ER-phagy: mechanisms, regulation, and diseases connected to the lysosomal clearance of the endoplasmic reticulum

Abstract

ER-phagy (reticulophagy) defines the degradation of portions of the endoplasmic reticulum (ER) within lysosomes or vacuoles. It is part of the self-digestion (i.e., autophagic) programs recycling cytoplasmic material and organelles, which rapidly mobilize metabolites in cells confronted with nutrient shortage. Moreover, selective clearance of ER subdomains participates in the control of ER size and activity during ER stress, the reestablishment of ER homeostasis after ER stress resolution, and the removal of ER parts in which aberrant and potentially cytotoxic material has been segregated. ER-phagy relies on the individual and/or concerted activation of the ER-phagy receptors, ER peripheral or integral membrane proteins that share the presence of LC3/Atg8-binding motifs in their cytosolic domains. ER-phagy involves the physical separation of portions of the ER from the bulk ER network and their delivery to the endolysosomal/vacuolar catabolic district. This last step is accomplished by a variety of mechanisms including macro-ER-phagy (in which ER fragments are sequestered by double-membrane autophagosomes that eventually fuse with lysosomes/vacuoles), micro-ER-phagy (in which ER fragments are directly engulfed by endosomes/lysosomes/vacuoles), or direct fusion of ER-derived vesicles with lysosomes/vacuoles. ER-phagy is dysfunctional in specific human diseases, and its regulators are subverted by pathogens, highlighting its crucial role for cell and organism life.

Keywords: ER-phagy; autophagy; disease; endoplasmic reticulum; lysosomal degradation.

Graphical abstract

FIGURE 1.

The mechanism of CMA. During CMA, KFERQ or KFERQ-like motifs are recognized by the cytosolic chaperone heat shock cognate 71-kDa protein (HSC70) and its cochaperones, including HSC70-interacting protein (CHIP), heat shock protein (HSP40), and HSC70–HSP90 organizing protein (HOP), leading to the assembly of a cargo-chaperone complex. This complex engages LAMP2A at lysosomes, and substrates are translocated into the lysosomal lumen via a process involving the multimerization of LAMP2A and lysosomal HSC70. Substrates are then broken down by lysosomal proteases, while the LAMP2A multimers disassemble for reuse. See glossary for abbreviations.

FIGURE 2.

The mechanism of macro-autophagy. The induction of macro-autophagy, often modulated by mTORC1 and/or AMPK, leads to the activation of the ULK kinase complex and the subsequent formation of the phagophore. The nucleation of the phagophore requires both the fusion of Atg9/ATG9A-positive vesicles with possibly other ones and the activity of the macro-autophagy-specific PI3K-III complex. The subsequent recruitment and engagement of the ATG2 proteins and the 2 Ub-like conjugation systems (but also other factors) drives the phagophore expansion and its closure into an autophagosome. Autophagosome maturation is characterized by the release in the cytoplasm of the components intervening during autophagosome biogenesis and the recruitment of factors mediating the docking and fusion with late endosomes and/or lysosomes. Exposure of the autophagosomal cargo to the lysosomal hydrolyses leads to its breakdown into basic metabolites. The major players mediating autophagosome biogenesis and consumption are indicated below each step of autophagy. See glossary for abbreviations.

FIGURE 3.

The mechanisms of micro-autophagy. During micro-autophagy, the cargo is directly engulfed by late endosomes and/or lysosomes/vacuoles. Micro-autophagy pathways are subdivided into type I, in which the lysosome/vacuole extrudes membrane projections that enwrap the cargo; type II, in which the lysosome/vacuole engulfs the cargo; and type III, in which the cargo is sequestered by late endosomes. Orange arrows indicate where the targeted cytoplasmic cargoes are engulfed. See glossary for abbreviations.

FIGURE 4.

Selective macro-autophagy. Selective types of macro-autophagy are initiated through 2 different mechanisms. In the first, ubiquitylation of the cargo triggers the binding of soluble autophagy receptors possessing an ubiquitin-binding domain, which in turn recruits both Atg8/LC3 proteins and FIP200 (or its yeast counterpart Atg11). This leads to the assembly and activation of the ATG machinery, which mediates the local formation of a phagophore and its expansion around the cargo. In the second mechanism, autophagy receptors embedded into the limiting membrane of a targeted organelle are activated, often through posttranslational modifications such as phosphorylation, which primes the organelle for degradation. Activated autophagy receptors recruit Atg8/LC3 proteins and FIP200/Atg11, and the local formation and expansion of the phagophore leads to the sequestration of the targeted organelle into an autophagosome.

FIGURE 5.

Selective micro-autophagy. Autophagy receptors can also mediate micro-autophagy upon their activation, possibly through direct or indirect binding to the cargo. In this context, it remains unknown how the autophagy receptors are recognized by endolysosomal compartments and trigger the engulfment of the cargo. There might be forms of micro-autophagy that do not require conventional autophagy receptors.

FIGURE 6.

Autophagy receptor-mediated vesicular transport. Probably direct or indirect binding of the cargo to the autophagy receptor triggers the formation of a transport vesicle carrying both the cargo and the autophagy receptors. These transport vesicles subsequently directly fuse with compartments of the endolysosomal system. It remains unclear whether all the vesicular transport pathways involved in the degradation of a portions of a determined organelle always require autophagy receptors.

FIGURE 7.

The 3 principal mechanisms of ER-phagy. ER fragments can be turned over by either macro- or micro-autophagy. Within these 2 pathways, ER fragmentation and sequestration into either autophagosomes or late endosomes/lysosomes/vacuoles are coordinated events. ER portions can also be directly transported to and fused with late endosomes and/or lysosomes/vacuoles. The different vesicular transport routes remain ill-characterized.

FIGURE 8.

Schematic overview of the mammalian ER-phagy receptors. For simplicity, LIR or GABARAP interacting region (GIR) motifs indicate sequences that have been shown to bind members of the Atg8/LC3 protein family. Those sequences include conventional LIR motifs, nonconventional LIR motifs, and Ub-interacting motifs. Factors required to recruit soluble autophagy receptors to the ER, like VAP proteins, UFL1, DDRGK1, and Ub, are also shown. RHD, reticulon-homology domain. See glossary for other abbreviations.

FIGURE 9.

Schematic overview of the yeast ER-phagy receptors. Atg39 and Atg40 have only been studied in S. cerevisiae. Epr1 has been characterized in S. pombe and is not present in S. cerevisiae. Scs2 and Scs22 are yeast members of the VAP protein family that recruit soluble Epr1 to the ER. RHD, reticulon-homology domain. See glossary for other abbreviations.

FIGURE 10.

Schematic overview of the plant ER-phagy receptors. Membrane-bound (AtDDRGK1) and cytosolic (AtUFL1) factors required to recruit soluble autophagy receptors to the ER are shown. RHD, reticulon-homology domain. See glossary for other abbreviations.

FIGURE 11.

Documented pleiotropic cues activating ER-phagy responses: nutrient depletions. They generate an internal pool of nutrients required for cell/organism survival. Pleiotropic signals triggered by nutrient starvation induce macro-ER-phagy, which is characterized by the sequestration of ER fragments within autophagosomes carrying bulk cargoes. This type of macro-ER-phagy involves most of the known ER-phagy receptors. Nutrient restrictions can also elicit other ER-phagy pathways, as shown in plants during light-dark cycles that result in carbon starvation. Mammalian, yeast, and plant ER-phagy receptors are in blue, green, and red, respectively. See glossary for abbreviations.

FIGURE 12.

ER stress sensors. AtbZIP17 and AtbZIP28 are the plant homologs of mammalian ATF6. See glossary for abbreviations.

FIGURE 13.

Documented pleiotropic cues activating ER-phagy responses: cellular stresses. They control ER expansion and/or eliminate ER portions containing damaged, aged, and/or toxic material. These pleiotropic signals are triggered by perturbation of calcium, redox, ions, sugar, protein and/or lipid homeostasis. In addition to inducing a variety of cell responses, this type of pleiotropic signals activates macro-ER-phagy, which is characterized by sequestration of ER fragments within autophagosome carrying bulk cargoes via unfolded protein responses. In yeast, direct capture of ER whorls by the vacuole through micro-ER-phagy has been reported. Mammalian, yeast, and plant ER-phagy receptors are in blue, green and red, respectively. See glossary for abbreviations.

FIGURE 14.

Documented ER-centric cues activating ER-phagy responses: recovery from ER stresses (recover-ER-phagy). It removes excess ER. The mammalian ER-phagy receptor is in blue. See glossary for abbreviations.

FIGURE 15.

ER-associated degradation and N-glycan processing. Slow mannose removal from N-glycans on terminally misfolded proteins by the ER-α-mannosidase I and EDEM glycosidases (mannose processing) generates N-glycans that display a terminal α1,6-bonded mannose residue (red circle). This is recognized by lectins such as OS-9 and ERLECTIN1 (mannose binding). These 2 lectins shuttle extensively demannosylated, terminally misfolded proteins to client-specific supramolecular complexes including membrane-embedded E3 Ub ligases (translocon). Retrotranslocation into the cytoplasm is followed by deglycosylation, polyubiquitylation, and proteasomal degradation. See glossary for abbreviations.

FIGURE 16.

Structure of the N-linked glycans. These oligosaccharides are preassembled on a dolichol lipid moiety and conjugated en bloc to an Asn residue in the consensus sequence Asn-X-Ser/Thr (N-X-S/T) of newly synthesized proteins, in which X can be any amino acid except a proline. N-glycans can be found on ER luminal proteins and in the luminal domains of integral ER membrane polypeptides. Inside the red-outlined circles, the green mannose residue elicits ERAD and the blue glucose residue elicits ERLAD.

FIGURE 17.

ER-to-lysosome-associated degradation (ERLAD) and N-glycan processing. Cycles of glucose removal by ER-resident α-glucosidases and glucose re-addition by UGGT1 (glucose processing) retain terminally misfolded proteins associated with CNX. The glucose residue ensuring CNX binding is shown as a red circle. CNX acts as a cargo receptor that, through interaction with specific ER-phagy receptors, elicits ERLAD. ER-to-lysosome-associated degradation is characterized by cargo segregation in determined regions of the ER, vesiculation/fragmentation of this discrete ER regions, and their turnover by macro-ER-phagy, micro-ER-phagy, or LC3-dependent vesicular transport to lysosomes/vacuoles. See glossary for abbreviations.

FIGURE 18.

Documented ER-centric cues activating ER-phagy responses: accumulation of misfolded proteins in the yeast ER. These ER-to-vacuole-associated degradation pathways remove aberrant gene products. Select examples are indicated in gray. Yeast ER-phagy receptors are in green. See glossary for abbreviations.

FIGURE 19.

Documented ER-centric cues activating ER-phagy responses: accumulation of misfolded proteins in the mammalian ER. These ER-to-lysosome-associated degradation pathways remove aberrant gene products. The engaged ER receptors and ER-phagy pathway depend on the client, cell type, and/or tissue. Select examples are indicated in gray. Mammalian ER-phagy receptors are in blue. See glossary for abbreviations.

FIGURE 20.

Documented ER-centric cues activating ER-phagy responses: ribosome stalling or pathogen invasion. They are important for the turnover of aberrant transcript, microbial gene products, or antimicrobial gene products (e.g., the Ago1 protein in A. thaliana cells infected with the Turnip yellows virus). Mammalian and plant ER-phagy receptors are in blue and red, respectively. See glossary for abbreviations.