Free DNA Concentration in E. coli Estimated by an Analysis of Competition for DNA Binding Proteins

Abstract

Transcription in E. coli is often controlled by the binding of specific gene-regulatory proteins. Binding of these proteins to their specific DNA binding sites occurs in the presence of a large excess of "nonspecific" genomic DNA. Binding to a specific DNA site thus depends on the concentration of regulatory protein, on its affinities for specific and competing nonspecific binding sites, and on the free concentrations of those sites. Although it is probable that genomic DNA is largely occluded by protein binding or by condensation in vivo, the actual extent to which the DNA is available to act as a competitor for specific binding (i.e. the effective concentration of nonspecific DNA) is not known. Because many regulatory interactions occur simultaneously in a cell, it is reasonable to expect that they will have evolved to function at equilibrium with a shared concentration of competing nonspecific DNA. This premise was the basis for this study. In vitro binding data were compiled for six regulatory proteins that function in E. coli, and used to calculate theoretical equilibrium binding distributions. The calculated distributions were used to evaluate the regulatory states of promoters according to models based on the equilibrium occupancies of regulatory sites. For four proteins whose DNA-binding affinities are modulated by ligand binding (CAP, lac repressor, trp repressor and ara C), regulation was assessed as the extent to which the presence of the modulator could affect the occupancy by protein of the specific sites (e.g. the difference in equilibrium occupancy by CAP of CAP binding sites between conditions of high and low concentrations of CAP's affinity modulator, cAMP). For two proteins whose site affinities are not modulated by ligand binding (λ repressor and λ- cro), regulation was assessed by specific site occupancy at equilibrium. These regulation profiles were compared to determine whether a single concentration of nonspecific competing DNA is compatible with effective regulation as defined for all of the systems. For five of the six modeled systems (CAP, trp repressor, araC, λ repressor and λ- cro), a free nonspecific DNA concentration on the order of 10 -4 M base pairs is compatible with regulation based on equilibria of the protein-DNA interactions. The lac repressor-operator system is an exception to these results: as has been shown previously, the regulation of operator binding by low molecular weight inducers increases with increasing concentrations of nonspecific DNA (von Hippel et al., 1974 Proc. natn. Acad. Sci. U.S.A. 71, 4808-4812). This discrepancy may indicate that the regulatory state of the lac operator depends on the lifetime of the repressor-operator complex, not simply its equilibrium fractional occupancy. With this exception, the results based on equilibria for the other five systems are consistent with regulation of transcription by protein binding in the presence of an effective DNA concentration [∼ 10 -4 M base pairs (b.p.)] that is less than 1% of the absolute concentration of total genomic DNA.