Proteomic Approach to Identification of Proteins Reactive for Abasic Sites in DNA

Robert A. Rieger, Elena I. Zaika, Weiping Xie, Francis Johnson, Arthur P. Grollman, Charles R. Iden, Dmitry O. Zharkov
2006 Molecular & Cellular Proteomics  
Apurinic/apyrimidinic (AP) sites, a prominent type of DNA damage, are repaired through the base excision repair mechanism in both prokaryotes and eukaryotes and may interfere with many other cellular processes. A full repertoire of AP site-binding proteins in cells is presently unknown, preventing reliable assessment of harm inflicted by these ubiquitous lesions and of their involvement in the flux of DNA metabolism. We present a proteomics-based strategy for assembling at least a partial
more » ... ast a partial catalogue of proteins capable of binding AP sites in DNA. The general scheme relies on the sensitivity of many AP site-bound protein species to NaBH 4 cross-linking. An affinity-tagged substrate is used to facilitate isolation of the cross-linked species, which are then separated and analyzed by mass spectrometry methods. We report identification of seven proteins from Escherichia coli (AroF, DnaK, MutM, PolA, TnaA, TufA, and UvrA) and two proteins from bakers' yeast (ARC1 and Ygl245wp) reactive for AP sites in this system. Molecular & Cellular Proteomics 5:858 -867, 2006. From the ‡Department of Pharmacology, §Laboratory of Chemical Biology, and ʈProteomic Center, Stony Brook University, Stony Brook, New York 11794 and the ‡ ‡Siberian Branch of the Russian Academy
doi:10.1074/mcp.m500224-mcp200 pmid:16474175 fatcat:ayzbmpr4jnfstjhg7y2dnwp6rq