Probing DNA Binding, DNA Opening, and Assembly of a Downstream Clamp/Jaw in Escherichia coli RNA Polymerase−λPR Promoter Complexes Using Salt and the Physiological Anion Glutamate

Transcription by all RNA polymerases (RNAPs) requires a series of large-scale conformational changes to form the transcriptionally competent open complex RPo. At the λPR promoter, Escherichia coli σ70 RNAP first forms a wrapped, closed 100 bp complex I1. The subsequent step opens the entire DNA bubble, creating the relatively unstable (open) complex I2. Additional conformational changes convert I2 to the stable RPo. Here we probe these events by dissecting the effects of Na+ salts of Glu, F, and Cl on each step in this critical process. Rapid mixing and nitrocellulose filter binding reveal that the binding constant for I1 at 25 °C is ∼30-fold larger in Glu than in Cl at the same Na+ concentration, with the same log−log salt concentration dependence for both anions. In contrast, both the rate constant and equilibrium constant for DNA opening (I1 to I2) are only weakly dependent on salt concentration, and the opening rate constant is insensitive to replacement of Cl with Glu. These very small effects of salt concentration on a process (DNA opening) that is strongly dependent on salt concentration in solution may indicate that the backbones of both DNA strands interact with polymerase throughout the process and/or that compensation is present between ion uptake and release. Replacement of Cl with Glu or F at 25 °C greatly increases the lifetime of RPo and greatly reduces its salt concentration dependence. By analogy to Hofmeister salt effects on protein folding, we propose that the excluded anions Glu and F drive the folding and assembly of the RNAP clamp/jaw domains in the conversion of I2 to RPo, while Cl does not. Because the Hofmeister effect of Glu or F largely compensates for the destabilizing Coulombic effect of any salt on the binding of this assembly to downstream promoter DNA, RPo remains long-lived even at 0.5 M Na+ in Glu or F salts. The observation that Eσ70 RPo complexes are exceedingly long-lived at moderate to high Glu concentrations argues that Eσ70 RNAP does not dissociate from strong promoters in vivo when the cytoplasmic glutamate concentration increases during osmotic stress.