Isolation and mass spectrometry analysis of Atg9 vesicles from Saccharomyces cerevisiae

Autophagy is a eukaryotic bulk degradation pathway that allows cells to degrade potentially harmful cytosolic components or to provide necessary nutrients during starvation. This cargo degradation is achieved by its sequestration within double membrane vesicles termed autophagosomes, which fuse with the vacuole where it is degraded. Atg (autophagy-related) proteins are the main group of proteins involved in this process and, interestingly, Atg9 is the only integral membrane yeast Atg protein absolutely required for autophagy progression. In the cell it resides in Golgi-derived vesicles, which are indispensable for the nucleation of the autophagosome. There is not much known about biochemical properties of these vesicles in particular their protein content apart from Atg9. To address this question and to identify putative interaction partners of Atg9, the Atg9-vesicles were isolated and submitted to mass spectrometry analysis.