Effects of σ factor competition are promoter initiation kinetics dependent

• Under stress, Escherichia coli alter σ factors numbers as a global gene regulation mechanism.
• These changes allow direct positive and indirect negative gene regulation.
• Sensitivity to indirect negative down-regulation differs widely between promoters.
• We show that sensitivity differs with ratio between closed and open complex formation.
• Promoters' sensitivity to indirect σ factor regulation is thus evolvable and adaptive.

In Escherichia coli, the expression of a σ factor is expected to indirectly down-regulate the expression of genes recognized by another σ factor, due to σ factor competition for a limited pool of RNA polymerase core enzymes. Evidence suggests that the sensitivity of genes to indirect down-regulation differs widely. We studied the variability in this sensitivity in promoters primarily recognized by RNAP holoenzymes carrying σ70. From qPCR and live single-cell, single-RNA measurements of the transcription kinetics of several σ70-dependent promoters in various conditions and from the analysis of σ factors population-dependent models of transcription initiation, we find that, the smaller is the time-scale of the closed complex formation relative to the open complex formation, the weaker is a promoter's responsiveness to changes in σ38 numbers. We conclude that, in E. coli, a promoter's responsiveness to indirect regulation by σ factor competition is determined by the sequence-dependent kinetics of the rate limiting steps of transcription initiation.

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