Figure 3

DndB binds to two regions in the promoter of the dndBCDE operon.

(A) Footprinting assays identifying two regions protected by DndB, BB1 and BB2, on both the coding and noncoding DNA strands. The palindromic motifs are shown in red letters. (B) The promoter sequence of the dndBCDE operon was analyzed using BPROM and Neutral Network Promoter Prediction online software. (C) EMSAs were performed on serial concentrations of DndB ranging from 0 to 300 nM with the DNA fragments B₁ and mutated B₁. The TACG in BB1 and CGTA in BB2 were replaced by GGTT and TTGG respectively, in the mutated B₁ fragment. Mutation of the B1 fragment impaired the DNA-binding activity of DndB. Shifted bands were recovered when the wild-type DNA B1 fragment was added.