Gene network analysis identifies a central post-transcriptional regulator of cellular stress survival

Abstract
Data availability
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Abstract

Cells adapt to shifts in their environment by remodeling transcription. Measuring changes in transcription at the genome scale is now routine, but defining the functional significance of individual genes within large gene expression datasets remains a major challenge. We applied a network-based algorithm to interrogate publicly available gene expression data to predict genes that serve major functional roles in Caulobacter crescentus stress survival. This approach identified GsrN, a conserved small RNA that is directly activated by the general stress sigma factor, σ^T, and functions as a potent post-transcriptional regulator of survival across distinct conditions including osmotic and oxidative stress. Under hydrogen peroxide stress, GsrN protects cells by base pairing with the leader of katG mRNA and activating expression of KatG catalase/peroxidase protein. We conclude that GsrN convenes a post-transcriptional layer of gene expression that serves a central functional role in Caulobacter stress physiology.

Data availability

The following data sets were generated

(2017) RNA-Seq gene expression analysis of ΔgsrN, gsrN-OE, and wild-type Caulobacter crescentus
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE106168).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE106168
(2017) Identification of RNAs that co-purify with the Caulobacter sRNA, GsrN
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE106171).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE106171
(2017) Caulobacter crescentus GsrN mutants proteome analysis
PXD008128.

https://www.ebi.ac.uk/pride/archive/projects/PXD008128

The following previously published data sets were used

(2013) Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE46915).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46915

Article and author information

Author details

Matthew Tien

Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-0006-9644
Aretha Fiebig

Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States

Competing interests
The authors declare that no competing interests exist.
Sean Crosson

Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States

For correspondence
scrosson@uchicago.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-1727-322X

Funding

National Institutes of Health (1R01GM087353)

Sean Crosson

National Institutes of Health (U19AI107792)

Sean Crosson

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.