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Chaperone-Mediated Autophagy (CMA) - Selection, Mechanism and RegulationAutophagy and selective autophagy -
Ribosomes, both freely cytosolic as well as connected to the endoplasmic reticulum ER , direct protein translation in a highly controlled manner in close collaboration with multiple co-factors. Besides its role in calcium and lipid homeostasis, the ER, together with its numerous resident chaperones and enzymes, surveys and facilitates the critical steps of protein maturation, folding and sorting, particularly of secretory and membrane proteins Gomez-Navarro and Miller, ; Hwang and Qi, It also serves in robust protein quality control by ensuring the removal of nascent misfolded polypeptides by the proteasome, through the process of ER-associated degradation ERAD Christianson and Ye, Beyond its role in ERAD, the proteasome is a highly sophisticated protease complex and a key regulator of protein destruction of a large majority of cellular proteins via the ubiquitin proteasome system UPS.
Often overlooked is the fact that these protein homeostasis machineries are themselves under homeostatic control, and have limited and highly variable half-lives. Especially under conditions of cellular stress, ribosomes, ER and proteasomes are substrates for selective degradation through complex mechanisms that are only recently beginning to emerge.
Macroautophagy hereafter autophagy is an evolutionarily conserved catabolic process in all eukaryotes, which mediates intracellular recycling of cytoplasmic components in order to maintain cellular homeostasis Dikic and Elazar, ; Levine and Kroemer, This degradation pathway involves the sequestration of intracellular material within double-membrane vesicles called autophagosomes, which eventually fuse with vacuoles in yeast and plants or lysosomes in metazoans , where the cargo is degraded by resident hydrolases Lawrence and Zoncu, Autophagy takes place during standard physiological conditions and in response to different types of stress, where it ensures intracellular clearance of damaged or superfluous organelles and proteins.
Hereby, it plays a crucial role in cellular physiology and is generally regarded as protective against a wide variety of diseases including neurodegeneration, cancer, infections, and cardiovascular disorders Levine and Kroemer, Autophagy was formerly considered to be a non-selective, bulk degradation pathway involving random uptake of cytoplasm by phagophores the precursors to autophagosomes , however, in recent years, tremendous progress has been made in understanding differential cargo targeting by autophagy through a process known as selective autophagy Johansen and Lamark, Autophagy can selectively target specific cellular components, including organelles such as the ER, mitochondria, peroxisomes or lysosomes, as well as larger protein complexes such as proteasomes, ribosomes or protein aggregates Kirkin and Rogov, A unifying principle, common to all types of selective autophagy, is the requirement of a receptor for specific cargo recognition.
The receptor-Atg8 interaction is mediated by so-called Atg8-interacting motifs AIM or LC3-interacting region LIR motifs, as well as some additional newly identified interaction domains Rogov et al. So far, of the almost 20 different types of selective autophagy that have been described, nearly half of them are ubiquitin-driven, including the processes of mitophagy, xenophagy, and aggrephagy Khaminets et al.
In this context, receptors directly bind the ubiquitin chains present on the cargo surface, through a ubiquitin-binding domain. Yet in other types of selective autophagy, including ER-phagy, the potential involvement of ubiquitin as signaling molecule is unclear and remains a topic for further investigation Wilkinson, An additional emerging feature of autophagy receptors, besides cargo recognition, is to control the spatiotemporal formation of autophagosomes.
Several receptors, including p62 and NDP52, have been described to promote autophagosome formation at the site of their cargo through the interaction with ULK1 and FIP Ravenhill et al.
In this review, we discuss the latest findings, which describe how and when autophagy can be used to selectively degrade the protein homeostasis safe-keepers: ribosomes, ER and proteasomes Figure 1.
Although these represent separately defined pathways, their physical and functional interplay is discussed, together with their implications for protein homeostasis in health and disease.
Figure 1. Selective autophagy of the protein homeostasis machinery. Ribosomes, proteasomes and the ER monitor and maintain protein homeostasis to ensure cellular functionality. These machineries are themselves targeted by selective autophagy as a means to regulate balanced cellular homeostasis and functionality.
This process is conserved from yeast to mammals, yet with several mechanistic differences. In yeast, Ubp3 and Snx4 play key roles in triggering proteasome degradation. Identified proteaphagy receptors include Rpn10 in plants, Cue5 in yeast and p62 in mammals. In yeast, ribosome de-ubiquitination by the Ubp3 complex comprising Ubp3, Bre5, Cdc48, and Ufd3 leads to degradation of the large subunit, which is antagonized by Ltn1-mediated ubiquitination.
In humans, the ribophagy receptor NUFIP1 links ribosomes to the autophagosome to direct their degradation. FAMB, RTN3L, SEC62, CCPG1, ATL3 and TEX have been identified as mammalian ER-phagy receptors. FAMB and CCPG1 are implicated in ER maintenance of polarized cells, such as sensory axons and pancreatic acinar cells and are preferentially involved in ER-phagy of ER sheets.
TEX, RTN3L and ATL3 have been attributed roles in ER-phagy of ER tubules. TEX induces ER membrane engulfment from ER tubule three-way junctions by promoting autophagosome growth from these sites. RTN3L induces tubule fragmentation, leading to subsequent engulfment and degradation.
SEC62 is essential for ER recovery after stress conditions with no clear preference to either ER sheets or tubules. ER sub-domain receptor preferences still require further experimental evidence, hence the division between the two is depicted by a less prominent stippled line. Zoom in far right : Protein homeostasis at the ER is coordinated by ribosomes and proteasomes that interact with the translocon complex to deliver newly synthesized proteins to the ER or receive proteins for degradation, respectively.
Proteins in green plants , proteins in blue yeast , proteins in black humans. As the core of the translational machinery, the ribosome is a key complex that mediates proper decoding of the genome in space and time and thus ensures correct cellular functionality.
The eukaryotic ribosome is a highly conserved complex composed of four ribosomal RNAs rRNAs and close to 80 ribosomal proteins. The small subunit 40S is composed of the 18S rRNA and 33 ribosomal proteins, while the large subunit 60S comprises three rRNAs 28S, 5.
Ribosome biogenesis is an energy consuming process that requires more than additional factors to ensure proper rRNA folding and incorporation of ribosomal proteins into mature ribosomes Peña et al. In recent years, we have learned that the ribosome pool is heterogenous in its composition and that numerous inherent ribosome properties can promote preferential translation of distinct cellular mRNAs Genuth and Barna, ; Emmott et al.
Ribosome heterogeneity stems from various factors, including sequence variants and chemical modifications of the rRNA Parks et al. Additionally, the differential subcellular localization of ribosomes and target mRNAs contributes to the concept of localized translation, especially relevant in highly polarized cells, such as intestinal epithelium or neurons Jung et al.
While increasing knowledge continues to reveal the complexity in key areas of ribosome biogenesis, structure and function, little is currently known about the turnover of ribosomes and its impact on cellular homeostasis, development and disease. The UPS has been shown to rapidly degrade excess ribosomal proteins that are not incorporated into functional ribosomes Sung et al.
This process is crucial for cell proliferation, since several unincorporated ribosomal proteins signal cell cycle arrest Zhou et al. Yet in their assembled form, ribosomal subunits cannot be dealt with by the proteasome, and other means must be employed to degrade these large macromolecular complexes.
Below, we discuss emerging evidence of selective ribosome degradation by the autophagy pathway. Ever since the early detection of autophagic vesicles by transmission electron microscopy in the s, ribosomes have been found inside autophagosomes Eskelinen et al.
It was long-assumed that these autophagosome-engulfed ribosomes were the result of bulk cytoplasmic degradation, until , where Kraft et al. Using an image-based screen of yeast mutants, the Ubp3 and Bre5 de-ubiquitinase complex was shown to be specifically required for degradation of the large ribosomal subunit Kraft et al.
In follow-up studies, the Ubp3 and Bre5 binding partners, Cdc48 and Ufd3, were identified as additional players in this process, as well as γ-Glutamyl kinase Ossareh-Nazari et al.
The Ubp3 complex de-ubiquitinates lysine 74 on Rpl25, the same residue that is ubiquitinated by the ribosome associated E3 ligase Ltn1. Interestingly, Ltn1 is also known for its role in ribosome-associated quality control RQC Bengtson and Joazeiro, ; Ossareh-Nazari et al.
While Ltn1 depletion alone does not influence ribophagy during nutrient starvation, it restores ribosome degradation in a Ubp3 null background. This antagonistic interplay between Ltn1 and the Ubp3 complex, through competition for the same site on Rpl25, was the first evidence of a dynamically regulated, specific ribophagy signal.
The specificity of this signal was further supported by the lack of effect of Ubp3 on bulk autophagy or on the small ribosomal subunit, suggesting the existence of distinct machinery for the turnover of each subunit Kraft et al.
Together, these findings led to a suggested model, in which the ubiquitination of Rpl25 serves to protect ribosomes from autophagy-mediated degradation.
Upon starvation, Ltn1 expression was shown to be largely decreased Ossareh-Nazari et al. In contrast to other forms of selective autophagy, where cargo ubiquitination generally signals for selective engulfment by the autophagosome Dikic and Elazar, , ribophagy intriguingly seems to involve the removal of a ubiquitin mark as the trigger, at least in yeast.
Still, several aspects remain unclear. For instance, it is not known how the de-ubiquitinated Rpl25 is recognized by the autophagy machinery or whether the removal of this post-translational modification may unmask an as yet unidentified signal. Moreover, the distinct mechanisms for degradation of the two subunits suggests the requirement for their dissociation prior to degradation, an area for future exploration.
Several findings over the last years have confirmed the occurrence of autophagy-mediated ribosome turnover in human cells. For instance, mass spectrometry studies of isolated autophagosomes have revealed ribosomal proteins as autophagic cargo in PANC-1, MCF-7 and HeLa cells Mancias et al.
Importantly, the kinetics of ribosome degradation appeared to be different from that of other cytoplasmic proteins and mitochondria, distinguishing this process from other forms of selective or bulk autophagy Kristensen et al.
While we have a growing mechanistic understanding of ribophagy in yeast, this process was only recently described in human cells. Making use of the pH-sensitive fluorophore Keima Katayama et al.
This is blocked by inhibiting autophagy initiation through Beclin 1 BECN1 knockout and phosphatidylinositol 3-kinase VPS34 inhibition by SAR, as well as by lysosomal inhibition using bafilomycin A1. Interestingly, while starvation and Torin1-induced degradation of RPL28 was reduced in ATG5 knockout cells, Keima-tagged RPS3 remained unaffected, highlighting potential differences in large and small subunit degradation pathways, similar to the observations from yeast An and Harper, The selectivity of ribophagy was further assessed by testing a panel of translation inhibitors and cellular stress agents, which unlike starvation, do not broadly induce bulk autophagy.
Interestingly, specific inhibitors of translation, such as cycloheximide, did not affect ribosome degradation, possibly attributed to the fact that cycloheximide locks ribosomes onto the mRNA and prevents subunit dissociation, a step, as discussed above, which may be important for ribophagy.
Alternatively, translational inhibition in itself may not provide sufficient signal for ribophagy induction.
In contrast, sodium arsenite, which induces stress granule formation and reversine, an inducer of chromosome mis-segregation, both stimulate ribosome degradation more specifically than mTORC1 inhibition, as assessed through comparison of multiple cargo types An and Harper, Unlike mTORC1-dependent ribophagy, both sodium arsenite and reversine-induced degradation of small and large subunits was similarly affected in ATG5 knockout cells, pointing toward different modes of ribosome degradation depending on the inducing stimulus.
The precise triggering signal of these ribophagy-inducing agents remains unknown. Adding to these findings, the first selective ribophagy receptor, nuclear fragile X mental retardation-interacting protein 1 NUFIP1 was recently described in human cell lines Wyant et al.
Upon mTORC1 inhibition, this nuclear protein re-localizes and accumulates in lysosomes. Through interaction studies, Wyant et al. In addition to defects in ribosome degradation, NUFIP1 knockout cells show reduced survival during long-term starvation 72 h , which is accompanied by reduced nucleoside and arginine levels.
Also in C. elegans , autophagy-dependent degradation of ribosomal RNA was suggested to play a key role in maintaining nucleotide homeostasis during animal development. In this model, the loss of the lysosomal T2 family endoribonuclease RNST-2 causes accumulation of rRNA and ribosomal proteins, leading to an embryonic lethal phenotype Liu et al.
As has been observed for several other types of selective autophagy, including ER-phagy and mitophagy, multiple receptors co-exist for each autophagy subtype Kirkin and Rogov, ; Wilkinson, , suggesting the existence of additional ribophagy receptors, depending on the initiating signal or cell type.
In summary, we have limited knowledge of ribosome degradation in yeast and mammals. Despite a functionally important de-ubiquitination signal on the large ribosomal subunit in yeast, the picture is far from complete and a selective receptor has yet to be identified. Interestingly, a number of studies have elucidated a broad occurrence of post-translational modifications on ribosomal proteins in response to several types of stress, including ubiquitinations and phosphorylations.
For instance in response to translational stalling Garzia et al. Apart from the well-described phosphorylation of RPS6 downstream of mTORC1 Biever et al.
From a functional perspective, the majority of these and other modifications remain to be understood, including their possible roles in ribosome turnover. Working in parallel with autophagy, which can eliminate a large variety of substrates, the UPS targets only single proteins and is limited by the size of the proteasome Kocaturk and Gozuacik, ; Marshall and Vierstra, Besides its essential roles in maintaining proteostasis, the proteasome broadly impacts cellular processes through the removal of e.
The eukaryotic proteasome is composed of two subunits, the core particle CP and the regulatory particle RP. The CP, also referred to as the 20S, is composed of four heptameric rings that stack up to form a barrel-like structure, forming the core of the protease complex.
The RP, or the 19S, contains two subcomplexes, the lid and base, that cap one or both sides of the CP. The RP is responsible for substrate recognition and unfolding, before feeding the targeted protein to the CP for degradation Livneh et al. The specificity of the UPS is guided by ubiquitination of proteins directed for degradation.
The RP base harbors proteins that recognize substrates by their ubiquitin modifications, while the RP lid removes the ubiquitin marks from substrate proteins prior to their degradation Albornoz et al. Proteasomes are highly mobile complexes that shuttle between the cytoplasm and the nucleus depending on the cell cycle, cellular growth and stress conditions Grice and Nathan, ; Livneh et al.
While the function of the proteasome is well-established, the fate of its own components and the regulation of their turnover is less well understood. The initial indication of autophagy targeting proteasomes was discovered in , when proteasomes were observed within autophagic vesicles and lysosomes of rat liver cells under starvation Cuervo et al.
Proteaphagy has since been shown to occur in plants, yeast and mammalian cells and to be a highly regulated process mediated through distinct mechanisms depending on the physiological context Marshall et al. In a pioneer study by Marshall et al.
Briefly, by GFP-tagging the CP protein Pag1 and the RP protein Rpn5a, the extent of vacuole-dependent GFP cleavage was used as a readout for proteaphagic flux. Using this assay, it was shown that autophagy of both proteasome subunits is induced upon nitrogen starvation and is dependent on Atg8 lipidation by Atg7 and Atg10 Marshall et al.
Even in fully fed plants, both proteasomal subunits accumulate in autophagy-deficient mutant strains, while the global proteasomal activity remains unchanged compared to wild type plants, suggesting a basal level of proteaphagy that mainly targets inactive proteasomes Marshall et al.
The same study showed that proteaphagy can also be induced by proteasome inactivation. Plants deficient for proteasome assembly rpt2a-2 , rpt4b-2 or treated with a proteasome inhibitor, MG, displayed increased levels of proteaphagy, while bulk autophagy, measured by lysosomal cleavage of GFP-Atg8, remained unchanged.
Distinct from starvation-induced proteaphagy, upon their inactivation, proteasomes themselves become heavily ubiquitinated.
The ensuing proteaphagy is dependent on Rpn10, an integral component of the RP, which is required for recognition of ubiquitinated substrates Marshall et al.
Unlike other proteasomal proteins, Rpn10 can also be found as a free cytoplasmic protein, not incorporated into the proteasome van Nocker et al. Free Rpn10 accumulates on inactivated proteasomes in a ubiquitin-dependent manner and serves as a proteaphagy receptor that simultaneously binds to ubiquitinated proteasomal subunits and to Atg8, via two distinct ubiquitin-interacting motifs UIMs Marshall et al.
The sequence of Rpn10 and its binding motifs are highly conserved among plants, however, the yeast and human homologs of Rpn10 PSMD4 in humans have neither been shown to interact with Atg8 nor to impact proteaphagy Marshall et al. To date, proteaphagy is best understood in yeast, where it is specifically induced during both proteasome inhibition and nitrogen starvation, while carbon starvation, which also induces bulk autophagy, does not stimulate proteaphagy Marshall and Vierstra, As in Arabidopsis , turnover of the yeast proteasome is directed by distinct, stimulus-dependent pathways, which are dependent on the core autophagy machinery Marshall et al.
Additionally, yeast proteaphagy depends on sorting nexin 4 Snx4, also known as Atg24 , which dimerizes with Snx41 or Snx42 to mediate turnover of both subunits during nitrogen starvation or proteasome inhibition.
Snx4 is dispensable for bulk autophagy, but was shown to be required for selective autophagy of proteasomes and in fact also ribosomes Nemec et al. An additional co-regulator of both ribophagy and proteaphagy is Ubp3, which regulates CP but not RP degradation during nitrogen starvation, through the removal of an inhibitory ubiquitin mark Kraft et al.
Thus, similarly to ribophagy, these findings suggest subunit-specific mechanisms for proteaphagy induction. This is further substantiated by experiments demonstrating that trapping the RP lid in the nucleus via an inducible tether does not affect the turnover of the RP base or the CP.
However, some interdependency may exist in the cytoplasm, since tethering either subunit to the plasma membrane does in fact impact degradation of the other subunit Haruki et al.
Similar to observations from Arabidopsis , clearance of inactive proteasomes is mechanistically distinct from starvation-induced proteaphagy. Following their inhibition, proteasomes undergo extensive ubiquitination and accumulate in cytoplasmic insoluble protein deposits IPODs , which are a prerequisite for proteaphagy Marshall et al.
Moreover, the ubiquitin binding-factor, coupling of ubiquitin to ER degradation-5 Cue5 , has been identified as an autophagy receptor of inactive proteasomes. It binds to ubiquitinated proteasomes via its CUE domain and to Atg8 via its AIM domain to sequester aggregated, inactive proteasomes for autophagic degradation Marshall et al.
Cue5 is specifically required for proteaphagy of chemically or genetically inactivated proteasomes, but does not play a role in starvation-induced proteaphagy Marshall et al.
Proteaphagy has been described in mammalian cells in response to amino acid starvation. Unlike in plants and yeast, the mammalian proteasome becomes ubiquitinated upon starvation, which is essential for its degradation by autophagy Marshall et al.
p62 can act as a selective proteaphagy receptor to mediate autophagosomal uptake of proteasomes in HeLa cells. The starvation-induced recognition of the ubiquitinated proteasome by p62 is mediated by its UBA domain, while its PB1 domain is dispensable for this process Cohen-Kaplan et al.
In contrast, the PB1 domain is responsible for pmediated substrate delivery to the proteasome for degradation Seibenhener et al. These findings interestingly place p62 as a decisive factor in the regulated balance between actively supporting proteasomal function vs.
targeting it for lysosomal decay. Overall, it seems that proteaphagy occurs broadly amongst different organisms, although mechanistic details differ and lack further characterization. While the existence of this process across species suggests its physiological importance, its biological implications remain largely unknown.
Especially worthy of further investigation is whether proteaphagy plays a protective role in maintaining a healthy cellular proteasome pool by selectively targeting those that are dysfunctional. Future studies will clarify these and other points and reveal the potential consequences of defective proteaphagy for human development and disease.
The ER is a versatile organelle and apart from its afore-mentioned roles in translation, folding, sorting and ERAD, it is also important for lipid synthesis and calcium storage and release Phillips and Voeltz, Structurally the ER consists of flat membrane sheets that are covered by ribosomes rough ER and branched tubules that are spread throughout the cytosol smooth ER.
Generally speaking, the rough ER is the predominant location of synthesis and translocation of luminal and secretory proteins, while the smooth tubules interact with various other organelles to influence their lipid composition or calcium levels Shibata et al. However, care must be taken to avoid oversimplifying the division between these two ER-subtypes.
As a dynamic organelle, the ER as a whole must adjust to accommodate the changing demands in cellular protein homeostasis.
Lysosomal degradation of ER components provides a means to adjust ER volume and ensure its functionality. The selective degradation of ER via the autophagy-lysosome pathway is termed ER-phagy and can be subdivided into macro-ER-phagy and micro-ER-phagy.
While macro-ER-phagy is dependent on the core autophagy machinery and is characterized by cargo engulfment into typical double-membrane vesicles, micro-ER-phagy is mainly independent of the autophagy machinery, where cargo is instead engulfed directly by endolysosomes Wilkinson, However, recent examples illustrate that the formation of micro-ER-phagy vesicles can, in some cases, involve core autophagy proteins Fregno et al.
We here focus on macro-ER-phagy from now on termed ER-phagy , by briefly reviewing some of its key molecular players and its implications for ER homeostasis.
For a more detailed overview of this pathway, we refer the reader to a number of recent comprehensive reviews on ER-phagy Grumati et al. Recently, a number of independent studies have revealed the existence of several specialized ER-phagy receptors.
This includes six mammalian receptors FAMB, RTN3L, SEC62, CCPG1, ATL3, and TEX Khaminets et al. Below follows a brief description of the six mammalian ER-phagy receptors, their ATG8 interactions and their biological roles in cellular fitness and disease.
Family with sequence similarity FAMB was the first ER-phagy receptor described in mammalian cells Khaminets et al. It contains a membrane-embedded reticulon-homology domain RHD , that allows it to bind and reshape ER membranes and a C-terminal LIR domain, both of which are crucial for its receptor function.
Interestingly, cells depleted of FAMB show a substantial increase in ER volume and its knockout in vivo leads to neurodegeneration in peripheral sensory neurons with an associated inflated ER phenotype Khaminets et al. A recent study found that misfolded procollagen in the ER is recognized by calnexin, which directly interacts with FAMB to form ER sub-domains that are degraded through ER-phagy Forrester et al.
Thus, FAMB is a crucial ER-phagy receptor with important implications in sensory axon maintenance and collagen production. Reticulon domain-containing proteins RTN reside in ER tubules, where they are able to bend and shape ER membranes Voeltz et al.
A unique member of this reticulon protein family is the long isoform of RTN3 RTN3L , recently characterized as an ER-phagy receptor, which harbors multiple LIR domains and specifically mediates ER tubule turnover Grumati et al.
RTN3L homo-dimerization leads to ER tubule fragmentation and subsequent lysosomal degradation of these fragmented tubules.
Bulk autophagic flux and ER sheet degradation remain unaffected in the RTN3 pan-isoform knockout. However, re-introduction of RTN3L alone into these knockouts is sufficient to rescue ER tubule degradation, emphasizing the specificity of this receptor and highlighting the existence of distinct ER subtype degradation pathways mediated through different receptors.
In contrast to FAMB , RTN3L deletion does not evoke any apparent phenotype in mice, nor are there any known human pathologies related to this protein. A third ER-phagy receptor is SEC62, part of the multiprotein translocon complex which imports nascent polypeptides from translating ribosomes into the ER lumen Linxweiler et al.
This transmembrane protein is required for ER-stress recovery in a manner that is dependent on a functional LIR domain at its C-terminus Fumagalli et al. Despite the essential involvement of LC3 and the lipidation machinery proteins in SECdependent ER degradation, this process does not require proteins of the canonical autophagy initiation machinery, such as ULK1, ULK2, ATG13, and ATG Thus, a recent study suggests that ER-phagy after stress recovery is an atypical type of piecemeal micro-autophagy, which is dependent on LC3 and SEC62 Loi et al.
Interestingly, mass spectrometry analysis of autolysosomal content revealed a selective panel of ER proteins, whose degradation is dependent on SEC62, including ER chaperones and protein disulfide isomerases, which are excluded from autophagosomes in SEC62 LIR mutant cells Fumagalli et al.
Other protein substrates, including ERAD proteins, are degraded independently of SEC62 function. Moreover, SEC62 has been found to be upregulated in several types of cancer, where it is associated with increased metastatic and invasive potential, as well as higher ER stress tolerance Greiner et al.
Cell cycle progression protein 1 CCPG1 is another ER-resident transmembrane ER-phagy receptor that binds to ATG8 proteins via its LIR domain and additionally binds directly to FIP, potentially linking it to the initiation of autophagosome formation at the site of the cargo Smith et al.
In support of this, in cultured cells, CCPG1 forms puncta, which are also positive for early phagophore markers including WIPI2 and ZFYVE1 also DFCP1.
Treatment with UPR inducers DTT, tunicamycin and thapsigargin were shown to drive CCPG1-dependent ER-phagy in a manner that was dependent on its binding to both ATG8 and FIP Interestingly, the CCPG1 gene is UPR-responsive, as both its mRNA and protein levels are upregulated upon induction of ER stress.
A pancreatic proteostasis defect was observed in a hypomorphic CCPG1 mouse model, characterized by depolarization of acinar cells of the exocrine pancreas, which was accompanied by the accumulation of ER-produced secretory proteins and ER-luminal chaperones Smith et al.
Interestingly, apart from the pancreatic organ damage, the adult gastric epithelium displayed a similar loss of polarity, suggesting the importance of CCPG1 in proteostatic maintenance and proper function of polarized cells Smith et al. An additional, recently identified ER-phagy receptor is atlastin GTPase 3 ATL3 , part of the atlastin protein family ATL1, ATL2, and ATL3 , which span ER membranes via two transmembrane domains and mediate ER membrane fusion via GTP-driven conformational changes Bian et al.
Important for its function as an ER-phagy receptor, ATL3 interacts specifically with GABARAP proteins but not LC3 proteins, and its knockout reduces the degradation of tubular ER membrane proteins Chen et al.
ATL3 mutations in humans cause hereditary sensory and autonomic neuropathy type I, which is associated with ER collapse, hallmarked by aberrantly tethered tubules Kornak et al.
Interestingly, the disease-linked ATL3 mutants lose their GABARAP binding potential and cannot mediate functional ER-phagy, possibly contributing to the partial ER network breakdown observed in patients Chen et al.
Finally, testis expressed protein TEX was recently discovered as a single pass, transmembrane selective ER-phagy receptor in two independent proteomic-based studies An et al.
While Chino et al. mutant LC3B K51A , An et al. Both studies show that TEX localizes to the ER with a transmembrane domain and is degraded during starvation in an autophagy-dependent manner.
Additionally, Chino et al. TEX accumulates at ER tubule three-way junctions that are already positive for ATG8 proteins. By using TEXAPEX2 proximity labeling to detect proteins in close vicinity, the authors identified not only ATG8 proteins, but also key proteins of the canonical autophagy machinery, such as VPS34 complex proteins, WIPI2 and p62 An et al.
These findings led them to hypothesize that TEX localizes to autophagosome isolation membranes at ER tubules and helps to form the growing autophagosome in a zipper-like fashion along the ER membrane. The identification of six mammalian ER-phagy receptors intuitively raises the discussion of functional redundancy.
One factor likely to contribute to the differential roles of ER-phagy receptors is their distinct binding patterns to different ATG8 proteins. For instance, when comparing the interactome of FAMB and RTN3L, it was shown that FAMB preferentially binds to LC3B and GABARAP-L2, while RTN3L predominantly binds to GABARAP-L1 Grumati et al.
Also, ATL3 specifically binds GABARAP- but not LC3 proteins Chen et al. Several emerging studies suggest distinct functions for LC3 and GABARAP proteins in various steps of the autophagy pathway, ranging from autophagosome formation to autophagosome-lysosome fusion Weidberg et al.
Similarly, some newly identified subtypes of selective autophagy depend specifically on selected ATG8 family members Holdgaard et al. The evolution of the six human homologs from the yeast Atg8 may reflect the need to meet increased complexity in higher organisms, with critical roles in differential cargo recruitment.
The extent to which these differences in ATG8 binding contribute to the distinct functions of the ER-phagy receptors remains a subject of future study. In a functional comparison of all receptors for their individual contributions to ER-phagy during starvation, Chino et al. The lack of effect of SEC62 and RTN3L might be attributed to their more specialized roles in recovery from ER stress in the case of SEC62 Fumagalli et al.
In line with this, Grumati et al. In HeLa cells, a triple knockout of TEX , FAMB , and CCPG1 nearly mimics a FIP knockout with regards to the potency of ER-phagy induction, as assessed by an ER-resident tandem RFP-GFP reporter, with the largest phenotypic contribution attributed to TEX Chino et al.
Although quantitative proteomics indicate an accumulation of ER resident proteins during amino acid starvation in TEX knockout cells, these cells did not display an enlarged ER area upon starvation or ER stress as previously seen for CCPG1 depletion Smith et al.
Undoubtedly, these and other studies will shed further light on the differences in ER-phagy receptors and ER-phagy subtypes, along with their individual implications in the development of disease. The cell is constantly challenged to deal with a shifting balance between protein production versus protein destruction in order to maintain and shape the dynamic state of proteome equilibrium.
One of the means to acquire this, is through the selective turnover of protein homeostasis safe-keepers, as described in this review and summarized in Figure 1. This occurs in a highly context-dependent manner, involving a number of co-regulatory factors and receptors, both in basal conditions, as well as in response to a broad variety of cellular stress.
Although ribophagy, proteaphagy and ER-phagy are known as distinct, separately regulated pathways, noteworthy connections exist. In fact, the ER serves as a platform for both ribosomes and proteasomes, accounting for their commonly observed intracellular co-localization.
Yet it also binds to the proteasome via the 19S RP and accordingly, a large fraction of cytoplasmic proteasomes associates with the ER membrane Kalies et al.
Thus, ribosomes and proteasomes can physically compete for binding to the SEC61 channel in a counterbalance between nascent peptide synthesis versus degradation upon misfolding Kalies et al. The physical association of ribosomes and proteasomes at the ER deserves considerable attention in future investigations of selective autophagy.
It raises the issue of by-stander autophagy, in which nearby components can be captured by autophagosomes alongside selective cargo. In line with this, a substantial amount of by-stander autophagy is reported even after relatively specific ribophagy-inducing treatments, such as sodium arsenite and reversine An and Harper, It is possible that this is due to a more general stress-response, which in addition to ribophagy, induces bulk autophagy in parallel.
Yet the close association of ribosomes with multiple additional cytoplasmic components, is also likely to play a role. their possible degradation through rough ER uptake during ER-phagy, is lacking. Yet the common observation of free, non-membrane-bound ribosomes within autophagic vesicles by electron microscopy, suggests a clear distinction between these Eskelinen, ; Zhuang et al.
For instance, a recent study identified SEC24C, essential for sorting cargo into COPII vesicles, to be important for FAMB and RTN3L mediated ER-phagy Cui et al.
SEC24C could potentially contribute to selective cargo-sorting during ER-phagy, in a similar fashion to its COPII vesicle-related sorting.
Importantly, the issue of by-stander autophagy can be largely extrapolated to several additional types of selective autophagy and emphasizes the importance of always controlling for alternative cargo degradation. It is noteworthy that common regulators of proteaphagy and ribophagy exist, such as Ubp3 and Snx4, with identified roles in both processes in yeast Kraft et al.
Additionally, Ubp3 has been identified as a negative regulator of mitophagy in yeast Müller et al. This mechanistic overlap may imply a biological cross-talk between these degradation pathways, which is a subject worthy of further investigation. Additional regulators have several independent biological roles, potentially linking functions between different pathways.
For instance, the E3 ubiquitin ligase Ltn1, a starvation-responsive signaling factor for ribophagy, also acts in the process of RQC by marking nascent polypeptide chains with ubiquitin to signal their proteasomal degradation Bengtson and Joazeiro, ; Ossareh-Nazari et al.
While significant functional consequences of ER-phagy subtypes are emerging, including the importance in sensory axon maintenance, collagen production and cellular polarization Khaminets et al. Although proteasomes and ribosomes are relatively stable complexes with half-lives ranging from 16 h in mouse embryonic fibroblasts to over 2 weeks in rat liver cells and other cell types Liebhaber et al.
This will undoubtedly impact fundamental cellular processes that have yet to be characterized in detail. In fact, the abundance of proteasomes and ribosomes suggests an enormous potential for lysosome-mediated replenishment of amino acids and especially nucleotides through rRNA recycling.
Moreover, the impact of proteaphagy and ribophagy in shaping the functional pools of proteasomes and ribosomes, respectively, is unknown.
As increasing light is shed on ribosome heterogeneity and its functional implications for translation and cellular fate Genuth and Barna, ; Emmott et al.
Ultimately, strengthening these avenues of research will shed light on valuable therapeutic intervention opportunities in several areas, including cancer and neurodegeneration.
CB, SB, and LF conceived the review topic, discussed its contents, and wrote the manuscript. This work was supported by the Lundbeck Foundation Fellowship R and the Danish Cancer Society Knæk Cancer grant RA The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
The authors thank Catharina Steentoft and Nikolaus Allan Watson for critical reading and commenting on the manuscript. Albornoz, N. Cellular responses to proteasome inhibition: molecular mechanisms and beyond.
doi: PubMed Abstract CrossRef Full Text Google Scholar. An, H. Systematic analysis of ribophagy in human cells reveals by-stander flux during selective autophagy.
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Christianson, J. Cleaning up in the endoplasmic reticulum: ubiquitin in charge. Cohen-Kaplan, V. One of these adaptor proteins is p p62 contains an LC3-interacting region and is believed to be a substrate for selective autophagy.
In addition, p62 contains a domain that binds ubiquitin chains, and mediates the recruitment of poly ubiquitinated protein aggregates and depolarized mitochondria to the autophagic machinery see page 11 for the details of selective autophagy. In fact, in liver- and brain-specific autophagy-deficient mice, overaccumulation of p62 occurs, and ubiquitin- and ppositive inclusion bodies are observed Fig.
There is increasing interest in the involvement of impaired autophagic degradation of p62 in these diseases. Custom MHC tetramer services.
Molecular Cancer volume 23Article number: 22 Selectice this article. Metrics details. Eukaryotic Autopphagy engage in Augophagy, an internal process of self-degradation through lysosomes. Autophagy can be classified as selective or non-selective depending on the way it chooses to degrade substrates. Specific cargo is delivered to autophagosomes by specific receptors, isolated and engulfed. In Autophagy and selective autophagy cells, autophagy prevents tumorigenesis through selective cleanup Augophagy damaged organelles and certain specific proteins such as p In contrast, autophagy selectkve tumor cells, which require Autophagy and selective autophagy amounts of Autophagy and selective autophagy, with amino autopphagy, fatty Heart health supplements, and glucose. Therefore, autophagy represents something of a double-edged sword in cancer: it functions as a tumor suppressor, but can also satisfy metabolic demands once tumors are established. In this chapter, we review the tumor-suppressive and oncogenic effects of autophagy which have been characterized using several approaches including transgenic mice and introduce the involvement of selective autophagy. This is a preview of subscription content, log in via an institution. Cancer Cell —
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