Free RNA polymerase and modeling global transcription in Escherichia coli

Abstract

Growth rate-dependent changes in the cytoplasmic concentration of free functional RNA polymerase, [ R f], affect the activity of all bacterial genes. Since [ R f] is not accessible to direct experimental quantitation, it can only be found indirectly from an evaluation of promoter activity data. Here, a theory has been derived to calculate [ R f] from the concentrations of total RNA polymerase and promoters in a model system with known Michaelis–Menten constants for the polymerase–promoter interactions. The theory takes transcript lengths and elongation rates into account and predicts how [ R f] changes with varying gene dosages. From experimental data on total concentrations of RNA polymerase and kinetic properties of different classes of promoters, the theory was developed into a mathematical model that reproduces the global transcriptional control in Escherichia coli growing at different rates. The model allows an estimation of the concentrations of free and DNA-bound RNA polymerase, as well as the partitioning of RNA polymerase into mRNA and stable RNA synthesizing fractions. According to this model, [ R f] is about 0.4 and 1.2 μM at growth rates corresponding to 1.0 and 2.5 doublings/h, respectively. The model accurately reflects a number of further experimental observations and suggests that the free RNA polymerase concentration increases with increasing growth rate.