Fig. 2

DzrR specifically binds to the promoter of desAB. A EMSA of DzrR binding to the promoter fragment of desAB. Free probes, i.e., biotin-labeled DNA fragment of P_desAB (222 bp) and biotin-labeled control DNA (60 bp), and P_desAB probe with DzrR (Bound probe) are indicated by arrows. B DNase I footprinting assay performed between DzrR and the promoter fragment of desAB labeled with FAM and HEX. C DzrR binding site in desAB promoter region. DzrR binding site, potential -35 and -10 regions, and start codon (ATG) of desA gene are indicated and underlined. D EMSA of DzrR binding to a 37-bp DNA fragment (P_desAB(37)) containing the DzrR protected region identified in DNase I footprinting assay (C). Free probe of P_desAB(37) (37 bp) and P_desAB(37) probe with DzrR (Bound probe) are indicated by arrows. In A and D, biotin-labeled DNA probes and biotin-labeled control DNA from EMSA kit were added at a final concentration of 20 fmol. In A, a concentration of 4 pmol unlabeled DNA fragment of P_desAB was added as a competitor for determining the specific binding of DzrR. In B, BSA (bovine serum albumin) was used as the negative control in DNase I footprinting assay for analyzing the specific region protected by DzrR