A COPII subunit acts with an autophagy receptor to target endoplasmic reticulum for degradation

ER-phagy keeps cells healthy In eukaryotic cells, about one-third of all proteins are targeted to the endoplasmic reticulum (ER), which serves as a hub for secretory protein traffic and quality control. Cui et al. studied a protein known as Lst1 in yeast and SEC24C in mammalian cells that is involved in loading secretory cargo into vesicles that are delivered to the Golgi complex. In response to stress caused by starvation or misfolded aggregate-prone secretory proteins, Lst1 acted to promote an additional function—ER-phagy. Together with autophagy receptors on the ER, Lst1 targeted ER domains for degradation to avert protein aggregation, thus preserving cellular health. Science, this issue p. 53 Different COPII coat subunits direct endoplasmic reticulum contents either to the secretory pathway or for ER-phagy INTRODUCTION 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. RATIONALE 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. RESULTS 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. CONCLUSION We discovered an unconventional function for a COPII cargo adaptor complex, Lst1/SEC24C-Sec23, in targeting domains of the ER for autophagy. Lst1/SEC24C-mediated ER-phagy was induced by nutrient deprivation or the expression of aggregation-prone proteins. In the latter case, ER-phagy prevented protein aggregation in the ER. Formation of Lst1/SEC24C-Sec23–containing ER-phagy sites (ERPHS) required Lnp1-stabilized ER junctions. ERPHS were found to be distinct from the Sec24-Sec23–containing ER exit sites (ERES) that bud canonical COPII-coated transport vesicles. Thus, our findings indicate that COPII cargo adaptors package distinct cargoes (ER domains or exported proteins) into membranes that are then directed onto alternate pathways, ER-phagy or the secretory pathway. The Lst1/SEC24C-Sec23 and Sec24-Sec23 cargo adaptor complexes could sort their distinct cargoes through an interaction with the cytoplasmic domain of an ER transmembrane protein: the ER-phagy receptor or an exported protein, respectively. These distinct ER-trafficking routes are regulated by separate stress-response pathways. ER-phagy depends on TOR-dependent autophagy transcriptional regulators, whereas protein homeostasis on the secretory pathway is modulated by the UPR. COPII cargo adaptors package cargoes onto two distinct pathways. ER-phagy, which can be induced by nutrient deprivation or expression of aggregation-prone proteins, occurs at ERPHS that contain Lst1/SEC24C-Sec23. The absence of Sec24 from the ERPHS distinguishes them from the Sec24-containing ERES, which bud conventional COPII vesicles that traffic to the Golgi. ER junctions stabilized by Lnp1 are important for the formation of the ERPHS. The COPII-cargo adaptor complex Lst1-Sec23 selectively sorts proteins into vesicles that bud from the endoplasmic reticulum (ER) and traffic to the Golgi. Improperly folded proteins are prevented from exiting the ER and are degraded. ER-phagy is an autophagic degradation pathway that uses ER-resident receptors. Working in yeast, we found an unexpected role for Lst1-Sec23 in ER-phagy that was independent from its function in secretion. Up-regulation of the stress-inducible ER-phagy receptor Atg40 induced the association of Lst1-Sec23 with Atg40 at distinct ER domains to package ER into autophagosomes. Lst1-mediated ER-phagy played a vital role in maintaining cellular homeostasis by preventing the accumulation of an aggregation-prone protein in the ER. Lst1 function appears to be conserved because its mammalian homolog, SEC24C, was also required for ER-phagy.