EcRBPome: a comprehensive database of all known <i>E. coli</i> RNA-binding proteins

Ghosh, Pritha; Guita, Niang; Offmann, Bernard; Sowdhamini, Ramanathan

doi:10.1101/268441

Cited by 1 publication

(1 citation statement)

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“…Global approaches revealed a plethora of new RBPs and RBP‐RNA interactions in eukaryotes, often involving unconventional RNA‐binding domains (RBDs; Hentze et al , ). In contrast, a few RBPs cooperating with sRNAs are known in bacteria (Holmqvist & Vogel, ; Babitzke et al , ), albeit ~6–7% of a typical bacterial proteome may feature RNA‐binding activity (Ghosh et al , ). Hfq, ProQ, and CsrA emerged as global RBPs governing large post‐transcriptional networks, either by facilitating the activities of base‐pairing sRNAs (Holmqvist et al , ; Santiago‐Frangos & Woodson, ) or by acting as pleiotropic mRNA repressor (Potts et al , ), but little is known beyond.…”

Section: Introductionmentioning

confidence: 99%

Small RNA ‐binding protein RapZ mediates cell envelope precursor sensing and signaling in Escherichia coli

et al. 2020

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The RNA‐binding protein RapZ cooperates with small RNAs (sRNAs) GlmY and GlmZ to regulate the glmS mRNA in Escherichia coli. Enzyme GlmS synthesizes glucosamine‐6‐phosphate (GlcN6P), initiating cell envelope biosynthesis. GlmZ activates glmS expression by base‐pairing. When GlcN6P is ample, GlmZ is bound by RapZ and degraded through ribonuclease recruitment. Upon GlcN6P depletion, the decoy sRNA GlmY accumulates through a previously unknown mechanism and sequesters RapZ, suppressing GlmZ decay. This circuit ensures GlcN6P homeostasis and thereby envelope integrity. In this work, we identify RapZ as GlcN6P receptor. GlcN6P‐free RapZ stimulates phosphorylation of the two‐component system QseE/QseF by interaction, which in turn activates glmY expression. Elevated GlmY levels sequester RapZ into stable complexes, which prevents GlmZ decay, promoting glmS expression. Binding of GlmY also prevents RapZ from activating QseE/QseF, generating a negative feedback loop limiting the response. When GlcN6P is replenished, GlmY is released from RapZ and rapidly degraded. We reveal a multifunctional sRNA‐binding protein that dynamically engages into higher‐order complexes for metabolite signaling.

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