title: Promoter Escape with Bacterial Two-component σ Factor Suggests Retention of σ Region Two in the Elongation Complex.
abstract: The transition from the formation of the RNA polymerase (RNAP)-promoter open complex step to the productive elongation complex step involves "promoter escape" of RNAP. From the structure of RNAP, a promoter escape model has been proposed that suggests that the interactions between σR4 and RNAP and σR4 and DNA are destabilized upon transition to elongation. This accounts for the reduced affinity of σ to RNAP and stochastic release of σ. However, as the loss of interaction of σR4 with RNAP results in the release of intact σ, assessing this interaction remains challenging to be experimentally verified. Here we study the promoter escape model using a two-component σ factor YvrI and YvrHa from Bacillus subtilis that independently contributes to the functions of σR4 and σR2 in a RNAP-promoter complex. Our results show that YvrI, which mimics σR4, is released gradually as transcription elongation proceeds, whereas YvrHa, which mimics σR2 is retained throughout the elongation complexes. Thus our result validates the proposed model for promoter escape and also suggests that promoter escape involves little or no change in the interaction of σR2 with RNAP.
authors.affiliation: Department of Chemistry, Bose Institute, 93/1 APC Road, Kolkata 700009, India.
authors.forename: Shreya
authors.initials: S
authors.lastname: Sengupta
authors.affiliation: Department of Chemistry, Bose Institute, 93/1 APC Road, Kolkata 700009, India.
authors.forename: Ranjit Kumar
authors.initials: RK
authors.lastname: Prajapati
authors.affiliation: Department of Chemistry, Bose Institute, 93/1 APC Road, Kolkata 700009, India. Electronic address: jayanta@jcbose.ac.in.
authors.forename: Jayanta
authors.initials: J
authors.lastname: Mukhopadhyay
mesh_terms: D001412:Bacillus subtilis / Q000378:metabolism*; D001426:Bacterial Proteins / Q000378:metabolism*; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D011401:Promoter Regions, Genetic
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D012321:DNA-Directed RNA Polymerases
keywords: Bacillus; RNA polymerase; YvrI and YvrHa; promoter; promoter escape; transcription; transcription initiation factor