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The 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 Lee, Lauren Shull, Lakshmi Batachari, Moira Dillon, Ciaran Evans, Johanna Hardin, Joseph T. Wade, Daniel M. Stoebel
doi: https://doi.org/10.1101/082537
Garrett T. Wong
1Department of Biology, Harvey Mudd College, Claremont CA
2Current address: Departments of Neuroscience, Genetics and Genome Sciences, Icahn School of Medicine at Mount Sinai.
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Richard P. Bonocora
3Wadsworth Center, New York State Department of Health, Albany NY
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Alicia N. Schep
1Department of Biology, Harvey Mudd College, Claremont CA
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Suzannah M. Beeler
1Department of Biology, Harvey Mudd College, Claremont CA
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Anna Lee
1Department of Biology, Harvey Mudd College, Claremont CA
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Lauren Shull
1Department of Biology, Harvey Mudd College, Claremont CA
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Lakshmi Batachari
1Department of Biology, Harvey Mudd College, Claremont CA
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Moira Dillon
1Department of Biology, Harvey Mudd College, Claremont CA
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Ciaran Evans
8Department of Mathematics, Pomona College, Claremont CA
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Johanna Hardin
8Department of Mathematics, Pomona College, Claremont CA
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Joseph T. Wade
3Wadsworth Center, New York State Department of Health, Albany NY
10Department of Biomedical Sciences, School of Public Health, University at Albany, SUNY, Albany NY
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  • For correspondence: joseph.wade@health.ny.gov stoebel@g.hmc.edu
Daniel M. Stoebel
1Department of Biology, Harvey Mudd College, Claremont CA
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  • For correspondence: joseph.wade@health.ny.gov stoebel@g.hmc.edu
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Abstract

The alternative sigma factor RpoS is a central regulator of a 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 show that 23% of genes in the E. coli genome are regulated by RpoS level, and we identify many RpoS-transcribed genes and promoters. We observe 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 a RpoS-regulated gene in sensitive or insensitive. Moreover, we show that sensitive and insensitive genes are enriched for specific functional classes, and that the (in)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.

Importance The sigma factor RpoS is a global regulator that controls the response to many stresses in Escherichia coli. Different 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 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 to coordinate specific cellular processes in response to stresses.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 21, 2016.
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The 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 Lee, Lauren Shull, Lakshmi Batachari, Moira Dillon, Ciaran Evans, Johanna Hardin, Joseph T. Wade, Daniel M. Stoebel
bioRxiv 082537; doi: https://doi.org/10.1101/082537
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The 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 Lee, Lauren Shull, Lakshmi Batachari, Moira Dillon, Ciaran Evans, Johanna Hardin, Joseph T. Wade, Daniel M. Stoebel
bioRxiv 082537; doi: https://doi.org/10.1101/082537

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