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

Gianluca Matera,Yael Altuvia,Milan Gerovac,Youssef El Mouali,Hanah Margalit,Jörg Vogel

doi:10.1016/j.molcel.2021.12.030

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.

Highlights

Gram-negative bacteria possess a unique cell envelope consisting of an outer membrane (OM) and an inner membrane (IM), separated by the periplasm (Silhavy et al, 2010; Vergalli et al, 2020)
RNA interaction by ligation and sequecing (RIL-seq) reveals the Salmonella RNA-RNA interactome To generate a map of Hfq-mediated RNA-RNA interactions, we performed RIL-seq in Salmonella during the early stationary growth phase (OD600 of 2.0), i.e., when the bacterium expresses most of its small non-coding RNAs (sRNAs) (Chao et al, 2012)
Cellular RNA-RNA pairs were revealed by co-immunoprecipitation of Hfq from a bacterial lysate of an hfq::33FLAG strain, fusion by RNA ligation, and identification of chimeric fragments via sequencing

Summary

Introduction

Gram-negative bacteria possess a unique cell envelope consisting of an outer membrane (OM) and an inner membrane (IM), separated by the periplasm (Silhavy et al, 2010; Vergalli et al, 2020). Additional specialized porins are expressed when specific nutrients are sensed in the environment; for example, detection of chitin-derived oligosaccharides induces the chitoporin ChiP (Figueroa-Bossi et al, 2009). Nutrient influx at the IM is mediated by selective transport systems, including the major peptide importer systems for dipeptides (Dpp) and oligopeptides (Opp), in addition to more specialized transporters. Many of these major OM and IM proteins are exceptionally abundant, with porins reaching 105 copies/cell, a number as high as that of ribosomal proteins (Li et al, 2014; Vergalli et al, 2020). Precise regulation of envelope proteins is a matter of cellular economy

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Discussion

Conclusion