Competition among seven Escherichia coli σ subunits: relative binding affinities to the core RNA polymerase

Seven different species of the RNA polymerase σ subunit exist in Escherichia coli, each binding to a single species of the core enzyme and thereby directing transcription of a specific set of genes. To test the σ competition model in the global regulation of gene transcription, all seven E.coli σ subunits have been purified and compared for their binding affinities to the same core RNA polymerase (E). In the presence of a fixed amount of σ(70), the principal σ for growth-related genes, the level of Eσ(70) holoenzyme formation increased linearly with the increase in core enzyme level, giving an apparent K(d) for the core enzyme of 0.26 nM. Mixed reconstitution experiments in the presence of a fixed amount of core enzyme and increasing amounts of an equimolar mixture of all seven σ subunits indicated that σ(70) is strongest in terms of core enzyme binding, followed by σ(N), σ(F), σ(E)/σ(FecI), σ(H) and σ(S) in decreasing order. The orders of core binding affinity between σ(70) and σ(N) and between σ(70) and σ(H) were confirmed by measuring the replacement of one core-associated σ by another σ subunit. Taken together with the intracellular σ levels, we tried to estimate the number of each holoenzyme form in growing E.coli cells.