Starving cells up-regulate the autophagy pathway, in which a double-membraned autophagosome engulfs cytoplasmic content and delivers it to lysosomes for degradation and recycling. Numerous organelles, including lipid droplets (LDs) and the endoplasmic reticulum (ER), have been proposed as the sources of autophagosomal membranes. Velázquez et al. reveal that LDs aren’t, in fact, required for autophagosome formation, but they do regulate autophagy by maintaining the function of the ER during cell starvation (1).
In 2013, Martin Graef and colleagues discovered that autophagosomes form at specialized regions of the ER called ER exit sites (2). After starting his own group at the Max Planck Institute for Biology of Ageing in Cologne, Germany, Graef wanted to investigate the effects of perturbing ER function in yeast. “What happens if we interfere with ER homeostasis? How does this affect autophagy and autophagosome biogenesis?” Graef says.
One possible way to disrupt ER homeostasis is to block the formation of LDs, organelles that emerge from the ER to store excess fatty acids. LDs themselves have been suggested as the membrane source for autophagosomes (3–5), but, when Graef and colleagues, led by graduate student Ariadna Velázquez, analyzed LD-deficient yeast, they quickly realized that LDs are dispensable for autophagosome biogenesis (1). True: LD-deficient yeast were unable to form autophagosomes and degrade autophagic substrates in response to starvation, reducing the cells’ ability to survive. But yeast treated with the autophagy-inducing drug rapamycin were perfectly capable of forming autophagosomes even in the absence of LDs. “This conditional phenotype means that lipid droplets must have some sort of regulatory function,” Graef explains. “They don’t simply act as a membrane source.”
“[Lipid droplets] don’t simply act as a membrane source.”
During starvation, LD-deficient cells formed numerous puncta containing the autophagosomal membrane marker Atg8. These puncta formed in the vicinity of ER exit sites, but they didn’t expand into proper autophagosomes, possibly because of defects in the ER. Indeed, Velázquez et al. found that the ER was chronically stressed in LD-deficient cells and, upon starvation, it collapsed into an abnormally shaped network of dilated tubules.
Elevated fatty acid levels cause a similar alteration in ER morphology. Starving yeast ramp up fatty acid synthesis and, in the absence of LDs, they wouldn’t be able to store these lipids and protect the ER. Accordingly, Velázquez et al. found that inhibiting fatty acid synthesis restored the ER’s normal morphology and partially rescued the ability of LD-deficient cells to form autophagosomes and survive starvation.
However, the failure to fully rescue autophagy suggested that starving cells face additional problems in the absence of LDs. Velázquez et al. analyzed the overall lipid content of LD-deficient yeast and found that their phosphatidylinositol levels were elevated, and their phosphatidic acid levels were decreased. The cells may increase production of phosphatidylinositol as an alternative way to buffer fatty acids in the absence of LDs, but phosphoinositides and phosphatidic acid have numerous signaling functions that could potentially interfere with autophagy. Sure enough, autophagosome formation and cell survival was partially rescued when the researchers corrected the phospholipid content of starving LD-deficient yeast. And autophagy was fully rescued when the researchers simultaneously restored phospholipid levels and inhibited fatty acid synthesis.
Thus, although LDs are dispensable for autophagosome biogenesis, they control autophagy by buffering fatty acids and regulating phospholipid levels in order to maintain the function of the ER. How defects in these processes end up inhibiting autophagosome formation remains unclear, however. “This is now a very important question,” Graef says. “How is the autophagy machinery affected? We don’t know that yet.”
Answering this question could be important because several neurodegenerative diseases and metabolic disorders, including obesity, are linked to lipid stress and impaired autophagy. “In the long run, it could be interesting to consider combining therapeutic approaches that reduce fatty acid synthesis and influence the cell’s phospholipid composition,” Graef says.