Stochastic Analysis Demonstrates the Dual Role of Hfq in Chaperoning E. coli Sugar Shock Response

Abstract

Small RNAs (sRNAs) play a crucial role in the regulation of bacterial gene expression by silencing the translation of target mRNAs. SgrS is an sRNA that relieves glucose-phosphate stress, or “sugar shock” in E. coli. The power of single cell measurements is their ability to obtain population level statistics that illustrate cell-to-cell variation. Here, we utilize single molecule super-resolution microscopy in single E. coli cells coupled with stochastic modeling to analyze glucose-phosphate stress regulation by SgrS. We present a kinetic model that captures the combined effects of transcriptional regulation, gene replication and chaperone mediated RNA silencing in the SgrS regulatory network. This more complete kinetic description, simulated stochastically, recapitulates experimentally observed cellular heterogeneity and characterizes the binding of SgrS to the chaperone protein Hfq as a slow process that not only stabilizes SgrS but also may be critical in restructuring the sRNA to facilitate association with its target ptsG mRNA.

Engineering global regulators for enhanced tolerance to multiple inhibitors by CRISPR‐enabled trackable genome engineering

“…The OD 600 at 60 h increased by about 66.07% in medium with 20 g/L sodium acetate compared to MG1655 (Figure S8), suggesting that knockout of sgrS conferred acetate tolerance. SgrS was found to be expressed during glucose‐phosphate stress, a condition associated with intracellular accumulation of glucose‐6‐phosphate caused by disruption of glycolytic flux in E. coli 73 . Under stress conditions, SgrS negatively regulates the translation and stability of the ptsG mRNA, encoding the major glucose transporter, by means of a base pairing‐dependent mechanism requiring the RNA chaperone Hfq 74 .…”

“…SgrS was found to be expressed during glucose-phosphate stress, a condition associated with intracellular accumulation of glucose-6-phosphate caused by disruption of glycolytic flux in E. coli. 73 Under stress conditions, SgrS negatively regulates the translation and stability of the ptsG mRNA, encoding the major glucose transporter, by means of a base pairing-dependent mechanism requiring the RNA chaperone Hfq. 74 SgrS thus downregulates the synthesis of glucose-6-phosphate, and further decreases glycolytic flux.…”

Improving Furfural Tolerance of Escherichia coli by Integrating Adaptive Laboratory Evolution with CRISPR-Enabled Trackable Genome Engineering (CREATE)

“…Small regulatory RNAs (sRNAs) are abundant in bacteria and have great vital roles in post-transcriptional gene expression regulation. Large regulons are controlled by many bacterial sRNAs, which perform important functions in cellular metabolism and physiology. , The synthesis of a variety of sRNAs is strictly regulated and expressed under specific conditions such as glucose-phosphate overload, oxidative stress, and acid stress . The rpoB gene encodes the β subunit of RNA polymerase.…”

Adaptive strategies of uropathogenic Escherichia coli CFT073: from growth in lab media to virulence during host cell adhesion

“…The upregulation of adhesins and porins and the downregulation of global regulators with respect to lab media showed the deep gene expression reset of CFT073 during the contact with host cells. Apart from Fnr, regulons governed by CRP, Hfq, Fur, and Zur encode several virulence genes (Banerjee et al 2020;Bianchi et al 2020;Patzer and Hantke 2000;Shimada et al 2011). The interplay among these global regulators that leads to the complex gene regulation cascades in response to environmental stimuli is still unknown and requires further studies.…”

“…In adherent bacteria, its expression was significantly downregulated in comparison with bacteria grown in LB and AU and paralleled the expression profile shown by crp (Tables 2 and 3). In view of these results, it can be speculated that the host cell environment causes a downregulation of hfq, which, in turn, influences the stability of several target RNAs, such as fur, gadAC, and manX (Bianchi et al 2020;Lin et al 2011). Indeed, this interconnected regulatory cascade composed by CRP-cAMP/Hfq coordinates metabolic pathways, membrane homeostasis, motility, envelope stress, and virulence during UPEC adhesion steps and bacterial intracellular lifestyle later on (Behzadi et al 2021).…”