The autophagosomal perspective

Macroautophagy is a degradative system that cells employ to degrade proteins, lipids, pathogens or whole organelles. Dysfunctional autophagy has been implicated in diseases ranging from cancer to neurodegeneration. Animal models lacking macroautophagy fail to preserve a functional liver or central nervous system, supporting the importance of autophagy in maintaining the health of these tissues. However, it is unclear why this degradative pathway is critical in maintaining homeostasis. All macroautophagic cargo are sequestered by the multilamellar organelle called the autophagosome. The formation of the autophagosome depends on the lipidation of a cytosolic protein LC3, so that it associates with the autophagosomal membrane throughout the autophagic process. Using a mouse model expressing GFP-LC3, we have developed an approach to immunopurify autophagosomes from different tissue, then identified their autophagosomal content using tandem-mass-tag (TMT) quantitative proteomics. We have found that the tissues rely on autophagy differently based on the turnover of their organelles as liver depended more on autophagy for ER turnover and brain relied on autophagy more for mitochondrial turnover and its synaptic vesicle homeostasis. Starvation can activate macroautophagy, and is the most studied means through which this pathway has been studied. The importance of autophagy activation in the liver during starvation has been well characterized whereas its importance in the brain has been debated. In this study, we have found that both the liver and brain rely on autophagic degradation of mitochondria differently during starvation. As expected, liver increases its autophagic response upon 24 hr nutrient deprivation, but surprisingly cargo capture transitions from whole mitochondrial turnover to piecemeal mitochondrial turnover. In contrast, in brain, mitochondria-turnover remains largely unchanged. Moreover, although neuronal cargo proteins also remained largely unchanged in response to nutrient deprivation, there was a robust response driven by the non-neuronal cells of the CNS including glial cells and brain endothelial cells, indicating how the discrete cell types of the CNS respond to this physiologic stressor differently. Taken together, this work reveals the tissue-specificity and cell-specificity in the physiological role of autophagy, providing insight in how vertebrates use autophagy to maintain health and react to stress.