Published April 11, 2022 | Version v1
Dataset Open

Sequence-dependent model of genes with dual σ factor preference

Description

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.

Notes

Funding provided by: Jane ja Aatos Erkon Säätiö
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100004012
Award Number: 10-10524-38

Funding provided by: Suomen Kulttuurirahasto
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100003125
Award Number:

Funding provided by: Suomalainen Tiedeakatemia
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100002342
Award Number:

Funding provided by: Tampere University Graduate Program*
Crossref Funder Registry ID:
Award Number:

Funding provided by: Pirkanmaan Rahasto
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100005431
Award Number:

Funding provided by: EDUFI Fellowship*
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