Molecular Mechanisms of ATG-9 Localization and Function in Neurons

Date of Award

Spring 2022

Document Type


Degree Name

Doctor of Philosophy (PhD)


Cell Biology

First Advisor

Colón-Ramos, Daniel


Autophagy is a cellular degradation pathway essential for neuronal health andfunction. Autophagosome biogenesis occurs at synapses, is locally regulated and increases in response to neuronal activity. The mechanisms that couple autophagosome biogenesis to synaptic activity remain unknown. In my thesis work, I determine that trafficking of ATG-9, the only transmembraneprotein in the core autophagy pathway, links the synaptic vesicle cycle with autophagy. ATG-9-positive vesicles in C. elegans are generated from the trans-Golgi network via AP- 3-dependent budding and delivered to presynaptic sites. At presynaptic sites, ATG-9 undergoes exo-endocytosis in an activity-dependent manner. Mutations that disrupt endocytosis, including a lesion in synaptojanin 1 associated with Parkinson’s disease, result in abnormal ATG-9 accumulation at clathrin-rich synaptic foci, and defects in activity-induced presynaptic autophagy. My findings uncover regulated key steps of ATG- 9 trafficking at presynaptic sites, and provide evidence that ATG-9 exo-endocytosis couples autophagosome biogenesis at presynaptic sites with the activity-dependent synaptic vesicle cycle. Furthermore, I also performed forward genetic screens, and identified a role for thelong isoform of the active zone protein Clarinet (CLA-1L) in regulating trafficking of autophagy protein ATG-9 at synapses, and presynaptic autophagy. I found mutations in CLA-1L result in abnormal accumulation of ATG-9 into clathrin-rich endocytic intermediates and that CLA-1L is specifically required for activity-induced presynaptic autophagy. My findings provide mechanistic insights into how active zone proteins regulate key steps of ATG-9 exo-endocytosis, a process that could couple the activity state of the neuron and autophagy. Together these studies support a model whereby ATG-9, regulated by active zoneproteins, couples the synaptic exo-endocytosis to autophagy and thus link synaptic autophagy to the activity state of the neuron.

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