The PCR products were purified using QiaQuick cleanup columns (Qiagen). Increasing amounts of purified His-protein were incubated with the labeled DNA fragment (2 to 5 pmol) for 30 min at room temperature in a binding buffer containing 10 mM Tris-Cl (pH7.4), 50 mM KCl, 0.5 mM DTT, 1 mM MgCl2, 4% glycerol, 0.05 mg/ml BSA, 0.05 mg/ml shared salmon sperm DNA and 0.5 mM EDTA, with a final volume of 10

μl [16, 21]. To achieve the OmpR phosphorylation, 25 mM fresh acetyl phosphate LY3039478 cost was added in the binding buffer and incubated with purified His-OmpR for 30 min, after which the labeled DNA was added for additional incubation for 30 min. To activate CRP, 2 mM cAMP was mixed with purified His-CRP in the DNA-binding reactions. To initiate DNA digestion, 10 μl of Ca2+/Mg2+ solution (5 mM CaCl2 and 10 mM MgCl2) was added, followed by incubation for 1 min at room temperature. Afterwards, the optimized RQ1 RNase-Free DNase I (Promega) was added to the reaction mixture, and the mixture was incubated at room temperature for 30 to 90 s. The cleavage reaction was stopped by adding 9 μl of the stop solution (200 mM

NaCl, 30 mM EDTA, and 1% SDS) followed by DNA extraction and precipitation. The partially digested DNA samples were then analyzed in a 6% polyacrylamide/8 M urea gel. Protected regions were identified by comparing these with the sequence ladders. For sequencing, the fmol® DNA Cycle Sequencing System (Promega) was used, and the final result was detected by autoradiography (Kodak film). Computational promoter analysis The 300 bp promoter regions Blasticidin S in vivo upstream of the start codon of each indicated gene was retrieved using the ‘ retrieve-seq ‘

program [27]. The ‘ matrices-paster’ tool [27] was used to match Glutamate dehydrogenase the relevant position-specific scoring matrix (PSSM) within the above promoter regions. Results Non-polar mutation of ompR or crp The ompR and crp null mutants designated as ΔompR and Δcrp, respectively, have been evaluated in the present study. Non-polar mutation of ompR has been confirmed previously with the complemented ompR mutant [12]. To prove the non-polar mutation of crp, we constructed the pRW50-harboring fusion promoter, which consisted of a promoter-proximal region of ompF and promoterless lacZ, and then transformed into WT, Δcrp and C-crp (the complemented crp mutant), respectively (Additional file 2). The ompF gene was positively regulated by CRP as determined by several distinct methods (see below). As expected, the ompF promoter activity (β-galactosidase activity) decreased significantly in Δcrp relative to WT grown in the TMH medium with the addition of 1 mM cAMP, but showed almost no difference between WT and C- crp. Direct regulation of ompC, F and X by CRP The quantitative RT-PCR analysis was also performed to compare the mRNA levels of each gene tested in Δcrp and WT in the presence of 1 mM cAMP.