Stable DNA opening within open promoter complexes is mediated by the RNA polymerase β′-jaw domain

Abstract

DNA opening for transcription-competent open promoter complex (OC) formation by the bacterial RNA polymerase (RNAP) relies upon a complex network of interactions between the structurally conserved and flexible modules of the catalytic β and β′-subunits, RNAP-associated σ-subunit, and the DNA. Here, we show that one such module, the β′-jaw, functions to stabilize the OC. In OCs formed by the major σ70- RNAP, the stabilizing role of the β′-jaw is not restricted to any particular melted DNA segment. In contrast, in OCs formed by the major variant σ54-RNAP, the β′-jaw and a conserved σ54 regulatory domain co-operate to stabilize the melted DNA segment immediately upstream of the transcription start site. Clearly, regulated communication between the mobile modules of the RNAP and the functional domain(s) of the σ subunit is required for stable DNA opening. © 2005 by The American Society for Biochemistry and Molecular Biology, Inc.