Poly(ADP-ribose) binds to specific domains in DNA damage checkpoint proteins

Poly(ADP-ribose) is formed in possibly all multicellular organisms by a fam iliy of poly(ADP-ribose) polymerases (PARPs). PARP-1, the best understood a nd until recently the only known member of this family, is a DNA damage sig nal protein catalyzing its automodification with multiple, variably sized A DP-ribose polymers that may contain up to 200 residues and several branchin g points. Through these polymers, PARP-1 can interact noncovalently with ot her proteins and alter their functions. Here we report the discovery of a p oly(ADP-ribose)-binding sequence motif in several important DNA damage chec kpoint proteins. The 20-amino acid motif contains two conserved regions: (i ) a cluster rich in basic amino acids and (ii) a pattern of hydrophobic ami no acids interspersed with basic residues. Using a combination of alanine s canning, polymer blot analysis, and photoaffinity labeling, we have identif ied poly(ADP-ribose)-binding sites in the following proteins: p53, p21(CIP1 /WAF1) xeroderma pigmentosum group A complementing protein, MSH6, DNA ligas e III, XRCC1, DNA polymerase epsilon, DNA-PKCS, Ku70, NF-kappaB, inducible nitric-oxide synthase , caspase-activated DNase, and telomerase. The poly(A DP-ribose)-binding motif was found to overlap with five important functiona l domains responsible for (i) protein-protein interactions, (ii) DNA bindin g, (iii) nuclear localization, (iv) nuclear export, and (v) protein degrada tion. Thus, PARPs may target specific signal network proteins via poly(ADP- ribose) and regulate their domain functions.