Open AccessInsights into transcriptional regulation and σ competition from an equilibrium model of RNA polymerase binding to DNA
Author(s) -
Irina Grigorova,
Naum J. Phleger,
Vivek K. Mutalik,
Carol A. Gross
Publication year - 2006
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.0600828103
Subject(s) - rna polymerase ii , sigma factor , polymerase , rna polymerase , microbiology and biotechnology , biology , transcription (linguistics) , rna polymerase i , promoter , rna , transcription factor ii d , dna , gene expression , rna dependent rna polymerase , genetics , gene , linguistics , philosophy
To explore scenarios that permit transcription regulation by activator recruitment of RNA polymerase and σ competitionin vivo , we used an equilibrium model of RNA polymerase binding to DNA constrained by the values of total RNA polymerase (E) and σ70 per cell measured in this work. Our numbers of E and σ70 per cell, which are consistent with most of the primary data in the literature, suggest thatin vivo (i ) only a minor fraction of RNA polymerase (<20%) is involved in elongation and (ii ) σ70 is in excess of total E. Modeling the partitioning of RNA polymerase between promoters, nonspecific DNA binding sites, and the cytoplasm suggested that even weak promoters will be saturated with Eσ70 in vivo unless nonspecific DNA binding by Eσ70 is rather significant. In addition, the model predicted that σs compete for binding to E only when their total number exceeds the total amount of RNA polymerase (excluding that involved in elongation) and that weak promoters will be preferentially subjected to σ competition.