Salt-dependent binding of Escherichia coli RNA polymerase to DNA and specific transcription by the core enzyme and holoenzyme

Abstract

The interaction of the Escherichia coli RNA polymerase with several forms of DNA has been studied by difference absorption spectroscopy, protection against endonucleases, and limited, specific initiation. The core enzyme is able to open duplex poly[d(A-T)] in 10 mM KCl. The core enzyme binds to promoters in linear DNA in a salt-dependent manner, but it does not bind to the same promoters in supercoiled DNA. The binding of the core enzyme is not as tight as that of the holoenzyme. The holoenzyme initiates specific transcription from promoters in a salt-dependent manner. The core enzyme also initiates specific transcription from the same promoters at approximately one-fifth the level of the holoenzyme with a different salt dependence. The profile of the salt dependence of specific transcription initiation varies with the promoter. The origin of differences between holoenzyme-DNA and core enzyme-DNA interactions and the mechanism whereby sigma improves transcriptional specificity are discussed in light of these data.