title: Effects of σ factor competition are promoter initiation kinetics dependent.
abstract: In Escherichia coli, the expression of a σ factor is expected to indirectly down-regulate the expression of genes recognized by another σ factor, due to σ factor competition for a limited pool of RNA polymerase core enzymes. Evidence suggests that the sensitivity of genes to indirect down-regulation differs widely. We studied the variability in this sensitivity in promoters primarily recognized by RNAP holoenzymes carrying σ(70). From qPCR and live single-cell, single-RNA measurements of the transcription kinetics of several σ(70)-dependent promoters in various conditions and from the analysis of σ factors population-dependent models of transcription initiation, we find that, the smaller is the time-scale of the closed complex formation relative to the open complex formation, the weaker is a promoter's responsiveness to changes in σ(38) numbers. We conclude that, in E. coli, a promoter's responsiveness to indirect regulation by σ factor competition is determined by the sequence-dependent kinetics of the rate limiting steps of transcription initiation.
authors.affiliation: Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, 33101 Tampere, Finland.
authors.forename: Vinodh K
authors.initials: VK
authors.lastname: Kandavalli
authors.affiliation: Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, 33101 Tampere, Finland.
authors.forename: Huy
authors.initials: H
authors.lastname: Tran
authors.affiliation: Laboratory of Biosystem Dynamics, Department of Signal Processing, Tampere University of Technology, 33101 Tampere, Finland. Electronic address: andre.ribeiro@tut.fi.
authors.forename: Andre S
authors.initials: AS
authors.lastname: Ribeiro
mesh_terms: D012321:DNA-Directed RNA Polymerases / Q000235:genetics* / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D020035:Holoenzymes / Q000235:genetics / Q000378:metabolism; D007700:Kinetics; D008957:Models, Genetic; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012808:Sigma Factor / Q000235:genetics* / Q000378:metabolism; D061785:Transcription Initiation, Genetic
chemical_list: D020035:Holoenzymes; D012808:Sigma Factor; C106402:RNA polymerase Esigma(38); C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases
keywords: Closed Complex Formation; In vivo Transcription dynamics; Open Complex Formation; Single RNA detection; σ Factors competition