Active recruitment of σ54-RNA polymerase to the Pu promoter of Pseudomonas putida : role of IHF and αCTD

The sequence elements determining the binding of the σ54-containing RNA polymerase (σ54-RNAP) to the Pu promoter of Pseudomonas putida have been examined. Contrary to previous results in related systems, we show that the integration host factor (IHF) binding stimulates the recruitment of the enzyme to the -12/-24 sequence motifs. Such a recruitment, which is fully independent of the activator of the system, XylR, requires the interaction of the C-terminal domain of the α subunit of RNAP with specific DNA sequences upstream of the IHF site which are reminiscent of the UP elements in σ70 promoters. Our data show that this interaction is mainly brought about by the distinct geometry of the promoter region caused by IHF binding and the ensuing DNA bending. These results support the view that binding of σ54-RNAP to a promoter is a step that can be subjected to regulation by factors (e.g. IHF) other than the sole intrinsic affinity of σ54-RNAP for the -12/-24 site.