Complex formation between activator and RNA polymerase as the basis for transcriptional activation by MarA and SoxS in Escherichia coli

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Abstract
Transcriptional activation in Escherichia coli is generally considered to proceed via the formation of an activator–DNA–RNA polymerase (RNP) ternary complex. Although the order of assembly of the three elements is thermodynamically irrelevant, a prevalent idea is that the activator–DNA complex is formed first, and recruitment of RNP to the binary complex occurs subsequently. We show here that the closely related activators, MarA, SoxS and Rob, which activate the same family of genes, are capable of forming complexes with RNP core or holoenzyme in the absence of DNA. In addition, we find that the ternary MarA–DNA–RNP and SoxS–DNA–RNP complexes are more stable than the corresponding Rob–DNA–RNP complex, although the binary Rob–DNA complex is often more stable than the corresponding MarA– or SoxS–DNA complexes. These results may help to explain certain puzzling aspects of the MarA/SoxS/ Rob system. We suggest that activator–RNP complexes scan the chromosome and bind promoters of the regulon more efficiently than either RNP or the activators alone.