The Bacterial Response Regulator ArcA Uses a Diverse Binding Site Architecture to Regulate Carbon Oxidation Globally
Figure 4
Analysis of predicted multiple DR elements by DNase I footprinting.
DNase I footprinting data for a subset of ArcA regulated promoters. The regions protected by ArcA-P are indicated with vertical lines with predicted DR elements indicated by filled boxes with arrows indicating the directional orientation of DR elements. The numbers indicate the position relative to the previously determined transcription start site. Predicted DR elements not protected by ArcA-P are indicated by dashed grey boxes while dashed black boxes represent protected regions where no DR element greater than 0 bits was predicted. Samples were electrophoresed with Maxam–Gilbert ladders (A+G) made using the same DNA (lane 1). ArcA-P protein concentrations are given from left to right in terms of nM total protein. (A) Coding strand of the astC promoter, (D) acs promoter, (E) putP promoter and (G) phoH promoter. ArcA-P: 0, 50, 100, 200, 400, 600 nM. (B) Coding strand of the trxC promoter and (H) dctA promoter. ArcA-P: 0, 100, 200, 400, 600, 1000 nM. (C) Coding strand of the icdA promoter. ArcA-P: 0, 50, 150, 300, 600, 1000 nM. (F) Coding strand of the paaA promoter. ArcA-P: 0, 100, 200, 400, 600 nM.