FIG. 3.

CtrA binding sites on oriRp. A DNase I footprinting assay of oriRp was performed with thrombin-cleaved CtrA (4 μg) and CtrA∼P (phosphorylated CtrA) (4 μg) (A) by using a HincII ³²P-end-labeled fragment (A) and with different amounts of thrombin-cleaved CtrA and CtrA∼P (0.05, 0.5, 1, and 2 μg) by using BamHI ³²P-end-labeled pMW1070 (B). The lines labeled with roman numerals indicate binding sites. The thick lines indicate enhanced binding by CtrA∼P. Five CtrA binding sites (sites I to V) on the HincII end-labeled oriRp fragment (A) and three of the five CtrA binding sites (sites III, IV, and V) on the BamHI end-labeled oriRp fragment (B) were detected. The schematic diagram of oriRp shows the positions of BamHI and HincII restriction sites flanking oriRp; the dumbbells indicate CtrA binding sites I to V. (C) Comparison of the sequences of all five oriRp CtrA binding sites to the Cori CtrA binding consensus sequence. The potential CzcR binding consensus sequence is TTWW-N7-TTWW, where W is A or T. Note that in site IV there are two potential DnaA boxes (underlined) overlapping the halves of the binding site.