A general model of the dynamics of genes with dual σ factor preference

Escherichia coli uses the ability of σ factors to recognize specific DNA sequences in order to quickly control large gene cohorts. While most genes respond to only one s factor, approximately 5% have dual s factor preference. The ones in significant numbers are ‘σ 70+38 genes’, responsive to σ 70 , which controls housekeeping genes, as well as to σ 38 , which activates genes during stationary growth and stresses. We show that σ 70+38 genes are almost as upregulated in stationary growth as genes responsive to σ 38 alone. Also, their response strengths to σ 38 are predictable from their promoter sequences. Next, we propose a sequence- and σ 38 level-dependent, analytical model of σ 70+38 genes applicable in the exponential, stationary, and in the transition period between the two growth phases. Finally, we propose a general model, applicable to other σ factors as well. This model can guide the design of synthetic circuits with sequence-dependent sensitivity and plasticity to transitions between the exponential and stationary growth phases. ### Competing Interest Statement The authors have declared no competing interest.