Sequence-dependent model of genes with dual σ factor preference
Baptista, Ines S.C.; Kandavalli, Vinodh; Chauhan, Vatsala; Bahrudeen, Mohamed N.M.; Almeida, Bilena L.B.; Palma, Cristina S.D.; Dash, Suchintak; Ribeiro, Andre S. (2022-04)
Baptista, Ines S.C.
Kandavalli, Vinodh
Chauhan, Vatsala
Bahrudeen, Mohamed N.M.
Almeida, Bilena L.B.
Palma, Cristina S.D.
Dash, Suchintak
Ribeiro, Andre S.
04 / 2022
194812
Julkaisun pysyvä osoite on
https://urn.fi/URN:NBN:fi:tuni-202204253523
https://urn.fi/URN:NBN:fi:tuni-202204253523
Kuvaus
Peer reviewed
Tiivistelmä
Escherichia coli uses σ factors to quickly control large gene cohorts during stress conditions. While most of its genes respond to a single σ factor, approximately 5% of them have dual σ factor preference. The most common are those responsive to both σ70, which controls housekeeping genes, and σ38, 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 σ38 and σ70, 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.
Kokoelmat
- TUNICRIS-julkaisut [16951]