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Sequence-dependent model of genes with dual σ factor preference

Citation

Baptista, Ines et al. (2022), Sequence-dependent model of genes with dual σ factor preference, Dryad, Dataset, https://doi.org/10.5061/dryad.jsxksn0b7

Abstract

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.

Funding

Jane ja Aatos Erkon Säätiö, Award: 10-10524-38

Suomen Kulttuurirahasto

Suomalainen Tiedeakatemia

Tampere University Graduate Program

Pirkanmaan Rahasto

EDUFI Fellowship