Figure 2 Regulation of ompC , F and X by CRP. a) Quantitative RT-PCR. The mRNA levels of each indicated gene were compared between Δcrp and WT. This figure shows the increased (positive number) or decreased (minus one) mean fold for each gene in Δcrp relative to WT. b) LacZ fusion reporter. A promoter-proximal region of each indicated gene was cloned into pRW50 containing a promotorless lacZ reporter gene, and transformed into WT or Δcrp to determine the promoter activity (β-Galactosidase activity in cellular Fedratinib research buy extracts). The empty

plasmid was also introduced into the corresponding strain as negative control, which gave extremely low promoter activity (data not shown). β-Galactosidase activity in each tested cellular extract was subtracted with that of negative control. This figure shows the increased (positive number) or decreased (minus one) mean fold for the detecting promoter activity in Δcrp 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 Δcrp. An oligonucleotide primer complementary to the RNA transcript of each gene was designed from a suitable position. The primer extension products were analyzed EPZ015938 with 8 M urea-6% acrylamide sequencing gel; lanes C, T, A, and G represent the Sanger sequencing reactions, respectively. On the right side, DNA sequences are shown from the bottom (5′) to the top (3′), and the transcription start sites were

underlined. d) DNase I footprinting. The labeled DNA probe was incubated with various amounts of purified His-CRP (lanes 1, 2, 3, 4, and 5 containing 0, 5, 10, 15 and 20 pmol, respectively) in the presence of 2 mM cAMP, and subjected to DNase I footprinting assay; lanes G, A, T, and C represent the Sanger sequencing reactions, respectively. ZD1839 concentration The protected regions (bold lines) are indicated on the right-hand side. The numbers indicated the nucleotide positions upstream the transcriptional start sites. In addition, primer extension experiments (Figure 1c) were conducted for ompC, F, and X to detect the yield of primer extension product that represented the relative activity of each target promoter in Δcrp or WT. A single promoter was check details transcribed for ompF or X, which was dependent on CRP. No primer extension product could be detected for ompC in both ΔompR and WT after repeated efforts, which might be due to the limitation of the primer extension assay. Meanwhile, the transcriptional levels of ompF or X in ΔompR and WT, determined by primer extension experiments herein (Figure 1c), was consistent with the RT-PCR and lacZ fusion reporter data. A previously described CRP consensus (PSSM) of Y.