title: Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12.
abstract: The alternative sigma factor RpoS is a central regulator of many stress responses inEscherichia coliThe level of functional RpoS differs depending on the stress. The effect of these differing concentrations of RpoS on global transcriptional responses remains unclear. We investigated the effect of RpoS concentration on the transcriptome during stationary phase in rich media. We found that 23% of genes in theE. coligenome are regulated by RpoS, and we identified many RpoS-transcribed genes and promoters. We observed three distinct classes of response to RpoS by genes in the regulon: genes whose expression changes linearly with increasing RpoS level, genes whose expression changes dramatically with the production of only a little RpoS ("sensitive" genes), and genes whose expression changes very little with the production of a little RpoS ("insensitive"). We show that sequences outside the core promoter region determine whether an RpoS-regulated gene is sensitive or insensitive. Moreover, we show that sensitive and insensitive genes are enriched for specific functional classes and that the sensitivity of a gene to RpoS corresponds to the timing of induction as cells enter stationary phase. Thus, promoter sensitivity to RpoS is a mechanism to coordinate specific cellular processes with growth phase and may also contribute to the diversity of stress responses directed by RpoS.IMPORTANCEThe sigma factor RpoS is a global regulator that controls the response to many stresses inEscherichia coliDifferent stresses result in different levels of RpoS production, but the consequences of this variation are unknown. We describe how changing the level of RpoS does not influence all RpoS-regulated genes equally. The cause of this variation is likely the action of transcription factors that bind the promoters of the genes. We show that the sensitivity of a gene to RpoS levels explains the timing of expression as cells enter stationary phase and that genes with different RpoS sensitivities are enriched for specific functional groups. Thus, promoter sensitivity to RpoS is a mechanism that coordinates specific cellular processes in response to stresses.
authors.affiliation: Department of Biology, Harvey Mudd College, Claremont, California, USA.
authors.forename: Garrett T
authors.initials: GT
authors.lastname: Wong
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, USA.
authors.forename: Richard P
authors.initials: RP
authors.lastname: Bonocora
authors.affiliation: Department of Biology, Harvey Mudd College, Claremont, California, USA.
authors.forename: Alicia N
authors.initials: AN
authors.lastname: Schep
authors.affiliation: Department of Biology, Harvey Mudd College, Claremont, California, USA.
authors.forename: Suzannah M
authors.initials: SM
authors.lastname: Beeler
authors.affiliation: Department of Biology, Harvey Mudd College, Claremont, California, USA.
authors.forename: Anna J
authors.initials: AJ
authors.lastname: Lee Fong
authors.affiliation: Department of Biology, Harvey Mudd College, Claremont, California, USA.
authors.forename: Lauren M
authors.initials: LM
authors.lastname: Shull
authors.affiliation: Department of Biology, Harvey Mudd College, Claremont, California, USA.
authors.forename: Lakshmi E
authors.initials: LE
authors.lastname: Batachari
authors.affiliation: Department of Biology, Harvey Mudd College, Claremont, California, USA.
authors.forename: Moira
authors.initials: M
authors.lastname: Dillon
authors.affiliation: Department of Mathematics, Pomona College, Claremont, California, USA.
authors.forename: Ciaran
authors.initials: C
authors.lastname: Evans
authors.affiliation: Department of Biology, Harvey Mudd College, Claremont, California, USA.
authors.forename: Carla J
authors.initials: CJ
authors.lastname: Becker
authors.affiliation: Department of Biology, Harvey Mudd College, Claremont, California, USA.
authors.forename: Eliot C
authors.initials: EC
authors.lastname: Bush
authors.affiliation: Department of Mathematics, Pomona College, Claremont, California, USA.
authors.forename: Johanna
authors.initials: J
authors.lastname: Hardin
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, USA joseph.wade@health.ny.gov stoebel@g.hmc.edu.|Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany, New York, USA.
authors.forename: Joseph T
authors.initials: JT
authors.lastname: Wade
authors.affiliation: Department of Biology, Harvey Mudd College, Claremont, California, USA joseph.wade@health.ny.gov stoebel@g.hmc.edu.
authors.forename: Daniel M
authors.identifier: http://orcid.org/0000-0002-9461-7567
authors.initials: DM
authors.lastname: Stoebel
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D015153:Blotting, Western; D048168:Escherichia coli K12 / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology*; D055106:Genome-Wide Association Study; D009154:Mutation; D011401:Promoter Regions, Genetic; D012808:Sigma Factor / Q000235:genetics / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D012808:Sigma Factor; C069567:sigma factor KatF protein, Bacteria
keywords: RpoS; promoters; stress response; transcriptional regulation; transcriptome; σS