The unfolded protein response (UPR) maintains homeostasis of the endoplasmic reticulum (ER) through a variety of mechanisms, including ER-associated degradation (ERAD). ERAD recognizes terminally misfolded or unassembled proteins and retrotranslocates them across the ER membrane into the cytosol, where they are degraded by the proteasome. Certain disease-associated, aggregation-prone proteins, however, cannot be cleared by ERAD and are disposed of by other pathways. Aggregation-prone proteins have been linked to a variety of neurodegenerative diseases, including a diverse group of disorders characterized as hereditary spastic paraplegias. Thus, understanding how these alternate disposal pathways function has important medical implications.

Autophagy of the ER (ER-phagy) is a disposal pathway that targets ER domains and sequesters them into autophagosomes for delivery to the vacuole or lysosome for degradation. When ER-phagy is induced, ER-phagy receptors recruit their binding partner, Atg8 in yeast or LC3 in mammals, to discrete sites on the ER to facilitate autophagosome formation. These sites are formed on a highly dynamic tubular ER network that is stabilized by Lnp1, a conserved protein that resides at the tubular ER junctions. Although ER-phagy occurs at discrete sites on the contiguous ER network, the receptors that load ER into autophagosomes are dispersed throughout the network. How specific sites on the ER are targeted for ER-phagy is unknown. We reasoned that cytosolic components might function with ER-phagy receptors to define these sites. COPII coat subunits were candidates for such factors because they are known to segregate membrane domains from the bulk ER. Correctly folded proteins destined to exit the ER are packaged by the COPII coat cargo adaptor complex Sec24-Sec23 into transport vesicles that bud from the ER and traffic to the Golgi.

In budding yeast, we discovered that the Sec24 paralog Lst1, which forms a COPII cargo adaptor complex with Sec23, is essential for ER-phagy. ER-phagy is typically induced in yeast with the drug rapamycin, a TOR (target of rapamycin) kinase inhibitor that mimics nutrient deprivation. Rapamycin treatment up-regulated the Atg40 ER-phagy receptor and increased the number of Atg40 puncta that colocalized with Lst1-Sec23. Atg40 also bound to Lst1. Other COPII coat subunits did not colocalize with or interact with Atg40. Highlighting the importance of ER dynamics in ER-phagy, the Lst1-Sec23 complex failed to colocalize with Atg40 puncta and Atg8 in Lnp1-depleted cells, which are defective in ER-phagy. Consistent with a role for Lst1 in packaging ER domains, Atg40 degradation during ER-phagy required Lst1. Furthermore, both Lst1 and Atg40 were needed to sequester ER domains into autophagosomes. We also found that ER stress induced by an overexpressed, aggregation-prone secretory protein up-regulated Atg40 expression to reduce protein aggregation in the ER. TOR-dependent autophagy transcriptional regulators, and not the UPR, modulated Atg40 expression. The role of Lst1 in ER-phagy appears to be conserved, because its mammalian homolog, SEC24C, was similarly required for ER-phagy. Specifically, we found that SEC24C was needed for the degradation of two mammalian ER-phagy receptors, FAM134B and RTN3. SEC24C function is especially critical in the central nervous system, because its depletion in postmitotic neurons leads to their death.

We discovered an unconventional function for a COPII cargo adaptor complex, Lst1/SEC24C-Sec23, in targeting …