title: An aromatic residue switch in enhancer-dependent bacterial RNA polymerase controls transcription intermediate complex activity.
abstract: The formation of the open promoter complex (RPo) in which the melted DNA containing the transcription start site is located at the RNA polymerase (RNAP) catalytic centre is an obligatory step in the transcription of DNA into RNA catalyzed by RNAP. In the RPo, an extensive network of interactions is established between DNA, RNAP and the σ-factor and the formation of functional RPo occurs via a series of transcriptional intermediates (collectively 'RPi'). A single tryptophan is ideally positioned to directly engage with the flipped out base of the non-template strand at the +1 site. Evidence suggests that this tryptophan (i) is involved in either forward translocation or DNA scrunching and (ii) in σ(54)-regulated promoters limits the transcription activity of at least one intermediate complex (RPi) before the formation of a fully functional RPo. Limiting RPi activity may be important in preventing the premature synthesis of abortive transcripts, suggesting its involvement in a general mechanism driving the RPi to RPo transition for transcription initiation.
authors.affiliation: Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK. s.wiesler@imperial.ac.uk
authors.forename: Simone C
authors.initials: SC
authors.lastname: Wiesler
authors.forename: Robert O J
authors.initials: RO
authors.lastname: Weinzierl
authors.forename: Martin
authors.initials: M
authors.lastname: Buck
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D001105:Archaea / Q000201:enzymology; D001419:Bacteria / Q000201:enzymology; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D017124:Conserved Sequence; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D056890:Eukaryota / Q000201:enzymology; D020035:Holoenzymes / Q000378:metabolism; D008969:Molecular Sequence Data; D009154:Mutation; D011401:Promoter Regions, Genetic; D024363:Transcription Initiation Site; D061785:Transcription Initiation, Genetic; D014364:Tryptophan / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D020035:Holoenzymes; D014364:Tryptophan; D004247:DNA; D012321:DNA-Directed RNA Polymerases