title: A dual switch controls bacterial enhancer-dependent transcription.
abstract: Bacterial RNA polymerases (RNAPs) are targets for antibiotics. Myxopyronin binds to the RNAP switch regions to block structural rearrangements needed for formation of open promoter complexes. Bacterial RNAPs containing the major variant σ(54) factor are activated by enhancer-binding proteins (bEBPs) and transcribe genes whose products are needed in pathogenicity and stress responses. We show that (i) enhancer-dependent RNAPs help Escherichia coli to survive in the presence of myxopyronin, (ii) enhancer-dependent RNAPs partially resist inhibition by myxopyronin and (iii) ATP hydrolysis catalysed by bEBPs is obligatory for functional interaction of the RNAP switch regions with the transcription start site. We demonstrate that enhancer-dependent promoters contain two barriers to full DNA opening, allowing tight regulation of transcription initiation. bEBPs engage in a dual switch to (i) allow propagation of nucleated DNA melting from an upstream DNA fork junction and (ii) complete the formation of the transcription bubble and downstream DNA fork junction at the RNA synthesis start site, resulting in switch region-dependent RNAP clamp closure and open promoter complex formation.
authors.affiliation: Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, UK. s.wiesler@imperial.ac.uk
authors.forename: Simone C
authors.initials: SC
authors.lastname: Wiesler
authors.forename: Patricia C
authors.initials: PC
authors.lastname: Burrows
authors.forename: Martin
authors.initials: M
authors.lastname: Buck
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D004268:DNA-Binding Proteins / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics; D004742:Enhancer Elements, Genetic; D004926:Escherichia coli / Q000187:drug effects / Q000201:enzymology / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000235:genetics; D017353:Gene Deletion; D015964:Gene Expression Regulation, Bacterial; D020035:Holoenzymes / Q000378:metabolism; D006868:Hydrolysis; D007783:Lactones / Q000494:pharmacology; D011401:Promoter Regions, Genetic; D011487:Protein Conformation; D051877:RNA Polymerase Sigma 54 / Q000235:genetics; D012097:Repressor Proteins / Q000378:metabolism; D024363:Transcription Initiation Site; D061785:Transcription Initiation, Genetic / Q000187:drug effects
chemical_list: D000900:Anti-Bacterial Agents; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D020035:Holoenzymes; D007783:Lactones; D012097:Repressor Proteins; C120334:gene 2 product, bacteriophage T7; C497751:rpoN protein, E coli; D000255:Adenosine Triphosphate; D012321:DNA-Directed RNA Polymerases; D051877:RNA Polymerase Sigma 54