Equipment Supplement: The mechanism and regulation of autophagy

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Autophagy represents a complex pathway of cellular homeostasis that functions in cytoprotection, but if dysregulated can cause cell death; a complete knowledge of regulation is critical for the potential modulation of this process for therapeutic purposes, and to increase our basic understanding of membrane dynamics and organelle biogenesis. Autophagy occurs in all eukaryotes, and the protein components of the autophagic machinery are conserved from yeast to mammals. The hallmark of this process is the formation of double- membrane cytosolic vesicles, autophagosomes, that contain cytoplasmic components sequestered by the phagophore, a unique transient compartment. After completion, the autophagosomes fuse with the lysosome/vacuole to release the inner vesicle that is broken down, allowing access to the cargo. Autophagy plays a role in various developmental processes and is associated with a range of pathophysiological conditions. The long-term goals of this proposal are to understand the mechanism of action of the autophagy- related proteins, how the process is regulated, and why specific mutations result in human disease. In the last 20 years, we have learned much about the molecular aspects of autophagy—42 autophagy- related (Atg) proteins have been identified, but we only have a cursory knowledge of their function. In addition, autophagic dysfunction is associated with numerous diseases in humans, including cancer, heart disease and neurodegeneration. Although autophagy is primarily cytoprotective, excessive autophagy is detrimental. Thus, we need a full understanding of the regulatory network in order to apply therapeutic interventions aimed at treating disease through autophagy modulation. In the next five years, we want to (1) understand the structure and function of the Atg proteins; (2) define the regulatory controls that allow autophagy induction, determine the switch between specific and non-specific types of autophagy, and maintain autophagy at appropriate levels; and (3) decipher the relationship between mutations affecting autophagy and diseases, with an ultimate goal of facilitating treatment. We are using yeast to investigate the molecular mechanism of autophagy; this is the best system for a molecular genetic and biochemical analysis of this complex process. Because of the high degree of conservation, however, the information we learn from yeast will be applicable to more complex eukaryotes. The experiments described in this proposal are significant because they will elucidate important links between upstream regulatory components and the machinery that carries out autophagy, providing the next step in a comprehensive analysis that links the signal transduction elements to the functional apparatus, advancing our knowledge of basic cell biology, and identifying targets for ultimate therapeutic intervention. The proposed research is innovative, because it is providing new, and in some cases paradigm-shifting, information about the regulatory and functional components of autophagy.