Mechanisms of Phagophore Nucleation and Expansion

Autophagy (Greek for self-eating) is a process in which cells encapsulate and finally degrade damaged and harmful material that accumulates in them. The encapsulation occurs by the formation of a membrane structure around the substances destined for degradation. When the membrane has fully enwrapped the harmful material is closes to form an autophagosome. The autophagosome subsequently fuses with the cells recycling stations, the lysosomes, wherein the material is broken down and the individual building blocks are recycled and reused. The whole process is analogous to a waste bag (the membrane) wrapping around the waste, just that in our cells the bag is made anew locally at the material. The process of autophagy is important for our health and defects in autophagy have been linked to severe disease such as neurodegeneration and cancer. An outstanding question in the field is how autophagosomes are formed, and in particular how the membrane grows around the material destined for degradation. The formation of autophagosomes is mediated by a number of proteins and protein complexes that have various biochemical activities. Among the many factors are vesicles containing the transmembrane protein Atg9, the Atg11 scaffold protein and the Atg2 protein, which is able to shuttle lipids between two separate membranes. We will investigate how the Atg11 protein helps to recruit the Atg9 vesicles to the material, which is destined for autophagic degradation. We will further study how the Atg2 protein is recruited to Atg9 vesicles and to how this step can be regulated by the Atg1 kinase. Finally, is planned to reconstitute the lipid transfer mediated growth of Atg9 vesicles around the cargo material. To this end, we will employ a combination of structural and biochemical reconstitution approaches, as well as cell biology using yeast to study how the interplay of these protein complexes mediates the formation of autophagosomes. Our studies promise to reveal fundamental insights into the enigmatic process by which cells form autophagosomes.