Analysis of Nucleotide Sequence-Dependent DNA Binding of Poly(ADP-ribose) Polymerase in a Purified System

Abstract

The enzymatic transfer of ADP-ribose from NAD to histone H(1) [defined as trans(oligo-ADP-ribosylation)] or to PARP-1 [defined as auto(poly-ADP-ribosylation)] requires binding of coenzymic DNA. The preceding paper [Kun, E., et al. (2004) Biochemistry 43, 210-216] shows that oligonucleotides of dsDNA can serve as coenzymic DNA for PARP-1 trans- or auto-modification activity. Results of DNA-protein binding (EMSA) experiments reported here demonstrate that short DNA oligonucleotides containing the 5'-TGTTG-3' nucleotide sequence motif preferentially bind to cloned PARP-1 in vitro. The same nucleotide sequence motif is responsible for striated myocyte-selective transcription of a contractile protein gene encoding cardiac troponin T (cTnT). Results of experiments reported here demonstrate that mutation of this motif also abolishes the differentiation-dependent activation of the transfected cTnT promoter in myoblasts cultured in vitro, indicating that nucleotide sequence-dependent binding of PARP-1 to promoter DNA of the cTnT gene is also necessary for differentiation-dependent activation. Thus, PARP-1 has two types of dsDNA binding activity: (1) nucleotide sequence-dependent binding, analyzed here with EMSA experiments, and (2) coenzymic binding, measured catalytically, which does not depend on the nucleotide sequence of the dsDNA. We hypothesize that the well-known association of PARP-1 with chromatin can be attributed to its stable binding to chromosomal dsDNA, some portion of which is likely to be nucleotide sequence-dependent binding. According to this hypothesis, the distribution of this protein-modifying enzyme in chromatin may be targeted to specific genomic loci and vary according to cell type and developmental stage.

The zinc-finger domains of PARP1 cooperate to recognize DNA strand breaks

“…Short-patch repair of DNA single-strand breaks is initiated by poly(ADP-ribose) polymerase-1 (PARP1) -a multi-domain enzyme activated by binding of its N-terminal DNA-binding domain (DBD) to DNA breaks [1][2][3][4][5] . Activated PARP1 utilises NAD + to Correspondence to: Andreas G. Ladurner; Laurence H. Pearl; Antony W. Oliver.…”

“…We have now determined the crystal structure of the human PARP1-DBD bound to a DNA break. Along with functional analysis of PARP1 recruitment to sites of DNA damage in vivo, the structure reveals a dimeric assembly whereby ZnF1 and ZnF2 domains from separate PARP1 molecules form a strand-break recognition module that helps activate PARP1 by facilitating its dimerization and consequent trans-automodification.Short-patch repair of DNA single-strand breaks is initiated by poly(ADP-ribose) polymerase-1 (PARP1) -a multi-domain enzyme activated by binding of its N-terminal DNA-binding domain (DBD) to DNA breaks [1][2][3][4][5] . Activated PARP1 utilises NAD + to Correspondence to: Andreas G. Ladurner; Laurence H. Pearl; Antony W. Oliver.…”

Uncoupling of the transactivation and transrepression functions of PARP1 protein

“…Such a sequence could be part of the genome of retrotransposable elements. The ability to bind sequence TGTTG has been previously reported for mammalian PARP1 (32). Sequence TGTTG is known to be an evolutionarily conserved flanking sequence for many retroviral and retrotransposable elements with long terminal repeats, such as copia and gypsy in Drosophila.…”

Differential regulation of CXC ligand 1 transcription in melanoma cell lines by poly(ADP-ribose) polymerase-1

“…Studies with PARP-1-deficient cells and animals have revealed diverse functions of PARP-1, including roles in anti-recombination and genomic instability, DNA replication, regulation of telomere function and transcriptional regulation (Simbulan-Rosenthal et al, 1999;Smulson et al, 2000;Cayuela et al, 2001). Although no consensus DNAbinding sequence for PARP-1 has been established, the ability of PARP-1 to bind DNA in a sequence-specific manner was demonstrated by Huang et al (2004), where PARP-1 preferentially bound to DNA oligonucleotides containing the 5 0 -TGTTG-3 0 nucleotide sequence motif (Simbulan-Rosenthal et al, 2003). PARP-1 has also been shown to activate the human T-cell leukemia virus type I Tax-mediated transcription in murine lymphocytic leukemia cells through sequence-specific binding to the Tax-responsive element TTGACGACAA (Zhang et al, 2002).…”