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Sequence-dependent model of genes with dual σ factor preference

2022-04Artigo científico Acesso aberto
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dc.contributor.authorBaptista, Inês S. C.
dc.contributor.authorKandavalli, Vinodh
dc.contributor.authorChauhan, Vatsala
dc.contributor.authorBahrudeen, Mohamed N. M.
dc.contributor.authorAlmeida, Bilena L. B.
dc.contributor.authorPalma, Cristina S. D.
dc.contributor.authorDash, Suchintak
dc.contributor.authorRibeiro, André S.
dc.contributor.institutionCTS - Centro de Tecnologia e Sistemas
dc.contributor.institutionUNINOVA-Instituto de Desenvolvimento de Novas Tecnologias
dc.contributor.pblElsevier
dc.date.accessioned2022-09-05T22:25:47Z
dc.date.available2022-09-05T22:25:47Z
dc.date.issued2022-04
dc.descriptionFunding Information: This work was supported by the Jane and Aatos Erkko Foundation [ 10-10524-38 to A.S.R]; Finnish Cultural Foundation [ 00200193 and 00212591 to I.S.C.B., and 50201300 to S.D.]; Pirkanmaa Regional Fund of the Finnish Cultural Foundation to V.K.; Suomalainen Tiedeakatemia to C.S.D.P.; Tampere University Graduate Program to V.C., M.N.M.B., and B.L.B.A.; EDUFI Fellowship [TM-19-11105 to S.D]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: © 2022 The Authors
dc.description.abstractEscherichia 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.en
dc.description.versionpublishersversion
dc.description.versionpublished
dc.format.extent9
dc.format.extent3433144
dc.identifier.doi10.1016/j.bbagrm.2022.194812
dc.identifier.issn1874-9399
dc.identifier.otherPURE: 46295225
dc.identifier.otherPURE UUID: fab6387b-972f-44ec-8f65-38e0b765c86e
dc.identifier.otherScopus: 85127225517
dc.identifier.otherPubMed: 35338024
dc.identifier.otherWOS: 000791277200001
dc.identifier.urihttp://hdl.handle.net/10362/143501
dc.identifier.urlhttps://www.scopus.com/pages/publications/85127225517
dc.language.isoeng
dc.peerreviewedyes
dc.subjectDual σ factor preference
dc.subjectE. coli
dc.subjectFlow cytometry
dc.subjectRNA-seq
dc.subjectSequence-dependent gene expression model
dc.subjectBiophysics
dc.subjectStructural Biology
dc.subjectBiochemistry
dc.subjectMolecular Biology
dc.subjectGenetics
dc.titleSequence-dependent model of genes with dual σ factor preferenceen
dc.typejournal article
degois.publication.firstPage1
degois.publication.issue3
degois.publication.lastPage9
degois.publication.titleBiochimica et Biophysica Acta - Gene Regulatory Mechanisms
degois.publication.volume1865
dspace.entity.typePublication
rcaap.rightsopenAccess

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