Proteomic Landscape of Endoplasmic Reticulum Remodeling During Neurogenesis via Combinatorial Selective ER-phagy

ABSTRACT: The endoplasmic reticulum (ER) functions in protein and lipid synthesis, calcium ion flux, and inter-organelle communication, all of which are driven by the ER proteome landscape. ER is remodeled in part through autophagy-dependent protein turnover involving membrane-embedded ER-phagy receptors1,2. A refined tubular ER network is formed in neurons within highly polarized dendrites and axons3,4. Autophagy-deficient neurons in vivo display axonal ER accumulation within synaptic ER boutons, associated with hyper-excitability,5 and the ER-phagy receptor FAM134B has been genetically linked with human sensory and autonomic neuropathy6,7. However, mechanisms and receptor selectivity underlying ER remodeling by autophagy in neurons is limited. Here, we employ genetic, proteomic and computational tools to create a quantitative landscape of ER proteome remodeling via selective autophagy during conversion of stem cells to induced neurons in vitro. Through analysis of single and combinatorial ER-phagy receptor mutants coupled with an allelic series computational framework, we delineate the extent to which each of five receptors contributes to both the magnitude of ER turnover by autophagy and the selectivity of clearance for individual ER proteins. We define specific subsets of reticulon-domain containing ER-tubule shaping proteins or luminal proteins as preferred clients for autophagic turnover via distinct receptors. Using spatial sensors and flux reporters, we demonstrate receptor-specific autophagic capture of ER in axons, which correlates with aberrant accumulation of ER in axonal structures in ER-phagy receptor or autophagy-deficient cells. This molecular inventory of ER proteome remodeling and versatile genetic toolkit provides a quantitative framework for understanding the contributions of individual ER-phagy receptors for reshaping this critical organelle during transitions in cell states.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Neuron, Embryonic Stem Cell

SUBMITTER: Melissa Hoyer  

LAB HEAD: Jeffrey Wade Harper

PROVIDER: PXD046646 | Pride | 2024-01-08

REPOSITORIES: Pride