Ubiquilin at a crossroads in protein degradation pathways

Ubiquilin proteins are conserved across all eukaryotes and function in the regulation of protein degradation. We found that ubiquilin functions to regulate macroautophagy and that the protein is also a substrate of chaperone-mediated autophagy.Key words: autophagy, cell death, LC3, protein turnover, ubiquitinUbiquilin proteins are present in all eukaryotes and appear to function in protein degradation pathways. Humans contain four ubiquilin genes each encoding a separate protein. The proteins are approximately 600 amino acids in length and share extensive homology with one another. They are characterized by an N-terminal sequence that is very similar to ubiquitin, called the ubiquitin-like domain (UBL), followed by a longer, more variable central domain, and terminate with a conserved 50-amino-acid sequence called a ubiquitin-associated domain (UBA). This structural organization is characteristic of proteins that function to deliver ubiquitinated proteins to the proteasome for degradation. In accordance with this function, the UBL domain of ubiquilin binds subunits of the proteasome, and its UBA domain binds to polyubiquitin chains that are typically conjugated onto proteins that are marked for destruction. Indeed, we recently showed that ubiquilin is recruited to the endoplasmic reticulum where it binds and promotes the degradation of misfolded proteins to the proteasome during ER-associated degradation (ERAD).Remarkably, ubiquilin was also recently reported to be involved in macroautophagy. The finding was based on colocalization of ubiquilin with autophagosomal marker LC3 in cells, and because overexpression of ubiquilin-1 suppresses and silencing of its expression enhances, starvation-induced cell death. In our recently published paper we describe our evidence linking ubiquilin to autophagy. We demonstrate that ubiquilin is indeed present in different structures associated with macroautophagy and that it is required for a critical step in autophagosome formation. Additionally, we also demonstrate that ubiquilin is a substrate of chaperone-mediated autophagy. The findings suggest that ubiquilin might play an important, and perhaps a crucial, role in dictating the pathway of protein degradation in cells.In previous studies we found that ubiquilin proteins expressed in normal growing HeLa cells are very stable with a rate of turnover in excess of 20 h. Because most long-lived proteins are degraded by autophagy, we felt it was important to distinguish whether ubiquilin localization in autophagosomes was simply related to the expected route of degradation of the protein or whether it was related to some special function in autophagy. Accordingly, our experiments were designed to distinguish between these two possibilities.Using double immunofluorescence microscopy we found that endogenous ubiquilin and LC3 proteins are present in puncta in HeLa cells. To ensure this was not an artifact of the staining procedure, we cotransfected HeLa cells with ubiquilin-1 and LC3 expression constructs that were tagged with either mRFP or GFP proteins and again found that the two expressed proteins are colocalized in puncta, irrespective of which tag was fused to the proteins. Further evidence supporting ubiquilin localization to autophagosomes was obtained by showing strong enrichment of ubiquilin proteins upon purification of autophagosomes from mouse liver and by the strong immunogold staining of the protein in autophagosomes in mouse brains in a transgenic mouse model of Alzheimer disease.To determine if ubiquilin localization to autophagosomes is mediated by interaction with LC3 we conducted immunoprecipitation experiments to examine whether the two proteins coimmunoprecipitate with each other. Indeed, our results showed that the two proteins coimmunoprecipitate with one another, indicating that they bind together in a complex. However, we did not detect any strong binding between bacterially expressed forms of the proteins, suggesting that the interaction between the proteins in cells might be mediated by a bridging factor(s).We next used a pH-sensitive tandem-tagged mCherry-GFP-LC3 reporter that is used to monitor maturation of autophagosomes to autolysosomes to determine whether ubiquilin is present during the different steps of macroautophagy. Indeed, we found that anti-ubiquilin staining is present throughout the different structures involved in the process, and interestingly, we also noted that the structures are enriched for K48- and K63-ubiquitin linkages. Because ubiquilin contains a UBA domain that binds ubiquitin chains we examined whether proteins containing K48- and K63-ubiquitin linkages coimmunoprecipitate with ubiquilin. Indeed, our immunoblots indicated that proteins containing both of these types of linkages coprecipitate with ubiquilin, consistent with the idea that ubiquilin might target proteins with diverse ubiquitin linkages for degradation by autophagy.To determine if ubiquilin is required for autophagy, we knocked down the ubiquilin-1 and -2 proteins in HeLa cells (which mainly express these two ubiquilin isoforms) by siRNA transfection and examined if loss of the proteins altered LC3-I and LC3-II levels. Interestingly, we found that ubiquilin knockdown over a 72 h time period is associated with a progressive increase in LC3-I levels and a concomitant decrease in LC3-II levels. Furthermore, ubiquilin knockdown led to an ∼45% reduction in the number of cells containing five or more autophagosomes. Based on these results we propose that ubiquilin is required for maturation of LC3-I to LC3-II, which we speculate might be related to the requirement of the protein in macroautophagy.We next asked if ubiquilin protein is consumed during autophagy. We examined this by treating HeLa cells with puromycin to induce protein misfolding and macroautophagy. Immunoblot analysis of the protein lysates examined at 2 h intervals over a 7 h period of exposure to puromycin revealed a direct correlation between stimulation of macroautophagy and a time-dependent decrease in the ubiquilin and LC3-II protein levels. The time-dependent decline in the proteins is inhibited by treatment of cells with two different autophagy inhibitors, 3-methyladenine and bafilomycin A₁. The results suggest that ubiquilin protein is consumed during macroautophagy.The consumption of ubiquilin during macroautophagy prompted us to examine if ubiquilin might also be involved in chaperone-mediated autophagy (CMA), which involves the active transport of proteins into lysosomes. Support for this idea arose because ubiquilin proteins contain two sequences that conform to a pentapeptide motif involved in CMA. An in vitro CMA assay using recombinant GST-ubiquilin-1 fusion protein and purified lysosomes confirmed ubiquilin is an active CMA substrate. The results suggested that ubiquilin can be consumed by two different types of autophagy, macroautophagy and CMA. We speculate that this dual mode of consumption may provide a potential switch whereby changes in ubiquilin levels beyond a certain threshold might trigger execution of either macroautophagy or CMA. The idea that such a switch exists stems from previous work that showed inhibition of CMA can lead to activation of macroautophagy and vice versa.Several intriguing new questions emerge from this and previous works, including what exact function ubiquilin serves in autophagy, particularly in the execution of macroautophagy and CMA. Is there a signal that instructs ubiquilin to choose between its known functions in autophagy and ERAD or is the choice random? What role do its different domains play in these processes? The answers to these questions are likely to be important because in previous studies we showed that overexpression of ubiquilin protects cells against potentially toxic mutant huntingtin proteins containing polyglutamine expansions. In our new work we also found that ubiquilin overexpression protects cells against starvation-induced cell death caused by mutations in presenilin-2 proteins. The underlying conclusion from these studies is that ubiquilin appears to play important roles in regulating protein degradation pathways that are likely to have important implications in cell survival. Clearly, understanding ubiquilin function in different protein degradation pathways could lead to novel approaches to prevent diseases associated with protein misfolding.     

TMEM59 defines a novel ATG16L1‐binding motif that promotes local activation of LC3

Selective autophagy underlies many of the important physiological roles that autophagy plays in multicellular organisms, but the mechanisms involved in cargo selection are poorly understood. Here we describe a molecular mechanism that can target conventional endosomes for autophagic degradation. We show that the human transmembrane protein TMEM59 contains a minimal 19‐amino‐acid peptide in its intracellular domain that promotes LC3 labelling and lysosomal targeting of its own endosomal compartment. Interestingly, this peptide defines a novel protein motif that mediates interaction with the WD‐repeat domain of ATG16L1, thus providing a mechanistic basis for the activity. The motif is represented with the same ATG16L1‐binding ability in other molecules, suggesting a more general relevance. We propose that this motif may play an important role in targeting specific membranous compartments for autophagic degradation, and therefore it may facilitate the search for adaptor proteins that promote selective autophagy by engaging ATG16L1. Endogenous TMEM59 interacts with ATG16L1 and mediates autophagy in response to Staphylococcus aureus infection.     

Ubiquilin at a crossroads in protein degradation pathways

Ubiquilin proteins are conserved across all eukaryotes and function in the regulation of protein degradation. We found that ubiquilin functions to regulate macroautophagy and that the protein is also a substrate of chaperone-mediated autophagy.     

Vrl1 relies on its VPS9‐domain to play a role in autophagy in Saccharomyces cerevisiae

Autophagy is an intracellular degradation process involving many Atg proteins, which are recruited hierarchically to regulate this process. Rab/Ypt GTPases and their activators, guanine nucleotide exchange factors (GEFs), which are critical for regulating vesicle trafficking, are also involved in autophagy. Previously, we reported that yeast Vps21 and its GEF Vps9 are required for autophagy. Later, a third yeast VPS9‐domain‐containing protein, V AR P‐l ike 1 (Vrl1), which was identified as a mutant in major laboratory strains, had partially overlapping functions with Vps9 in trafficking. In this study, we showed that Vrl1 performed roles in autophagy, and its VPS9‐domain was crucial for its role in autophagy. We found that localization of Vrl1 differed from the other two VPS9‐domain‐containing proteins, Vps9 and Muk1, and only Vrl1 changed from multipoint to diffusion after starvation. Like Vps9, Vrl1 suppressed autophagic defects caused by the VPS9 deletion. We further showed that these VPS9‐domain‐containing proteins, Vps9, Muk1, and Vrl1, all co‐localized with Atg8 on autophagosomes in cells blocked in any late step of starvation‐induced autophagy, with Vrl1 most often co‐localizing with Atg8. A small portion (<25%) of these VPS9‐domain‐containing proteins were degraded through autophagy. However, a large portion (>60%) of Vrl1 decreased independently of autophagy. We propose that Vrl1 may regulate autophagy in a similar way as Vps9, and the level of Vrl1 partly decreases through both autophagy‐dependent and ‐independent routes.     

NBR1 and p62 as cargo receptors for selective autophagy of ubiquitinated targets

Autophagy is an evolutionary conserved cell survival process for degradation of long-lived proteins, damaged organelles and protein aggregates. The mammalian proteins p62 and NBR1 are selectively degraded by autophagy and can act as cargo receptors or adaptors for the autophagic degradation of ubiquitinated substrates. Despite differing in size and primary sequence, both proteins share a similar domain architecture containing an N-terminal PB1 domain, a LIR motif interacting with ATG8 family proteins, and a C-terminal UBA domain interacting with ubiquitin. The LIR motif is essential for their autophagic degradation, indicating that ATG8 family proteins are responsible for the docking of p62 and NBR1 to nucleating autophagosomes. p62 and NBR1 co-operate in the sequestration of misfolded and ubiquitinated proteins in p62 bodies and are both required for their degradation by autophagy. Here we discuss the role of p62 and NBR1 in degradation of ubiquitinated cargoes and the putative role of LIR as a general motif for docking of proteins to ATG8 family proteins.     

Antagonism of Beclin 1‐dependent autophagy by BCL‐2 at the endoplasmic reticulum requires NAF‐1

In addition to mitochondria, BCL‐2 is located at the endoplasmic reticulum (ER) where it is a constituent of several distinct complexes. Here, we identify the BCL‐2‐interacting protein at the ER, nutrient‐deprivation autophagy factor‐1 (NAF‐1)—a bitopic integral membrane protein whose defective expression underlies the aetiology of the neurodegenerative disorder Wolfram syndrome 2 (WFS2). NAF‐1 contains a two iron–two sulphur coordinating domain within its cytosolic region, which is necessary, but not sufficient for interaction with BCL‐2. NAF‐1 is displaced from BCL‐2 by the ER‐restricted BH3‐only protein BIK and contributes to regulation of BIK‐initiated autophagy, but not BIK‐dependent activation of caspases. Similar to BCL‐2, NAF‐1 is found in association with the inositol 1,4,5‐triphosphate receptor and is required for BCL‐2‐mediated depression of ER Ca²⁺ stores. During nutrient deprivation as a physiological stimulus of autophagy, BCL‐2 is known to function through inhibition of the autophagy effector and tumour suppressor Beclin 1. NAF‐1 is required in this pathway for BCL‐2 at the ER to functionally antagonize Beclin 1‐dependent autophagy. Thus, NAF‐1 is a BCL‐2‐associated co‐factor that targets BCL‐2 for antagonism of the autophagy pathway at the ER.     

The Machado–Joseph disease deubiquitylase ataxin‐3 interacts with LC3C/GABARAP and promotes autophagy

The pathology of spinocerebellar ataxia type 3, also known as Machado‐Joseph disease, is triggered by aggregation of toxic ataxin‐3 (ATXN3) variants containing expanded polyglutamine repeats. The physiological role of this deubiquitylase, however, remains largely unclear. Our recent work showed that ATX‐3, the nematode orthologue of ATXN3, together with the ubiquitin‐directed segregase CDC‐48, regulates longevity in Caenorhabditis elegans. Here, we demonstrate that the long‐lived cdc‐48.1; atx‐3 double mutant displays reduced viability under prolonged starvation conditions that can be attributed to the loss of catalytically active ATX‐3. Reducing the levels of the autophagy protein BEC‐1 sensitized worms to the effect of ATX‐3 deficiency, suggesting a role of ATX‐3 in autophagy. In support of this conclusion, the depletion of ATXN3 in human cells caused a reduction in autophagosomal degradation of proteins. Surprisingly, reduced degradation in ATXN3‐depleted cells coincided with an increase in the number of autophagosomes while levels of lipidated LC3 remained unaffected. We identified two conserved LIR domains in the catalytic Josephin domain of ATXN3 that directly interacted with the autophagy adaptors LC3C and GABARAP in vitro. While ATXN3 localized to early autophagosomes, it was not subject to lysosomal degradation, suggesting a transient regulatory interaction early in the autophagic pathway. We propose that the deubiquitylase ATX‐3/ATXN3 stimulates autophagic degradation by preventing superfluous initiation of autophagosomes, thereby promoting an efficient autophagic flux important to survive starvation.     

Bovine herpesvirus type 4 infection modulates autophagy in a permissive cell line

Bovine herpesvirus type 4 (BoHV‐4), like other herpesviruses, induces a series of alterations in the host cell that modify the intracellular environment in favor of viral replication, survival and spread. This research examined the impact of BoHV‐4 infection on autophagy in BoHV‐4 infected Madin Darby bovine kidney (MDBK) cells. Protein extracts of BoHV‐4 infected and control MDBK cells were subjected to Western blot. The concentrations of the autophagy and apoptosis‐related proteins Beclin 1, p21, PI3 kinase, Akt1/2, mTOR, phospho mTOR, p62 and the light chain three (LC3) were normalized to the actin level and expressed as the densitometric ratio. Western blot analysis of virus‐infected cells revealed that autophagic degradation pathway was induced in the late phase of BoHV‐4 infection. After 48 h post‐infection the protein LC3II, which is essential for autophagy was found to be markedly increased, while infection of MDBK cells with BoHV‐4 resulted in a depletion of p62 levels. Becline 1, PI3 kinase, Akt1/2 and p21 expression increased between 24 and 48 h post‐infection. Surprisingly, mTOR and its phosphorylated form, which are negative regulators of autophagy, also increased after 24 h post‐infection. In conclusion, our findings suggest that BoHV‐4 has developed mechanisms for modulation of autophagy that are probably part of a strategy designed to enhance viral replication and to evade the immune system. Additional studies on the relationship between autophagy and BoHV‐4 replication and survival, in both lytic and latent replication phases, are needed to understand the role of autophagy in BoHV‐4 pathogenesis. J. Cell. Biochem. 114: 1529–1535, 2013. © 2013 Wiley Periodicals, Inc.     

Enhanced Proteostasis in Post-ischemic Stroke Mouse Brains by Ubiquilin-1 Promotes Functional Recovery

Stroke is pathologically associated with oxidative stress, protein damage, and neuronal loss. We previously reported that overexpression of a ubiquitin-like protein, ubiquilin-1 (Ubqln), protects neurons against ischemia-caused brain injury, while knockout of the gene exacerbates cerebral ischemia-caused neuronal damage and delays functional recovery. Although these observations indicate that Ubqln is a potential therapeutic target, transgenic manipulation-caused overexpression of Ubqln occurs before the event of ischemic stroke, and it remains unknown whether delayed Ubqln overexpression in post-ischemic brains within a clinically relevant time frame is still beneficial. To address this question, we generated lentiviruses (LVs) either overexpressing or knocking down mouse Ubqln, and treated post-ischemic stroke mice 6 h following the middle cerebral artery occlusion with the LVs before animal behaviors were evaluated at day 1, 3, 5, and 7. Our data indicate that post-ischemic overexpression of Ubqln significantly promoted functional recovery, whereas post-ischemic downregulation of Ubqln expression delays functional recovery. To further understand the mechanisms underlying how Ubqln functions, we also isolated protein aggregates from the brains of wild-type mice or the mice overexpressing Ubqln following ischemia/reperfusion. Western blot analysis indicates that overexpression of Ubqln significantly reduced the accumulation of protein aggregates. These observations not only suggest that Ubqln is a useful candidate for therapeutic intervention for ischemic stroke but also highlight the significance of proteostasis in functional recovery following stroke.     

Tumor suppressor Tsc1 is a new Hsp90 co‐chaperone that facilitates folding of kinase and non‐kinase clients

The tumor suppressors Tsc1 and Tsc2 form the tuberous sclerosis complex (TSC), a regulator of mTOR activity. Tsc1 stabilizes Tsc2; however, the precise mechanism involved remains elusive. The molecular chaperone heat‐shock protein 90 (Hsp90) is an essential component of the cellular homeostatic machinery in eukaryotes. Here, we show that Tsc1 is a new co‐chaperone for Hsp90 that inhibits its ATPase activity. The C‐terminal domain of Tsc1 (998–1,164 aa) forms a homodimer and binds to both protomers of the Hsp90 middle domain. This ensures inhibition of both subunits of the Hsp90 dimer and prevents the activating co‐chaperone Aha1 from binding the middle domain of Hsp90. Conversely, phosphorylation of Aha1‐Y223 increases its affinity for Hsp90 and displaces Tsc1, thereby providing a mechanism for equilibrium between binding of these two co‐chaperones to Hsp90. Our findings establish an active role for Tsc1 as a facilitator of Hsp90‐mediated folding of kinase and non‐kinase clients—including Tsc2—thereby preventing their ubiquitination and proteasomal degradation.     

Conformational flexibility of BECN1: Essential to its key role in autophagy and beyond

BECN1 (Beclin 1), a highly conserved eukaryotic protein, is a key regulator of autophagy, a cellular homeostasis pathway, and also participates in vacuolar protein sorting, endocytic trafficking, and apoptosis. BECN1 is important for embryonic development, the innate immune response, tumor suppression, and protection against neurodegenerative disorders, diabetes, and heart disease. BECN1 mediates autophagy as a core component of the class III phosphatidylinositol 3‐kinase complexes. However, the exact mechanism by which it regulates the activity of these complexes, or mediates its other diverse functions is unclear. BECN1 interacts with several diverse protein partners, perhaps serving as a scaffold or interaction hub for autophagy. Based on extensive structural, biophysical and bioinformatics analyses, BECN1 consists of an intrinsically disordered region (IDR), which includes a BH3 homology domain (BH3D); a flexible helical domain (FHD); a coiled‐coil domain (CCD); and a β‐α‐repeated autophagy‐specific domain (BARAD). Each of these BECN1 domains mediates multiple diverse interactions that involve concomitant conformational changes. Thus, BECN1 conformational flexibility likely plays a key role in facilitating diverse protein interactions. Further, BECN1 conformation and interactions are also modulated by numerous post‐translational modifications. A better structure‐based understanding of the interplay between different BECN1 conformational and binding states, and the impact of post‐translational modifications will be essential to elucidating the mechanism of its multiple biological roles.     

Mitophagy defects arising from BNip3 loss promote mammary tumor progression to metastasis

BNip3 is a hypoxia‐inducible protein that targets mitochondria for autophagosomal degradation. We report a novel tumor suppressor role for BNip3 in a clinically relevant mouse model of mammary tumorigenesis. BNip3 delays primary mammary tumor growth and progression by preventing the accumulation of dysfunctional mitochondria and resultant excess ROS production. In the absence of BNip3, mammary tumor cells are unable to reduce mitochondrial mass effectively and elevated mitochondrial ROS increases the expression of Hif‐1α and Hif target genes, including those involved in glycolysis and angiogenesis—two processes that are also markedly increased in BNip3‐null tumors. Glycolysis inhibition attenuates the growth of BNip3‐null tumor cells, revealing an increased dependence on autophagy for survival. We also demonstrate that BNIP3 deletion can be used as a prognostic marker of tumor progression to metastasis in human triple‐negative breast cancer (TNBC). These studies show that mitochondrial dysfunction—caused by defects in mitophagy—can promote the Warburg effect and tumor progression, and suggest better approaches to stratifying TNBC for treatment.     

Golgi membrane‐associated degradation pathway in yeast and mammals

Autophagy is a cellular process that degrades subcellular constituents, and is conserved from yeast to mammals. Although autophagy is believed to be essential for living cells, cells lacking Atg5 or Atg7 are healthy, suggesting that a non‐canonical degradation pathway exists to compensate for the lack of autophagy. In this study, we show that the budding yeast Saccharomyces cerevisiae, which lacks Atg5, undergoes bulk protein degradation using Golgi‐mediated structures to compensate for autophagy when treated with amphotericin B1, a polyene antifungal drug. We named this mechanism Golgi membrane‐associated degradation (GOMED) pathway. This process is driven by the disruption of PI(4)P‐dependent anterograde trafficking from the Golgi, and it also exists in Atg5‐deficient mammalian cells. Biologically, when an Atg5‐deficient β‐cell line and Atg7‐deficient β‐cells were cultured in glucose‐deprived medium, a disruption in the secretion of insulin granules from the Golgi occurred, and GOMED was induced to digest these (pro)insulin granules. In conclusion, GOMED is activated by the disruption of PI(4)P‐dependent anterograde trafficking in autophagy‐deficient yeast and mammalian cells.     

PI4P-signaling pathway for the synthesis of a nascent membrane structure in selective autophagy

Phosphoinositides regulate a wide range of cellular activities, including membrane trafficking and biogenesis, via interaction with various effector proteins that contain phosphoinositide binding motifs. We show that in the yeast Pichia pastoris, phosphatidylinositol 4'-monophosphate (PI4P) initiates de novo membrane synthesis that is required for peroxisome degradation by selective autophagy and that this PI4P signaling is modulated by an ergosterol-converting PpAtg26 (autophagy-related) protein harboring a novel PI4P binding GRAM (glucosyltransferase, Rab-like GTPase activators, and myotubularins) domain. A phosphatidylinositol-4-OH kinase, PpPik1, is the primary source of PI4P. PI4P concentrated in a protein-lipid nucleation complex recruits PpAtg26 through an interaction with the GRAM domain. Sterol conversion by PpAtg26 at the nucleation complex is necessary for elongation and maturation of the membrane structure. This study reveals the role of the PI4P-signaling pathway in selective autophagy, a process comprising multistep molecular events that lead to the de novo membrane formation.     

Beclin 1 self‐association is independent of autophagy induction by amino acid deprivation and rapamycin treatment

Autophagy, a process of self‐digestion of cellular constituents, regulates the balance between protein synthesis and protein degradation. Beclin 1 represents an important component of the autophagic machinery. It interacts with proteins that positively regulate autophagy, such as Vps34, UVRAG, and Ambra1, as well as with anti‐apoptotic proteins such as Bcl‐2 via its BH3‐like domain to negatively regulate autophagy. Thus, Beclin 1 interactions with several proteins may regulate autophagy. To identify novel Beclin 1 interacting proteins, we utilized a GST‐Beclin 1 fusion protein. Using mass spectroscopic analysis, we identified Beclin 1 as a protein that interacts with GST‐Beclin 1. Further examination by cross linking and co‐immunoprecipitation experiments confirmed that Beclin 1 self‐interacts and that the coiled coil and the N‐terminal region of Beclin 1 contribute to its oligomerization. Importantly, overexpression of vps34, UVRAG, or Bcl‐x_L, had no effect on Beclin 1 self‐interaction. Moreover, this self‐interaction was independent of autophagy induction by amino acid deprivation or rapamycin treatment. These results suggest that full‐length Beclin 1 is a stable oligomer under various conditions. Such an oligomer may provide a platform for further protein–protein interactions. J. Cell. Biochem. 110: 1262–1271, 2010. Published 2010 Wiley‐Liss, Inc.     

GFP‐LC3 labels organised smooth endoplasmic reticulum membranes independently of autophagy

Disruption of autophagy leads to accumulation of intracellular multilamellar inclusions morphologically similar to organised smooth endoplasmic reticulum (OSER) membranes. However, the relation of these membranous compartments to autophagy is unknown. The purpose of this study was to test whether OSER plays a role in the autophagic protein degradation pathway. Here, GFP‐LC3 is shown to localise to the OSER membranes induced by calnexin expression both in transiently transfected HEK293 cells and in mouse embryo fibroblasts. In contrast to GFP‐LC3, endogenous LC3 is excluded from these membranes under normal conditions as well as after cell starvation. Furthermore, YFP‐Atg5, a protein essential for autophagy and known to reside on autophagic membranes, is excluded from the calnexin‐positive inclusion structures. In cells devoid of Atg5, a protein essential for autophagy and known to reside on autophagic membranes, colocalisation of calnexin with GFP‐LC3 within the multilamellar bodies is preserved. I show that calnexin, a protein enriched in the OSER, is not subject to autophagic or lysosomal degradation. Finally, GFP‐LC3 targeting to these membranes is independent of its processing and insensitive to drugs modulating autophagic and lysosomal protein degradation. These observations are inconsistent with a role of autophagic/lysosomal degradation in clearance of multilamellar bodies comprising OSER. Furthermore, GFP‐LC3, a fusion protein widely used as a marker for autophagic vesicles and pre‐autophagic compartments, may be trapped in this compartment and this artefact must be taken into account if the construct is used to visualise autophagic membranes. J. Cell. Biochem. 107: 86–95, 2009. © 2009 Wiley‐Liss, Inc.     

α‐Synuclein toxicity in yeast and human cells is caused by cell cycle re‐entry and autophagy degradation of ribonucleotide reductase 1

α‐Synuclein (aSyn) toxicity is associated with cell cycle alterations, activation of DNA damage responses (DDR), and deregulation of autophagy. However, the relationships between these phenomena remain largely unknown. Here, we demonstrate that in a yeast model of aSyn toxicity and aging, aSyn expression induces Ras2‐dependent growth signaling, cell cycle re‐entry, DDR activation, autophagy, and autophagic degradation of ribonucleotide reductase 1 (Rnr1), a protein required for the activity of ribonucleotide reductase and dNTP synthesis. These events lead to cell death and aging, which are abrogated by deleting RAS2, inhibiting DDR or autophagy, or overexpressing RNR1. aSyn expression in human H4 neuroglioma cells also induces cell cycle re‐entry and S‐phase arrest, autophagy, and degradation of RRM1, the human homologue of RNR1, and inhibiting autophagic degradation of RRM1 rescues cells from cell death. Our findings represent a model for aSyn toxicity that has important implications for understanding synucleinopathies and other age‐related neurodegenerative diseases.     

CCPG1 is a noncanonical autophagy cargo receptor essential for reticulophagy and pancreatic ER proteostasis

Reticulophagy is the conserved macroautophagic/autophagic degradation of the endoplasmic reticulum (ER) in response to ER stress or general nutrient deprivation. Sequestration of the ER by phagophores plays an important role in regulating ER size and homeostasis. In their recent work, Smith et al. have discovered that the ER-localized protein CCPG1 is a novel mammalian reticulophagy receptor that interacts with core autophagy machinery components—LC3, GABARAP and RB1CC1—and regulates reticulophagy.     

Autophagy and Cancer Therapy

Autophagy is a dynamic process of protein degradation which is typically observed during nutrient deprivation. Recently, interest in autophagy has been renewed among oncologists, because different types of cancer cells undergo autophagy after various anticancer therapies. This type of non-apoptotic cell death has been documented mainly by observing morphological changes, e.g., numerous autophagic vacuoles in the cytoplasm of dying cells. Thus, autophagic cell death is considered programmed cell death type II, whereas apoptosis is programmed cell death type I. These two types of cell death are predominantly distinctive, but many studies demonstrate cross-talk between them. Whether autophagy in cancer cells causes death or protects cells is controversial. In multiple studies, autophagy has been inhibited pharmacologically or genetically, resulting in contrasting outcomes—survival or death—depending on the specific context. Interestingly, the regulatory pathways of autophagy share several molecules with the oncogenic pathways activated by tyrosine kinase receptors. Tumor suppressors such as Beclin 1, PTEN, and p53 also play an important role in autophagy induction. Taken together, these accumulating data may lead to development of new cancer therapies that manipulate autophagy.