FIGURE 5.

Interactions of MtrA with the upstream regions of bldD and whiI. (A) For EMSAs, a fixed amount of labeled probe containing the intergenic region upstream of the indicated gene was incubated in reactions containing no MtrA (lane 1), or 1.6 or 3.2 μg MtrA (lanes 2 and 3, respectively). The DNA fragments used as probes were amplified by PCR. The length of the probe for each upstream region is: bldD (282 bp), bldKA (265 bp), whiE-ORF1 (267 bp), and whiI (293 bp). The arrow indicates the position of free probes, and arrowheads indicate the position of the shifted probes. DNase I footprinting assays of the coding strand of bldD (B) and whiI (C). The upper electropherograms in red are the control reactions without addition of MtrA protein. The reactions including MtrA are shown below in blue. The MtrA-protected regions are indicated by the dotted rectangles. The superimposed electropherograms shows the sequencing reactions. The nucleotide sequence of the MtrA-protected region for each gene is marked by bold italics and a double arrow, and the numbers indicate position relative to the TSP of each gene. The potential MtrA sequence is underlined.