Figure 6.

Effect of chromosome relaxation on RNAP binding on TopoI promoter(s). (A) Schematic of the experimental design. Negative supercoiling may bring the −35 and −10 elements of topoI promoter(s) on the same phase of DNA thus enhancing the RNAP-promoter interaction. (B) Exponentially grown M. smegmatis cells were treated with novobiocin (100 μg/ml) for 6 h. The treated cells were subjected to ChIP using anti-RpoB antibody. The immunoprecipitated DNA was analyzed for the enrichment of promoter region of various genes by qRT-PCR using primers flanking the promoter region. (C) Model representing the SST of TopoI. Sub-optimal spacer length between −10 and −35 elements align them out of phase affecting the optimal RNAP-promoter interaction. Additionally upstream gene transcription affects the DNA topology restricting the topoI activity. The negative supercoiling activity of DNA gyrase maintains the optimal topology of the topoI promoter aligning the −35 and −10 elements in the appropriate orientation required for the optimal transcription. Conditions leading to the chromosome relaxation reduce the topoI expression by altering optimal orientation of −35 and −10 elements. The error bars represent the SD obtained from three independent experiments.*P < 0.01, ns: not significant (P > 0.1).