Combinatorial selective ER-phagy remodels the ER during neurogenesis

SUMMARY

The endoplasmic reticulum (ER) has a vast proteomic landscape to perform many diverse functions including protein and lipid synthesis, calcium ion flux, and inter-organelle communication. The ER proteome is remodeled in part through membrane-embedded receptors linking ER to degradative autophagy machinery (selective ER-phagy)^{1, 2}. A refined tubular ER network^{3, 4} is formed in neurons within highly polarized dendrites and axons^{5, 6}. Autophagy-deficient neurons in vivo display axonal ER accumulation within synaptic ER boutons,⁷ and the ER-phagy receptor FAM134B has been genetically linked with human sensory and autonomic neuropathy^{8, 9}. However, mechanisms, including receptor selectivity, that define ER remodeling by autophagy in neurons are limited. Here, we combine a genetically tractable induced neuron (iNeuron) system for monitoring extensive ER remodeling during differentiation with proteomic and computational tools to create a quantitative landscape of ER proteome remodeling via selective autophagy. Through analysis of single and combinatorial ER-phagy receptor mutants, we delineate the extent to which each receptor contributes to both magnitude and selectivity of ER clearance via autophagy for individual ER protein cargos. We define specific subsets of ER curvature-shaping proteins or lumenal proteins as preferred clients for distinct receptors. Using spatial sensors and flux reporters, we demonstrate receptor-specific autophagic capture of ER in axons, which correlates with aberrant ER accumulation in axons of ER-phagy receptor or autophagy-deficient neurons. This molecular inventory of ER proteome remodeling and versatile genetic toolkit provides a quantitative framework for understanding contributions of individual ER-phagy receptors for reshaping ER during cell state transitions.