Metabolism regulation by autophagy

The goal of this project is to obtain insights into how autophagy regulates cell metabolism under different nutritional conditions. Increasing evidences are showing that induction of autophagy allows stem cells and certain cell types to change their fate and enter specific developmental and differentiation programs, which is accompanied by change in energy production from glycolysis to phosphorylative oxidation. It remains unclear , however, which is the identity of the factors degraded by autophagy that trigger this metabolic change. It is imaginable that a metabolic shift involves turnover of specific cellular factors and therefore it would be mediated by a selective type of autophagy, which will require one or more autophagic receptors. To unveil how eukaryotic cells regulate their metabolism through autophagy, we will exploit yeast Saccharomyces cerevisiae. The unique advantages of this model system is that nutritional conditions can be easily modified by changing the culture medium, and yeast possess just one autophagy receptor involved in the turnover of cytoplasmic components, i.e. Cue5. Our strategy is to practically change nutritional conditions and determine what Cue5 is transporting to the vacuole (the yeast counterpart of the mammalian lysosome).

The ESR will change yeast metabolism by transferring cells into medium lacking nitrogen or carbon, or containing pyruvate or oleic acid as the sole carbon source, before monitoring the turnover of Cue5 biochemically. Once determined the time when Cue5 is delivered into the vacuole, the ESR will immune-isolate this autophagy receptor and identify the bound proteins by mass spectrometry. Geontological analysis of the identified proteins will reveal the cellular pathways in the metabolic shift will be subsequently proven by inhibiting them with specific drug (if available) or by knocking out key enzymes. This approach will also allow to isolate biomarkers to follow autophagy progression under specific nutritional conditions. The ESR will also explore whether the same marker proteins and pathways are involved in metabolic shifts in mammalian cells, taking advantage of the expertise available within DRIVE.