The [γ-32P]-labeled upstream region of each genes (10 fmol of target DNA probes) were incubated with the purified Zur protein in the presence of 100 μM ZnCl2. 0, 1.25, 2.5, 5, 5, 5 and 0 pmol of Zur were used in lanes 1 to 4 and C1 to C3, respectively. The mixtures were directly subjected to 4% polyacrylamide gel electrophoresis. For lanes 1 to 4, the retarded DNA band with decreased mobility turned up, which presumably represented the Zur-DNA complex. To confirm the specificity of the HSP inhibitor binding complexes, either a 200-fold molar excess of DNA Damage inhibitor nonspecific competitor (2 pmol of unlabeled znuA DNA without its predicted binding region in lane C1) or a 200-fold molar excess of specific competitor (2 pmol

of unlabeled target DNA probe in lane C2) was added to the binding mixture. 2 pmol of an unrelated protein, i.e., purified rabbit anti-F1 antibody, were included in lane C3. Both znuA and znuC gave positive EMSA results. Since these two genes had overlapped upstream regions and shared a single predicted Zur site, the EMSA data of only znuA rather than znuC was presented herein. The EMSA experiments still included three additional VX-661 in vivo genes, astC, astA and rovA (Fig. 3). As expected, the negative control rovA gave negative EMSA result. astC and astA were the first and second genes of the astCADBE operon, respectively. The whole operon was induced by Zur

as determined by cDNA microarray, and real-time RT-PCR confirmed the up-regulation of astC by Zur (Additional file 5). astA gave a high score value (8.2) in the computational promoter analysis, while astC presented a

very low value of 4.4 (Table 1). Both of astC and astA gave the negative EMSA results (Fig. 3). Herein, neither astCADB nor astADB was thought to be under the direct control of Zur by directly binding to a cis-acting element within corresponding upstream promoter region. Zur represses promoter activity of znuA, znuCB and ykgM-rpmJ2 To further validate the effect of Zur on the promoter activity of znuCB, znuA and ykgM-rpmJ2, we constructed oxyclozanide the znuC::lacZ, znuA::lacZ and ykgM::lacZ fusion promoters each consisting of an upstream DNA of the corresponding gene, and then each of them was transformed into WT and Δzur, respectively. The β-galactosidase production of these lacZ fusions was measured in both WT and Δzur, which represented the promoter activity of the corresponding gene in each strain. It should be noted that the zur mutation had an effect on the copy number of recombinant or empty pRS551 plasmid, and accordingly a normalized Miller unit was used to calculate the fold change in the activity of each fusion promoter in Δzur in relative to WT (Table 2). For each of the three genes, there was a significant increase of β-galactosidase activity in Δzur compared to WT when they grew in TMH with the addition of zinc. Thus, Zur repressed the promoter activities of znuC, znuA and ykgM.