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bioRxiv · 10.1101/2021.11.17.468920

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

Calado Baptista, I. S.·Kandavalli, V.·Chauhan, V.·Mohamed Bahrudeen, M. N.·Almeida, B. L. d. B.·Palma, C. S. D.·Dash, S.·Ribeiro, A.
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Abstract

Escherichia coli uses {sigma} factors to quickly control large gene cohorts during stress conditions. While most of its genes respond to a single {sigma} factor, approximately 5% of them have dual {sigma} factor preference. The most common are those responsive to both {sigma}70, which controls housekeeping genes, and {sigma}38, which activates genes during stationary growth and stresses. Using RNA-seq and flow-cytometry measurements, we show that {sigma}70+38 genes are nearly as upregulated in stationary growth as {sigma}38 genes. Moreover, we find a clear quantitative relationship between their promoter sequence and their response strength to changes in {sigma}38 levels. We then propose and validate a sequence dependent model of {sigma}70+38 genes, with dual sensitivity to {sigma}38 and {sigma}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 {sigma} factor combinations. Given this, promoters controlling {sigma}70+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.

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Calado Baptista, I. S., Kandavalli, V., Chauhan, V., Mohamed Bahrudeen, M. N., Almeida, B. L. d. B., Palma, C. S. D., Dash, S., Ribeiro, A.. 2021-11-19. A general model of the dynamics of genes with dual σ factor preference. https://doi.org/10.1101/2021.11.17.468920

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