The studies in this proposal are aimed at understanding the role of secretory machinery on two different types of autophagy pathways that use autophagosomes, bulk autophagy and the selective autophagy of the endoplasmic reticulum (ER). Defects in autophagy have been linked to cancer and a variety of human diseases, including neurodegenerative diseases. Autophagy is a conserved catabolic process that targets cellular components for degradation. When autophagy is induced, membranes coalesce to engulf components targeted for degradation. Once these membranes seal to form an autophagosome their contents are delivered to the lysosome or vacuole for degradation. My laboratory has shown the importance of the Rab GTPase Ypt1 (Rab1 in mammals) in initiating these events. When cells are starved for nutrients, bulk autophagy is upregulated to rapidly make more nutrients. The high demand for membrane to make more autophagosomes during starvation leads to a dramatic reorganization of intracellular membranes. We have shown that the secretory pathway is downregulated during starvation and membranes from the secretory pathway are redirected to the bulk autophagy pathway. Furthermore, we found that phosphorylation of secretory machinery plays a key role in reprogramming membranes for bulk autophagy. A future goal of our studies is to identify the kinases that trigger the conserved membrane rearrangement events that take place during starvation in yeast (Saccharomyces cerevisiae) and mammalian cells. We will also address the requirements for fusing autophagosomal membranes with membranes from the early secretory pathway. Selective autophagy pathways use cargo receptors to degrade toxic aggregates and damaged organelle subdomains. These receptors link cargo, that is targeted for degradation, to the autophagy machinery. Our studies on autophagy have now expanded to include the selective degradation of the ER, also called ER-phagy. Understanding ER-phagy is of therapeutic importance as this pathway appears to be essential for the clearance of toxic aggregates from the ER. How ER-phagy targets damaged domains of the ER for degradation and severs these domains from the rest of the network remains unknown. We initiated a genetic screen in yeast and have identified key conserved factors that act in ER-phagy. Some of these factors are components of the early secretory pathway that also work in conjunction with Atg40. Atg40 is a conserved cargo receptor that has been implicated in the packaging of ER subdomains into autophagosomes. A goal of our studies is to understand how Atg40 works with these newly identified conserved components to target and sever ER subdomains during ER-phagy in both yeast and mammalian cells.
Bulk autophagy rapidly supplies nutrients to starving cells, and autophagy of the endoplasmic reticulum (ER) clears toxic proteins from the ER. Our studies are focused on understanding how these two different autophagy pathways use secretory machinery and membranes derived from the secretory pathway to maintain homeostasis during cell stress. These studies are likely to advance our understanding of cancer and certain neurological diseases.
