title: A protein-induced DNA bend increases the specificity of a prokaryotic enhancer-binding protein.
abstract: 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 transcribed by Escherichia coli RNA polymerase holoenzyme containing the alternate sigma factor sigma54, regulatory proteins bound at more distally located enhancer sites can activate transcription via DNA looping by taking advantage of the increasing flexibility of DNA over longer distances. While this second mechanism offers a greater possible flexibility in the location of these binding sites, it is not clear how the specificity offered by the proximity of the regulatory protein and the polymerase intrinsic to the first mechanism is maintained. Here we demonstrate that integration host factor (IHF), a protein that induces a sharp bend in DNA, acts both to inhibit DNA-looping-dependent transcriptional activation by an inappropriate enhancer-binding protein and to facilitate similar activation by an appropriate enhancer-binding protein. These opposite effects have the consequence of increasing the specificity of activation of a promoter that is susceptible to regulation by proteins bound to a distal site.
authors.affiliation: Laboratory of Genetics, The Rockefeller University, New York, New York 10021, USA. dworkin@biosun.harvard.edu
authors.forename: J
authors.initials: J
authors.lastname: Dworkin
authors.forename: A J
authors.initials: AJ
authors.lastname: Ninfa
authors.forename: P
authors.initials: P
authors.lastname: Model
mesh_terms: D001426:Bacterial Proteins / Q000187:drug effects / Q000235:genetics / Q000494:pharmacology; D001665:Binding Sites / Q000187:drug effects; D004247:DNA / Q000737:chemistry* / Q000187:drug effects; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000187:drug effects / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D004742:Enhancer Elements, Genetic / Q000502:physiology; D004926:Escherichia coli / Q000737:chemistry; D029968:Escherichia coli Proteins; D034982:Integration Host Factors; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic / Q000187:drug effects; D051877:RNA Polymerase Sigma 54; D012680:Sensitivity and Specificity; D012808:Sigma Factor / Q000378:metabolism; D015534:Trans-Activators / Q000187:drug effects / Q000235:genetics; D015533:Transcriptional Activation / Q000187:drug effects
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D034982:Integration Host Factors; C098954:PspF protein, E coli; D012808:Sigma Factor; D015534:Trans-Activators; C497751:rpoN protein, E coli; D004247:DNA; D012321:DNA-Directed RNA Polymerases; D051877:RNA Polymerase Sigma 54