title: The flap domain is required for pause RNA hairpin inhibition of catalysis by RNA polymerase and can modulate intrinsic termination.
abstract: Bacterial RNA polymerase (RNAP) responds to formation of RNA secondary structures (hairpins) in newly synthesized RNA. Depending on the spacing of the hairpin from the RNA 3' end and the intervening RNA sequence, the hairpin can prolong pausing or cause transcriptional termination. At the his pause site, the pause hairpin contacts a flexible domain on RNAP called the flap, which forms a critical part of a hairpin-interaction site on the enzyme. We report that pause hairpin-flap interaction stabilizes an inhibited configuration of RNAP's active site without changing RNAP's translocation register. The distal part of the flap (the flap tip) is required for the hairpin to affect the active site, but not for hairpin formation. In contrast, the flap tip is not required for intrinsic termination, but can modulate it at suboptimal termination signals.
authors.affiliation: Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA.
authors.forename: Innokenti
authors.initials: I
authors.lastname: Toulokhonov
authors.forename: Robert
authors.initials: R
authors.lastname: Landick
mesh_terms: D001665:Binding Sites; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D008957:Models, Genetic; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D014176:Protein Biosynthesis; D017434:Protein Structure, Tertiary; D012313:RNA / Q000737:chemistry* / Q000378:metabolism
chemical_list: D012313:RNA; D012321:DNA-Directed RNA Polymerases