title: The elongation factor RfaH and the initiation factor sigma bind to the same site on the transcription elongation complex.
abstract: RNA polymerase is a target for numerous regulatory events in all living cells. Recent studies identified a few "hot spots" on the surface of bacterial RNA polymerase that mediate its interactions with diverse accessory proteins. Prominent among these hot spots, the beta' subunit clamp helices serve as a major binding site for the initiation factor sigma and for the elongation factor RfaH. Furthermore, the two proteins interact with the nontemplate DNA strand in transcription complexes and thus may interfere with each other's activity. We show that RfaH does not inhibit transcription initiation but, once recruited to RNA polymerase, abolishes sigma-dependent pausing. We argue that this apparent competition is due to a steric exclusion of sigma by RfaH that is stably bound to the nontemplate DNA and clamp helices, both of which are necessary for the sigma recruitment to the transcription complex. Our findings highlight the key regulatory role played by the clamp helices during both initiation and elongation stages of transcription.
authors.affiliation: Department of Microbiology, Ohio State University, 484 West Twelfth Avenue, Columbus, OH 43210, USA.
authors.forename: Anastasiya
authors.initials: A
authors.lastname: Sevostyanova
authors.forename: Vladimir
authors.initials: V
authors.lastname: Svetlov
authors.forename: Dmitry G
authors.initials: DG
authors.lastname: Vassylyev
authors.forename: Irina
authors.initials: I
authors.lastname: Artsimovitch
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010445:Peptide Elongation Factors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding; D020836:Protein Structure, Quaternary; D012808:Sigma Factor / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D010445:Peptide Elongation Factors; D012808:Sigma Factor; D004247:DNA