Computation-Directed Identification of OxyR DNA Binding Sites in Escherichia coli

• DOI: 10.1128/jb.183.15.4571-4579.2001
• Publication Date: 2002-07-27T09:58:18Z
• Authors: Ming Zheng; Xunde Wang; Bernard Doan; Karen A. Lewis; Thomas D. Schneider; Gisela Storz
• Keywords: Footprinting; DNA footprinting; Hypersensitive site; DNA binding site

ABSTRACT A computational search was carried out to identify additional targets for the Escherichia coli OxyR transcription factor. This approach predicted binding sites upstream of dsbG , encoding a periplasmic disulfide bond chaperone-isomerase; fhuF protein required iron uptake; and within yfdI . DNase I footprinting assays confirmed that oxidized bound site centered 54 bp gene 238 known in promoter region divergently transcribed ahpC gene. Although new near Northern blotting primer extension showed -proximal led induction second ahpCF transcript, while leads both transcripts. Oxidized 40 by footprinting, but these further revealed higher-affinity promoter. Interestingly, two overlapped with regions Fur repressor. Expression analysis repressed hydrogen peroxide an OxyR-dependent manner. Finally, experiments be coding sequence These results demonstrate versatile modes regulation illustrate need learn more about ensembles transcripts E. genome.