Sequence-dependent model of genes with dual σ factor preference.

Escherichia coli uses σ factors to quickly control large gene cohorts during stress conditions. While most of its genes respond to a single σ factor, approximately 5% of them have dual σ factor preference. The most common are those responsive to both σ, which controls housekeeping genes, and σ, which activates genes during stationary growth and stresses. Using RNA-seq and flow-cytometry measurements, we show that 'σ genes' are nearly as upregulated in stationary growth as 'σ genes'. Moreover, we find a clear quantitative relationship between their promoter sequence and their response strength to changes in σ levels. We then propose and validate a sequence dependent model of σ genes, with dual sensitivity to σ and σ, that is applicable in the exponential and stationary growth phases, as well in the transient period in between. We further propose a general model, applicable to other stresses and σ factor combinations. Given this, promoters controlling σ genes (and variants) could become important building blocks of synthetic circuits with predictable, sequence-dependent sensitivity to transitions between the exponential and stationary growth phases.