Autophagy is a catabolic pathway with multifaceted roles in cellular homeostasis. This process is also involved in the antiviral response at multiple levels, including the direct elimination of intruding viruses (virophagy), the presentation of viral antigens, the fitness of immune cells, and the inhibition of excessive inflammatory reactions. In line with its central role in immunity, viruses have evolved mechanisms to interfere with or to evade the autophagic process, and in some cases, even to harness autophagy or constituents of the autophagic machinery for their replication. Given the devastating consequences of the current COVID-19 pandemic, the question arises whether manipulating autophagy might be an expedient approach to fight the novel coronavirus SARS-CoV-2. In this piece, we provide a short overview of the evidence linking autophagy to coronaviruses and discuss whether such links may provide actionable targets for therapeutic interventions.

Sulforaphane (SFN) is a compound [1-isothiocyanato-4-(methylsulfinyl)-butane] found in broccoli and other cruciferous vegetables that is currently of interest because of its potential as a chemopreventive and a chemotherapeutic drug. Recent studies in a diverse range of cellular and animal models have shown that SFN is involved in multiple intracellular pathways that regulate xenobiotic metabolism, inflammation, cell death, cell cycle progression, and epigenetic regulation. In order to better understand the mechanisms of action behind SFN-induced cell death, we undertook an unbiased genome wide screen with the yeast knockout (YKO) library to identify SFN sensitive (SFN^S) mutants. The mutants were enriched with knockouts in genes linked to vacuolar function suggesting a link between this organelle and SFN’s mechanism of action in yeast. Our subsequent work revealed that SFN increases the vacuolar pH of yeast cells and that varying the vacuolar pH can alter the sensitivity of yeast cells to the drug. In fact, several mutations that lower the vacuolar pH in yeast actually made the cells resistant to SFN (SFN^R). Finally, we show that human lung cancer cells with more acidic compartments are also SFN^R suggesting that SFN’s mechanism of action identified in yeast may carry over to higher eukaryotic cells.

Synthesis of glucosamine-6-phosphate (GlcN6P) by the enzyme GlmS initiates bacterial cell envelope biosynthesis. To ensure ongoing synthesis, GlcN6P homeostasis is required. Escherichia coli achieves this through a post-transcriptional control mechanism comprising the RNA-binding protein RapZ and small RNAs (sRNAs) GlmY and GlmZ. GlmZ stimulates glmS translation by base-pairing. When GlcN6P is abundant, GlmZ is cleaved and inactivated by endoribonuclease RNase E. Cleavage depends on RapZ, which binds GlmZ and recruits RNase E. Decreasing GlcN6P concentrations provoke up-regulation of the decoy sRNA GlmY which sequesters RapZ, thereby suppressing GlmZ decay. In our current study we identify RapZ as the GlcN6P sensor. GlcN6P-free RapZ interacts with and stimulates phosphorylation of the two-component system (TCS) QseE/QseF triggering glmY expression. Thereby generated GlmY sequesters RapZ into stable complexes, allowing for glmS expression. Sequestration by GlmY also disables RapZ to stimulate QseE/QseF, providing a negative feed-back loop limiting the response. When GlcN6P is replenished, GlmY is released from RapZ and rapidly degraded. Our work has revealed a complex regulatory scenario, in which an RNA binding protein senses a metabolite and communicates with two sRNAs, a TCS and ribonuclease RNase E to achieve metabolite homeostasis.