The association between Hfq and RNase E in long-term nitrogen starvedEscherichia coli

Abstract

The regulation of bacterial gene expression is underpinned by the synthesis and degradation of mRNA. 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). The ubiquitous bacterial chaperone Hfq bound to sRNAs interacts with the RNA degradosome for the sRNA guided degradation of target mRNAs. The association between RNase E and Hfq has never been observed in live bacteria. We now show that in long-term nitrogen starved E. coli, both RNase E and Hfq co-localise in a single, large focus. This subcellular assembly, which we refer to as the H-body, also includes components of the RNA degradosome, namely, the helicase RhlB and the exoribonuclease polynucleotide phosphorylase. We further show that H-bodies are important for E. coli to optimally survive sustained nitrogen starvation. Collectively, the properties and features of the H-body suggests that it represents a hitherto unreported example of subcellular compartmentalisation of a process(s) associated with RNA management in stressed bacteria.

Polyribosome-Dependent Clustering of Membrane-Anchored RNA Degradosomes To Form Sites of mRNA Degradation in Escherichia coli

“…The loss of an RNase E-mCherry signal in TIRF mode after chloramphenicol treatment strongly suggests that RNA degradosomes in the foci are not membrane attached. Recent work has shown that nitrogen starvation in E. coli triggers a stress response that results in the formation of foci containing RNA degradosomes and the RNA chaperone Hfq ( 63 , 64 ). By analogy, we propose that the foci formed by chloramphenicol treatment are part of a stress response induced by the inhibition of translation elongation.…”

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

“…The copyright holder for this preprint (which this version posted April 1, 2022. ; https://doi.org/10.1101/2022.04.01.486790 doi: bioRxiv preprint 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.…”

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.…”