2018
DOI: 10.7554/elife.33684
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Gene network analysis identifies a central post-transcriptional regulator of cellular stress survival

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… Show more

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Cited by 18 publications
(51 citation statements)
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References 86 publications
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“…1B ). This protective effect is consistent with peroxide stress protection conferred by full-length gsrN overexpression ( gsrN ++ ), reported in our previous study (11).…”
Section: Resultssupporting
confidence: 92%
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“…1B ). This protective effect is consistent with peroxide stress protection conferred by full-length gsrN overexpression ( gsrN ++ ), reported in our previous study (11).…”
Section: Resultssupporting
confidence: 92%
“…GsrN is a small RNA (sRNA) that undergoes endonucleolytic processing, and functions as a potent regulator of both oxidative stress and osmotic stress survival in Caulobacter crescentus (11). Expression of the processed 5’ fragment of GsrN is necessary and sufficient to protect cells from hydrogen peroxide exposure.…”
Section: Resultsmentioning
confidence: 99%
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“…While hundreds of sRNAs are known to exist in C. crescentus (Schrader et al, 2014; Zhou et al, 2015), only three have been functionally explored. Two trans-encoded sRNAs who can silence target mRNAs through base pairing were found to be slightly enriched in BR-bodies ( crfA 0.67 and chvR 0.27) (Frohlich et al, 2018; Landt et al, 2010), while another was found to be slightly depleted ( gsrN -0.24) (Tien et al, 2018). Pairing of sRNAs with mRNAs typically occurs through the Lsm protein Hfq (Santiago-Frangos and Woodson, 2018; Vogel and Luisi, 2011), and we observe that 252/257 of these RNAs that associate with Hfq (Assis et al, 2019) are enriched in BR-bodies (Table S1).…”
Section: Resultsmentioning
confidence: 99%
“…Regulation of TonB-dependent receptors, as for outer membrane proteins in general, is often post-transcriptionally controlled by small noncoding RNAs (sRNAs) [18]. Caulobacter encodes 133 sRNAs [19], of which only a few have been characterized, but in these cases they appear to be components of stress-response signaling pathways [20, 21]. The sRNA ChvR was recently shown to downregulate a single TonB-dependent receptor of unknown function, ChvT, in response to acid stress, starvation or DNA damage [22].…”
Section: Introductionmentioning
confidence: 99%