Lysosomal Interaction of Akt with Phafin2: A Critical Step in the Induction of Autophagy

Autophagy is an evolutionarily conserved mechanism for the gross disposal of intracellular proteins in mammalian cells and dysfunction in this pathway has been associated with human disease. Although the serine threonine kinase Akt is suggested to play a role in this process, little is known about the molecular mechanisms by which Akt induces autophagy. Using a yeast two-hybrid screen, Phafin2 (EAPF or PLEKHF2), a lysosomal protein with a unique structure of N-terminal PH (pleckstrin homology) domain and C-terminal FYVE (Fab 1, YOTB, Vac 1, and EEA1) domain was found to interact with Akt. A sucrose gradient fractionation experiment revealed that both Akt and Phafin2 co-existed in the same lysosome enriched fraction after autophagy induction. Confocal microscopic analysis and BiFC analysis demonstrated that both Akt and Phafin2 accumulate in the lysosome after induction of autophagy. BiFC analysis using PtdIns (3)P interaction defective mutant of Phafin2 demonstrated that lysosomal accumulation of the Akt-Phafin2 complex and subsequent induction of autophagy were lysosomal PtdIns (3)P dependent events. Furthermore, in murine macrophages, both Akt and Phafin2 were required for digestion of fluorescent bacteria and/or LPS-induced autophagy. Taken together, these findings establish that lysosomal accumulation of Akt and Phafin2 is a critical step in the induction of autophagy via an interaction with PtdIns (3)P.     

Suppression of autophagy permits successful enzyme replacement therapy in a lysosomal storage disorder—murine Pompe disease

Autophagy, an intracellular system for delivering portions of cytoplasm and damaged organelles to lysosomes for degradation/recycling, plays a role in many physiological processes and is disturbed in many diseases. We recently provided evidence for the role of autophagy in Pompe disease, a lysosomal storage disorder in which acid alpha-glucosidase, the enzyme involved in the breakdown of glycogen, is deficient or absent. Clinically the disease manifests as a cardiac and skeletal muscle myopathy. The current enzyme replacement therapy (ERT) clears lysosomal glycogen effectively from the heart but less so from skeletal muscle. In our Pompe model, the poor muscle response to therapy is associated with the presence of pools of autophagic debris. To clear the fibers of the autophagic debris, we have generated a Pompe model in which an autophagy gene, Atg7, is inactivated in muscle. Suppression of autophagy alone reduced the glycogen level by 50–60%. Following ERT, muscle glycogen was reduced to normal levels, an outcome not observed in Pompe mice with genetically intact autophagy. The suppression of autophagy, which has proven successful in the Pompe model, is a novel therapeutic approach that may be useful in other diseases with disturbed autophagy.Key words: Pompe disease, lysosomal glycogen storage, myopathy, Atg7, enzyme replacement therapy     

The Immune System GTPase GIMAP6 Interacts with the Atg8 Homologue GABARAPL2 and Is Recruited to Autophagosomes

The GIMAPs (GTPases of the immunity-associated proteins) are a family of small GTPases expressed prominently in the immune systems of mammals and other vertebrates. In mammals, studies of mutant or genetically-modified rodents have indicated important roles for the GIMAP GTPases in the development and survival of lymphocytes. No clear picture has yet emerged, however, of the molecular mechanisms by which they perform their function(s). Using biotin tag-affinity purification we identified a major, and highly specific, interaction between the human cytosolic family member GIMAP6 and GABARAPL2, one of the mammalian homologues of the yeast autophagy protein Atg8. Chemical cross-linking studies performed on Jurkat T cells, which express both GIMAP6 and GABARAPL2 endogenously, indicated that the two proteins in these cells readily associate with one another in the cytosol under normal conditions. The GIMAP6-GABARAPL2 interaction was disrupted by deletion of the last 10 amino acids of GIMAP6. The N-terminal region of GIMAP6, however, which includes a putative Atg8-family interacting motif, was not required. Over-expression of GIMAP6 resulted in increased levels of endogenous GABARAPL2 in cells. After culture of cells in starvation medium, GIMAP6 was found to localise in punctate structures with both GABARAPL2 and the autophagosomal marker MAP1LC3B, indicating that GIMAP6 re-locates to autophagosomes on starvation. Consistent with this finding, we have demonstrated that starvation of Jurkat T cells results in the degradation of GIMAP6. Whilst these findings raise the possibility that the GIMAPs play roles in the regulation of autophagy, we have been unable to demonstrate an effect of GIMAP6 over-expression on autophagic flux.     

Autophagy impairment as a key feature for acetaminophen-induced ototoxicity

Macroautophagy/autophagy is a highly conserved self-digestion pathway that plays an important role in cytoprotection under stress conditions. Autophagy is involved in hepatotoxicity induced by acetaminophen (APAP) in experimental animals and in humans. APAP also causes ototoxicity. However, the role of autophagy in APAP-induced auditory hair cell damage is unclear. In the present study, we investigated autophagy mechanisms during APAP-induced cell death in a mouse auditory cell line (HEI-OC1) and mouse cochlear explant culture. We found that the expression of LC3-II protein and autophagic structures was increased in APAP-treated HEI-OC1 cells; however, the degradation of SQSTM1/p62 protein, the yellow puncta of mRFP-GFP-LC3 fluorescence, and the activity of lysosomal enzymes decreased in APAP-treated HEI-OC1 cells. The degradation of p62 protein and the expression of lysosomal enzymes also decreased in APAP-treated mouse cochlear explants. These data indicate that APAP treatment compromises autophagic degradation and causes lysosomal dysfunction. We suggest that lysosomal dysfunction may be directly responsible for APAP-induced autophagy impairment. Treatment with antioxidant N-acetylcysteine (NAC) partially alleviated APAP-induced autophagy impairment and apoptotic cell death, suggesting the involvement of oxidative stress in APAP-induced autophagy impairment. Inhibition of autophagy by knocking down of Atg5 and Atg7 aggravated APAP-induced ER and oxidative stress and increased apoptotic cell death. This study provides a better understanding of the mechanism responsible for APAP ototoxicity, which is important for future exploration of treatment strategies for the prevention of hearing loss caused by ototoxic medications.Subject terms: Macroautophagy, Hair cell     

Self-eating to grow and kill: autophagy in filamentous ascomycetes

Autophagy is a tightly controlled degradation process in which eukaryotic cells digest their own cytoplasm containing protein complexes and organelles in the vacuole or lysosome. Two types of autophagy have been described: macroautophagy and microautophagy. Both types can be further divided into nonselective and selective processes. Molecular analysis of autophagy over the last two decades has mostly used the unicellular ascomycetes Saccharomyces cerevisiae and Pichia pastoris. Genetic analysis in these yeasts has identified 36 autophagy-related (atg) genes; many are conserved in all eukaryotes, including filamentous ascomycetes. However, the autophagic machinery also evolved significant differences in fungi, as a consequence of adaptation to diverse fungal lifestyles. Intensive studies on autophagy in the last few years have shown that autophagy in filamentous fungi is not only involved in nutrient homeostasis but in other cellular processes such as cell differentiation, pathogenicity and secondary metabolite production. This mini-review focuses on the specific roles of autophagy in filamentous fungi.     

Autophosphorylation Within the Atg1 Activation Loop Is Required for Both Kinase Activity and the Induction of Autophagy in Saccharomyces cerevisiae

Autophagy is an evolutionarily conserved degradative pathway that has been implicated in a number of physiological events important for human health. This process was originally identified as a response to nutrient deprivation and is thought to serve in a recycling capacity during periods of nutritional stress. Autophagy activity appears to be highly regulated and multiple signaling pathways are known to target a complex of proteins that contains the Atg1 protein kinase. The data here extend these observations and identify a particular phosphorylation event on Atg1 as a potential control point within the autophagy pathway in Saccharomyces cerevisiae. This phosphorylation occurs at a threonine residue, T226, within the Atg1 activation loop that is conserved in all Atg1 orthologs. Replacing this threonine with a nonphosphorylatable residue resulted in a loss of Atg1 protein kinase activity and a failure to induce autophagy. This phosphorylation required the presence of a functional Atg1 kinase domain and two known regulators of Atg1 activity, Atg13 and Atg17. Interestingly, the levels of this modification were found to increase dramatically upon exposure to conditions that induce autophagy. In addition, T226 phosphorylation was associated with an autophosphorylated form of Atg1 that was found specifically in cells undergoing the autophagy process. In all, these data suggest that autophosphorylation within the Atg1 activation loop may represent a point of regulatory control for this degradative process.MACROAUTOPHAGY (hereafter referred to as autophagy) is a highly conserved process of self-degradation that is essential for cell survival during periods of nutrient limitation (Tsukada and Ohsumi 1993). During autophagy, a double membrane grows out from a specific nucleation site, known as the pre-autophagosomal structure, or PAS, in Saccharomyces cerevisiae and the phagophore assembly site in mammals (Suzuki and Ohsumi 2007). This membrane encapsulates bulk protein and other constituents of the cytoplasm and ultimately targets this material to the vacuole/lysosome for degradation (Xie and Klionsky 2007). Recent studies have linked this pathway to a number of processes important for human health, including tumor suppression, innate immunity, and neurological disorders, like Huntington''s disease (Rubinsztein et al. 2007; Levine and Kroemer 2008). Determining how this pathway is regulated is therefore important for our understanding of these processes and our attempts to manipulate autophagy in clinically beneficial ways.Most of the molecular components of the autophagy pathway were initially characterized in the budding yeast, S. cerevisiae, but orthologs of many of these Atg proteins have since been found in other eukaryotes (Tsukada and Ohsumi 1993; Meijer et al. 2007). A complex of proteins that contains the Atg1 protein kinase is of special interest and appears to be a key point of regulatory control within this pathway (Kamada et al. 2000; Budovskaya et al. 2005; He and Klionsky 2009; Stephan et al. 2009). In S. cerevisiae, genetic and biochemical data indicate that this complex is targeted by at least three different signaling pathways. Two of these pathways, involving the Tor and cAMP-dependent protein kinases, inhibit this process, whereas the AMP-activated protein kinase is needed for the full induction of autophagy (Noda and Ohsumi 1998; Wang et al. 2001; Budovskaya et al. 2004; Stephan and Herman 2006; Kamada et al. 2010). The manner in which these signaling pathways regulate Atg1 activity and the precise role of this kinase in the autophagy process are presently matters of intense scrutiny.Although Atg1 kinase activity is required for the induction of autophagy, relatively little is known about how this enzyme is regulated in vivo. Two proteins associated with Atg1, Atg13 and Atg17, have been shown to be required for full Atg1 kinase activity both in vitro and in vivo (Kamada et al. 2000; Stephan et al. 2009). The roles of these proteins appear to be conserved through evolution as functional homologs of both have been identified in fruit flies and/or mammals (Hara et al. 2008; Chan et al. 2009; Chang and Neufeld 2009; Ganley et al. 2009; Hosokawa et al. 2009; Jung et al. 2009; Mercer et al. 2009). However, it is not yet clear precisely how these proteins stimulate Atg1 activity. In this study, we show that Atg1 is autophosphorylated within the activation loop and that this phosphorylation is required for both Atg1 kinase activity and the induction of autophagy. The activation loop is a structurally conserved element within the kinase domain and phosphorylation within this loop is often a necessary prerequisite for efficient substrate binding and/or phosphotransfer in the catalytic site (Johnson et al. 1996; Nolen et al. 2004). This loop generally corresponds to the sequence between two signature elements within the core kinase domain, the DFG and APE motifs (Hanks and Hunter 1995). Phosphorylation within this loop tends to result in a more ordered structure for this region and the proper positioning of key elements within the catalytic core of the kinase domain (Knighton et al. 1991; Johnson and O''reilly 1996; Huse and Kuriyan 2002). We found that Atg1 activation loop phosphorylation was correlated with the onset of autophagy and that replacing the site of phosphorylation with a phosphomimetic residue led to constitutive Atg1 autophosphorylation in vivo. In all, the data here suggest that Atg1 phosphorylation within its activation loop may be an important point of regulation within the autophagy pathway and models that discuss these data are presented.     

Endocytosis and Autophagy: Exploitation or Cooperation?

Autophagy is a lysosome-mediated degradative system that is a highly conserved pathway present in all eukaryotes. In all cells, double-membrane autophagosomes form and engulf cytoplasmic components, delivering them to the lysosome for degradation. Autophagy is essential for cell health and can be activated to function as a recycling pathway in the absence of nutrients or as a quality-control pathway to eliminate damaged organelles or even to eliminate invading pathogens. Autophagy was first identified as a pathway in mammalian cells using morphological techniques, but the Atg (autophagy-related) genes required for autophagy were identified in yeast genetic screens. Despite tremendous advances in elucidating the function of individual Atg proteins, our knowledge of how autophagosomes form and subsequently interact with the endosomal pathway has lagged behind. Recent progress toward understanding where and how both the endocytotic and autophagic pathways overlap is reviewed here.Autophagy is a lysosome-mediated pathway for the degradation of cytosolic proteins and organelles, which is essential for cell homeostasis, development, and for the prevention of several human diseases and infection (Choi et al. 2013). Importantly, autophagy cannot occur without an active lysosome. However, it is becoming increasingly recognized that the endosomal pathway plays a greater role than just providing the degradative enzymes found in the lysosome. Recent data suggest that in mammalian cells multiple contributions from several stages of the endocytic pathway are essential for efficient autophagy. Here we outline the autophagic pathway and then address the recent data on how different endosomal compartments contribute to autophagy, and the molecular machinery required for the interaction of the endosome and lysosome during the formation, and consumption of the autophagosome. Given the model emerging that the amino-acid-sensitive autophagic pathway originates from the endoplasmic reticulum (ER), several questions arise, including how do recognition and productive interaction occur between an ER-derived membrane and endosomes? How are these interactions mediated, and which are essential for efficient autophagy?     

ULK1��ATG13��FIP200 Complex Mediates mTOR Signaling and Is Essential for Autophagy

Autophagy is a degradative process that recycles long-lived and faulty cellular components. It is linked to many diseases and is required for normal development. ULK1, a mammalian serine/threonine protein kinase, plays a key role in the initial stages of autophagy, though the exact molecular mechanism is unknown. Here we report identification of a novel protein complex containing ULK1 and two additional protein factors, FIP200 and ATG13, all of which are essential for starvation-induced autophagy. Both FIP200 and ATG13 are critical for correct localization of ULK1 to the pre-autophagosome and stability of ULK1 protein. Additionally, we demonstrate by using both cellular experiments and a de novo in vitro reconstituted reaction that FIP200 and ATG13 can enhance ULK1 kinase activity individually but both are required for maximal stimulation. Further, we show that ATG13 and ULK1 are phosphorylated by the mTOR pathway in a nutrient starvation-regulated manner, indicating that the ULK1·ATG13·FIP200 complex acts as a node for integrating incoming autophagy signals into autophagosome biogenesis.Macroautophagy (herein referred to as autophagy) is a catabolic process whereby long-lived proteins and damaged organelles are shuttled to lysosomes for degradation. This process is conserved in all eukaryotes. Under normal growth conditions a housekeeping level of autophagy exists. Under stress, such as nutrient starvation, autophagy is strongly induced resulting in the engulfment of cytosolic components and organelles in specialized double-membrane structures termed autophagosomes. Following fusion of the outer autophagosomal membrane with lysosomes, the inner membrane and its cytoplasmic cargo are degraded and recycled (1–3). Recent work has implicated autophagy in many disease pathologies, including cancer, neurodegeneration, as well as in eliminating intracellular pathogens (4–8).The morphology of autophagy was first described in mammalian cells over 50 years ago (9). However, it is only recently through yeast genetic screens, that multiple autophagy-related (ATG) genes have been identified (10–12). The yeast ATG proteins have been classified into four major groups: the Atg1 protein kinase complex, the Vps34 phosphatidylinositol 3-phosphate kinase complex, the Atg8/Atg12 conjugation systems, and the Atg9 recycling complex (13). Even though many ATG genes are now known, most of which have functional homologs in mammalian cells (14, 15), the molecular mechanism by which they sense the initial triggers and subsequently dictate autophagy-specific intracellular membrane events is far from understood.In yeast, one of the earliest autophagy-specific events is believed to involve the Atg1 protein kinase complex. Atg1 is a serine/threonine protein kinase and a key autophagy-regulator (16). Atg1 is complexed to at least two other proteins during autophagy, Atg13 and Atg17, both of which are required for normal Atg1 function and autophagosome generation (17–19). Classical signaling pathways such as the cAMP-dependent kinase (PKA) pathway or the Tor kinase pathway appear to converge upon this complex, placing Atg1 at an early stage during autophagosome biogenesis (20–22). Atg1 phosphorylation by PKA blocks its association with the forming autophagosome (21), while the Tor pathway hyperphosphorylates Atg13 causing a reduced affinity of Atg13 for Atg1, resulting in repression of autophagy (17, 19). In contrast, nutrient starvation or inhibition of Tor leads to dephosphorylation of Atg13 thus increased Atg1 complex formation and kinase activity, resulting in stimulation of autophagy (19). Surprisingly, the physiological substrates of Atg1 kinase have not been identified; thus how Atg1 transduces upstream autophagic signaling is undefined. Recently, mammalian homologs of Atg1 have been identified as ULK1 and ULK2 (Unc-51-like kinase)² (23–25). ULK1 and ULK2 are ubiquitously expressed and localize to the isolation membrane, or forming autophagosome, upon nutrient starvation (25); RNAi-mediated depletion of ULK1 in HEK293 cells compromises autophagy (23, 24). The exact role of ULK1 versus ULK2 in autophagy is unclear, and it is possible some redundancy exists between the two isoforms (26).Given the conservation of autophagy from yeast to man, it is interesting to note that no mammalian counterpart to yeast Atg13 or Atg17 had been identified until very recently. The protein FIP200 (focal adhesion kinase family-interacting protein of 200 kDa) was identified as an autophagy-essential binding partner of both ULK1 and ULK2 (25), and it has been speculated that FIP200 might be the equivalent of yeast Atg17, despite low sequence similarity (25, 27).In this study, we delve deeper into the molecular regulation of ULK1 to gain a better insight into how mammalian signaling pathways affect autophagy initiation. We describe here the identification of a triple complex consisting of ULK1, FIP200, and the mammalian equivalent of Atg13. This complex is required not only for localization of ULK1 to the isolation membrane but also for maximal kinase activity. In addition, both ATG13 and ULK1 are kinase substrates in the mTOR pathway and thus might function to sense nutrient starvation. Therefore, this study defines the role of mammalian ULK1-ATG13-FIP200 complex in mediating the initial autophagic triggers and to transduce the signal to the core autophagic machinery.     

Alfy-dependent elimination of aggregated proteins by macroautophagy: Can there be too much of a good thing?

Degradation of different cargo by macroautophagy is emerging as a highly selective process which relies upon specific autophagy receptors and adapter molecules that link the cargo with the autophagic molecular machinery. We have recently reported that the large phsophatidylinositol-3-phosphate (PtdIns(3)P)-binding protein Alfy (Autophagy-linked FYVE protein) is required for selective degradation of aggregated proteins. Although depletion of Alfy inhibits Atg5-dependent aggregate degradation, overexpression of Alfy results in Atg5-dependent aggregate clearance and neuroprotection. Alfy-mediated degradation requires the ability of Alfy to directly interact with Atg5. This ability to interact with the core autophagic machinery may cause Alfy to diminish the responsiveness to nonselective autophagic degradation as measured by long-lived protein degradation. Thus, increasing Alfy-mediated protein degradation may be beneficial in some organs, but may be detrimental in others.Key words: autophagy, protein aggregates, neurodegeneration, Alfy, aggregation, degradation     

Cytosolic clearance of replication-deficient mutants reveals Francisella tularensis interactions with the autophagic pathway

Cytosolic bacterial pathogens must evade intracellular innate immune recognition and clearance systems such as autophagy to ensure their survival and proliferation. The intracellular cycle of the bacterium Francisella tularensis is characterized by rapid phagosomal escape followed by extensive proliferation in the macrophage cytoplasm. Cytosolic replication, but not phagosomal escape, requires the locus FTT0369c, which encodes the dipA gene (deficient in intracellular replication A). Here, we show that a replication-deficient, ∆dipA mutant of the prototypical SchuS4 strain is eventually captured from the cytosol of murine and human macrophages into double-membrane vacuoles displaying the late endosomal marker, LAMP1, and the autophagy-associated protein, LC3, coinciding with a reduction in viable intracellular bacteria. Capture of SchuS4ΔdipA was not dipA-specific as other replication-deficient bacteria, such as chloramphenicol-treated SchuS4 and a purine auxotroph mutant SchuS4ΔpurMCD, were similarly targeted to autophagic vacuoles. Vacuoles containing replication-deficient bacteria were labeled with ubiquitin and the autophagy receptors SQSTM1/p62 and NBR1, and their formation was decreased in macrophages from either ATG5-, LC3B- or SQSTM1-deficient mice, indicating recognition by the ubiquitin-SQSTM1-LC3 pathway. While a fraction of both the wild-type and the replication-impaired strains were ubiquitinated and recruited SQSTM1, only the replication-defective strains progressed to autophagic capture, suggesting that wild-type Francisella interferes with the autophagic cascade. Survival of replication-deficient strains was not restored in autophagy-deficient macrophages, as these bacteria died in the cytosol prior to autophagic capture. Collectively, our results demonstrate that replication-impaired strains of Francisella are cleared by autophagy, while replication-competent bacteria seem to interfere with autophagic recognition, therefore ensuring survival and proliferation.     

Autophagy in the pathogenesis of myelodysplastic syndrome and acute myeloid leukemia

Autophagy is a conserved cellular pathway responsible for the sequestration of spent organelles and protein aggregates from the cytoplasm and their delivery into lysosomes for degradation. Autophagy plays an important role in adaptation to starvation, in cell survival, immunity, development and cancer. Recent evidence in mice suggests that autophagic defects in hematopoietic stem cells (HSCs) may be implicated in leukemia. Indeed, mice lacking Atg7 in HSCs develop an atypical myeloproliferation resembling human myelodysplastic syndrome (MDS) progressing to acute myeloid leukemia (AML). Our studies suggest that accumulation of damaged mitochondria and reactive oxygen species result in cell death of the majority of progenitor cells and, possibly, concomitant transformation of some surviving ones. Interestingly, bone marrow cells from MDS patients are characterized by mitochondrial abnormalities and increased cell death. A role for autophagy in the transformation to cancer has been proposed in other cancer types. This review focuses on autophagy in human MDS development and progression to AML within the context of the role of mitochondria, apoptosis and reactive oxygen species (ROS) in its pathogenesis.Key words: autophagy, mitophagy, Atg7, hematopoiesis, HSCs, myelodysplastic syndrome, acute myeloid leukemia     

Regulation and Function of Autophagy during Cell Survival and Cell Death

Autophagy is an important catabolic process that delivers cytoplasmic material to the lysosome for degradation. Autophagy promotes cell survival by elimination of damaged organelles and proteins aggregates, as well as by facilitating bioenergetic homeostasis. Although autophagy has been considered a cell survival mechanism, recent studies have shown that autophagy can promote cell death. The core mechanisms that control autophagy are conserved between yeast and humans, but animals also possess genes that regulate autophagy that are not present in yeast. These regulatory differences may be explained by the need to control autophagy in a cell context-specific manner in multicellular animals, such as during cell survival and cell death. Autophagy was thought to be a bulk cytoplasmic degradation mechanism, but recent studies have shown that specific cargo is recruited for degradation. This suggests the possibility that either cell survival or death may be regulated by selective autophagic clearance of cytoplasmic material. Here we summarize the mechanisms that regulate autophagy and how they may contribute to cell survival and death.Autophagy (self-eating) is an evolutionarily conserved catabolic process that is used to deliver cytoplasmic materials, including organelles and proteins, to the lysosome for degradation. Three types of autophagy have been described, including macroautophagy, microautophagy, and chaperone-mediated autophagy (Mizushima and Komatsu 2011). Although macroautophagy involves the fusion of the double membrane autophagosome and lysosomes, microautophagy is poorly understood and thought to involve direct uptake of material by the lysosome via a process that appears similar to pinocytosis. By contrast, chaperone-mediated autophagy is a biochemical mechanism to import proteins into the lysosome; it depends on a signature sequence and interaction with protein chaperones. Here we will focus on macroautophagy (hereafter called autophagy) because of our knowledge of this process in cell survival and cell death.Autophagy was likely first observed when electron microscopy was used to observe “dense bodies” containing mitochondria in mouse kidneys (Clark 1957). Five years later, it was reported that rat hepatocytes exposed to glucagon possessed membrane-bound vesicles that were rich in mitochondria and endoplasmic reticulum (Ashford and Porter 1962). Almost simultaneously, it was shown that these membrane-bound vesicles contained lysosomal hydrolases (Novikoff and Essner 1962). In 1965 de Duve coined the term “autophagy” (Klionsky 2008).The delivery of cytoplasmic material to the lysosome by autophagy involves membrane formation and fusion events (Fig. 1). First an isolation membrane, also known as a phagophore, must be initiated from a membrane source known as the phagophore assembly site (PAS). de Duve suggested that the smooth endoplasmic reticulum could be the source of autophagosome membrane (de Duve and Wattiaux 1966), and subsequent studies have supported this possibility (Dunn 1990; Axe et al. 2008). Although controversial, mitochondria and plasma membrane could also supply membranes for the formation of the autophagosomes under different conditions (Hailey et al. 2010; Ravikumar et al. 2010). The elongating isolation membrane surrounds cargo that is ultimately enclosed in the double membrane autophagosome. Once the autophagosome is formed, it fuses with lysosomes (known as the vacuole in yeasts and plants) to form autolysosomes in which the cargo is degraded by lysosomal hydrolases. At this stage lysosomes must reform so that subsequent autophagy may occur (Yu et al. 2010).Open in a separate windowFigure 1.Macroautophagy (autophagy) delivers cytoplasmic cargo to lysosomes for degradation, and involves membrane formation and fusion. The isolation membrane is initiated from a membrane source known as the from the phagophore assembly site (PAS). The isolation membrane surrounds cargo, including organelles and proteins, to form a double membrane autophagosome. Autophagosomes fuse with lysosomes to form autolysosomes in which the cargo is degraded by lysosomal hydrolases.     

Autophagy plays a WASHing game

EMBO J (2013) 32: 2685–2696 doi:10.1038/emboj.2013.189; published online August232013Beclin 1 is a crucial regulator of autophagy. It forms a complex with ATG14L, VPS34 or the class III phosphatidylinositol 3-kinase AMBRA1 to control autophagosome formation. A study in this issue of The EMBO Journal (Xia et al, 2013) reports that WASH, a protein known to regulate endosomal sorting, hampers autophagy by inhibiting the AMBRA1-dependent polyubiquitylation of Beclin 1. This modification is required to promote VPS34 activity and to initiate autophagy during starvation.Macroautophagy (hereafter called autophagy) is a lysosomal degradation pathway for cytoplasmic components. Autophagy is initiated by the formation of a double-membrane bound vacuole, the autophagosome that sequesters the autophagic cargo and eventually fuses with the lysosomal compartment, leading to cargo degradation. Autophagy plays a major role in cytoplasm homeostasis by removing protein aggregates and controlling organelle quality, and it is stimulated to promote cell survival during stressful situations, such as nutrient starvation and microbial infection. Autophagosome formation is dependent on evolutionarily conserved Atg (Autophagy-related) proteins initially identified in yeast (Mizushima et al, 2011). They function in complexes or functional modules on a membrane known as the phagophore that matures into the autophagosome via several stages (initiation, elongation and sealing). Phosphatidylinositol 3-phosphate kinase complex I (PI3K complex I) plays a key role in the initiation step. In this complex, Beclin 1 (the mammalian homologue of yeast Atg6) interacts with ATG14L, AMBRA1, and class III PI3K or VPS34 (Cecconi and Levine, 2008; Figure 1). The activity of this complex, which produces the lipid phosphatidylinositol 3-phosphate (PI3P) to recruit Atg18 homologues (WIPIs), has to be tightly regulated to keep autophagy under control.Open in a separate windowFigure 1Role of WASH in autophagosome formation. WASH interacts with Beclin 1 via a sequence (121–221) that is not involved in endosomal sorting. In the absence of WASH, when autophagy is stimulated by nutrient deprivation, Beclin 1 interacts with VPS34 (and its adaptor VPS15), ATG14L and AMBRA1. In this complex, Beclin 1 is polyubiquitylated by AMBRA1, which acts as an E3 ligase. The activation of VPS34 produces PI3P at the phagophore to recruit WIPI proteins, and then triggers the machinery to elongate and seal the membrane, thus forming an autophagosome. The VAC domain of WASH involved in endosomal sorting is not required for autophagy regulation.In this issue of The EMBO Journal, Xia et al (2013) demonstrate that WASH (Wiskott-Aldrich syndrome protein (WASP) and SCAR homologue) regulates autophagosome formation in response to nutrient starvation by influencing the ubiquitylation of Beclin 1. WASH forms a complex with four other proteins and plays an essential role in endosomal sorting by promoting actin polymerization to facilitate segregation of endosomal proteins (Seaman et al, 2013). Using WASH−/− mice, Xia et al (2013) observe that WASH deficiency causes embryonic lethality (E7.5−E9.5) with massive apoptosis-independent cell death and the accumulation of autophagic structures. However, whether autophagy is instrumental in the cell death observed in WASH−/− embryos remains to be investigated. From a series of classical readouts, the authors conclude that WASH downregulates starvation-induced autophagy. Interestingly, WASH is detected on the autophagosomal membrane before and after closure of the autophagosome, but not on the autolysosomes (organelles formed when the autophagosome fuses with the lysosome). The authors first show that WASH has distinct roles in autophagy and in endosomal sorting, because deletion of the VCA domain of WASH that is required for its endosomal function and the knockdown of FAM21 (a protein that directs WASH to the endosomal membrane) do not influence autophagy. They then show that WASH interacts with the coil-coiled domain of Beclin 1. WASH depletion induces more VPS34 to interact with Beclin 1, leading to augmented formation of PtdIns3P and increased recruitment of WIPI-1 to the autophagosomal membrane. However, WASH does not influence the stability of Beclin 1, although it does regulate its K63-linked polyubiquitylation at position K437 during starvation (K63-linked polyubiquitylation suggests a regulatory role, whereas K48-linked polyubiquitylation is frequently associated with protein degradation). Overexpression of WASH reduces the ubiquitylation of Beclin 1, and the K437R Beclin 1 mutant that cannot be ubiquitylated has a low level of interaction with VPS34, which prevents the stimulation of autophagy by starvation (Figure 1). Recently, Beclin 1 has been shown to be ubiquitylated at position K117 during TLR4-induced autophagy (Shi and Kehrl, 2010). Interestingly, Xia et al (2013) show that the K117R Beclin 1 mutant is still ubiquitylated in response to nutrient starvation. Finally, the authors identify the substrate-specific E3 ubiquitin ligase for Beclin 1 in this context. They exclude TRAF6 and NEDD4, two E3 ligases reported to ubiquitylate Beclin 1 (Kuang et al, 2013). AMBRA1, which regulates autophagy in the PI3K complex I, is also known as DCAF3 and interacts with the Cullin 4–DDB1 E3 ligase complex (Jin et al, 2006). Following in vitro E3 ligase assays, Xia et al (2013) conclude that AMBRA1 is the substrate receptor for Beclin 1 ubiquitylation at position K437, adding Cullin4/DDB1 and AMBRA1 to the list of E3 ligases involved in autophagy (Kuang et al, 2013). The finding that WASH and AMBRA1 compete to regulate starvation-induced autophagy raises several questions: how do WASH and AMBRA1 influence one another''s binding to Beclin 1? WASH is evolutionarily conserved, although it is not present in yeast (Linardopoulou et al, 2007)—does it also reduce starvation-induced autophagy in non-mammalian cells? WASH has recently been reported to be required for the lysosomal digestion of autophagy cargo in Dictyostelium during starvation (King et al, 2013). Does this mean that the function of WASH in autophagy has evolved from controlling cargo degradation to forming autophagosomes? Xia et al (2013) do not report any association between WASH and the lysosomal compartment during autophagy; the role of WASH in autophagosome maturation calls for further investigation. Finally, a recent report demonstrates that AMBRA1 interacts with the E3 ligase TRAF6 to ubiquitylate ULK1 (the mammalian orthologue of the yeast Atg1) and to ensure its subsequent stabilization and function (Nazio et al, 2013). ULK1 is part of a complex that acts with PI3K complex 1 to regulate the initiation of autophagy (Mizushima et al, 2011). How are these two AMBRA1-dependent ubiquitylation processes coordinated to control autophagy? In conclusion, both the study reported here (Xia et al, 2013) and the recent study of Nazio et al (2013) clearly demonstrate that AMBRA1 plays a central role in regulating the initiation of autophagy.     

Death by over-eating: The Gaucher disease associated gene GBA1, identified in a screen for mediators of autophagic cell death,is necessary for developmental cell death in Drosophila midgut

Autophagy is critical for homeostasis and cell survival during stress, but can also lead to cell death, a little understood process that has been shown to contribute to developmental cell death in lower model organisms, and to human cancer cell death. We recently reported¹ Dasari SK, Bialik S, Levin-Zaidman S, Levin-Salomon V, Merrill AH, Jr., Futerman AH, Kimchi A. Signalome-wide rnai screen identifies gba1 as a positive mediator of autophagic cell death. Cell Death Differ. 2017;24(7):1288-1302. https://doi.org/10.1038/cdd.2017.80. PMID:28574511[Crossref], [PubMed], [Web of Science ®] [Google Scholar] on our thorough molecular and morphologic characterization of an autophagic cell death system involving resveratrol treatment of lung carcinoma cells. To gain mechanistic insight into this death program, we performed a signalome-wide RNAi screen for genes whose functions are necessary for resveratrol-induced death. The screen identified GBA1, the gene encoding the lysosomal enzyme glucocerebrosidase, as an important mediator of autophagic cell death. Here we further show the physiological relevance of GBA1 to developmental cell death in midgut regression during Drosophila metamorphosis. We observed a delay in midgut cell death in two independent Gba1a RNAi lines, indicating the critical importance of Gba1a for midgut development. Interestingly, loss-of-function GBA1 mutations lead to Gaucher Disease and are a significant risk factor for Parkinson Disease, which have been associated with defective autophagy. Thus GBA1 is a conserved element critical for maintaining proper levels of autophagy, with high levels leading to autophagic cell death.     

The molecular mechanism of Atg13 function in autophagy induction: What is hidden behind the data?

Atg13 is an essential subunit of the Atg1 autophagy initiation complex in yeast and its mammalian counterpart, ATG13, is indispensable for autophagy induction by the ULK1 complex. The N terminus of the protein folds into a HORMA domain, an architecture that has been revealed by crystallography.^1-4 Jao CC, Ragusa MJ, Stanley RE, Hurley JH. A HORMA domain in Atg13 mediates PI 3-kinase recruitment in autophagy. P Natl Acad Sci USA 2013; 110:5486-91; PMID:23509291; http://dx.doi.org/10.1073/pnas.1220306110 Suzuki SW, Yamamoto H, Oikawa Y, Kondo-Kakuta C, Kimura Y, Hirano H, Ohsumi Y. Atg13 HORMA domain recruits Atg9 vesicles during autophagosome formation. P Natl Acad Sci USA 2015; 112:3350-5; PMID:25737544; http://dx.doi.org/10.1073/pnas.1421092112 Suzuki H, Kaizuka T, Mizushima NNoda NN. Structure of the Atg101-Atg13 complex reveals essential roles of Atg101 in autophagy initiation. Nat Struct Mol Biol 2015; 22:572-81; PMID:26030876; http://dx.doi.org/10.1038/nsmb.3036 Qi SQ, Kim DJ, Stjepanovic G, Hurley JH. Structure of the human Atg13-Atg101 HORMA heterodimer: An interaction hub within the Ulk1 complex. Structure 2015; 23:1848-57; PMID:26299944; http://dx.doi.org/10.1016/j.str.2015.07.011  In human cells, the ATG13 HORMA domain interacts directly with ATG14, a subunit of the class III phosphatidylinositol 3-kinase complex.⁵ Park JM, Jung CH, Seo M, Otto NM, Grunwald D, Kim KH, Moriarity B, Kim YM, Starker C, Nho RS, et al. The Ulk1 complex mediates mTORC1 signaling to the autophagy initiation machinery via binding and phosphorylating Atg14. Autophagy 2016; 12:547-64; PMID:27046250; http://dx.doi.org/10.1080/15548627.2016.1140293[Taylor & Francis Online], [Web of Science ®] [Google Scholar] In budding yeast, the HORMA domain of Atg13 recruits Atg14, but a direct interaction remains to be proven.¹ Jao CC, Ragusa MJ, Stanley RE, Hurley JH. A HORMA domain in Atg13 mediates PI 3-kinase recruitment in autophagy. P Natl Acad Sci USA 2013; 110:5486-91; PMID:23509291; http://dx.doi.org/10.1073/pnas.1220306110[Crossref], [PubMed], [Web of Science ®] [Google Scholar] The amino acid sequence that follows the HORMA domain does not adopt any 3-dimensional structure on its own; therefore, it is termed an intrinsically disordered region (IDR). Here we discuss the results of 2 recent studies in light of previous reports on Atg13 from yeast. Together, they yield an insight into the molecular mechanism for the function of this intriguing protein, and reveal why Atg13, as well as the mammalian homolog ATG13, cannot have a structurally rigid architecture.     

Ubiquitin Regulates GGA3-mediated Degradation of BACE1

BACE1 (β-site amyloid precursor protein-cleaving enzyme 1) is a membrane-tethered member of the aspartyl proteases, essential for the production of β-amyloid, a toxic peptide that accumulates in the brain of subjects affected by Alzheimer disease. The BACE1 C-terminal fragment contains a DXXLL motif that has been shown to bind the VHS (VPS27, Hrs, and STAM) domain of GGA1–3 (Golgi-localized γ-ear-containing ARF-binding proteins). GGAs are trafficking molecules involved in the transport of proteins containing the DXXLL signal from the Golgi complex to endosomes. Moreover, GGAs bind ubiquitin and traffic synthetic and endosomal ubiquitinated cargoes to lysosomes. We have previously shown that depletion of GGA3 results in increased BACE1 levels and activity because of impaired lysosomal degradation. Here, we report that the accumulation of BACE1 is rescued by the ectopic expression of GGA3 in H4 neuroglioma cells depleted of GGA3. Accordingly, the overexpression of GGA3 reduces the levels of BACE1 and β-amyloid. We then established that mutations in the GGA3 VPS27, Hrs, and STAM domain (N91A) or in BACE1 di-leucine motif (L499A/L500A), able to abrogate their binding, did not affect the ability of ectopically expressed GGA3 to rescue BACE1 accumulation in cells depleted of GGA3. Instead, we found that BACE1 is ubiquitinated at lysine 501 and is mainly monoubiquitinated and Lys-63-linked polyubiquitinated. Finally, a GGA3 mutant with reduced ability to bind ubiquitin (GGA3L276A) was unable to regulate BACE1 levels both in rescue and overexpression experiments. These findings indicate that levels of GGA3 tightly and inversely regulate BACE1 levels via interaction with ubiquitin sorting machinery.     

Mechanisms of mitochondria and autophagy crosstalk

Autophagy is a cellular survival pathway that recycles intracellular components to compensate for nutrient depletion and ensures the appropriate degradation of organelles. Mitochondrial number and health are regulated by mitophagy, a process by which excessive or damaged mitochondria are subjected to autophagic degradation. Autophagy is thus a key determinant for mitochondrial health and proper cell function. Mitophagic malfunction has been recently proposed to contribute to progressive neuronal loss in Parkinson disease. In addition to autophagy''s significance in mitochondrial integrity, several lines of evidence suggest that mitochondria can also substantially influence the autophagic process. The mitochondria''s ability to influence and be influenced by autophagy places both elements (mitochondria and autophagy) in a unique position where defects in one or the other system could increase the risk to various metabolic and autophagic related diseases.Key words: autophagy, mitochondria, fission, fusion, apoptosis     

Up for grabs; trashing peroxisomes

EMBO J 31 13, 2852–2868 (2012); published online May292012Together with the proteasome, autophagy is one of the major catabolic pathways of the cell. In response to cellular needs or environmental cues, this transport route targets specific structures for degradation into the mammalian lysosomes or the yeast and plant vacuoles. The mechanisms allowing exclusive autophagic elimination of unwanted structures are currently the object of intensive investigations. The emerging picture is that there is a series of autophagy receptors that determines the specificity of the different selective types of autophagy. How cargo binding and recognition is regulated by these receptors, however, is largely unknown. In their study, Motley et al (2012) have shed light into the molecular principles underlying the turnover of excess peroxisomes in the budding yeast Saccharomyces cerevisiae.Peroxisomes perform a series of crucial functions and their number is regulated in response to the metabolic demands of the cell. After proliferation and when no more required, a selective type of autophagy called pexophagy degrades superfluous peroxisomes (Manjithaya et al, 2010). This turnover allows the cell to save the energy required for the maintenance of excess organelles and to generate metabolites that can be used to carry out other functions. Like all selective types of autophagy, pexophagy relies on the conserved core of the autophagy-related (Atg) machinery, but also requires additional proteins that confer specificity of the pathway such as cargo selection and membrane dynamics (Manjithaya et al, 2010). It is still unclear, however, which peroxisomal protein allows the recognition of peroxisomes by the autophagosomes. Although Pex3 and Pex14 have previously been indicated as possible suspects (Bellu et al, 2001, 2002; Farre et al, 2008), their specific contribution to pexophagy was difficult to establish. Deletion of either PEX3 or PEX14, as well as most other PEX genes, leads to defects in peroxisome biogenesis, which makes the dissection of their contribution to peroxisome degradation very difficult to assess. Motley et al (2012) have elegantly exploited S. cerevisiae genetics to isolate pex3 alleles specifically impaired in pexophagy and could thus demonstrate that Pex3 (and not Pex14) mediates the selective engulfment of peroxisomes by autophagosomes. In support to this result, the authors have also identified a new protein, Atg36, which binds Pex3 (Figure 1). Importantly, Atg36 interacts with Atg11, an autophagy adaptor involved in numerous selective types of autophagy in yeast, thereby bringing peroxisomes to the site where autophagosomes will be generated and coordinating the activation of the Atg machinery at this location (Kim et al, 2001; Reggiori et al, 2005; Monastyrska et al, 2008). Atg36, however, is only present in S. cerevisiae and related yeasts. Methylotrophic yeasts, in contrast, appear to have a different protein with the same properties, Atg30 (Farre et al, 2008). It is unclear, however, whether Atg30 is the functional counterpart of Atg36 because these two proteins do not display similarities in their amino-acid sequence.Open in a separate windowFigure 1Schematic representation for a putative Pex3 checkpoint. The peroxisomal integral membrane protein Pex3 acts as a master regulator to determine peroxisome fate. Organelle abundance is regulated by formation of new organelles, and their subsequent segregation (inheritance) and degradation. A new paradigm has been uncovered, whereby Pex3 controls peroxisome abundance through the regulated binding to specific co-factors. At the endoplasmic reticulum (ER), together with Pex19, it initiates biogenesis of new peroxisomes. At the peroxisomal membrane, it ensures that both mother and daughter cells obtain the correct number of peroxisomes, whereas when the organelles become dispensable, Pex3 can initiate their selective degradation. To keep peroxisomes in the mother cell during cell division, Pex3 associates with Inp1 and tether peroxisomes to cortical actin patches. Under pexophagy-inducing conditions, Pex3 binds the newly identified pexophagy factor Atg36 and delivers peroxisomes to the site of autophagosome formation for subsequent degradation into the vacuole.While it is unmistakable that Atg36 (and Atg30) is essential for pexophagy, it remains unclear whether this protein is an autophagy receptor. This class of molecules has four characteristics (Kraft et al, 2010). First, each autophagy receptor binds a specific cargo. Second, they often interact with adaptor proteins, which function as scaffolds that bring the cargo–receptor complex in contact with the core Atg machinery to allow the specific sequestration of the cargo. Third, they possess at least one LC3-interacting region (LIR) motif that enables them to interact with the LC3/Atg8 pool present in the interior autophagomes and assures the hermetic enwrapping of the cargo into these vesicles. Fourth, autophagy receptors are degraded in the lysosome/vacuole together with the cargo that they bind to. While Atg36 (and Atg30) binds both the cargo and the adaptor protein Atg11, this protein does not appear to be turned over in the vacuole during pexophagy and a LIR motif has not been pinpointed yet. Consequently, it is unclear whether Atg36 is a new type of autophagy receptor or acts together with a not yet identified autophagy receptor involved in pexophagy.A very interesting concept emerging from the work of Motley et al (2012) is that a single protein, that is, Pex3, could be the central regulator of peroxisome homoeostasis (Figure 1). Pex3 is involved in peroxisome biogenesis, segregation and degradation (Bellu et al, 2002; Hoepfner et al, 2005; Farre et al, 2008; Munck et al, 2009; Ma et al, 2011). As a result, the cell could regulate peroxisome abundance by modulating Pex3 function and/or its array of interactions. In this context, it would be particularly interesting to determine whether Pex3 is also the decision maker of a quality control mechanism that eliminates peroxisomes when not correctly assembled and thus dysfunctional, or when not accurately distributed during cell division. Clearly, additional experiments are needed to understand how Pex3 regulates peroxisome homoeostasis, but this protein and this organelle could represent a convenient system to unveil the principles that regulate the steady-state level of other subcellular compartments.     

ATG3-dependent autophagy mediates mitochondrial homeostasis in pluripotency acquirement and maintenance

Pluripotent stem cells, including induced pluripotent and embryonic stem cells (ESCs), have less developed mitochondria than somatic cells and, therefore, rely more heavily on glycolysis for energy production.^1-3 Zhang J, Nuebel E, Daley GQ, Koehler CM, Teitell MA. Metabolic regulation in pluripotent stem cells during reprogramming and self-renewal. Cell Stem Cell 2012; 11:589-95; PMID:23122286; http://dx.doi.org/10.1016/j.stem.2012.10.005 Vessoni AT, Muotri AR, Okamoto OK. Autophagy in stem cell maintenance and differentiation. Stem Cells Dev 2012; 21:513-20; PMID:22066548; http://dx.doi.org/10.1089/scd.2011.0526 Suhr ST, Chang EA, Tjong J, Alcasid N, Perkins GA, Goissis MD, Ellisman MH, Perez GI, Cibelli JB. Mitochondrial rejuvenation after induced pluripotency. PLoS One 2010; 5:e14095; PMID:21124794; http://dx.doi.org/10.1371/journal.pone.0014095  However, how mitochondrial homeostasis matches the demands of nuclear reprogramming and regulates pluripotency in ESCs is largely unknown. Here, we identified ATG3-dependent autophagy as an executor for both mitochondrial remodeling during somatic cell reprogramming and mitochondrial homeostasis regulation in ESCs. Dysfunctional autophagy by Atg3 deletion inhibited mitochondrial removal during pluripotency induction, resulting in decreased reprogramming efficiency and accumulation of abnormal mitochondria in established iPSCs. In Atg3 null mouse ESCs, accumulation of aberrant mitochondria was accompanied by enhanced ROS generation, defective ATP production and attenuated pluripotency gene expression, leading to abnormal self-renewal and differentiation. These defects were rescued by reacquisition of wild-type but not lipidation-deficient Atg3 expression. Taken together, our findings highlight a critical role of ATG3-dependent autophagy for mitochondrial homeostasis regulation in both pluripotency acquirement and maintenance.