title: rRNA promoter regulation by nonoptimal binding of sigma region 1.2: an additional recognition element for RNA polymerase.
abstract: Regulation of transcription initiation is generally attributable to activator/repressor proteins that bind to specific DNA sequences. However, regulators can also achieve specificity by binding directly to RNA polymerase (RNAP) and exploiting the kinetic variation intrinsic to different RNAP-promoter complexes. We report here a previously unknown interaction with Escherichia coli RNAP that defines an additional recognition element in bacterial promoters. The strength of this sequence-specific interaction varies at different promoters and affects the lifetime of the complex with RNAP. Selection of rRNA promoter mutants forming long-lived complexes, kinetic analyses of duplex and bubble templates, dimethylsulfate footprinting, and zero-Angstrom crosslinking demonstrated that sigma subunit region 1.2 directly contacts the nontemplate strand base two positions downstream of the -10 element (within the "discriminator" region). By making a nonoptimal sigma1.2-discriminator interaction, rRNA promoters create the short-lived complex required for specific responses to the RNAP binding factors ppGpp and DksA, ultimately accounting for regulation of ribosome synthesis.
authors.affiliation: Department of Bacteriology, University of Wisconsin-Madison, 420 Henry Mall, 53706, USA.
authors.forename: Shanil P
authors.initials: SP
authors.lastname: Haugen
authors.forename: Melanie B
authors.initials: MB
authors.lastname: Berkmen
authors.forename: Wilma
authors.initials: W
authors.lastname: Ross
authors.forename: Tamas
authors.initials: T
authors.lastname: Gaal
authors.forename: Christopher
authors.initials: C
authors.lastname: Ward
authors.forename: Richard L
authors.initials: RL
authors.lastname: Gourse
mesh_terms: D001483:Base Sequence; D018983:DNA Footprinting; D012321:DNA-Directed RNA Polymerases / Q000235:genetics / Q000502:physiology*; D004926:Escherichia coli / Q000201:enzymology; D029968:Escherichia coli Proteins / Q000235:genetics / Q000502:physiology; D007202:Indicators and Reagents; D008958:Models, Molecular; D009154:Mutation; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012808:Sigma Factor / Q000235:genetics / Q000378:metabolism*; D013463:Sulfuric Acid Esters; D013698:Templates, Genetic; D014158:Transcription, Genetic; D012407:rRNA Operon
chemical_list: D029968:Escherichia coli Proteins; D007202:Indicators and Reagents; D012808:Sigma Factor; D013463:Sulfuric Acid Esters; C090751:dksA protein, E coli; D012321:DNA-Directed RNA Polymerases; C007482:dimethyl sulfate