Interaction between E. coli RNA polymerase and the tetR promoter from pSC101: homologies and differences with other E. coli promoter systems from close contact point studies

Abstract

The interaction between E. coli RNA polymerase and the tetR promoter from pSC101, was studied by protection and premodification experiments, using dimethyl sulfate, methylation of single stranded cytosines, and DNAase I footprinting. Whereas qualitative and quantitative results from the chemical approach conform to patterns already displayed by other promoter systems, hypersensitive sites to DNAase I attack differ from those of other promoters. Distribution and nature of the contacts suggest that regions of the promoter sequence participates differently in complex formation. The involvement of major and minor grooves of the double helix in the complex with the enzyme, differs along the promoter. After a comparison of the results from seven different promoters, a pattern of conserved contacts seem to appear. Comparison of temperature dependence of local unwinding around the transcription start site (detected by the appearance of single stranded cytosines), and DNAase I footprinting, reveals that the process leading to stable complex formation can be achieved without disruption of base-pairing.