Insights into transcriptional regulation and σ competition from an equilibrium model of RNA polymerase binding to DNA

Abstract

To explore scenarios that permit transcription regulation by activator recruitment of RNA polymerase and σ competition in vivo , we used an equilibrium model of RNA polymerase binding to DNA constrained by the values of total RNA polymerase (E) and σ 70 per cell measured in this work. Our numbers of E and σ 70 per cell, which are consistent with most of the primary data in the literature, suggest that in vivo ( i ) only a minor fraction of RNA polymerase (<20%) is involved in elongation and ( ii ) σ 70 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 Eσ 70 in vivo unless nonspecific DNA binding by Eσ 70 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.