Sequence-dependent model of genes with dual s factor preference

Escherichia coli uses s factors to quickly control large gene cohorts during stress conditions. While most of its genes respond to a single s factor, approximately 5% of them have dual s factor preference. The most common are those responsive to both s70, which controls housekeeping genes, and s38, which activates genes during stationary growth and stresses. Using RNA-seq and flow-cytometry measurements, we show that 's70+38 genes' are nearly as upregulated in stationary growth as 's38 genes'. Moreover, we find a clear quantitative relationship between their promoter sequence and their response strength to changes in s38 levels. We then propose and validate a sequence dependent model of s70+38 genes, with dual sensitivity to s38 and s70, 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 s factor combinations. Given this, promoters controlling s70+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. Overall design: Examination of genome-wide responses under exponential and stationary growth phase conditions