A PROTEIN-INDUCED DNA BEND INCREASES THE SPECIFICITY OF A PROKARYOTICENHANCER-BINDING PROTEIN

Control of transcription in prokaryotes often involves direct contact of regulatory proteins with RNA polymerase from binding sites located adjacent to the target promoter. Alternatively, in the case of genes t ranscribed by Escherichia coli RNA polymerase holoenzyme containing th e alternate sigma factor sigma(54), regulatory proteins bound at more distally located enhancer sites can activate transcription via DNA loo ping by taking advantage of the increasing flexibility of DNA over lon ger distances. While this second mechanism offers a greater possible f lexibility in the location of these binding sites, it is not clear how the specificity offered by the proximity of the regulatory protein an d the polymerase intrinsic to the first mechanism is maintained. Here we demonstrate that integration host factor (IHF), a protein that indu ces a sharp bend in DNA, acts both to inhibit DNA-looping-dependent tr anscriptional activation by an inappropriate enhancer-binding protein and to facilitate similar activation by an appropriate enhancer-bindin g protein. These opposite effects have the consequence of increasing t he specificity of activation of a promoter that is susceptible to regu lation by proteins bound to a distal site.