Sequence-dependent model of genes with dual σ factor preference

<p class="MsoNormal"><em>Escherichia coli</em> uses <span>s</span> factors to quickly control large gene cohorts during stress conditions. While most of its genes respond to a single <span>s</span> factor, approximately 5% of them have dual <span>s</span> factor preference. The most common are those responsive to both <span>s</span>⁷⁰, which controls housekeeping genes, and <span>s</span>³⁸, which activates genes during stationary growth and stresses. Using RNA-seq and flow-cytometry measurements, we show that 'σ⁷⁰⁺³⁸ genes' are nearly as upregulated in stationary growth as 'σ³⁸ genes'. Moreover, we find a clear quantitative relationship between their promoter sequence and their response strength to changes in σ³⁸ levels. We then propose and validate a sequence dependent model of σ⁷⁰⁺³⁸ genes, with dual sensitivity to <span>s</span>³⁸and <span>s</span>⁷⁰, 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 σ⁷⁰⁺³⁸ 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.</p>