Free RNA polymerase and modeling global transcription in Escherichia coli

Biochimie. 2003 Jun;85(6):597-609. doi: 10.1016/s0300-9084(03)00105-6.

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 microM 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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • DNA, Bacterial / genetics
  • DNA, Bacterial / metabolism
  • DNA-Directed RNA Polymerases / metabolism*
  • Escherichia coli / enzymology*
  • Escherichia coli / genetics*
  • Gene Expression Regulation, Bacterial
  • Kinetics
  • Models, Genetic*
  • Promoter Regions, Genetic / genetics
  • Transcription, Genetic / genetics*

Substances

  • DNA, Bacterial
  • DNA-Directed RNA Polymerases