Quantitation and biochemical characterization of autophagy's role in aging Autophagy, a highly conserved intracellular protein-, lipid-, and organelle-degradation pathway, has been implicated in prolonging longevity and forestalling aging and age-related diseases including neurodegeneration, cardiomyopathy, diabetes, and cancer. This process involves the sequestration of cytosolic components within a double-membrane vesicle, the autophagosome, and the subsequent delivery of the cargo to the lysosome/vacuole where it is degraded. Once thought to nonspecifically degrade and recycle cytosolic components, more recent work has revealed that specific cargos are subject to autophagic degradation, including protein aggregates, ribosomes, mitochondria and select cytosolic proteins. Genetic knockouts targeting integral autophagy genes have demonstrated links between the aforementioned diseases, longevity/lifespan and autophagic capacity. However, the importance of nonspecific autophagy and the various forms of specific autophagy in relation to aging is currently underexplored. This work aims to quantitatively characterize the flux of these classes of autophagy with age. These experiments will utilize advanced pulse-labeling mass spectrometry techniques that I have recently developed to precisely quantify autophagic degradation globally in the model organisms S. cerevisiae and C. elegans. These data will identify selective autophagic pathways that are misregulated as cells age, providing novel targets for future pharmacological intervention in age-related disorders. Critically, the mentored phase of this work will provide essential training in the biology of autophagy and aging as well as guidance in working with model systems of aging/longevity (i.e. C. elegans and S. cerevisiae). This training will complement my extensive prior training in biochemistry, biophysics, and computational biology, thus facilitating my transition to independence. Throughout this critical transitional phase, I will receive mentoring and guidance from a distinguished committee of autophagy, aging, and biochemistry experts. Many have hypothesized that selective autophagic cargos are targeted for degradation using specific receptor proteins. However, only a few such proteins have been identified. During the independent phase, I aim to biochemically identify and characterize receptor proteins required for specific forms of aging-related autophagy identified above. Finally, the mechanisms by which autophagic capacity decreases with age are unknown. I will apply recently developed, innovative pulse-labeling mass spectrometry approaches to measure the detailed kinetics of autophagy in aging cells, thereby identifying the biochemical reaction limiting overall autophagic flux. Identification of these receptors and rate-limiting reactions will provide novel targets for he future development of therapeutics to treat age-related, autophagy-dependent diseases.
In all eukaryotes, the removal of harmful protein aggregates, dysfunctional organelles and the general maintenance of cellular protein homeostasis depends on autophagy, a highly-conserved degradation pathway. Through an unknown mechanism, autophagy is thought to decrease in capacity as organisms age, and this attenuation has been correlated with age-related diseases including neurodegeneration, cardiomyopathy, and cancer. This research aims to precisely quantify how autophagy changes with age, identify proteins responsible for targeting intracellular material for degradation, and uncover biochemical reactions that limit autophagic activity in aging cells; these data will be critical in the future development of therapeutics targeting age-related, autophagy-dependent diseases.
|Davis, Joseph H; Williamson, James R (2017) Structure and dynamics of bacterial ribosome biogenesis. Philos Trans R Soc Lond B Biol Sci 372:|
|Tan, Yong Zi; Baldwin, Philip R; Davis, Joseph H et al. (2017) Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat Methods 14:793-796|
|Davis, Joseph H; Tan, Yong Zi; Carragher, Bridget et al. (2016) Modular Assembly of the Bacterial Large Ribosomal Subunit. Cell 167:1610-1622.e15|