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Co-regulation by bent DNA. Functional substitutions of the integration host factor site at sigma 54-dependent promoter Pu of the upper-TOL operon by intrinsically curved sequences.

The role of integration host factor (IHF) in the regulation of the sigma 54-dependent promoter Pu of the TOL plasmid of Pseudomonas putida has been examined. We have selected in vivo insertions of intrinsically curved DNA that restore the responsiveness of an IHF-binding site deletion variant of Pu to the cognate activator of the system, XylR. We found five Pu derivatives which had inserted a core sequence with 6 phased [A]6 tracts, flanked by different lengths of DNA at the location of the former IHF site. They displayed 40-100% of the activity of Pu, were independent of IHF, and maintained the overall geometry of the wild-type promoter. The induction patterns of Pu, compared to those of hybrid promoters, were virtually indistinguishable. This supports the notion that, in native conditions, IHF co-regulates the system by providing a structural aid for promoter architecture and not by interacting directly with the RNA polymerase, as it has been suggested with other known IHF-dependent promoters.