New insights into autophagy regulation using yeast Saccharomyces cerevisiae

Autophagy, from two Greek words meaning “self-eating”, is a catabolic pathway allowing the degradations of cellular components during stress conditions such as scarce nutrients. Defects in autophagy are associated with numerous human diseases. As a result, an in-depth understanding of autophagy regulation may lead to the identification of attractive new therapeutic targets. During autophagy, specific actors called Atg proteins associate at the phagophore assembly sites (PAS) to mediate the formation of vesicles, called autophagosomes, which sequester and deliver to lysosomes/vacuoles the structures targeted to destruction. Atg4 is a protease that cleaves Atg8 to both promote its association to the PAS and remove it from the complete autophagosomes. Atg4 activity needs to be highly regulated to correctly orchestrate autophagosome biogenesis. In this thesis, we discovered that Atg4 associates to the PAS through Atg8 binding and this recruitment depends on a domain in Atg4, called APEAR, which is essential for Atg4 function in autophagy. We also found that Atg1 kinase modifies a specific site of Atg4, blocking the binding to Atg8 and the removal of Atg8 from the autophagosome. These two major molecular mechanisms are crucial for controlling Atg4 activity and consequently also autophagy. The transmembrane protein Atg9, similarly to Atg4 and Atg8, is essential for autophagy. Using a microscopy-based screen, we identified Atg proteins that participate in the movement of Atg9-containing vesicles to and from the PAS. Given the relevance of autophagy in human diseases, our findings represent an important step towards the discovery of new therapeutic targets.