Autophagy is an intracellular degradation system for the removal of harmful, bulky material from the cytoplasm. Autophagy thereby ensures cellular homeostasis and protects us from diseases such as neurodegeneration, cancer and uncontrolled infections. This is achieved by the sequestration of this material, referred to as the cargo, within double membrane organelles termed autophagosomes. Upon induction of autophagy, autophagosomes form de novo and are first observed as small membrane structures known as phagophores (or isolation membranes). These phagophores gradually expand and sequester the cargo as they grow. After closure of the phagophores, the resulting autophagosomes fuse with lysosomes (or the vacuole in yeast) wherein their inner membrane and the cargo are degraded. The biogenesis of autophagosomes is mediated by various proteins referred to as the autophagy machinery. How this machinery is orchestrated to generate autophagosomes was the subject of this project. Particular attention was given to selective autophagy, wherein defined cargo material is specifically targeted by the autophagy machinery. In order to obtain mechanistic insights into selective autophagy, especially with regard to which factors are sufficient for a given sub-reaction a reconstitution approach was conducted. These biochemical experiments were combined with cell and structural biology. Studying the cytoplasm-to-vacuole targeting pathway, a specialized selective autophagy-like process in yeast, as well as the selective autophagy of ubiquitinated proteins in mammalian cell, we found that the autophagy machinery is recruited to the cargo via cargo receptors. Thus, phagophores are not preformed but their formation is initiated directly at the cargo. Furthermore, we found that Atg9 vesicles, which are components of the autophagy machinery, function as platforms for the assembly of the autophagy machinery and thereby form seed for establishment of membrane contact sites driving the expansion of these vesicles into phagophores via lipid transfer.
