bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2019‒10‒20
fourteen papers selected by
Viktor Korolchuk
Newcastle University


  1. Aging Cell. 2019 Oct 17. e13051
    Herzog LK, Kevei É, Marchante R, Böttcher C, Bindesbøll C, Lystad AH, Pfeiffer A, Gierisch ME, Salomons FA, Simonsen A, Hoppe T, Dantuma NP.
      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.
    Keywords:   Caenorhabditis elegans ; atx-3 ; DUB; ataxin-3; autophagy; ubiquitin
    DOI:  https://doi.org/10.1111/acel.13051
  2. EMBO J. 2019 Oct 18. e101994
    Gu Y, Princely Abudu Y, Kumar S, Bissa B, Choi SW, Jia J, Lazarou M, Eskelinen EL, Johansen T, Deretic V.
      Mammalian homologs of yeast Atg8 protein (mAtg8s) are important in autophagy, but their exact mode of action remains ill-defined. Syntaxin 17 (Stx17), a SNARE with major roles in autophagy, was recently shown to bind mAtg8s. Here, we identified LC3-interacting regions (LIRs) in several SNAREs that broaden the landscape of the mAtg8-SNARE interactions. We found that Syntaxin 16 (Stx16) and its cognate SNARE partners all have LIR motifs and bind mAtg8s. Knockout of Stx16 caused defects in lysosome biogenesis, whereas a Stx16 and Stx17 double knockout completely blocked autophagic flux and decreased mitophagy, pexophagy, xenophagy, and ribophagy. Mechanistic analyses revealed that mAtg8s and Stx16 control several properties of lysosomal compartments including their function as platforms for active mTOR. These findings reveal a broad direct interaction of mAtg8s with SNAREs with impact on membrane remodeling in eukaryotic cells and expand the roles of mAtg8s to lysosome biogenesis.
    Keywords:   GABARAP ; SNARE ; TOR ; autophagy; lysosome
    DOI:  https://doi.org/10.15252/embj.2019101994
  3. Mol Cell. 2019 Oct 09. pii: S1097-2765(19)30694-X. [Epub ahead of print]
    Takahashi D, Moriyama J, Nakamura T, Miki E, Takahashi E, Sato A, Akaike T, Itto-Nakama K, Arimoto H.
      Protein silencing represents an essential tool in biomedical research. Targeted protein degradation (TPD) strategies exemplified by PROTACs are rapidly emerging as modalities in drug discovery. However, the scope of current TPD techniques is limited because many intracellular materials are not substrates of proteasomal clearance. Here, we described a novel targeted-clearance strategy (autophagy-targeting chimera [AUTAC]) that contains a degradation tag (guanine derivatives) and a warhead to provide target specificity. As expected from the substrate scope of autophagy, AUTAC degraded fragmented mitochondria as well as proteins. Mitochondria-targeted AUTAC accelerated both the removal of dysfunctional fragmented mitochondria and the biogenesis of functionally normal mitochondria in patient-derived fibroblast cells. Cytoprotective effects against acute mitochondrial injuries were also seen. Canonical autophagy is viewed as a nonselective bulk decomposition system, and none of the available autophagy-inducing agents exhibit useful cargo selectivity. With its target specificity, AUTAC provides a new modality for research on autophagy-based drugs.
    Keywords:  AUTAC; Down syndrome; K63-linked polyubiquitin; PROTACs; S-guanylation; autophagy; cargo-specific degrader; drug discovery; mitophagy; targeted protein degradation
    DOI:  https://doi.org/10.1016/j.molcel.2019.09.009
  4. J Mol Biol. 2019 Oct 15. pii: S0022-2836(19)30559-5. [Epub ahead of print]
    Gross A, Graef M.
      Autophagy is a highly conserved catabolic pathway critical for stress responses and the maintenance of cellular homeostasis. Defective autophagy contributes to the etiology of an increasing number of diseases including cancer, neurodegeneration, and diabetes. Cells have to integrate complex metabolic information in order to counteract metabolic challenges ranging from carbon, nitrogen, and phosphate to metal ion limitations. An unparalleled variety of cytoplasmic materials in size and nature can be transported into the lytic compartment for degradation and recycling by transient double-membrane compartments, termed autophagosomes, during macroautophagy. In this review, we will outline our current mechanistic understanding of how cells regulate the initiation of macroautophagy to target substrates nonselectively or selectively. With an emphasis on findings in the yeast system, we will describe the emerging principles underlying the regulation of autophagy substrate recognition, which critically shapes the scope of stress-adapted autophagy responses upon diverse metabolic challenges.
    Keywords:  Autophagy; homeostasis; metabolism; selective autophagy; starvation
    DOI:  https://doi.org/10.1016/j.jmb.2019.09.005
  5. Neuropharmacology. 2019 Oct 14. pii: S0028-3908(19)30379-X. [Epub ahead of print] 107812
    Singer E, Walter C, Fabbro D, Rageot D, Beaufils F, Wymann MP, Rischert N, Riess O, Hillmann P, Nguyen HP.
      One of the pathological hallmarks of Huntington disease (HD) is accumulation of the disease-causing mutant huntingtin (mHTT), which leads to the disruption of a variety of cellular functions, ultimately resulting in cell death. Induction of autophagy, for example by the inhibition of mechanistic target of rapamycin (mTOR) signaling, has been shown to reduce HTT levels and aggregates. While rapalogs like rapamycin allosterically inhibit the mTOR complex 1 (TORC1), ATP-competitive mTOR inhibitors suppress activities of TORC1 and TORC2 and have been shown to be more efficient in inducing autophagy and reducing protein levels and aggregates than rapalogs. The ability to cross the blood-brain barrier of first generation catalytic mTOR inhibitors has so far been limited, and therefore sufficient target coverage in the brain could not be reached. Two novel, brain penetrant compounds - the mTORC1/2 inhibitor PQR620, and the dual pan-phosphoinositide 3-kinase (PI3K) and mTORC1/2 kinase inhibitor PQR530 - were evaluated by assessing their potential to induce autophagy and reducing mHTT levels. For this purpose, expression levels of autophagic markers and well-defined mTOR targets were analyzed in STHdh cells and HEK293T cells and in mouse brains. Both compounds potently inhibited mTOR signaling in cell models as well as in mouse brain. As proof of principle, reduction of aggregates and levels of soluble mHTT were demonstrated upon treatment with both compounds. Originally developed for cancer treatment, these second generation mTORC1/2 and PI3K/mTOR inhibitors show brain penetrance and efficacy in cell models of HD, making them candidate molecules for further investigations in HD.
    Keywords:  Aggregation; Catalytic mTOR inhibition; Huntingtin; Huntington disease; Neurodegeneration
    DOI:  https://doi.org/10.1016/j.neuropharm.2019.107812
  6. Cells. 2019 Oct 15. pii: E1255. [Epub ahead of print]8(10):
    Wang J, Wu MY, Su H, Lu J, Chen X, Tan J, Lu JH.
      Nitric oxide (NO) is an important mediator of inflammation response and the production of NO has been linked to a variety of diseases, including tumors, inflammation and central nervous system diseases. In macrophages, a high level of NO is generated by iNOS during inflammatory responses triggered by cytokines or pathogens. Autophagy, a cellular bulk degradation process via lysosome, has been implicated in many disease conditions including inflammation. In this study, we have reported the previously unknown role of autophagy in regulating iNOS levels in macrophages, both under basal and Lipopolysaccharides (LPS)-induced conditions. Our data showed that iNOS levels accumulated upon autophagy inhibition and decreased upon autophagy induction. iNOS interacted and co-localized with autophagy receptor p62/SQSTM1, especially under LPS-stimulated condition in macrophages. Moreover, the immunostaining data revealed that iNOS also co-localizes with the autophagosome marker LC3 and lysosome marker LAMP1, especially under lysosomal inhibition conditions, indicating iNOS is an autophagy substrate. Finally, we showed that autophagy negatively regulated the generation of NO in macrophages, which is consistent with the changes of iNOS levels. Collectively, our study revealed a previously unknown mechanism by which autophagy regulates iNOS levels to modulate NO production during inflammation.
    Keywords:  NO; autophagy; iNOS; macrophage; p62/SQSTM1
    DOI:  https://doi.org/10.3390/cells8101255
  7. Mol Cell. 2019 Oct 14. pii: S1097-2765(19)30696-3. [Epub ahead of print]
    Freyre CAC, Rauher PC, Ejsing CS, Klemm RW.
      Physical contact between organelles is vital to the function of eukaryotic cells. Lipid droplets (LDs) are dynamic organelles specialized in lipid storage that interact physically with mitochondria in several cell types. The mechanisms coupling these organelles are, however, poorly understood, and the cell-biological function of their interaction remains largely unknown. Here, we discover in adipocytes that the outer mitochondrial membrane protein MIGA2 links mitochondria to LDs. We identify an amphipathic LD-targeting motif and reveal that MIGA2 binds to the membrane proteins VAP-A or VAP-B in the endoplasmic reticulum (ER). We find that in adipocytes MIGA2 is involved in promoting triglyceride (TAG) synthesis from non-lipid precursors. Our data indicate that MIGA2 links reactions of de novo lipogenesis in mitochondria to TAG production in the ER, thereby facilitating efficient lipid storage in LDs. Based on its presence in many tissues, MIGA2 is likely critical for lipid and energy homeostasis in a wide spectrum of cell types.
    Keywords:  adipocyte differentiation; lipid droplet expansion; mass spectrometry lipidomics; organelle contact sites; transcriptomics of adipocyte differentiation
    DOI:  https://doi.org/10.1016/j.molcel.2019.09.011
  8. Aging Cell. 2019 Oct 18. e13050
    Marín-Aguilar F, Lechuga-Vieco AV, Alcocer-Gómez E, Castejón-Vega B, Lucas J, Garrido C, Peralta-Garcia A, Pérez-Pulido AJ, Varela-López A, Quiles JL, Ryffel B, Flores I, Bullón P, Ruiz-Cabello J, Cordero MD.
      While NLRP3-inflammasome has been implicated in cardiovascular diseases, its role in physiological cardiac aging is largely unknown. During aging, many alterations occur in the organism, which are associated with progressive impairment of metabolic pathways related to insulin resistance, autophagy dysfunction, and inflammation. Here, we investigated the molecular mechanisms through which NLRP3 inhibition may attenuate cardiac aging. Ablation of NLRP3-inflammasome protected mice from age-related increased insulin sensitivity, reduced IGF-1 and leptin/adiponectin ratio levels, and reduced cardiac damage with protection of the prolongation of the age-dependent PR interval, which is associated with atrial fibrillation by cardiovascular aging and reduced telomere shortening. Furthermore, old NLRP3 KO mice showed an inhibition of the PI3K/AKT/mTOR pathway and autophagy improvement, compared with old wild mice and preserved Nampt-mediated NAD+ levels with increased SIRT1 protein expression. These findings suggest that suppression of NLRP3 prevented many age-associated changes in the heart, preserved cardiac function of aged mice and increased lifespan.
    Keywords:  NLRP3-inflammasome; autophagy; cardiac aging; longevity; morbidity; mortality
    DOI:  https://doi.org/10.1111/acel.13050
  9. EMBO Mol Med. 2019 Oct 14. e10469
    Chen G, Xie W, Nah J, Sauvat A, Liu P, Pietrocola F, Sica V, Carmona-Gutierrez D, Zimmermann A, Pendl T, Tadic J, Bergmann M, Hofer SJ, Domuz L, Lachkar S, Markaki M, Tavernarakis N, Sadoshima J, Madeo F, Kepp O, Kroemer G.
      Caloric restriction mimetics (CRMs) are natural or synthetic compounds that mimic the health-promoting and longevity-extending effects of caloric restriction. CRMs provoke the deacetylation of cellular proteins coupled to an increase in autophagic flux in the absence of toxicity. Here, we report the identification of a novel candidate CRM, namely 3,4-dimethoxychalcone (3,4-DC), among a library of polyphenols. When added to several different human cell lines, 3,4-DC induced the deacetylation of cytoplasmic proteins and stimulated autophagic flux. At difference with other well-characterized CRMs, 3,4-DC, however, required transcription factor EB (TFEB)- and E3 (TFE3)-dependent gene transcription and mRNA translation to trigger autophagy. 3,4-DC stimulated the translocation of TFEB and TFE3 into nuclei both in vitro and in vivo, in hepatocytes and cardiomyocytes. 3,4-DC induced autophagy in vitro and in mouse organs, mediated autophagy-dependent cardioprotective effects, and improved the efficacy of anticancer chemotherapy in vivo. Altogether, our results suggest that 3,4-DC is a novel CRM with a previously unrecognized mode of action.
    Keywords:   TFEB ; TFE3; caloric restriction; caloric restriction mimetic; cardioprotection
    DOI:  https://doi.org/10.15252/emmm.201910469
  10. Nature. 2019 Oct 16.
    Hoshino A, Wang WJ, Wada S, McDermott-Roe C, Evans CS, Gosis B, Morley MP, Rathi KS, Li J, Li K, Yang S, McMannus MJ, Bowman C, Potluri P, Levin M, Damrauer S, Wallace DC, Holzbaur ELF, Arany Z.
      Mitochondrial homeostasis vitally depends on mitophagy, the programmed degradation of mitochondria. The roster of proteins known to participate in mitophagy remains small. We devised here a multidimensional CRISPR/Cas9 genetic screen, using multiple mitophagy reporter systems and pro-mitophagy triggers, and uncover numerous new components of Parkin-dependent mitophagy1. Unexpectedly, we identify the adenine nucleotide translocator (ANT) complex as required for mitophagy in multiple cell types. While pharmacological inhibition of ANT-mediated ADP/ATP exchange promotes mitophagy, genetic ablation of ANT paradoxically suppresses mitophagy. Importantly, ANT promotes mitophagy independently of its nucleotide translocase catalytic activity. Instead, the ANT complex is required for inhibition of the presequence translocase TIM23, leading to PINK1 stabilization, in response to bioenergetic collapse. ANT modulates TIM23 indirectly via interaction with TIM44, known to regulate peptide import through TIM232. Mice lacking ANT1 reveal blunted mitophagy and consequent profound accumulation of aberrant mitochondria. Disease-causing human mutations in ANT1 abrogate binding to TIM44 and TIM23 and inhibit mitophagy. Together, these data identify a novel and essential function for ANT as a fundamental mediator of mitophagy in health and disease.
    DOI:  https://doi.org/10.1038/s41586-019-1667-4
  11. Autophagy. 2019 Oct 17. 1-2
    Yang Y, Valionyte E, Kelly J, Luo S.
      Macroautophagy/autophagy cargo receptor SQSTM1/p62 puncta or clustering formation is critical for its function in cargo recognition and LC3 interaction. Evidence suggests that SQSTM1 puncta formation is a process of liquid-liquid phase separation. It is poorly understood how SQSTM1 liquid-liquid phase separation is regulated. We found that cytoplasmic DAXX enhances SQSTM1 puncta formation, and further demonstrated that DAXX drives SQSTM1 liquid phase condensation through increasing SQSTM1 oligomerization. DAXX promotes SQSTM1 recruitment of KEAP1, subsequently activating an NFE2L2/NRF2-mediated stress response. This study suggests a new mechanism of SQSTM1 phase condensation by a protein-protein interaction, and indicates that cytoplasmic DAXX can play a role to regulate redox homeostasis.
    Keywords:  Autophagy; DAXX; SQSTM1; phase condensation; selective autophagy
    DOI:  https://doi.org/10.1080/15548627.2019.1677323
  12. J Vis Exp. 2019 Sep 17.
    Ryzhikov M, Eubanks A, Haspel JA.
      Cells employ several methods for recycling unwanted proteins and other material, including lysosomal and non-lysosomal pathways. The main lysosome-dependent pathway is called autophagy, while the primary non-lysosomal method for protein catabolism is the ubiquitin-proteasome system. Recent studies in model organisms suggest that the activity of both autophagy and the ubiquitin-proteasome system is not constant across the day but instead varies according to a daily (circadian) rhythm. The ability to measure biological rhythms in protein turnover is important for understanding how cellular quality control is achieved and for understanding the dynamics of specific proteins of interest. Here we present a standardized protocol for quantifying autophagic and proteasomal flux in vivo that captures the circadian component of protein turnover. Our protocol includes details for mouse handling, tissue processing, fractionation, and autophagic flux quantification using mouse liver as the starting material.
    DOI:  https://doi.org/10.3791/60133
  13. Sci Rep. 2019 Oct 15. 9(1): 14828
    Ishii A, Kurokawa K, Hotta M, Yoshizaki S, Kurita M, Koyama A, Nakano A, Kimura Y.
      Cellular heat stress can cause damage, and significant changes, to a variety of cellular structures. When exposed to chronically high temperatures, yeast cells invaginate vacuolar membranes. In this study, we found that the expression of Atg8, an essential autophagy factor, is induced after chronic heat stress. In addition, without Atg8, vacuolar invaginations are induced conspicuously, beginning earlier and invaginating vacuoles more frequently after heat stress. Our results indicate that Atg8's invagination-suppressing functions do not require Atg8 lipidation, in contrast with autophagy, which requires Atg8 lipidation. Genetic analyses of vps24 and vps23 further suggest that full ESCRT machinery is necessary to form vacuolar invaginations irrespective of Atg8. In contrast, through a combined mutation with the vacuole BAR domain protein Ivy1, vacuoles show constitutively enhanced invaginated structures. Finally, we found that the atg8Δivy1Δ mutant is sensitive against agents targeting functions of the vacuole and/or plasma membrane (cell wall). Collectively, our findings revealed that Atg8 maintains vacuolar membrane homeostasis in an autophagy-independent function by coordinating with other cellular factors.
    DOI:  https://doi.org/10.1038/s41598-019-51254-1
  14. J Cell Biol. 2019 Oct 17. pii: jcb.201902184. [Epub ahead of print]
    Gomez RC, Wawro P, Lis P, Alessi DR, Pfeffer SR.
      LRRK2 kinase mutations cause familial Parkinson's disease and increased phosphorylation of a subset of Rab GTPases. Rab29 recruits LRRK2 to the trans-Golgi and activates it there, yet some of LRRK2's major Rab substrates are not on the Golgi. We sought to characterize the cell biology of LRRK2 activation. Unlike other Rab family members, we show that Rab29 binds nucleotide weakly, is poorly prenylated, and is not bound to GDI in the cytosol; nevertheless, Rab29 only activates LRRK2 when it is membrane bound and GTP bound. Mitochondrially anchored, GTP-bound Rab29 is both a LRRK2 substrate and activator, and it drives accumulation of active LRRK2 and phosphorylated Rab10 on mitochondria. Importantly, mitochondrially anchored LRRK2 is much less capable of phosphorylating plasma membrane-anchored Rab10 than soluble LRRK2. These data support a model in which LRRK2 associates with and dissociates from distinct membrane compartments to phosphorylate Rab substrates; if anchored, LRRK2 can modify misdelivered Rab substrates that then become trapped there because GDI cannot retrieve them.
    DOI:  https://doi.org/10.1083/jcb.201902184