A novel role for the Escherichia coli RNA chaperone Hfq in the adaptive response to nitrogen starvation

Abstract

Nitrogen is an essential nutrient for bacterial survival and growth, being a constituent of almost all cellular building blocks, including nucleotides, amino acids, and cell wall components. The adaptive response to nitrogen starvation in Escherichia coli has been well characterised at the transcriptional level, but relatively little beyond that. Moreover, the role of post-transcriptional regulation of gene expression is being increasingly recognised as a vital facet of bacterial adaptive responses to stress. Therefore, the ubiquitous post-transcriptional regulatory protein Hfq was chosen as a surrogate to study the post-transcriptional basis of the adaptive response to nitrogen starvation. Here, we demonstrate a requirement of Hfq for optimal survival, and maintenance of cellular metabolism, during long-term nitrogen starvation. Using single-molecule tracking photoactivatable localisation microscopy (SM-PALM), we present a novel property of Hfq in long-term nitrogen starved bacteria whereby it forms a single, distinct focus. The Hfq foci form gradually as nitrogen starvation persists, correlating with Hfq’s role in regulating cellular metabolism. Notably, the Hfq foci rapidly disperse when bacteria are replenished with nitrogen, thus cementing the idea that the Hfq foci play a role in the adaptive response to nitrogen starvation. Moreover, we establish that the above described Hfq foci contains the components of the RNA degradosome – namely RNase E, PNPase and RhlB. This discovery suggests that the Hfq foci/RNA degradosome structure in nitrogen starved bacteria may have a role in managing the fate of RNA in stressed bacteria functioning akin to analogous liquid-liquid phase separated (LLPS) structures described in stressed eukaryotic cells. Hence, we term the Hfq foci/RNA degradosome structure the H-body. Our investigation reveals that H-bodies share several features of LLPS structures. Although many details of the mechanistic basis and prevalence of H-bodies yet remain elusive, their discovery most likely heralds a new facet of post transcriptional gene regulation in bacteria.