The association between Hfq and RNase E in long‐term nitrogen‐starved Escherichia coli

Abstract

Under conditions of nutrient adversity, bacteria adjust metabolism to minimize cellular energy usage. This is often achieved by controlling the synthesis and degradation of RNA. In Escherichia coli, RNase E is the central enzyme involved in RNA degradation and serves as a scaffold for the assembly of the multiprotein complex known as the RNA degradosome. The activity of RNase E against specific mRNAs can also be regulated by the action of small RNAs (sRNA). In this case, the ubiquitous bacterial chaperone Hfq bound to sRNAs can interact with the RNA degradosome for the sRNA guided degradation of target RNAs. The RNA degradosome and Hfq have never been visualized together in live bacteria. We now show that in long‐term nitrogen starved E. coli, both RNase E and Hfq co‐localize in a single, large focus. This subcellular assembly, which we refer to as the H‐body, forms by a liquid‐liquid phase separation type mechanism and includes components of the RNA degradosome, namely, the helicase RhlB and the exoribonuclease polynucleotide phosphorylase. The results support the existence of a hitherto unreported subcellular compartmentalization of a process(s) associated with RNA management in stressed bacteria.

A 3’ UTR-derived small RNA connecting nitrogen and carbon metabolism in enteric bacteria

“…While 29 little is known about TmaR, this protein affects polar localization of enzymes of the phosphotransferase system (PTS) (55). Hfq can form polar foci under conditions of nitrogen starvation (56), raising the question of whether there is a connection between this phenomenon and the interaction between the GlnZ and tmaR RNAs. Conceivably further understanding of the GlnZ role in the regulation of these targets could give insights into the physiological response to low ammonium.…”

The Histone H1-Like Protein AlgP Facilitates Even Spacing of Polyphosphate Granules in Pseudomonas aeruginosa

“…One class of large subcellular bodies of particular interest in this context are Hfq-based assemblies. Hfq has been suggested to form several types of biomolecular condensates which may have distinct functions in E. coli : two types of RNA-based assemblies, Hfq-foci and H-bodies, both involved in RNA processing during nitrogen starvation, and DNA-based assemblies, specifically the formation of heterochromatin ( 12 , 36 , 37 ). In the context of heterochromatin, Hfq has been shown in vitro to form phase separated assemblies with DNA and polyP ( 12 ).…”

A Compensatory RNase E Variation Increases Iron Piracy and Virulence in Multidrug-ResistantPseudomonas aeruginosaduring Macrophage Infection

“…Future studies will examine the role of this virulence system in the host cell damage and bacterial escape using different rne mutants. RNase E or homologs were also involved in bacterial virulence and metabolic adaption under stress conditions in different bacterial species 51,55,63,64 . We speculate that the stress induced by phagocytosis triggers the secretion of virulence factors by the bacteria to survive the phagocytic process and eliminate a threat.…”