Fig 9.

Missing-nucleoside footprints of the P_exsC and P_pcrG promoter regions. P_exsC (A) or P_pcrG (B) promoter probes labeled with ³²P on the forward or reverse strand were treated with hydroxyl radicals, incubated with ExsA_His, and subjected to nondenaturing electrophoresis in a typical EMSA reaction. The unbound band and the ExsA-bound band corresponding to shift product 2 (representing ExsA bound to both sites 1 and 2) were eluted from the gel, separated by denaturing electrophoresis, and visualized by phosphorimaging. Maxam-Gilbert sequencing ladders (A+G) were included for orientation. The locations of the GnC and TGnnA sequences in binding site 1 and binding site 2 are indicated. (C) Summary of the footprinting data for the forward and reverse strands. The conserved GnC and TGnnA sequences (bold with larger typeface), adenine-rich region (gray box), and positions of ExsA binding sites 1 and 2 are indicated. Nucleotides indicated with arrows are those present in the unbound samples and required for maximal ExsA binding. (D) Proposed model for the binding of ExsA to site 1 in the P_exoT promoter region. The amino acid residues that are proposed to contribute to base-specific recognition of the coding or noncoding strand of the P_exoT promoter region are indicated.