Sequence-dependent model of genes with dual σ 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
‘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 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 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.