Fig. 3

PhaR binding to DNA fragments containing the promoter regions of phaP paralogs (a–c), phaR (d), phaZ paralogs (e and f), and others (g and h). Various amounts of purified PhaR-His₆ were incubated with a fixed amount of DNA fragments containing the promoter regions as indicated; (a) phaP1 (bll5155), (b) phaP4 (bll7395), (c) phaP5 (blr2887), and (d) phaR (blr0227), (e) phaZ1 (blr0908), (f) phaZ3 (blr0899), (g) cyoA (blr0149), and (h) blr2367. The reactions were subjected to gel mobility shift assays as described in the main text. Each of the gels has eight lanes containing serially increased amounts of PhaR-His₆ from left to right to give 0, 1.72, 3.44, 6.88, 13.8, 27.5, 55, and 110 nM, respectively. Positions for DNA-protein complex and free DNA fragments are indicated with arrowheads on the left side of the panels. As a negative control (NC), a constant amount of the DNA fragment corresponding to part of the phaP1 coding region is included, which is another PCR fragment amplified using the primer pairs EMSA-phaP1-ORF-F/EMSA-phaP1-ORF-R (Additional file 1: Table S1)