pestis 201 and then cloned directionally into the respective Bam HI and Hind III sites of plasmid pET28a. This was later verified through DNA sequencing. The recombinant plasmid encoding a His-protein was transformed into BL21λDE3 cells. Over-expression of His-OmpR in the LB medium was induced by adding 1 mM isopropyl-b-D-thiogalactoside. AMN-107 The over-expressed protein was purified under native conditions with nickel-loaded

HiTrap Chelating Sepharose columns (Amersham). The purified and eluted protein was concentrated to a final concentration of 0.1 to 0.3 mg/ml with the Amicon Ultra-15 (Millipore), which was confirmed by SDS-PAGE for purity. The purified protein was stored at -80°C. DNase I footprinting The promoter DNA regions (Table 1) were prepared by PCR amplification performed with the promoter-specific primer pairs (see Additional file 1 for primer sequences), including a 5′-32P-labeled primer (either forward or reverse) and its non-labeled counterpart. 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-HCl (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. Afterwards, 25 mM of fresh acetyl phosphate was added in the binding buffer and incubated with purified His-OmpR for 30 min to this website achieve the OmpR phosphorylation, after which the labeled DNA was added for additional incubation for 30 min. Prior to 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. The optimized RQ1 RNase-Free DNase I (Promega) was then added to the reaction mixture, which was subsequently incubated at room temperature for 30 to 90 s. The cleavage reaction was stopped by adding 9 μl of Farnesyltransferase the stop solution (200 mM NaCl, 30 mM EDTA and 1% SDS) followed by DNA extraction and precipitation. The partially

Proteasome structure 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. The result was detected by autoradiography (Kodak film). Computational promoter analysis The 300 bp promoter regions upstream of the start codon of each indicated gene were retrieved with the ‘ retrieve-seq ‘ program [28]. The ‘ matrices-paster’ tool [28] was used to match the relevant position-specific scoring matrix (PSSM) within the above promoter regions. Environmental stress experiments Y. pestis strain 201 inoculated into TMH was grown to the early logarithm phase at 26°C. To determine the effect of high osmolarity stress on Y. pestis, the log-phase cells were kept incubated at 26°C for 20 min in the presence of 1.