase

Changes in genomic DNA caused by exposure to the cytotoxic alkylating agent, 2,2'-dichlorodiethyl sulfide (sulfur mustard; HD), alone or in combination with selective inhibitors of poly(ADP-ribose) polymerase (PARP), were analyzed as a function of HD concentration and post-exposure time. Preparations of human peripheral blood lymphocytes were exposed to HD (1x10(-8) M-1x10(-3) M), and incubated at 37 degrees C for 0-24 h. Total genomic DNA was extracted from these cells and compared with DNA from control cells of the same donor using agarose gel electrophoresis. The effects of HD on genomic DNA depended on the HD concentration and the length of the post-exposure time interval. DNA fragmentation was detected as early as 2 h after exposure to 3x10(-4) M HD, or at 24 h after exposure to 6x10(-6) M HD. The qualitative DNA pattern, as well as the extent of DNA fragmentation, changed with post-exposure time. Exposure to HD caused a time-dependent shift in the DNA cleavage pattern from an oligonucleosome-sized 'DNA ladder' characteristic of apoptotic cell death, to a 'broad band' pattern characteristic of necrotic cell death. DNA fragmentation was not observed if cells were killed with heat or with Lewisite. Treatment of cells with selective PARP inhibitors consistently altered the DNA fragmentation caused by HD exposure. The inhibitors arrested DNA fragmentation at the DNA ladder stage. This effect only was observed if the PARP inhibitors were applied within 8 h of HD exposure. We conclude that early inhibition of PARP activity can induce a switch in the mechanism of cell death caused by HD. Such a switch may be useful therapeutically to convert a lytic, pro-inflammatory cell death that includes the disintegration of dying cells (necrosis), into a slower, programmed cell death that includes absorption of dying cells (apoptosis).