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Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12

Wong, Garrett T. and Bonocora, Richard P. and Schep, Alicia N. and Beeler, Suzannah M. and Lee Fong, Anna J. and Shull, Lauren M. and Batachari, Lakshmi E. and Dillon, Moira and Evans, Ciaran and Becker, Carla J. and Bush, Eliot C. and Hardin, Johanna and Wade, Joseph T. and Stoebel, Daniel M. (2017) Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12. Journal of Bacteriology, 199 (7). Art. No. e00755-16. ISSN 0021-9193. PMCID PMC5350281. doi:10.1128/JB.00755-16.

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The alternative sigma factor RpoS is a central regulator of many stress responses in Escherichia coli. The 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 the E. coli genome 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.

Item Type:Article
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URLURL TypeDescription CentralArticle Material
Schep, Alicia N.0000-0002-3915-0618
Beeler, Suzannah M.0000-0002-1930-4827
Evans, Ciaran0000-0003-3256-011X
Stoebel, Daniel M.0000-0002-9461-7567
Additional Information:© 2017 American Society for Microbiology. Received 21 October 2016. Accepted 12 January 2017. Accepted manuscript posted online 23 January 2017. We thank Rachael Kretsch for experimental help and Robert Drewell, Xuelin Wu, Jae Hur, Keith Derbyshire, and Todd Gray for helpful discussions. This work was supported by HHMI Undergraduate Science Education award 52007544 to Harvey Mudd College and by the NIH Director's New Innovator Award Program grant 1DP2OD007188 (to J.T.W.). Accession number(s).RNA-seq data were deposited in the GEO database with accession number GSE87856. ChIP-seq data were deposited in ArrayExpress with accession number E-MTAB-5339.
Funding AgencyGrant Number
Howard Hughes Medical Institute (HHMI)52007544
Subject Keywords:RpoS; promoters; σ^S; stress response; transcriptional regulation; transcriptome
Issue or Number:7
PubMed Central ID:PMC5350281
Record Number:CaltechAUTHORS:20170417-114538266
Persistent URL:
Official Citation:Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12 Garrett T. Wong, Richard P. Bonocora, Alicia N. Schep, Suzannah M. Beeler, Anna J. Lee Fong, Lauren M. Shull, Lakshmi E. Batachari, Moira Dillon, Ciaran Evans, Carla J. Becker, Eliot C. Bush, Johanna Hardin, Joseph T. Wade, and Daniel M. Stoebel J. Bacteriol. April 2017 199:7 17 e00755-16; Accepted manuscript posted online 23 January 2017, doi:10.1128/JB.00755-16
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:76601
Deposited By: George Porter
Deposited On:17 Apr 2017 19:48
Last Modified:15 Nov 2021 17:01

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