DNase I footprinting of P vpsL complexes on ( A ) nontemplate DNA and ( B ) template DNA. GA corresponds to G+A ladder. VpsR, c-di-GMP and/or RNAP are present as indicated. To the right of each gel image, a schematic indicates the −10 and −35 regions and the +1. The VpsR binding site is indicated as a dashed black line. DNase I protection regions and hypersensitive sites seen with the activated complex of RNAP, VpsR, c-di-GMP and DNA are depicted as black rectangles and horizontal arrows, respectively. The dashed red boxes indicate the regions of DNA where the protection/enhancement within and immediately adjacent to the VpsR binding site changes when comparing complexes containing RNAP with or without VpsR or c-di-GMP to the activated complex. (See text for details.)