These results further verified the above RT-PCR data for ompF and X. However, we failed to detect the primer Selleckchem NCT-501 extension product for ompC in both ΔompR and WT after repeated efforts using different primers. This could be attributed to the failure to synthesize the primer extension product for ompC

by polymerase. Figure 2 Regulation of ompC , F and X by OmpR. a) Real-time RT-PCR. The mRNA levels of each indicated gene were compared between ΔompR and WT. This figure shows the increased (positive number) or decreased (minus one) mean fold for each gene in ΔompR relative to WT. b) LacZ fusion reporter. A promoter-proximal region of each indicated gene was cloned into pRW50 containing a promoterless lacZ reporter gene, and transformed into WT or ΔompR to determine the promoter activity (β-galactosidase activity in cellular extracts). The empty plasmid was also introduced Cell Cycle inhibitor into each strain as negative control, which gave extremely low promoter

activity (data not shown). Positive and minus numbers check details indicate the increased and decreased mean folds, respectively, for the detecting promoter activity in ΔompR relative to WT. c) Primer extension. Primer extension assays were performed for each indicated gene using total RNAs isolated from the exponential-phase of WT or ΔompR. An oligonucleotide primer complementary to the RNA transcript of each gene was designed from a suitable position. The primer extension products were analyzed with 8 M urea-6% acrylamide sequencing gel. Lanes C, T, A, and G represent the Sanger sequencing reactions; on the right side, DNA sequences are shown from the bottom (5′) to the top (3′), and the transcription start sites are underlined. d) DNase I footprinting. The labeled DNA probe was incubated with various amounts of purified His-OmpR (lanes 1, 2, 3, 4, and 5 contained 0, 5, 10, 15 and 20 pmol, respectively) with the addition of acetyl phosphate, and subjected

to DNase I footprinting assay. Lanes G, A, T, and C represent the Sanger sequencing reactions, and theprotected regions (bold lines) are indicated on the right-hand side. The numbers indicate the nucleotide positions Florfenicol upstream of the transcriptional start sites. Given that OmpR consensus-like sequences were found within the promoter regions of ompC, F and X (Table 1), DNase I footprinting experiments (Figure 2d) were subsequently performed with both coding and non-coding strands of the corresponding promoter-proximal DNA fragments. The purified His-OmpR-P protein protected a single distinct region (OmpR-binding site) within each target promoter region in a dose-dependent pattern. Taken together, the OmpR regulator stimulated the expression of ompC, F, and X through the process of OmpR-promoter DNA association.