title: Mechanism of specific recognition of the aidB promoter by sigma(S)-RNA polymerase.
abstract: Transcription of the Escherichia coli aidB gene is controlled by an Esigma(S)-dependent promoter (PaidB) and is poorly transcribed by the Esigma(70) form of RNA polymerase in the absence of additional factors. In this report, we investigate the interaction between PaidB and either the Esigma(70) or the Esigma(S) forms of RNA polymerase in vitro. We show that although Esigma(70) can bind the aidB promoter, its interaction with the promoter results in the formation of an open complex inefficient in transcription initiation and sensitive to heparin challenge. Deletion of the C residue at position -13 of PaidB (Delta-13C) slightly impaired transcription initiation by Esigma(S), consistent with the role of -13C as a specific feature of Esigma(S)-dependent promoters. However, Esigma(S) could still bind and initiate transcription from the Delta-13C mutant aidB promoter more efficiently than Esigma(70), suggesting that sequence elements other than the -13C play an important role in specific promoter recognition by Esigma(S).
authors.affiliation: Swiss Federal Institute of Environmental Technology (EAWAG), Uberlandstrasse 133, CH-8600 Dübendorf, Switzerland.
authors.forename: Stephan
authors.initials: S
authors.lastname: Lacour
authors.forename: Annie
authors.initials: A
authors.lastname: Kolb
authors.forename: Alexander Jakob
authors.initials: AJ
authors.lastname: Boris Zehnder
authors.forename: Paolo
authors.initials: P
authors.lastname: Landini
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism*; D001483:Base Sequence; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins; D006493:Heparin / Q000494:pharmacology; D046911:Macromolecular Substances; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D023282:Nuclease Protection Assays; D011401:Promoter Regions, Genetic / Q000502:physiology*; D011485:Protein Binding / Q000187:drug effects / Q000502:physiology; D012808:Sigma Factor / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: C090096:AidB protein, E coli; D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D046911:Macromolecular Substances; D012808:Sigma Factor; C069567:sigma factor KatF protein, Bacteria; D006493:Heparin; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases