Participation of IHF and a distant UP element in the stimulation of the phage lambda P sub(L) promoter

We have previously identified a UP element in the phage lambda P sub(L) promoter, centred at position -90 from the transcription start site. Integration host factor (IHF), a heterodimeric DNA-binding and-bending protein, binds upstream of the lambda P sub(L) promoter in a region overlapping the UP element. Stimulation of transcription by IHF requires an intact alpha CTD and affects the initial binding of RNA polymerase to the promoter. We propose a model for the stimulation of P sub(L) by IHF in which IHF bends the DNA to bring the distal UP sequence in closer proximity to the promoter core sequences to allow the docking of the alpha CTD of RNA polymerase. Furthermore, IHF may also participate in protein-protein interactions with the alpha CTD. In support of this model, we found that alanine substitutions in alpha CTD at positions 265, 268, 270 and 275 reduced P sub(L) promoter activity. Mutations in the IHF DNA binding site, as well as IHF mutant proteins exhibiting a decreased ability to bend the DNA, were both defective in stimulating the P sub(L) promoter. In addition, some of the mutated IHF residues are clustered at a protein surface that interacts with the UP DNA sequence. These residues may also participate in protein-protein interactions with the alpha CTD.