title: Opening and closing of the bacterial RNA polymerase clamp.
abstract: Using single-molecule fluorescence resonance energy transfer, we have defined bacterial RNA polymerase (RNAP) clamp conformation at each step in transcription initiation and elongation. We find that the clamp predominantly is open in free RNAP and early intermediates in transcription initiation but closes upon formation of a catalytically competent transcription initiation complex and remains closed during initial transcription and transcription elongation. We show that four RNAP inhibitors interfere with clamp opening. We propose that clamp opening allows DNA to be loaded into and unwound in the RNAP active-center cleft, that DNA loading and unwinding trigger clamp closure, and that clamp closure accounts for the high stability of initiation complexes and the high stability and processivity of elongation complexes.
authors.affiliation: Howard Hughes Medical Institute, Waksman Institute, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
authors.forename: Anirban
authors.initials: A
authors.lastname: Chakraborty
authors.forename: Dongye
authors.initials: D
authors.lastname: Wang
authors.forename: Yon W
authors.initials: YW
authors.lastname: Ebright
authors.forename: You
authors.initials: Y
authors.lastname: Korlann
authors.forename: Ekaterine
authors.initials: E
authors.lastname: Kortkhonjia
authors.forename: Taiho
authors.initials: T
authors.lastname: Kim
authors.forename: Saikat
authors.initials: S
authors.lastname: Chowdhury
authors.forename: Sivaramesh
authors.initials: S
authors.lastname: Wigneshweraraj
authors.forename: Herbert
authors.initials: H
authors.lastname: Irschik
authors.forename: Rolf
authors.initials: R
authors.lastname: Jansen
authors.forename: B Tracy
authors.initials: BT
authors.lastname: Nixon
authors.forename: Jennifer
authors.initials: J
authors.lastname: Knight
authors.forename: Shimon
authors.initials: S
authors.lastname: Weiss
authors.forename: Richard H
authors.initials: RH
authors.lastname: Ebright
mesh_terms: D004258:DNA Polymerase III / Q000737:chemistry* / Q000187:drug effects; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods; D015964:Gene Expression Regulation, Bacterial; D011487:Protein Conformation; D014158:Transcription, Genetic
chemical_list: C101139:beta subunit, DNA polymerase III; D004258:DNA Polymerase III