Global RNA interactome of Salmonella discovers a 5' UTR sponge for the MicF small RNA that connects membrane permeability to transport capacity

Mol Cell. 2022 Feb 3;82(3):629-644.e4. doi: 10.1016/j.molcel.2021.12.030. Epub 2022 Jan 20.

Abstract

The envelope of Gram-negative bacteria is a vital barrier that must balance protection and nutrient uptake. Small RNAs are crucial regulators of the envelope composition and function. Here, using RIL-seq to capture the Hfq-mediated RNA-RNA interactome in Salmonella enterica, we discover envelope-related riboregulators, including OppX. We show that OppX acts as an RNA sponge of MicF sRNA, a prototypical porin repressor. OppX originates from the 5' UTR of oppABCDF, encoding the major inner-membrane oligopeptide transporter, and sequesters MicF's seed region to derepress the synthesis of the porin OmpF. Intriguingly, OppX operates as a true sponge, storing MicF in an inactive complex without affecting its levels or stability. Conservation of the opp-OppX-MicF-ompF axis in related bacteria suggests that it serves an important mechanism, adjusting envelope porosity to specific transport capacity. These data also highlight the resource value of this Salmonella RNA interactome, which will aid in unraveling RNA-centric regulation in enteric pathogens.

Keywords: MicF; RIL-seq; RNA sponges; Salmonella; envelope cross-talk; oppA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5' Untranslated Regions*
  • Biological Transport
  • Cell Membrane / genetics*
  • Cell Membrane / metabolism
  • Escherichia coli Proteins / genetics*
  • Escherichia coli Proteins / metabolism
  • Gene Expression Regulation, Bacterial
  • Host Factor 1 Protein / genetics*
  • Host Factor 1 Protein / metabolism
  • Host-Pathogen Interactions
  • Permeability
  • Porins / genetics
  • Porins / metabolism
  • RNA, Bacterial / genetics*
  • RNA, Bacterial / metabolism
  • RNA-Seq
  • Salmonella enterica / genetics*
  • Salmonella enterica / metabolism
  • Salmonella enterica / pathogenicity

Substances

  • 5' Untranslated Regions
  • Escherichia coli Proteins
  • Hfq protein, E coli
  • Host Factor 1 Protein
  • OmpF protein
  • Porins
  • RNA, Bacterial