bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2020‒01‒26
twenty papers selected by
Viktor Korolchuk
Newcastle University

  1. J Mol Biol. 2020 Jan 21. pii: S0022-2836(20)30068-1. [Epub ahead of print]
    Honda S, Arakawa S, Yamaguchi H, Torii S, Tajima-Sakurai H, Tsujioka M, Murohashi M, Shimizu S.
      Autophagy is a cellular process that degrades intracellular components, including misfolded proteins and damaged organelles. Many neurodegenerative diseases are considered to progress via the accumulation of misfolded proteins and damaged organelles; therefore, autophagy functions in regulating disease severity. There are at least two types of autophagy (canonical autophagy and alternative autophagy), and canonical autophagy has been applied to therapeutic strategies against various types of neurodegenerative diseases. In contrast, the role of alternative autophagy has not yet been clarified, but it is speculated to be involved in the pathogenesis of various neurodegenerative diseases, including Alzheimer disease.
    Keywords:  Alzheimer disease; GOMED; alternative autophagy; canonical autophagy; neurodegenerative disease
  2. Autophagy. 2020 Jan 23.
    Stefely JA, Zhang Y, Freiberger EC, Kwiecien NW, Thomas HE, Davis AM, Lowry ND, Vincent CE, Shishkova E, Clark NA, Medvedovic M, Coon JJ, Pagliarini DJ, Mercer CA.
      Macroautophagy/autophagy is suppressed by MTOR (mechanistic target of rapamycin kinase) and is an anticancer target under active investigation. Yet, MTOR-regulated autophagy remains incompletely mapped. We used proteomic profiling to identify proteins in the MTOR-autophagy axis. Wild-type (WT) mouse cell lines and cell lines lacking individual autophagy genes (Atg5 or Ulk1/Ulk2) were treated with an MTOR inhibitor to induce autophagy and cultured in media with either glucose or galactose. Mass spectrometry proteome profiling revealed an elevation of known autophagy proteins and candidates for new autophagy components, including CALCOCO1 (calcium binding and coiled-coil domain protein 1). We show that CALCOCO1 physically interacts with MAP1LC3C, a key protein in the machinery of autophagy. Genetic deletion of CALCOCO1 disrupted autophagy of the endoplasmic reticulum (reticulophagy). Together, these results reveal a role for CALCOCO1 in MTOR-regulated selective autophagy. More generally, the resource generated by this work provides a foundation for establishing links between the MTOR-autophagy axis and proteins not previously linked to this pathway.
    Keywords:  ATG5; CALCOCO1; MAP1LC3; MTOR; ULK1; ULK2; mass spectrometry proteomics; reticulophagy; selective autophagy
  3. J Mol Biol. 2020 Jan 20. pii: S0022-2836(20)30067-X. [Epub ahead of print]
    Cavalli G, Cenci S.
      Autophagy - conventional for macroautophagy - is a major recycling strategy that ensures cellular homeostasis through the selective engulfment of cytoplasmic supramolecular cargos in double membrane vesicles and their rapid dispatch to the lysosome for digestion. As autophagy operates in the cytoplasm, its interference with secretory proteins, i.e. proteins destined to the plasma membrane or the extracellular space, generally synthesized and routed within the endoplasmic reticulum (ER), has been relatively overlooked in the past. However, mounting evidence reveals that autophagy in fact heavily regulates protein secretion through diverse mechanisms. First, autophagy is closely involved in the unconventional secretion of leaderless proteins, a pool of proteins destined extracellularly, but lacking an ER-targeted leader sequence, and thus manufactured in the cytosol. Autophagy-related (ATG) genes now appear instrumental to the underlying pathways, hence the recently coined concept of secretory autophagy, or better ATG gene-dependent secretion. Indeed, ATG genes regulate unconventional protein secretion at multiple levels, ranging from intracellular inflammatory signaling, e.g. through the control of mitochondrial health and inflammasome activity, to trafficking of leaderless proteins. Moreover, perhaps less expectedly, autophagy also participates in the control of conventional secretion, intersecting the secretory apparatus at multiple points, though with surprising differences among professional secretory cell types that disclose remarkable and unpredicted specificity. This review synopsizes the multiple mechanisms whereby autophagy interfaces with conventional and unconventional protein secretory pathways and discusses the relative teleology. Altogether, the diverse controls exerted on protein secretion broaden and deepen the homeostatic significance of autophagy within the cell.
    Keywords:  autophagy; endoplasmic reticulum; inflammation; protein secretion; quality control
  4. Protein Sci. 2020 Jan 20.
    Taniguchi S, Toyoshima M, Takamatsu T, Mima J.
      In macroautophagy, de novo formation of the double membrane-bound organelles, termed autophagosomes, is essential for engulfing and sequestering the cytoplasmic contents to be degraded in the lytic compartments such as vacuoles and lysosomes. Atg8-family proteins have been known to be responsible for autophagosome formation via membrane tethering and fusion events of precursor membrane structures. Nevertheless, how Atg8 proteins act directly upon autophagosome formation still remains enigmatic. Here, to further gain molecular insights into Atg8-mediated autophagic membrane dynamics, we study the two representative human Atg8 orthologs, LC3B and GATE-16, by quantitatively evaluating their intrinsic potency to physically tether lipid membranes in a chemically defined reconstitution system using purified Atg8 proteins and synthetic liposomes. Both LC3B and GATE-16 retained the capacities to trigger efficient membrane tethering at the protein-to-lipid molar ratios ranging from 1:100 to 1:5,000. These human Atg8-mediated membrane tethering reactions require trans-assembly between the membrane-anchored forms of LC3B and GATE-16 and can be reversibly and strictly controlled by the membrane attachment and detachment cycles. Strikingly, we further uncovered distinct membrane curvature dependences of LC3B- and GATE-16-mediated membrane tethering reactions: LC3B can drive tethering more efficiently than GATE-16 for highly-curved small vesicles (e.g. 50 nm in diameter), although GATE-16 turns out to be a more potent tether than LC3B for flatter large vesicles (e.g. 200 and 400 nm in diameter). Our findings establish curvature-sensitive trans-assembly of human Atg8-family proteins in reconstituted membrane tethering, which recapitulates an essential subreaction of the biogenesis of autophagosomes in vivo. This article is protected by copyright. All rights reserved.
    Keywords:  Atg8; GATE-16; LC3B; autophagosome; autophagy; membrane reconstitution; membrane tethering
  5. Nat Commun. 2020 Jan 23. 11(1): 440
    Jakobi AJ, Huber ST, Mortensen SA, Schultz SW, Palara A, Kuhm T, Shrestha BK, Lamark T, Hagen WJH, Wilmanns M, Johansen T, Brech A, Sachse C.
      p62/SQSTM1 is an autophagy receptor and signaling adaptor with an N-terminal PB1 domain that forms the scaffold of phase-separated p62 bodies in the cell. The molecular determinants that govern PB1 domain filament formation in vitro remain to be determined and the role of p62 filaments inside the cell is currently unclear. We here determine four high-resolution cryo-EM structures of different human and Arabidopsis PB1 domain assemblies and observed a filamentous ultrastructure of p62/SQSTM1 bodies using correlative cellular EM. We show that oligomerization or polymerization, driven by a double arginine finger in the PB1 domain, is a general requirement for lysosomal targeting of p62. Furthermore, the filamentous assembly state of p62 is required for autophagosomal processing of the p62-specific cargo KEAP1. Our results show that using such mechanisms, p62 filaments can be critical for cargo uptake in autophagy and are an integral part of phase-separated p62 bodies.
  6. Int J Mol Sci. 2020 Jan 16. pii: E578. [Epub ahead of print]21(2):
    Germain K, Kim PK.
      The removal of damaged or superfluous organelles from the cytosol by selective autophagy is required to maintain organelle function, quality control and overall cellular homeostasis. Precisely how substrate selectivity is achieved, and how individual substrates are degraded during selective autophagy in response to both extracellular and intracellular cues is not well understood. The aim of this review is to highlight pexophagy, the autophagic degradation of peroxisomes, as a model for selective autophagy. Peroxisomes are dynamic organelles whose abundance is rapidly modulated in response to metabolic demands. Peroxisomes are routinely turned over by pexophagy for organelle quality control yet can also be degraded by pexophagy in response to external stimuli such as amino acid starvation or hypoxia. This review discusses the molecular machinery and regulatory mechanisms governing substrate selectivity during both quality-control pexophagy and pexophagy in response to external stimuli, in yeast and mammalian systems. We draw lessons from pexophagy to infer how the cell may coordinate the degradation of individual substrates by selective autophagy across different cellular cues.
    Keywords:  metabolism; organelle quality control; peroxisomes; selective autophagy
  7. J Nutr. 2020 Jan 21. pii: nxz301. [Epub ahead of print]
    Zhu M, Wang XQ.
      Mechanistic target of rapamycin complex 1 (mTORC1) is a highly evolutionarily conserved serine/threonine kinase that regulates cell growth and metabolism in response to multiple environmental cues, such as nutrients, hormones, energy, and stress. Deregulation of mTORC1 can lead to diseases such as diabetes, obesity, and cancer. A series of small GTPases, including Rag, Ras homolog enriched in brain (Rheb), adenosine diphosphate ribosylation factor 1 (Arf1), Ras-related protein Ral-A, Ras homolog (Rho), and Rab, are involved in regulating mTORC1 in response to nutrients, and mTORC1 is differentially regulated via these small GTPases according to specific conditions. Leucine and arginine sensing are considered to be well-confirmed amino acid-sensing signals, activating mTORC1 via a Rag GTPase-dependent mechanism as well as the Ragulator complex and vacuolar H+-adenosine triphosphatase (v-ATPase). Glutamine promotes mTORC1 activation via Arf1 independently of the Rag GTPase. In this review, we summarize current knowledge regarding the regulation of mTORC1 activity by small GTPases in response to nutrients, focusing on the function of small GTPases in mTORC1 activation and how small GTPases are regulated by nutrients.
    Keywords:  arginine; glutamine; leucine; mTORC1; small GTPases
  8. J Mol Biol. 2020 Jan 18. pii: S0022-2836(20)30069-3. [Epub ahead of print]
    Peker N, Gozuacik D.
      Cells of an organism face with various types of insults during their lifetime. Exposure to toxins, metabolic problems, ischemia/reperfusion, physical trauma, genetic diseases, neurodegenerative diseases are among the conditions that trigger cellular stress responses. In this context, autophagy is one of the mechanisms that supports cell survival under stressful conditions. Autophagic vesicle engulf the cargo and transport it to lysosome for degradation and turnover. As such, autophagy eliminates abnormal proteins, clears damaged organelles, limits oxidative stress and helps to improve metabolic balance. Nervous system cells and particularly post-mitotic neurons are highly sensitive to a spectrum of insults, and autophagy emerges as one of the key stress response mechanism, ensuring health and survival of these vulnerable cell types. In this review, we will overview mechanisms through which cells cope with stress, and how these stress responses regulate autophagy, with a special focus on the nervous system.
    Keywords:  autophagy; cellular stress; nervous system; neurodegenerative disease; neuron
  9. Autophagy. 2020 Jan 22. 1-15
    Jo DS, Park SJ, Kim AK, Park NY, Kim JB, Bae JE, Park HJ, Shin JH, Chang JW, Kim PK, Jung YK, Koh JY, Choe SK, Lee KS, Cho DH.
      Quality control of peroxisomes is essential for cellular homeostasis. However, the mechanism underlying pexophagy is largely unknown. In this study, we identified HSPA9 as a novel pexophagy regulator. Downregulation of HSPA9 increased macroautophagy/autophagy but decreased the number of peroxisomes in vitro and in vivo. The loss of peroxisomes by HSPA9 depletion was attenuated in SQSTM1-deficient cells. In HSPA9-deficient cells, the level of peroxisomal reactive oxygen species (ROS) increased, while inhibition of ROS blocked pexophagy in HeLa and SH-SY5Y cells. Importantly, reconstitution of HSPA9 mutants found in Parkinson disease failed to rescue the loss of peroxisomes, whereas reconstitution with wild type inhibited pexophagy in HSPA9-depleted cells. Knockdown of Hsc70-5 decreased peroxisomes in Drosophila, and the HSPA9 mutants failed to rescue the loss of peroxisomes in Hsc70-5-depleted flies. Taken together, our findings suggest that the loss of HSPA9 enhances peroxisomal degradation by pexophagy.
    Keywords:  Drosophila; HSPA9; Parkinson disease; ROS; peroxisome; pexophagy
  10. Autophagy. 2020 Jan 20. 1-2
    Takahashi D, Arimoto H.
      Targeted degradation is a promising new modality in drug discovery that makes it possible to reduce intracellular protein levels with small molecules. It is a complementary approach to the conventional protein knockdown typically used in laboratories and may offer a way to approach the currently undruggable human proteome. Recently, the first autophagy-mediated degraders, called AUTACs, were developed based on observations in a xenophagy study.
    Keywords:  AUTAC; PROTAC; drug discovery; guanylation; mitophagy; targeted degradation
  11. Cell. 2020 Jan 23. pii: S0092-8674(19)31397-2. [Epub ahead of print]180(2): 296-310.e18
    Hughes CE, Coody TK, Jeong MY, Berg JA, Winge DR, Hughes AL.
      Mitochondria and lysosomes are functionally linked, and their interdependent decline is a hallmark of aging and disease. Despite the long-standing connection between these organelles, the function(s) of lysosomes required to sustain mitochondrial health remains unclear. Here, working in yeast, we show that the lysosome-like vacuole maintains mitochondrial respiration by spatially compartmentalizing amino acids. Defects in vacuole function result in a breakdown in intracellular amino acid homeostasis, which drives age-related mitochondrial decline. Among amino acids, we find that cysteine is most toxic for mitochondria and show that elevated non-vacuolar cysteine impairs mitochondrial respiration by limiting intracellular iron availability through an oxidant-based mechanism. Cysteine depletion or iron supplementation restores mitochondrial health in vacuole-impaired cells and prevents mitochondrial decline during aging. These results demonstrate that cysteine toxicity is a major driver of age-related mitochondrial deterioration and identify vacuolar amino acid compartmentation as a cellular strategy to minimize amino acid toxicity.
    Keywords:  V-ATPase; aging; amino acid; cysteine; iron; lysosome; mitochondria; vacuole; yeast
  12. Curr Biol. 2020 Jan 20. pii: S0960-9822(19)31592-1. [Epub ahead of print]30(2): R89-R91
    Peng W, Jewell JL.
      Amino acid signaling through the Rag GTPases promotes mTORC1 lysosomal localization and subsequent activation. Two new cryo-EM structures examine the architecture of the Rag GTPase heterodimers complexed with mTORC1.
  13. Mitochondrion. 2020 Jan 20. pii: S1567-7249(19)30230-2. [Epub ahead of print]
    Garza-Lombó C, Pappa A, Panayiotidis MI, Franco R.
      Autophagy is a ubiquitous homeostatic mechanism for the degradation or turnover of cellular components. Degradation of mitochondria via autophagy (mitophagy) is involved in a number of physiological processes including cellular homeostasis, differentiation and aging. Upon stress or injury, mitophagy prevents the accumulation of damaged mitochondria and the increased steady state levels of reactive oxygen species leading to oxidative stress and cell death. A number of human diseases, particularly neurodegenerative disorders, have been linked to the dysregulation of mitophagy. In this mini-review, we aimed to review the molecular mechanisms involved in the regulation of mitophagy and their relationship with redox signaling and oxidative stress.
    Keywords:  autophagy; fission; fusion; mitochondrial dynamics
  14. Autophagy. 2020 Jan 23.
    Yao W, Li Y, Wu L, Wu C, Zhang Y, Liu J, He Z, Wu X, Lu C, Wang L, Zhong H, Hong Z, Xu S, Liu W, Yi C.
      How energy deprivation induces macroautophagy/autophagy is not fully understood. Here, we show that Atg11, a receptor protein for cargo recognition in selective autophagy, is required for the initiation of glucose starvation-induced autophagy. Upon glucose starvation, Atg11 facilitates the interaction between Snf1 and Atg1, thus is required for Snf1-dependent Atg1 activation. Phagophore assembly site (PAS) formation requires Atg11 via its control of the association of Atg17 with Atg29-Atg31. The binding of Atg11 with Atg9 is crucial for recruiting Atg9 vesicles to the PAS and, thus, glucose starvation-induced autophagy. We propose Atg11 as a key initiation factor controlling multiple key steps in energy deprivation-induced autophagy.
    Keywords:  Atg11; Atg9; PAS; Snf1; glucose starvation-induced autophagy
  15. Antioxid Redox Signal. 2020 Jan 22.
    Liu L, Liao X, Wu H, Li Y, Zhu Y, Chen Q.
      Mitochondria are the cellular powerhouses for ATP synthesis through oxidative phosphorylation (OXPHOS), and the centers for fatty acid β-oxidation, metabolite synthesis, ROS production, innate immunity and apoptosis. To fulfill these critical functions, mitochondrial quality and homeostasis must be well maintained to avoid potential damage to the cell. Abnormal mitochondrial quality contributes to aging and age-related disorders, such as metabolic syndrome, cancers and neurodegenerative diseases. Mitophagy is a cellular process that selectively removes damaged or superfluous mitochondria by autolysosomal degradation and is regarded as one of the major mechanisms responsible for mitochondrial quality control. To date, distinct mitophagy pathways have been discovered, including receptor-mediated mitophagy and ubiquitin-dependent mitophagy, of which the PINK1/Parkin-dependent mechanism is the best characterized to date. Emerging knowledge of these pathways shows that they play important roles in sensing mitochondrial stress and signaling for metabolic adaptations. Here, we provide a review on the molecular mechanisms for mitophagy and its interplay with cellular metabolism, with a particular focus on its role in metabolic and aging related disorders.
  16. Autophagy. 2020 Jan 20. 1-3
    Ejlerskov P, Rubinsztein DC, Pocock R.
      Loss of IFNB/interferon-β in mice causes a Parkinson disease-like phenotype where many features, including SNCA/α-synuclein and MAPT/tau accumulation, can be attributed to a late-stage block in autophagic flux. Recently, we identified a mechanism that can explain this phenotype. We found that IFNB induces expression of Mir1, a microRNA that can reduce the levels of TBC1D15, a RAB GTPase-activating protein. Induction of this pathway decreases RAB7 activity and thereby stimulates macroautophagy/autophagy. The relevance of these key players is deeply conserved from humans to Caenorhabditis elegans, highlighting the importance of this ancient autophagy regulatory pathway.
    Keywords:  Autophagy; Huntington disease; Parkinson disease; TBC1D15; interferon-beta; miR-1; proteinopathies
  17. Nat Commun. 2020 Jan 24. 11(1): 481
    Barinda AJ, Ikeda K, Nugroho DB, Wardhana DA, Sasaki N, Honda S, Urata R, Matoba S, Hirata KI, Emoto N.
      Vascular senescence is thought to play a crucial role in an ageing-associated decline of organ functions; however, whether vascular senescence is causally implicated in age-related disease remains unclear. Here we show that endothelial cell (EC) senescence induces metabolic disorders through the senescence-associated secretory phenotype. Senescence-messaging secretomes from senescent ECs induced a senescence-like state and reduced insulin receptor substrate-1 in adipocytes, which thereby impaired insulin signaling. We generated EC-specific progeroid mice that overexpressed the dominant negative form of telomeric repeat-binding factor 2 under the control of the Tie2 promoter. EC-specific progeria impaired systemic metabolic health in mice in association with adipose tissue dysfunction even while consuming normal chow. Notably, shared circulation with EC-specific progeroid mice by parabiosis sufficiently transmitted the metabolic disorders into wild-type recipient mice. Our data provides direct evidence that EC senescence impairs systemic metabolic health, and thus establishes EC senescence as a bona fide risk for age-related metabolic disease.
  18. J Clin Invest. 2020 Jan 21. pii: 133264. [Epub ahead of print]
    Xie Y, Zhao Y, Shi L, Li W, Chen K, Li M, Chen X, Zhang H, Li T, Yu MI, Yao X, Shao D, Ke Z, Li J, Chen Y, Zhang X, Cui J, Cui S, Leng Q, Cadwell K, Li X, Wei H, Zhang H, Li H, Xiao H.
      While the Western-diet and dysbiosis are the most prominent environmental factors associated with inflammatory bowel diseases (IBDs), the corresponding host factors and cellular mechanisms remain poorly defined. Here we report that the TSC1-mTOR pathway in the gut epithelium represents a metabolic and innate immune checkpoint for intestinal dysfunction and inflammation. mTOR hyperactivation triggered by the Western-diet or Tsc1-ablation led to epithelium necroptosis, barrier disruption, and predisposition to DSS (dextran sulfate sodium)-induced colitis and inflammation-associated colon cancer. Mechanistically, our results uncovered a critical role for TSC1-mTOR in restraining the expression and activation of RIPK3 in the gut epithelium through Trim11-mediated ubiquitination and autophagy-dependent degradation. Notably, microbiota-depletion by antibiotics or gnotobiotics attenuated RIPK3 expression and activation, thereby alleviating epithelial necroptosis and colitis driven by mTOR hyperactivation. mTOR primarily impinged on RIPK3 to potentiate TNF- and microbial PAMP-induced necroptosis, and hyperactive mTOR and aberrant necroptosis were intertwined in human IBDs. Together, our data reveal a previously unsuspected link between the Western-diet, microbiota and necroptosis, and identify the mTOR-RIPK3-necroptosis axis as a driving force for intestinal inflammation and cancer.
    Keywords:  Apoptosis survival pathways; Cell Biology; Inflammation; Inflammatory bowel disease; Innate immunity
  19. Sci Rep. 2020 Jan 22. 10(1): 993
    Seo MK, Hien LT, Park MK, Choi AJ, Seog DH, Kim SH, Park SW, Lee JG.
      The group II metabotropic glutamate 2/3 (mGlu2/3) receptor antagonist LY341495 produces antidepressant-like effects by acting on mammalian target of rapamycin complex 1 (mTORC1) signaling and α-amino-3-hydroxy-5-methylisoxazole-4-propionate (AMPA) receptors in rodent. We investigated whether LY341495 affects neuroplasticity via these mechanisms in rat primary hippocampal cultures under conditions of dexamethasone (DEX)-induced neurotoxicity. Ketamine was used for comparison. Hippocampal cultures were treated with LY341495 under conditions of DEX-induced toxicity. Changes in mTORC1-mediated proteins were determined by Western blotting analyses. Changes in dendritic outgrowth and spine density were evaluated via immunostaining. LY341495 significantly prevented DEX-induced decreases in the levels of mTORC1, 4E-BP1, and p70S6K phosphorylation as well as the levels of the synaptic proteins. These effects were blocked by pretreatment with the AMPA receptor inhibitor 2,3-dihydroxy-6-nitro-7sulfamoyl-benzo(f)quinoxaline (NBQX) and the mTORC1 inhibitor rapamycin. LY341495 significantly attenuated DEX-induced decreases in dendritic outgrowth and spine density. Pretreatment with rapamycin and NBQX blocked these effects of LY341495. Further analyses indicted that induction of BDNF expression produced by LY341495 was blocked by pretreatment with NBQX and rapamycin. LY341495 has neuroplastic effects by acting on AMPA receptor-mTORC1 signaling under neurotoxic conditions. Therefore, activation of AMPA receptor and mTORC1 signaling, which enhance neuroplasticity, may be novel targets for new antidepressants.
  20. Cell Death Differ. 2020 Jan 22.
    Di Rienzo M, Romagnoli A, Antonioli M, Piacentini M, Fimia GM.
      Autophagy, a main intracellular catabolic process, is induced in response to a variety of cellular stresses to promptly degrade harmful agents and to coordinate the activity of prosurvival and prodeath processes in order to determine the fate of the injured cells. While the main components of the autophagy machinery are well characterized, the molecular mechanisms that confer selectivity to this process both in terms of stress detection and cargo engulfment have only been partly elucidated. Here, we discuss the emerging role played by the E3 ubiquitin ligases of the TRIM family in regulating autophagy in physiological and pathological conditions, such as inflammation, infection, tumorigenesis, and muscle atrophy. TRIM proteins employ different strategies to regulate the activity of the core autophagy machinery, acting either as scaffold proteins or via ubiquitin-mediated mechanisms. Moreover, they confer high selectivity to the autophagy-mediated degradation as described for the innate immune response, where TRIM proteins mediate both the engulfment of pathogens within autophagosomes and modulate the immune response by controlling the stability of signaling regulators. Importantly, the elucidation of the molecular mechanisms underlying the regulation of autophagy by TRIMs is providing important insights into how selective types of autophagy are altered under pathological conditions, as recently shown in cancer and muscular dystrophy.