Regulation of the kinetics of the interaction of Escherichia coli RNA polymerase with the lambda PR promoter by salt concentration.

Abstract

The rate of formation of transcriptionally competent open complexes between Escherichia coli RNA polymerase (RNAP) and the lambda PR promoter is extraordinarily sensitive to the nature and concentration of the electrolyte ions in the solution. The pseudo-first-order time constant of open complex formation tau obsd, determined in excess RNAP at 25 degrees C as a function of NaCl concentration, is proportional to the concentration product [Na+]12 [RNAP]-1. Consequently, tau obsd is far more sensitive to changes in the salt concentration than to changes in the concentration of RNAP. The origin of this effect is the release of the thermodynamic equivalent of 12 monovalent ions in the process of closed complex formation at the lambda PR promoter. In more complex ionic mixtures, ion-specific stoichiometric effects on tau obsd are observed. These are not ionic strength effects but are instead both valence and species specific. Both the association and dissociation rate constants of RNAP at the lambda PR promoter are strongly salt dependent, varying (in NaCl) as [Na+]-12 and [Na+]8, respectively. Consequently, the equilibrium constant characterizing open complex formation at this promoter varies with [Na+]-20. Electrostatic interactions and counterion release are the major contributors to the binding free energy driving open complex formation in a dilute salt solution. Since the in vivo ionic environment of E. coli (and other cells) is highly variable, these large salt effects are almost certainly of physiological significance. Variations in the intracellular concentrations of inorganic and organic ions, including polyamines, must exert both global and also promoter-specific regulatory effects on the initiation of transcription, as well as on numerous other protein-nucleic acid interactions.