bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2020–06–14
forty-four papers selected by
Viktor Korolchuk, Newcastle University
  1. Puncta intended: connecting the dots between autophagy and cell stress networks.
  2. MERIT, a cellular system coordinating lysosomal repair, removal and replacement.
  3. Emerging roles of ATG proteins and membrane lipids in autophagosome formation.
  4. Coordination of Rheb lysosomal membrane interactions with mTORC1 activation.
  5. A heterodimeric SNX4:SNX7 SNX-BAR autophagy complex coordinates ATG9A trafficking for efficient autophagosome assembly.
  6. Vac8 determines phagophore assembly site vacuolar localization during nitrogen starvation-induced autophagy.
  7. Mitotic phosphorylation of the ULK complex regulates cell cycle progression.
  8. ULK1-ATG13 and their mitotic phospho-regulation by CDK1 connect autophagy to cell cycle.
  9. FBXL4 deficiency increases mitochondrial removal by autophagy.
  10. Live imaging of intra-lysosome pH in cell lines and primary neuronal culture using a novel genetically encoded biosensor.
  11. Autophagosome biogenesis and human health.
  12. CALCOCO1 acts with VAMP-associated proteins to mediate ER-phagy.
  13. ALS/FTD mutations in UBQLN2 impede autophagy by reducing autophagosome acidification through loss of function.
  14. Autophagy as an emerging target for COVID-19: lessons from an old friend, chloroquine.
  15. Phosphorylation of eukaryotic initiation factor-2α (eIF2α) in autophagy.
  16. Protein translocation into the ERGIC: an upstream event of secretory autophagy.
  17. Cell-Clearing Systems Bridging Repeat Expansion Proteotoxicity and Neuromuscular Junction Alterations in ALS and SBMA.
  18. Detection of p62/SQSTM1 Aggregates in Cellular Models of CCM Disease by Immunofluorescence.
  19. Autophagic Pathways to Clear the Tau Aggregates in Alzheimer's Disease.
  20. cGMP via PKG activates 26S proteasomes and enhances degradation of proteins, including ones that cause neurodegenerative diseases.
  21. Curcumin blunts epithelial-mesenchymal transition of hepatocytes to alleviate hepatic fibrosis through regulating oxidative stress and autophagy.
  22. Mechanisms of neurodegeneration in Parkinson's disease: keep neurons in the PINK1.
  23. Dual Targeting of BRAF and mTOR Signaling in Melanoma Cells with Pyridinyl Imidazole Compounds.
  24. TBC1D5-Catalyzed Cycling of Rab7 Is Required for Retromer-Mediated Human Papillomavirus Trafficking during Virus Entry.
  25. Trehalose against Alzheimer's Disease: Insights into a Potential Therapy.
  26. Cu(II) disrupts autophagy-mediated lysosomal degradation of oligomeric Aβ in microglia via mTOR-TFEB pathway.
  27. The C9orf72-SMCR8-WDR41 complex is a GAP for small GTPases.
  28. Autophagy controls the induction and developmental decline of NMDAR-LTD through endocytic recycling.
  29. PEBP1 acts as a rheostat between prosurvival autophagy and ferroptotic death in asthmatic epithelial cells.
  30. TECPR1 promotes aggrephagy by direct recruitment of LC3C autophagosomes to lysosomes.
  31. Autophagy-mediated apoptosis eliminates aneuploid cells in a mouse model of chromosome mosaicism.
  32. Sestrin2 as a potential therapeutic target for cardiovascular diseases.
  33. miRNA-182/Deptor/mTOR axis regulates autophagy to reduce intestinal ischaemia/reperfusion injury.
  34. "LRRK2: Autophagy and Lysosomal Activity".
  35. Aggresome-Like Formation Promotes Resistance to Proteotoxicity in Cells from Long-Lived Species.
  36. Nanoparticles induce autophagy via mTOR pathway inhibition and reactive oxygen species generation.
  37. Ischemic postconditioning attenuates acute kidney injury following intestinal ischemia-reperfusion through Nrf2-regulated autophagy, anti-oxidation, and anti-inflammation in mice.
  38. Human telomerase reverse transcriptase positively regulates mitophagy by inhibiting the processing and cytoplasmic release of mitochondrial PINK1.
  39. ULK complex organization in autophagy by a C-shaped FIP200 N-terminal domain dimer.
  40. Mitophagy in Hypertension-Associated Premature Vascular Aging.
  41. Atg21 organizes Atg8 lipidation at the contact of the vacuole with the phagophore.
  42. GTR1 Affects Nitrogen Consumption and TORC1 Activity in Saccharomyces cerevisiae Under Fermentation Conditions.
  43. Autophagy Induced by ROS Aggravates Testis Oxidative Damage in Diabetes via Breaking the Feedforward Loop Linking p62 and Nrf2.
  44. Crosstalk dynamics between the circadian clock and the mTORC1 pathway.
  1. Autophagy. 2020 Jun 07. 1-6
    Puncta intended: connecting the dots between autophagy and cell stress networks.
    Cally J Ho, Gayathri Samarasekera, Katharina Rothe, Jing Xu, Kevin C Yang, Emily Leung, Michelle Chan, Xiaoyan Jiang, Sharon M Gorski.
      Proteome profiling and global protein-interaction approaches have significantly improved our knowledge of the protein interactomes of autophagy and other cellular stress-response pathways. New discoveries regarding protein complexes, interaction partners, interaction domains, and biological roles of players that are part of these pathways are emerging. The fourth Vancouver Autophagy Symposium showcased research that expands our understanding of the protein interaction networks and molecular mechanisms underlying autophagy and other cellular stress responses in the context of distinct stressors. In the keynote presentation, Dr. Wade Harper described his team's recent discovery of a novel reticulophagy receptor for selective autophagic degradation of the endoplasmic reticulum, and discussed molecular mechanisms involved in ribophagy and non-autophagic ribosomal turnover. In other presentations, both omic and targeted approaches were used to reveal molecular players of other cellular stress responses including amyloid body and stress granule formation, anastasis, and extracellular vesicle biogenesis. Additional topics included the roles of autophagy in disease pathogenesis, autophagy regulatory mechanisms, and crosstalk between autophagy and cellular metabolism in anti-tumor immunity. The relationship between autophagy and other cell stress responses remains a relatively unexplored area in the field, with future investigations required to understand how the various processes are coordinated and connected in cells and tissues.
    ABBREVIATIONS: A-bodies: amyloid bodies; ACM: amyloid-converting motif; AMFR/gp78: autocrine motility factor receptor; ATG: autophagy-related; ATG4B: autophagy related 4B cysteine peptidase; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CAR T: chimeric antigen receptor T; CASP3: caspase 3; CCPG1: cell cycle progression 1; CAR: chimeric antigen receptor; CML: chronic myeloid leukemia; CCOCs: clear cell ovarian cancers; CVB3: coxsackievirus B3; CRISPR-Cas9: clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9; DDXs: DEAD-box helicases; EIF2S1/EIF-2alpha: eukaryotic translation initiation factor 2 subunit alpha; EIF2AK3: eukaryotic translation initiation factor 2 alpha kinase 3; ER: endoplasmic reticulum; EV: extracellular vesicle; FAO: fatty acid oxidation; GABARAP: GABA type A receptor-associated protein; ILK: integrin linked kinase; ISR: integrated stress response; MTOR: mechanistic target of rapamycin kinase; MPECs: memory precursory effector T cells; MAVS: mitochondrial antiviral signaling protein; NBR1: NBR1 autophagy cargo receptor; PI4KB/PI4KIIIβ: phosphatidylinositol 4-kinase beta; PLEKHM1: pleckstrin homology and RUN domain containing M1; RB1CC1: RB1 inducible coiled-coil 1; RTN3: reticulon 3; rIGSRNAs: ribosomal intergenic noncoding RNAs; RPL29: ribosomal protein L29; RPS3: ribosomal protein S3; S. cerevisiae: Saccharomyces cerevisiae; sEV: small extracellular vesicles; S. pombe: Schizosaccharomyces pombe; SQSTM1: sequestosome 1; SF3B1: splicing factor 3b subunit 1; SILAC-MS: stable isotope labeling with amino acids in cell culture-mass spectrometry; SNAP29: synaptosome associated protein 29; TEX264: testis expressed 264, ER-phagy receptor; TNBC: triple-negative breast cancer; ULK1: unc-51 like autophagy activating kinase 1; VAS: Vancouver Autophagy Symposium.
    Keywords:  Cellular stress responses; Vancouver autophagy symposium; macroautophagy; proteomics; selective autophagy
    DOI:  https://doi.org/10.1080/15548627.2020.1775394
  2. Autophagy. 2020 Jun 10.
    MERIT, a cellular system coordinating lysosomal repair, removal and replacement.
    Jingyue Jia, Aurore Claude-Taupin, Yuexi Gu, Seong Won Choi, Ryan Peters, Bhawana Bissa, Michal H Mudd, Lee Allers, Sandeep Pallikkuth, Keith A Lidke, Michelle Salemi, Brett Phinney, Muriel Mari, Fulvio Reggiori, Vojo Deretic.
      Membrane integrity is essential for cellular survival and function. The spectrum of mechanisms protecting cellular and intracellular membranes is not fully known. Our recent work has uncovered a cellular system termed MERIT for lysosomal membrane repair, removal and replacement. Specifically, lysosomal membrane damage induces, in succession, ESCRT-dependent membrane repair, macroautophagy/autophagy-dominant removal of damaged lysosomes, and initiation of lysosomal biogenesis via transcriptional programs. The MERIT system is governed by galectins, a family of cytosolically synthesized lectins recognizing β-galactoside glycans. We found in this study that LGALS3 (galectin 3) detects membrane damage by detecting exposed lumenal glycosyl groups, recruits and organizes ESCRT components PDCD6IP/ALIX, CHMP4A, and CHMPB at damaged sites on the lysosomes, and facilitates ESCRT-driven repair of lysosomal membrane. At later stages, LGALS3 cooperates with TRIM16, an autophagy receptor-regulator, to engage autophagy machinery in removal of excessively damaged lysosomes. In the absence of LGALS3, repair and autophagy are less efficient, whereas TFEB nuclear translocation increases to compensate lysosomal deficiency via de novo lysosomal biogenesis. The MERIT system protects endomembrane integrity against a broad spectrum of agents damaging the endolysosomal network including lysosomotropic drugs, Mycobacterium tuberculosis, or neurotoxic MAPT/tau.
    Keywords:  Autophagy; ESCRT; TFEB; TRIM; tauopathies; transferrin receptor; tuberculosis
    DOI:  https://doi.org/10.1080/15548627.2020.1779451
  3. Cell Discov. 2020 ;6 32
    Emerging roles of ATG proteins and membrane lipids in autophagosome formation.
    Taki Nishimura, Sharon A Tooze.
      Autophagosome biogenesis is a dynamic membrane event, which is executed by the sequential function of autophagy-related (ATG) proteins. Upon autophagy induction, a cup-shaped membrane structure appears in the cytoplasm, then elongates sequestering cytoplasmic materials, and finally forms a closed double membrane autophagosome. However, how this complex vesicle formation event is strictly controlled and achieved is still enigmatic. Recently, there is accumulating evidence showing that some ATG proteins have the ability to directly interact with membranes, transfer lipids between membranes and regulate lipid metabolism. A novel role for various membrane lipids in autophagosome formation is also emerging. Here, we highlight past and recent key findings on the function of ATG proteins related to autophagosome biogenesis and consider how ATG proteins control this dynamic membrane formation event to organize the autophagosome by collaborating with membrane lipids.
    Keywords:  Endoplasmic reticulum; Macroautophagy
    DOI:  https://doi.org/10.1038/s41421-020-0161-3
  4. F1000Res. 2020 ;pii: F1000 Faculty Rev-450. [Epub ahead of print]9
    Coordination of Rheb lysosomal membrane interactions with mTORC1 activation.
    Brittany Angarola, Shawn M Ferguson.
      A complex molecular machinery converges on the surface of lysosomes to ensure that the growth-promoting signaling mediated by mechanistic target of rapamycin complex 1 (mTORC1) is tightly controlled by the availability of nutrients and growth factors. The final step in this activation process is dependent on Rheb, a small GTPase that binds to mTOR and allosterically activates its kinase activity. Here we review the mechanisms that determine the subcellular localization of Rheb (and the closely related RhebL1 protein) as well as the significance of these mechanisms for controlling mTORC1 activation. In particular, we explore how the relatively weak membrane interactions conferred by C-terminal farnesylation are critical for the ability of Rheb to activate mTORC1. In addition to supporting transient membrane interactions, Rheb C-terminal farnesylation also supports an interaction between Rheb and the δ subunit of phosphodiesterase 6 (PDEδ). This interaction provides a potential mechanism for targeting Rheb to membranes that contain Arl2, a small GTPase that triggers the release of prenylated proteins from PDEδ. The minimal membrane targeting conferred by C-terminal farnesylation of Rheb and RhebL1 distinguishes them from other members of the Ras superfamily that possess additional membrane interaction motifs that work with farnesylation for enrichment on the specific subcellular membranes where they engage key effectors. Finally, we highlight diversity in Rheb membrane targeting mechanisms as well as the potential for alternative mTORC1 activation mechanisms across species.
    Keywords:  Rheb; cancer; lysosome; mTOR; membranes; signaling
    DOI:  https://doi.org/10.12688/f1000research.22367.1
  5. J Cell Sci. 2020 Jun 08. pii: jcs.246306. [Epub ahead of print]
    A heterodimeric SNX4:SNX7 SNX-BAR autophagy complex coordinates ATG9A trafficking for efficient autophagosome assembly.
    Zuriñe Antón, Virginie M S Betin, Boris Simonetti, Colin J Traer, Naomi Attar, Peter J Cullen, Jon D Lane.
      The sorting nexins (SNXs) are a family of peripheral membrane proteins that direct protein trafficking decisions within the endocytic network. Emerging evidence in yeast and mammalian cells implicates a sub-group of SNXs in selective and non-selective forms of (macro)autophagy. Using siRNA and CRISPR-Cas9, we demonstrate that the SNX-BAR protein, SNX4, is needed for efficient LC3 lipidation and autophagosome assembly in mammalian cells. SNX-BARs exist as homo- and heterodimers, and we show that SNX4 forms functional heterodimers with either SNX7 or SNX30 that associate with tubulovesicular endocytic membranes. Detailed image-based analysis during the early stages of autophagosome assembly reveal that SNX4:SNX7 is the autophagy-specific SNX-BAR heterodimer, required for efficient recruitment/retention of core autophagy regulators at the nascent isolation membrane. SNX4 partially co-localises with juxtanuclear ATG9A-positive membranes, with our data linking the SNX4 autophagy defect to the mis-trafficking and/or retention of ATG9A in the Golgi region. Together, our findings show that the SNX4:SNX7 heterodimer coordinates ATG9A trafficking within the endocytic network to establish productive autophagosome assembly sites, thus extending knowledge of SNXs as positive regulators of autophagy.
    Keywords:  ATG9A; Autophagy; Endosomes; SNX30; SNX4; SNX7; Sorting nexin
    DOI:  https://doi.org/10.1242/jcs.246306
  6. Autophagy. 2020 Jun 08.
    Vac8 determines phagophore assembly site vacuolar localization during nitrogen starvation-induced autophagy.
    Damian Gatica, Xin Wen, Heesun Cheong, Daniel J Klionsky.
      Macroautophagy/autophagy is a key catabolic process in which different cellular components are sequestered inside double-membrane vesicles called autophagosomes for subsequent degradation. In yeast, autophagosome formation occurs at the phagophore assembly site (PAS), a specific perivacuolar location that works as an organizing center for the recruitment of different autophagy-related (Atg) proteins. How the PAS is localized to the vacuolar periphery is not well understood. Here we show that the vacuolar membrane protein Vac8 is required for correct vacuolar localization of the PAS. We provide evidence that Vac8 anchors the PAS to the vacuolar membrane by binding Atg13 and recruiting the Atg1 initiation complex. VAC8 deletion or mislocalization of the protein reduce autophagy activity, highlighting the importance of both the PAS and the correct vacuolar localization of the Atg1 initiation complex for efficient and robust autophagy.
    Keywords:  Atg13; PAS; autophagosomes; lysosome; vacuole
    DOI:  https://doi.org/10.1080/15548627.2020.1776474
  7. PLoS Biol. 2020 Jun;18(6): e3000718
    Mitotic phosphorylation of the ULK complex regulates cell cycle progression.
    Akinori Yamasaki, Yui Jin, Yoshinori Ohsumi.
      Autophagy is an intracellular degradation pathway targeting organelles and macromolecules, thereby regulating various cellular functions. Phosphorylation is a key posttranscriptional protein modification implicated in the regulation of biological function including autophagy. Under asynchronous conditions, autophagy activity is predominantly suppressed by mechanistic target of rapamycin (mTOR) kinase, but whether autophagy-related genes (ATG) proteins are phosphorylated differentially throughout the sequential phases of the cell cycle remains unclear. In this issue, Li and colleagues report that cyclin-dependent kinase 1 (CDK1) phosphorylates the ULK complex during mitosis. This phosphorylation induces autophagy and, surprisingly, is shown to drive cell cycle progression. This work reveals a yet-unappreciated role for autophagy in cell cycle progression and enhances our understanding of the specific phase-dependent autophagy regulation during cellular growth and proliferation.
    DOI:  https://doi.org/10.1371/journal.pbio.3000718
  8. PLoS Biol. 2020 Jun;18(6): e3000288
    ULK1-ATG13 and their mitotic phospho-regulation by CDK1 connect autophagy to cell cycle.
    Zhiyuan Li, Xiaofei Tian, Xinmiao Ji, Junjun Wang, Hanxiao Chen, Dongmei Wang, Xin Zhang.
      Unc-51-like autophagy activating kinase 1 (ULK1)-autophagy-related 13 (ATG13) is the most upstream autophagy initiation complex that is phosphorylated by mammalian target-of-rapamycin complex 1 (mTORC1) and AMP-activated protein kinase (AMPK) to induce autophagy in asynchronous conditions. However, their phospho-regulation and functions in mitosis and cell cycle remain unknown. Here we show that ULK1-ATG13 complex is differentially regulated throughout the cell cycle, especially in mitosis, in which both ULK1 and ATG13 are highly phosphorylated by the key cell cycle machinery cyclin-dependent kinase 1 (CDK1)/cyclin B. Combining mass spectrometry and site-directed mutagenesis, we found that CDK1-induced ULK1-ATG13 phosphorylation promotes mitotic autophagy and cell cycle progression. Moreover, double knockout (DKO) of ULK1 and ATG13 could block cell cycle progression and significantly decrease cancer cell proliferation in cell line and mouse models. Our results not only bridge the mutual regulation between the core machinery of autophagy and mitosis but also illustrate the positive function of ULK1-ATG13 and their phosphorylation by CDK1 in mitotic autophagy regulation.
    DOI:  https://doi.org/10.1371/journal.pbio.3000288
  9. EMBO Mol Med. 2020 Jun 11. e11659
    FBXL4 deficiency increases mitochondrial removal by autophagy.
    David Alsina, Oleksandr Lytovchenko, Aleksandra Schab, Ilian Atanassov, Florian A Schober, Min Jiang, Camilla Koolmeister, Anna Wedell, Robert W Taylor, Anna Wredenberg, Nils-Göran Larsson.
      Pathogenic variants in FBXL4 cause a severe encephalopathic syndrome associated with mtDNA depletion and deficient oxidative phosphorylation. To gain further insight into the enigmatic pathophysiology caused by FBXL4 deficiency, we generated homozygous Fbxl4 knockout mice and found that they display a predominant perinatal lethality. Surprisingly, the few surviving animals are apparently normal until the age of 8-12 months when they gradually develop signs of mitochondrial dysfunction and weight loss. One-year-old Fbxl4 knockouts show a global reduction in a variety of mitochondrial proteins and mtDNA depletion, whereas lysosomal proteins are upregulated. Fibroblasts from patients with FBXL4 deficiency and human FBXL4 knockout cells also have reduced steady-state levels of mitochondrial proteins that can be attributed to increased mitochondrial turnover. Inhibition of lysosomal function in these cells reverses the mitochondrial phenotype, whereas proteasomal inhibition has no effect. Taken together, the results we present here show that FBXL4 prevents mitochondrial removal via autophagy and that loss of FBXL4 leads to decreased mitochondrial content and mitochondrial disease.
    Keywords:  FBXL4; autophagy; mitochondrial disease; mtDNA; oxidative phosphorylation
    DOI:  https://doi.org/10.15252/emmm.201911659
  10. Autophagy. 2020 Jun 09. 1-19
    Live imaging of intra-lysosome pH in cell lines and primary neuronal culture using a novel genetically encoded biosensor.
    Amy H Ponsford, Thomas A Ryan, Andrea Raimondi, Emanuele Cocucci, Susanne A Wycislo, Florian Fröhlich, Laura E Swan, Massimiliano Stagi.
      Disorders of lysosomal physiology have increasingly been found to underlie the pathology of a rapidly growing cast of neurodevelopmental disorders and sporadic diseases of aging. One cardinal aspect of lysosomal (dys)function is lysosomal acidification in which defects trigger lysosomal stress signaling and defects in proteolytic capacity. We have developed a genetically encoded ratiometric probe to measure lysosomal pH coupled with a purification tag to efficiently purify lysosomes for both proteomic and in vitro evaluation of their function. Using our probe, we showed that lysosomal pH is remarkably stable over a period of days in a variety of cell types. Additionally, this probe can be used to determine that lysosomal stress signaling via TFEB is uncoupled from gross changes in lysosomal pH. Finally, we demonstrated that while overexpression of ARL8B GTPase causes striking alkalinization of peripheral lysosomes in HEK293 T cells, peripheral lysosomes per se are no less acidic than juxtanuclear lysosomes in our cell lines.
    ABBREVIATIONS: ARL8B: ADP ribosylation factor like GTPase 8B; ATP: adenosine triphosphate; ATP5F1B/ATPB: ATP synthase F1 subunit beta; ATP6V1A: ATPase H+ transporting V1 subunit A; Baf: bafilomycin A1; BLOC-1: biogenesis of lysosome-related organelles complex 1; BSA: bovine serum albumin; Cos7: African green monkey kidney fibroblast-like cell line; CQ: chloroquine; CTSB: cathepsin B; CYCS: cytochrome c, somatic; DAPI: 4',6-diamidino -2- phenylindole; DIC: differential interference contrast; DIV: days in vitro; DMEM: Dulbecco's modified Eagle's medium;‎ E8: embryonic day 8; EEA1: early endosome antigen 1; EGTA: ethylene glycol-bis(β-aminoethyl ether)-N,N,N',N'-tetraacetic acid; ER: endoplasmic reticulum; FBS: fetal bovine serum; FITC: fluorescein isothiocyanate; GABARAPL2: GABA type A receptor associated protein like 2; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GOLGA2/GM130: golgin A2; GTP: guanosine triphosphate; HEK293T: human embryonic kidney 293 cells, that expresses a mutant version of the SV40 large T antigen; HeLa: Henrietta Lacks-derived cell; HEPES: 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid; HRP: horseradish peroxidase; IGF2R/ciM6PR: insulin like growth factor 2 receptor; LAMP1/2: lysosomal associated membrane protein 1/2; LMAN2/VIP36: lectin, mannose binding 2; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MTORC1: mechanistic target of rapamycin kinase complex 1; PCR: polymerase chain reaction; PDL: poly-d-lysine; PGK1p: promotor from human phosphoglycerate kinase 1; PIKFYVE: phosphoinositide kinase, FYVE-type zinc finger containing; PPT1/CLN1: palmitoyl-protein thioesterase 1; RPS6KB1/p70: ribosomal protein S6 kinase B1; STAT3: signal transducer and activator of transcription 3; TAX1BP1: Tax1 binding protein 1; TFEB: transcription factor EB; TGN: trans-Golgi network; TGOLN2/TGN46: trans-Golgi network protein 2; TIRF: total internal reflection fluorescence; TMEM106B: transmembrane protein 106B; TOR: target of rapamycin; TRPM2: transient receptor potential cation channel subfamily M member 2; V-ATPase: vacuolar-type proton-translocating ATPase; VPS35: VPS35 retromer complex component.
    Keywords:  Chloroquine; MTOR protein; V-type ATPase; fluorescence microscopy; lysosomes; pH
    DOI:  https://doi.org/10.1080/15548627.2020.1771858
  11. Cell Discov. 2020 ;6 33
    Autophagosome biogenesis and human health.
    Tsuyoshi Kawabata, Tamotsu Yoshimori.
      Autophagy degrades the cytoplasmic contents engulfed by autophagosomes. Besides providing energy and building blocks during starvation via random degradation, autophagy selectively targets cytotoxic components to prevent a wide range of diseases. This preventive activity of autophagy is supported by many studies using animal models and reports identifying several mutations in autophagy-related genes that are associated with human genetic disorders, which have been published in the past decade. Here, we summarize the molecular mechanisms of autophagosome biogenesis involving the proteins responsible for these genetic disorders, demonstrating a role for autophagy in human health. These findings will help elucidate the underlying mechanisms of autophagy-related diseases and develop future medications.
    Keywords:  Macroautophagy; Protein quality control
    DOI:  https://doi.org/10.1038/s41421-020-0166-y
  12. EMBO J. 2020 Jun 11. e2019103649
    CALCOCO1 acts with VAMP-associated proteins to mediate ER-phagy.
    Thaddaeus Mutugi Nthiga, Birendra Kumar Shrestha, Eva Sjøttem, Jack-Ansgar Bruun, Kenneth Bowitz Larsen, Zambarlal Bhujabal, Trond Lamark, Terje Johansen.
      The endoplasmic reticulum (ER) plays important roles in protein synthesis and folding, and calcium storage. The volume of the ER and expression of its resident proteins are increased in response to nutrient stress. ER-phagy, a selective form of autophagy, is involved in the degradation of the excess components of the ER to restore homeostasis. Six ER-resident proteins have been identified as ER-phagy receptors so far. In this study, we have identified CALCOCO1 as a novel ER-phagy receptor for the degradation of the tubular ER in response to proteotoxic and nutrient stress. CALCOCO1 is a homomeric protein that binds directly to ATG8 proteins via LIR- and UDS-interacting region (UIR) motifs acting co-dependently. CALCOCO1-mediated ER-phagy requires interaction with VAMP-associated proteins VAPA and VAPB on the ER membranes via a conserved FFAT-like motif. Depletion of CALCOCO1 causes expansion of the ER and inefficient basal autophagy flux. Unlike the other ER-phagy receptors, CALCOCO1 is peripherally associated with the ER. Therefore, we define CALCOCO1 as a soluble ER-phagy receptor.
    Keywords:   FFAT ; VAPA ; Autophagy; CALCOCO1; ER-phagy
    DOI:  https://doi.org/10.15252/embj.2019103649
  13. Proc Natl Acad Sci U S A. 2020 Jun 08. pii: 201917371. [Epub ahead of print]
    ALS/FTD mutations in UBQLN2 impede autophagy by reducing autophagosome acidification through loss of function.
    Josephine J Wu, Ashley Cai, Jessie E Greenslade, Nicole R Higgins, Cong Fan, Nhat T T Le, Micaela Tatman, Alexandra M Whiteley, Miguel A Prado, Birger V Dieriks, Maurice A Curtis, Christopher E Shaw, Teepu Siddique, Richard L M Faull, Emma L Scotter, Daniel Finley, Mervyn J Monteiro.
      Mutations in UBQLN2 cause amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and other neurodegenerations. However, the mechanism by which the UBQLN2 mutations cause disease remains unclear. Alterations in proteins involved in autophagy are prominent in neuronal tissue of human ALS UBQLN2 patients and in a transgenic P497S UBQLN2 mouse model of ALS/FTD, suggesting a pathogenic link. Here, we show UBQLN2 functions in autophagy and that ALS/FTD mutant proteins compromise this function. Inactivation of UBQLN2 expression in HeLa cells reduced autophagic flux and autophagosome acidification. The defect in acidification was rescued by reexpression of wild type (WT) UBQLN2 but not by any of the five different UBQLN2 ALS/FTD mutants tested. Proteomic analysis and immunoblot studies revealed P497S mutant mice and UBQLN2 knockout HeLa and NSC34 cells have reduced expression of ATP6v1g1, a critical subunit of the vacuolar ATPase (V-ATPase) pump. Knockout of UBQLN2 expression in HeLa cells decreased turnover of ATP6v1g1, while overexpression of WT UBQLN2 increased biogenesis of ATP6v1g1 compared with P497S mutant UBQLN2 protein. In vitro interaction studies showed that ATP6v1g1 binds more strongly to WT UBQLN2 than to ALS/FTD mutant UBQLN2 proteins. Intriguingly, overexpression of ATP6v1g1 in UBQLN2 knockout HeLa cells increased autophagosome acidification, suggesting a therapeutic approach to overcome the acidification defect. Taken together, our findings suggest that UBQLN2 mutations drive pathogenesis through a dominant-negative loss-of-function mechanism in autophagy and that UBQLN2 functions as an important regulator of the expression and stability of ATP6v1g1. These findings may have important implications for devising therapies to treat UBQLN2-linked ALS/FTD.
    Keywords:  UBQLN2; amyotrophic lateral sclerosis; autophagy; ubiquilin; vacuolar ATPase pump
    DOI:  https://doi.org/10.1073/pnas.1917371117
  14. Autophagy. 2020 Jun 10.
    Autophagy as an emerging target for COVID-19: lessons from an old friend, chloroquine.
    Srinivasa Reddy Bonam, Sylviane Muller, Jagadeesh Bayry, Daniel J Klionsky.
      During the last week of December 2019, Wuhan (China) was confronted with the first case of respiratory tract disease 2019 (coronavirus disease 2019, COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Due to the rapid outbreak of the transmission (~3.64 million positive cases and high mortality as of May 5, 2020), the world is looking for immediate and better therapeutic options. Still, much information is not known, including origin of the disease, complete genomic characterization, mechanism of transmission dynamics, extent of spread, possible genetic predisposition, clinical and biological diagnosis, complete details of disease-induced pathogenicity, and possible therapeutic options. Although several known drugs are already under clinical evaluation with many in repositioning strategies, much attention has been paid to the aminoquinoline derivates, chloroquine (CQ) and hydroxychloroquine (HCQ). These molecules are known regulators of endosomes/lysosomes, which are subcellular organelles central to autophagy processes. By elevating the pH of acidic endosomes/lysosomes, CQ/HCQ inhibit the autophagic process. In this short perspective, we discuss the roles of CQ/HCQ in the treatment of COVID-19 patients and propose new ways of possible treatment for SARS-CoV-2 infection based on the molecules that selectivity target autophagy.
    Keywords:  COVID-19; SARS-CoV-2; autophagy; coronavirus; cytokine storm syndrome
    DOI:  https://doi.org/10.1080/15548627.2020.1779467
  15. Cell Death Dis. 2020 Jun 08. 11(6): 433
    Phosphorylation of eukaryotic initiation factor-2α (eIF2α) in autophagy.
    Juliette Humeau, Marion Leduc, Giulia Cerrato, Friedemann Loos, Oliver Kepp, Guido Kroemer.
      The integrated stress response is characterized by the phosphorylation of eukaryotic initiation factor-2α (eIF2α) on serine 51 by one out of four specific kinases (EIF2AK1 to 4). Here we provide three series of evidence suggesting that macroautophagy (to which we refer to as autophagy) induced by a variety of distinct pharmacological agents generally requires this phosphorylation event. First, the induction of autophagic puncta by various distinct compounds was accompanied by eIF2α phosphorylation on serine 51. Second, the modulation of autophagy by >30 chemically unrelated agents was partially inhibited in cells expressing a non-phosphorylable (S51A) mutant of eIF2α or lacking all four eIF2α kinases, although distinct kinases were involved in the response to different autophagy inducers. Third, inhibition of eIF2α phosphatases was sufficient to stimulate autophagy. In synthesis, it appears that eIF2α phosphorylation is a central event for the stimulation of autophagy.
    DOI:  https://doi.org/10.1038/s41419-020-2642-6
  16. Autophagy. 2020 Jun 10. 1-3
    Protein translocation into the ERGIC: an upstream event of secretory autophagy.
    Lei Liu, Min Zhang, Liang Ge.
      Macroautophagy/autophagy was recently shown to regulate unconventional protein secretion through a process called secretory autophagy. How the secretory cargo selectively enters into the secretory autophagosome has been a central question. Our recent studies indicate that cargo translocation into the ER-Golgi intermediate compartment, a compartment contributing membranes to the forming autophagosome, acts as a mechanism for secretory cargo entry into the vesicle and may be an early step for secretory autophagy.
    Keywords:  Autophagy; ERGIC; HSP90; TMED10; membrane trafficking; protein translocation; unconventional protein secretion
    DOI:  https://doi.org/10.1080/15548627.2020.1768668
  17. Int J Mol Sci. 2020 Jun 04. pii: E4021. [Epub ahead of print]21(11):
    Cell-Clearing Systems Bridging Repeat Expansion Proteotoxicity and Neuromuscular Junction Alterations in ALS and SBMA.
    Fiona Limanaqi, Carla Letizia Busceti, Francesca Biagioni, Federica Cantini, Paola Lenzi, Francesco Fornai.
      The coordinated activities of autophagy and the ubiquitin proteasome system (UPS) are key to preventing the aggregation and toxicity of misfold-prone proteins which manifest in a number of neurodegenerative disorders. These include proteins which are encoded by genes containing nucleotide repeat expansions. In the present review we focus on the overlapping role of autophagy and the UPS in repeat expansion proteotoxicity associated with chromosome 9 open reading frame 72 (C9ORF72) and androgen receptor (AR) genes, which are implicated in two motor neuron disorders, amyotrophic lateral sclerosis (ALS) and spinal-bulbar muscular atrophy (SBMA), respectively. At baseline, both C9ORF72 and AR regulate autophagy, while their aberrantly-expanded isoforms may lead to a failure in both autophagy and the UPS, further promoting protein aggregation and toxicity within motor neurons and skeletal muscles. Besides proteotoxicity, autophagy and UPS alterations are also implicated in neuromuscular junction (NMJ) alterations, which occur early in both ALS and SBMA. In fact, autophagy and the UPS intermingle with endocytic/secretory pathways to regulate axonal homeostasis and neurotransmission by interacting with key proteins which operate at the NMJ, such as agrin, acetylcholine receptors (AChRs), and adrenergic beta2 receptors (B2-ARs). Thus, alterations of autophagy and the UPS configure as a common hallmark in both ALS and SBMA disease progression. The findings here discussed may contribute to disclosing overlapping molecular mechanisms which are associated with a failure in cell-clearing systems in ALS and SBMA.
    Keywords:  AR; C9ORF72; GSK3b; HSPB8; TFEB; autophagy; beta2 adrenergic receptors; mTOR; nicotinic acetylcholine receptors; proteasome
    DOI:  https://doi.org/10.3390/ijms21114021
  18. Methods Mol Biol. 2020 ;2152 417-426
    Detection of p62/SQSTM1 Aggregates in Cellular Models of CCM Disease by Immunofluorescence.
    Saverio Marchi, Saverio Francesco Retta, Paolo Pinton.
      Cerebral cavernous malformations (CCM) is a familial or sporadic rare disorder that is characterized by capillary vascular lesions with a mulberry-like appearance on MRI scans. Three distinct genes have been associated to CCM disease, known as CCM1/KRIT1, CCM2/MGC4607, and CCM3/PDCD10. Loss-of-functions mutations on these genes lead to deregulation in multiple signaling pathways, thereby resulting in disturbed vessel organization and function. Insufficient autophagy has been observed upon downregulation of all three CCM genes, both in cells and human patient tissues, revealed as aberrant accumulation of the autophagy receptor p62/SQSTM1. The autophagic process is conceived as an adaptive response to stress and is essential for the maintenance of cellular homeostasis. The aim of this review is to briefly summarize the current knowledge on the role of autophagy in CCM disease and to furnish a detailed protocol for detecting and measuring p62/SQSTM1 cytoplasmic aggregates through immunofluorescence technique.
    Keywords:  Autophagy; Cerebral cavernous malformations; Protein aggregates; mTORC1 signaling; p62/SQSMT1
    DOI:  https://doi.org/10.1007/978-1-0716-0640-7_30
  19. Cell Mol Neurobiol. 2020 Jun 11.
    Autophagic Pathways to Clear the Tau Aggregates in Alzheimer's Disease.
    Nalini Vijay Gorantla, Subashchandrabose Chinnathambi.
      Tau is a microtubule-associated protein with an intrinsically unstructured conformation. Tau is subjected to several pathological post-translational modifications (PTMs), leading to its loss of interaction with microtubules and accumulation as neurofibrillary tangles (NFTs) in neurons. Tau aggregates impede functions of endoplasmic reticulum and mitochondria leading to the generation of oxidative stress and in turn amplifying the Tau aggregation. Tau is channelled to chaperones for folding into their native form, which otherwise causes its degradation and clearance. Cellular response triggers the activation of ubiquitin-proteasome system or autophagy to facilitate Tau degradation, based on the PTMs or mutations associated with Tau. Further, autophagy can be selective where Hsc70 interacts with Tau in monomeric, oligomeric and aggregated form and drives its clearance by chaperone-mediated autophagy pathway (CMA). Lysosome-associated membrane proteins-2A (LAMP-2A) is the key player of CMA that recognises Hsc70-Tau complex and triggers the downstream cascade. Thus, it becomes challenging for mutant Tau to be cleared by CMA as it loses its affinity for Hsc70 and LAMP-2A. In such a scenario, Tau might be degraded by macroautophagy otherwise sequestered by aggresomes. Henceforth, the degradation of Tau and its blockage that is associated with various PTMs of Tau would explain the dynamics of Tau degradation or accumulation in AD. Further, unveiling the role of accessory proteins involved in these degradation pathways would help in understanding their loss of function and preventing Tau clearance.
    Keywords:  Alzheimer’s disease; Chaperone-mediated autophagy; Lysosome-associated membrane proteins-2A; Macroautophagy; Neurofibrillary tangles; Tau; Tau degradation; Ubiquitin–proteasome system
    DOI:  https://doi.org/10.1007/s10571-020-00897-0
  20. Proc Natl Acad Sci U S A. 2020 Jun 08. pii: 202003277. [Epub ahead of print]
    cGMP via PKG activates 26S proteasomes and enhances degradation of proteins, including ones that cause neurodegenerative diseases.
    Jordan J S VerPlank, Sylwia D Tyrkalska, Angeleen Fleming, David C Rubinsztein, Alfred L Goldberg.
      Because raising cAMP enhances 26S proteasome activity and the degradation of cell proteins, including the selective breakdown of misfolded proteins, we investigated whether agents that raise cGMP may also regulate protein degradation. Treating various cell lines with inhibitors of phosphodiesterase 5 or stimulators of soluble guanylyl cyclase rapidly enhanced multiple proteasome activities and cellular levels of ubiquitinated proteins by activating protein kinase G (PKG). PKG stimulated purified 26S proteasomes by phosphorylating a different 26S component than is modified by protein kinase A. In cells and cell extracts, raising cGMP also enhanced within minutes ubiquitin conjugation to cell proteins. Raising cGMP, like raising cAMP, stimulated the degradation of short-lived cell proteins, but unlike cAMP, also markedly increased proteasomal degradation of long-lived proteins (the bulk of cell proteins) without affecting lysosomal proteolysis. We also tested if raising cGMP, like cAMP, can promote the degradation of mutant proteins that cause neurodegenerative diseases. Treating zebrafish models of tauopathies or Huntington's disease with a PDE5 inhibitor reduced the levels of the mutant huntingtin and tau proteins, cell death, and the resulting morphological abnormalities. Thus, PKG rapidly activates cytosolic proteasomes, protein ubiquitination, and overall protein degradation, and agents that raise cGMP may help combat the progression of neurodegenerative diseases.
    Keywords:  cGMP; proteasome phosphorylation; protein degradation; protein kinase G
    DOI:  https://doi.org/10.1073/pnas.2003277117
  21. Redox Biol. 2020 May 30. pii: S2213-2317(20)30549-8. [Epub ahead of print]36 101600
    Curcumin blunts epithelial-mesenchymal transition of hepatocytes to alleviate hepatic fibrosis through regulating oxidative stress and autophagy.
    Desong Kong, Zili Zhang, Liping Chen, Weifang Huang, Feng Zhang, Ling Wang, Yu Wang, Peng Cao, Shizhong Zheng.
      The massive production and activation of myofibroblasts (MFB) is key to the development of liver fibrosis. In many studies, it has been proven that hepatocytes are an important part of MFB, and can be transformed into MFB through epithelial-mesenchymal transition (EMT) during hepatic fibrogenesis. In our previous study, we confirmed that curcumin inhibited EMT procession and differentiation of hepatocytes into MFB. In addition, in previous studies, it has been shown that autophagy plays an important role in the regulation of cellular EMT procession. In the current study, we showed that curcumin inhibited TGF-β/Smad signaling transmission by activating autophagy, thereby inhibiting EMT. The mechanism of degradative polyubiquitylation of Smad2 and Smad3 is likely through inhibiting tetratricopeptide repeat domain 3 (TTC3) and by inducing ubiquitylation and proteasomal degradation of Smad ubiquitination regulatory factor 2 (SMURF2), which on account of the increase of autophagy in hepatocytes. Curcumin inhibits levels of reactive oxygen species (ROS) and oxidative stress in hepatocytes by activating PPAR-α, and regulates upstream signaling pathways of autophagy AMPK and PI3K/AKT/mTOR, leading to an increase of the autophagic flow in hepatocytes. In this study, we confirm that curcumin effectively reduced the occurrence of EMT in hepatocytes and inhibited production of the extracellular matrix (ECM) by activating autophagy, which provides a potential novel therapeutic strategy for hepatic fibrosis.
    Keywords:  Autophagy; Curcumin; Epithelial-mesenchymal transition (EMT); Hepatic fibrosis; Hepatocytes; Oxidative stress
    DOI:  https://doi.org/10.1016/j.redox.2020.101600
  22. Mech Ageing Dev. 2020 Jun 03. pii: S0047-6374(20)30073-7. [Epub ahead of print] 111277
    Mechanisms of neurodegeneration in Parkinson's disease: keep neurons in the PINK1.
    Francesco Brunelli, Enza Maria Valente, Giuseppe Arena.
      Extensive studies on PINK1, whose mutations are a confirmed cause of Parkinson's disease (PD), have been conducted in animal models or immortalized cell lines. These include initial ground-breaking discoveries on mitophagy, which demonstrated that PINK1 recruits Parkin on depolarized mitochondria, initiating a signalling cascade eventually resulting in their autophagic degradation. Not all features of this complex molecular pathway have been reproduced in mammalian or human neurons, undermining the hypothesis proposing mitophagy as the most relevant biochemical link between PINK1 deficiency and PD pathogenesis. Experiments in murine primary neurons examined another possible neuroprotective function of PINK1, namely its involvement in mitochondrial motility along axons and dendrites. PINK1 interacts with Miro, a component of the motor/adaptor complex binding mitochondria to microtubules and allowing their movement to and from cellular processes. Distinct subcellular pools of PINK1, cytosolic and mitochondrial, appear to regulate anterograde and retrograde transport, respectively. Technological advancements today allow researchers to de-differentiate fibroblasts into induced pluripotent stem cells and re-differentiate them into dopaminergic neurons. Few studies based on this technique address possible neuroprotective effects of PINK1, including mitophagy and mitochondrial homeostasis, but underline the need for a broader characterization of its function in neurons.
    Keywords:  Induced pluripotent stem cells (iPSC); Mitochondrial function; Neurodegeneration; PINK1; Parkinson's disease
    DOI:  https://doi.org/10.1016/j.mad.2020.111277
  23. Cancers (Basel). 2020 Jun 10. pii: E1516. [Epub ahead of print]12(6):
    Dual Targeting of BRAF and mTOR Signaling in Melanoma Cells with Pyridinyl Imidazole Compounds.
    Veronika Palušová, Tereza Renzová, Amandine Verlande, Tereza Vaclová, Michaela Medková, Linda Cetlová, Miroslava Sedláčková, Hana Hříbková, Iva Slaninová, Miriama Krutá, Vladimír Rotrekl, Hana Uhlířová, Aneta Křížová, Radim Chmelík, Pavel Veselý, Michaela Krafčíková, Lukáš Trantírek, Kay Oliver Schink, Stjepan Uldrijan.
      BRAF inhibitors can delay the progression of metastatic melanoma, but resistance usually emerges, leading to relapse. Drugs simultaneously targeting two or more pathways essential for cancer growth could slow or prevent the development of resistant clones. Here, we identified pyridinyl imidazole compounds SB202190, SB203580, and SB590885 as dual inhibitors of critical proliferative pathways in human melanoma cells bearing the V600E activating mutation of BRAF kinase. We found that the drugs simultaneously disrupt the BRAF V600E-driven extracellular signal-regulated kinase (ERK) mitogen-activated protein kinase (MAPK) activity and the mechanistic target of rapamycin complex 1 (mTORC1) signaling in melanoma cells. Pyridinyl imidazole compounds directly inhibit BRAF V600E kinase. Moreover, they interfere with the endolysosomal compartment, promoting the accumulation of large acidic vacuole-like vesicles and dynamic changes in mTOR signaling. A transient increase in mTORC1 activity is followed by the enrichment of the Ragulator complex protein p18/LAMTOR1 at contact sites of large vesicles and delocalization of mTOR from the lysosomes. The induced disruption of the endolysosomal pathway not only disrupts mTORC1 signaling, but also renders melanoma cells sensitive to endoplasmic reticulum (ER) stress. Our findings identify new activities of pharmacologically relevant small molecule compounds and provide a biological rationale for the development of anti-melanoma therapeutics based on the pyridinyl imidazole core.
    Keywords:  BRAF V600E; BRAF inhibitor; ER stress; endosome; lysosome; mTORC1; melanoma; pyridinyl imidazole; small molecule drug
    DOI:  https://doi.org/10.3390/cancers12061516
  24. Cell Rep. 2020 Jun 09. pii: S2211-1247(20)30730-0. [Epub ahead of print]31(10): 107750
    TBC1D5-Catalyzed Cycling of Rab7 Is Required for Retromer-Mediated Human Papillomavirus Trafficking during Virus Entry.
    Jian Xie, Erin N Heim, Mac Crite, Daniel DiMaio.
      During virus entry, human papillomaviruses are sorted by the cellular trafficking complex, called retromer, into the retrograde transport pathway to traffic from the endosome to downstream cellular compartments, but regulation of retromer activity during HPV entry is poorly understood. Here we selected artificial proteins that modulate cellular proteins required for HPV infection and discovered that entry requires TBC1D5, a retromer-associated, Rab7-specific GTPase-activating protein. Binding of retromer to the HPV L2 capsid protein recruits TBC1D5 to retromer at the endosome membrane, which then stimulates hydrolysis of Rab7-GTP to drive retromer disassembly from HPV and delivery of HPV to the retrograde pathway. Although the cellular retromer cargos CIMPR and DMT1-II require only GTP-bound Rab7 for trafficking, HPV trafficking requires cycling between GTP- and GDP-bound Rab7. Thus, ongoing cargo-induced membrane recruitment, assembly, and disassembly of retromer complexes drive HPV trafficking.
    Keywords:  HPV; Rab7B; TBC1D5; functional genetics screen; proximity ligation assay; retrograde; retromer; senescence; traptamer
    DOI:  https://doi.org/10.1016/j.celrep.2020.107750
  25. Bioessays. 2020 Jun 09. e1900195
    Trehalose against Alzheimer's Disease: Insights into a Potential Therapy.
    Masoomeh Khalifeh, Morgayn I Read, George E Barreto, Amirhossein Sahebkar.
      Trehalose is a natural disaccharide with a remarkable ability to stabilize biomolecules. In recent years, trehalose has received growing attention as a neuroprotective molecule and has been tested in experimental models for different neurodegenerative diseases. Although the underlying neuroprotective mechanism of trehalose's action is unclear, one of the most important hypotheses is autophagy induction. The chaperone-like activity of trehalose and the ability to modulate inflammatory responses has also been reported. There is compelling evidence that the dysfunction of autophagy and aggregation of misfolded proteins contribute to the pathogenesis of Alzheimer's disease (AD) and other neurodegenerative disorders. Therefore, given the linking between trehalose and autophagy induction, it appears to be a promising therapy for AD. Herein, the published studies concerning the use of trehalose as a potential therapy for AD are summarized, providing a rationale for applying trehalose to reduce Alzheimer's pathology.
    Keywords:  Alzheimer's disease; amyloid β; autophagy; tau; treatment; trehalose
    DOI:  https://doi.org/10.1002/bies.201900195
  26. Toxicol Appl Pharmacol. 2020 Jun 05. pii: S0041-008X(20)30214-3. [Epub ahead of print] 115090
    Cu(II) disrupts autophagy-mediated lysosomal degradation of oligomeric Aβ in microglia via mTOR-TFEB pathway.
    Xiaofang Tan, Huifeng Guan, Y Yang, Shenying Luo, Lina Hou, Hongzhuan Chen, Juan Li.
      Copper dyshomeostasis is involved in the pathogenesis of Alzheimer's disease (AD). Microglia play a major role in the proteolytic clearance of oligomeric β-amyloid (Aβo). Here, we investigated whether Cu(II) affects microglial Aβo clearance and whether this effect involves autophagy-lysosomal pathway. Microtubule associated protein 1 light chain 3 (LC3)-II and p62 protein levels and autophagic flux in Cu(II)-treated microglia were detected. Aβo clearance was detected by enzyme-linked immunosorbent assay (ELISA) and immunofluorescence. In vivo, Cu(II) and Aβo were injected into mouse hippocampus to evaluate Aβ clearance. The results showed that Cu(II) inhibited phagocytic uptake and intracellular degradation of Aβo in microglial cultures. Additionally, Cu(II) elevated LC3-II and p62 protein levels and impaired autophagic flux. It also inhibited transcription factor EB (TFEB) expression and lysosomal biogenesis. Moreover, Cu(II) activated mammalian target of rapamycin kinase (mTOR), an upstream signaling of TFEB. The mTOR inhibitor PP242 ameliorated Cu(II)-impaired TFEB expression, lysosomal biogenesis, autophagic flux, and Aβo clearance in microglia. In vivo, Cu(II) inhibited microglial Aβo clearance in mouse hippocampus, an effect accompanied with activation of mTOR and impairment of TFEB expression and lysosomal biogenesis. Collectively, our results suggest that Cu(II) reduces microglial Aβo clearance through disrupting lysosomal biogenesis and autophagic flux. This effect could involve modulation of mTOR-TFEB axis and was prevented by pharmacological antagonism of mTOR. This study reveals a novel mechanism for Cu(II) involvement in AD. Our results implicate that rescue of Cu(II)-impaired autophagy-mediated lysosomal degradation may provide a new strategy to benefit multiple neurodegenerative disorders.
    Keywords:  Autophagy; Copper; Microglia; β-Amyloid clearance
    DOI:  https://doi.org/10.1016/j.taap.2020.115090
  27. Autophagy. 2020 Jun 10.
    The C9orf72-SMCR8-WDR41 complex is a GAP for small GTPases.
    Dan Tang, Jingwen Sheng, Liangting Xu, Chuangye Yan, Shiqian Qi.
      Massive expansions of the hexanucleotide in C9orf72 are the primary genetic origins of familial amyotrophic lateral sclerosis (ALS) and frontal temporal dementia (FTD). Current studies have found that this repeat sequence participates in the disease process by producing neurotoxic substances and reducing the level of C9orf72 protein; however, the progress in the functional study of C9orf72 is slow. Recently, a stable complex, consisting of C9orf72, SMCR8, and WDR41, has been implicated in regulating membrane trafficking and macroautophagy. We reported the cryo-electron microscopy (cryo-EM) structure of the C9orf72-SMCR8-WDR41 complex (CSW complex), unveiling that the CSW complex is a dimer of heterotrimers. Intriguingly, in the heterotrimer of the C9orf72-SMCR8-WDR41, C9orf72 interacts with SMCR8 in a manner similar to the FLNC-FNIP2 complex. Nevertheless, WDR41 is connected to the DENN domain of SMCR8 through its N-terminal β-strand and C-terminal helix but does not directly interact with C9orf72. Notably, the C9orf72-SMCR8 complex was demonstrated to act as a GAP for RAB8A and RAB11A in vitro.
    Keywords:  ALS; DENN domain; FTD; Longin domain; RAB; autophagy; cryo-EM; dimer; membrane
    DOI:  https://doi.org/10.1080/15548627.2020.1779473
  28. Nat Commun. 2020 Jun 12. 11(1): 2979
    Autophagy controls the induction and developmental decline of NMDAR-LTD through endocytic recycling.
    Hongmei Shen, Huiwen Zhu, Debabrata Panja, Qinhua Gu, Zheng Li.
      NMDA receptor-dependent long-term depression (NMDAR-LTD) is a long-lasting form of synaptic plasticity. Its expression is mediated by the removal of AMPA receptors from postsynaptic membranes. Under basal conditions, endocytosed AMPA receptors are rapidly recycled back to the plasma membrane. In NMDAR-LTD, however, they are diverted to late endosomes for degradation. The mechanism for this switch is largely unclear. Additionally, the inducibility of NMDAR-LTD is greatly reduced in adulthood. The underlying mechanism and physiological significance of this phenomenon are elusive. Here, we report that autophagy inhibition is essential for the induction and developmental dampening of NMDAR-LTD. Autophagy is inhibited during NMDAR-LTD to decrease endocytic recycling. Autophagy inhibition is both necessary and sufficient for LTD induction. In adulthood, autophagy is up-regulated to make LTD induction harder, thereby preventing the adverse effect of excessive LTD on memory consolidation. These findings reveal the unrecognized functions of autophagy in synaptic plasticity, endocytic recycling, and memory.
    DOI:  https://doi.org/10.1038/s41467-020-16794-5
  29. Proc Natl Acad Sci U S A. 2020 Jun 08. pii: 201921618. [Epub ahead of print]
    PEBP1 acts as a rheostat between prosurvival autophagy and ferroptotic death in asthmatic epithelial cells.
    Jinming Zhao, Haider H Dar, Yanhan Deng, Claudette M St Croix, Zhipeng Li, Yoshinori Minami, Indira H Shrivastava, Yulia Y Tyurina, Emily Etling, Joel C Rosenbaum, Tadao Nagasaki, John B Trudeau, Simon C Watkins, Ivet Bahar, Hülya Bayır, Andy P VanDemark, Valerian E Kagan, Sally E Wenzel.
      Temporally harmonized elimination of damaged or unnecessary organelles and cells is a prerequisite of health. Under Type 2 inflammatory conditions, human airway epithelial cells (HAECs) generate proferroptotic hydroperoxy-arachidonoyl-phosphatidylethanolamines (HpETE-PEs) as proximate death signals. Production of 15-HpETE-PE depends on activation of 15-lipoxygenase-1 (15LO1) in complex with PE-binding protein-1 (PEBP1). We hypothesized that cellular membrane damage induced by these proferroptotic phospholipids triggers compensatory prosurvival pathways, and in particular autophagic pathways, to prevent cell elimination through programmed death. We discovered that PEBP1 is pivotal to driving dynamic interactions with both proferroptotic 15LO1 and the autophagic protein microtubule-associated light chain-3 (LC3). Further, the 15LO1-PEBP1-generated ferroptotic phospholipid, 15-HpETE-PE, promoted LC3-I lipidation to stimulate autophagy. This concurrent activation of autophagy protects cells from ferroptotic death and release of mitochondrial DNA. Similar findings are observed in Type 2 Hi asthma, where high levels of both 15LO1-PEBP1 and LC3-II are seen in HAECs, in association with low bronchoalveolar lavage fluid mitochondrial DNA and more severe disease. The concomitant activation of ferroptosis and autophagy by 15LO1-PEBP1 complexes and their hydroperoxy-phospholipids reveals a pathobiologic pathway relevant to asthma and amenable to therapeutic targeting.
    Keywords:  asthma; autophagy; ferroptosis
    DOI:  https://doi.org/10.1073/pnas.1921618117
  30. Nat Commun. 2020 Jun 12. 11(1): 2993
    TECPR1 promotes aggrephagy by direct recruitment of LC3C autophagosomes to lysosomes.
    Lisa Wetzel, Stéphane Blanchard, Sowmya Rama, Viola Beier, Anna Kaufmann, Thomas Wollert.
      The accumulation of protein aggregates is involved in the onset of many neurodegenerative diseases. Aggrephagy is a selective type of autophagy that counteracts neurodegeneration by degrading such aggregates. In this study, we found that LC3C cooperates with lysosomal TECPR1 to promote the degradation of disease-related protein aggregates in neural stem cells. The N-terminal WD-repeat domain of TECPR1 selectively binds LC3C which decorates matured autophagosomes. The interaction of LC3C and TECPR1 promotes the recruitment of autophagosomes to lysosomes for degradation. Augmented expression of TECPR1 in neural stem cells reduces the number of protein aggregates by promoting their autophagic clearance, whereas knockdown of LC3C inhibits aggrephagy. The PH domain of TECPR1 selectively interacts with PtdIns(4)P to target TECPR1 to PtdIns(4)P containing lysosomes. Exchanging the PH against a tandem-FYVE domain targets TECPR1 ectopically to endosomes. This leads to an accumulation of LC3C autophagosomes at endosomes and prevents their delivery to lysosomes.
    DOI:  https://doi.org/10.1038/s41467-020-16689-5
  31. Nat Commun. 2020 Jun 11. 11(1): 2958
    Autophagy-mediated apoptosis eliminates aneuploid cells in a mouse model of chromosome mosaicism.
    Shruti Singla, Lisa K Iwamoto-Stohl, Meng Zhu, Magdalena Zernicka-Goetz.
      The high incidence of aneuploidy in the embryo is considered the principal cause for low human fecundity. However, the prevalence of aneuploidy dramatically declines as pregnancy progresses, with the steepest drop occurring as the embryo completes implantation. Despite the fact that the plasticity of the embryo in dealing with aneuploidy is fundamental to normal development, the mechanisms responsible for eliminating aneuploid cells are unclear. Here, using a mouse model of chromosome mosaicism, we show that aneuploid cells are preferentially eliminated from the embryonic lineage in a p53-dependent process involving both autophagy and apoptosis before, during and after implantation. Moreover, we show that diploid cells in mosaic embryos undertake compensatory proliferation during the implantation stages to confer embryonic viability. Together, our results indicate a close link between aneuploidy, autophagy, and apoptosis to refine the embryonic cell population and ensure only chromosomally fit cells proceed through development of the fetus.
    DOI:  https://doi.org/10.1038/s41467-020-16796-3
  32. Pharmacol Res. 2020 Jun 04. pii: S1043-6618(20)31298-6. [Epub ahead of print] 104990
    Sestrin2 as a potential therapeutic target for cardiovascular diseases.
    Gao Anbo, Li Feng, Zhou Qun, Chen Linxi.
      Sestrin2 is a cysteine sulfinyl reductase that plays crucial roles in regulation of antioxidant actions. Sestrin2 provides cytoprotection against multiple stress conditions, including hypoxia, endoplasmic reticulum (ER) stress and oxidative stress. Recent research reveals that upregulation of Sestrin2 is induced by various transcription factors such as p53 and activator protein 1 (AP-1), which further promotes AMP-activated protein kinase (AMPK) activation and inhibits mammalian target of rapamycin protein kinase (mTOR) signaling. Sestrin2 triggers autophagy activity to reduce cellular reactive oxygen species (ROS) levels by promoting nuclear factor erythroid 2 (NF-E2)-related factor 2 (Nrf2) activation and Kelch-like ECH-associated protein 1 (Keap1) degradation, which plays a pivotal role in homeostasis of metabolic regulation. Under hypoxia and ER stress conditions, elevated Sestrin2 expression maintains cellular homeostasis through regulation of antioxidant genes. Sestrin2 is responsible for diminishing cellular ROS accumulation through autophagy via AMPK activation, which displays cardioprotection effect in cardiovascular diseases. In this review, we summarize the recent understanding of molecular structure, biological roles and biochemical functions of Sestrin2, and discuss the roles and mechanisms of Sestrin2 in autophagy, hypoxia and ER stress. Understanding the precise functions and exact mechanism of Sestrin2 in cellular homeostasis will provide the evidence for future experimental research and aid in the development of novel therapeutic strategies for cardiovascular diseases.
    Keywords:  Autophagy; Cardiovascular diseases; Endoplasmic reticulum stress; Oxidative stress; Sestrin2
    DOI:  https://doi.org/10.1016/j.phrs.2020.104990
  33. J Cell Mol Med. 2020 Jun 08.
    miRNA-182/Deptor/mTOR axis regulates autophagy to reduce intestinal ischaemia/reperfusion injury.
    Yunsheng Li, Yanhua Luo, Baochuan Li, Lijun Niu, Jiaxin Liu, Xiaoyun Duan.
      It had been reported miR-182 was down-regulated after intestinal ischaemia/reperfusion (I/R) damage. However, its role and potential mechanisms are still unknown. This study was aimed to elucidate the function of miR-182 in intestinal I/R injury and the underlying mechanisms. The model of intestinal injury was constructed in wild-type and Deptor knockout (KO) mice. Haematoxylin-eosin staining, Chiu's score and diamine oxidase were utilized to detect intestinal damage. RT-qPCR assay was used to detected miR-182 expression. Electronic microscopy was used to detect autophagosome. Western blot was applied to detect the expression of Deptor, S6/pS6, LC3-II/LC3-I and p62. Dual-luciferase reporter assay was used to verify the relationship between miR-182 and Deptor. The results showed miR-182 was down-regulated following intestinal I/R. Up-regulation of miR-182 reduced intestinal damage, autophagy, Deptor expression and enhanced mTOR activity following intestinal I/R. Moreover, suppression of autophagy reduced intestinal damage and inhibition of mTOR by rapamycin aggravated intestinal damage following intestinal I/R. Besides, damage of intestine was reduced and mTOR activity was enhanced in Deptor KO mice. In addition, Deptor was the target gene of miR-182 and was indispensable for the protection of miR-182 on intestine under I/R condition. Together, our research implicated up-regulation of miR-182 inhibited autophagy to alleviate intestinal I/R injury via mTOR by targeting Deptor.
    Keywords:  Deptor; autophagy; ischaemia reperfusion injury; mTOR; miR-182
    DOI:  https://doi.org/10.1111/jcmm.15420
  34. Front Neurosci. 2020 ;14 498
    "LRRK2: Autophagy and Lysosomal Activity".
    Marta Madureira, Natalie Connor-Robson, Richard Wade-Martins.
      It has been 15 years since the Leucine-rich repeat kinase 2 (LRRK2) gene was identified as the most common genetic cause for Parkinson's disease (PD). The two most common mutations are the LRRK2-G2019S, located in the kinase domain, and the LRRK2-R1441C, located in the ROC-COR domain. While the LRRK2-G2019S mutation is associated with increased kinase activity, the LRRK2-R1441C exhibits a decreased GTPase activity and altered kinase activity. Multiple lines of evidence have linked the LRRK2 protein with a role in the autophagy pathway and with lysosomal activity in neurons. Neurons rely heavily on autophagy to recycle proteins and process cellular waste due to their post-mitotic state. Additionally, lysosomal activity decreases with age which can potentiate the accumulation of α-synuclein, the pathological hallmark of PD, and subsequently lead to the build-up of Lewy bodies (LBs) observed in this disorder. This review provides an up to date summary of the LRRK2 field to understand its physiological role in the autophagy pathway in neurons and related cells. Careful assessment of how LRRK2 participates in the regulation of phagophore and autophagosome formation, autophagosome and lysosome fusion, lysosomal maturation, maintenance of lysosomal pH and calcium levels, and lysosomal protein degradation are addressed. The autophagy pathway is a complex cellular process and due to the variety of LRRK2 models studied in the field, associated phenotypes have been reported to be seemingly conflicting. This review provides an in-depth discussion of different models to assess the normal and disease-associated role of the LRRK2 protein on autophagic function. Given the importance of the autophagy pathway in Parkinson's pathogenesis it is particularly relevant to focus on the role of LRRK2 to discover novel therapeutic approaches that restore lysosomal protein degradation homeostasis.
    Keywords:  G2019S; GTPase; LRRK2; Parkinson’s disease; R1441C; autophagy; kinase; lysosomes
    DOI:  https://doi.org/10.3389/fnins.2020.00498
  35. J Gerontol A Biol Sci Med Sci. 2020 Jun 09. pii: glaa069. [Epub ahead of print]
    Aggresome-Like Formation Promotes Resistance to Proteotoxicity in Cells from Long-Lived Species.
    Bharath Sunchu, Ruben T Riordan, Zhen Yu, Ido Almog, Jovita Dimas-Munoz, Andrew C Drake, Viviana I Perez.
      The capacity of cells to maintain proteostasis declines with age, causing rapid accumulation of damaged proteins and protein aggregates, which plays an important role in age-related disease etiology. While our group and others have identified that proteostasis is enhanced in long-lived species, there are no data on whether this leads to better resistance to proteotoxicity. We compared the sensitivity of cells from long- (naked mole rat [NMR]) and short- (Mouse) lived species to proteotoxicity, by measuring the survival of fibroblasts under polyglutamine (polyQ) toxicity, a well-established model of protein aggregation. Additionally, to evaluate the contribution of proteostatic mechanisms to proteotoxicity resistance, we down-regulated a key protein of each mechanism (autophagy-ATG5; ubiquitin-proteasome-PSMD14; and chaperones-HSP27) in NMR fibroblasts. Furthermore, we analyzed the formation and subcellular localization of inclusions in long- and short-lived species. Here, we show that fibroblasts from long-lived species are more resistant to proteotoxicity than their short-lived counterparts. Surprisingly, this does not occur because the NMR cells have less polyQ82 protein aggregates, but rather they have an enhanced capacity to handle misfolded proteins and form protective perinuclear and aggresome-like inclusions. All three proteostatic mechanisms contribute to this resistance to polyQ toxicity but autophagy has the greatest effect. Overall, our data suggest that the resistance to proteotoxicity observed in long-lived species is not due to a lower level of protein aggregates but rather to enhanced handling of the protein aggregates through the formation of aggresome-like inclusions, a well-recognized protective mechanism against proteotoxicty.
    Keywords:   Proteotoxicity; Aggresomes-like inclusions; Long-lived species
    DOI:  https://doi.org/10.1093/gerona/glaa069
  36. Nanomedicine (Lond). 2020 Jun 12.
    Nanoparticles induce autophagy via mTOR pathway inhibition and reactive oxygen species generation.
    Lu Jia, Shuang-Li Hao, Wan-Xi Yang.
      Due to their unique physicochemical properties, nanoparticles (NPs) have been increasingly developed for use in various fields. However, there has been both growing negative concerns with toxicity and positive realization of opportunities in nanomedicine, coming from the growing understanding of the associations between NPs and the human body, particularly relating to their cellular autophagic effects. This review summarizes NP-induced autophagy via the modulation of the mTOR signaling pathway and other associated signals including AMPK and ERK and also demonstrates how reactive oxygen species generation greatly underlies the regulation processes. The perspectives in this review aim to contribute to NP design, particularly in consideration of nanotoxicity and the potential for the precise application of NPs in nanomedicine.
    Keywords:  autophagy; lysosome; mTOR signaling pathway; nanoparticle; reactive oxygen species
    DOI:  https://doi.org/10.2217/nnm-2019-0387
  37. FASEB J. 2020 Jun 10.
    Ischemic postconditioning attenuates acute kidney injury following intestinal ischemia-reperfusion through Nrf2-regulated autophagy, anti-oxidation, and anti-inflammation in mice.
    Rong Chen, Zi Zeng, Yun-Yan Zhang, Chen Cao, Hui-Min Liu, Wei Li, Yang Wu, Zhong-Yuan Xia, Daqing Ma, Qing-Tao Meng.
      Intestinal ischemia-reperfusion (IIR) often occurs during and following major cardiovascular or gut surgery and causes significant organ including kidney injuries. This study was to investigate the protective effect of intestinal ischemic postconditioning (IPo) on IIR-induced acute kidney injury (AKI) and the underling cellular signaling mechanisms with focus on the Nrf2/HO-1. Adult C57BL/6J mice were subjected to IIR with or without IPo. IIR was established by clamping the superior mesenteric artery (SMA) for 45 minutes followed by 120 minutes reperfusion. Outcome measures were: (i) Intestinal and renal histopathology; (ii) Renal function; (iii) Cellular signaling changes; (iv) Oxidative stress and inflammatory responses. IPo significantly attenuated IIR-induced kidney injury. Furthermore, IPo significantly increased both nuclear Nrf2 and HO-1 expression in the kidney, upregulated autophagic flux, inhibited IIR-induced inflammation and reduced oxidative stress. The protective effect of IPo was abolished by the administration of Nrf2 inhibitor (Brusatol) or Nrf2 siRNA. Conversely, a Nrf2 activator t-BHQ has a similar protective effect to that of IPo. Our data indicate that IPo protects the kidney injury induced by IIR, which was likely mediated through the Nrf2/HO-1 cellular signaling activation.
    Keywords:  Nrf2/HO-1 pathway; acute kidney injury; autophagy; intestinal ischemia-reperfusion; ischemic postconditioning
    DOI:  https://doi.org/10.1096/fj.202000274R
  38. Cell Death Dis. 2020 Jun 08. 11(6): 425
    Human telomerase reverse transcriptase positively regulates mitophagy by inhibiting the processing and cytoplasmic release of mitochondrial PINK1.
    Woo Hyun Shin, Kwang Chul Chung.
      Mutations in the phosphatase and tensin homologue-induced putative kinase 1 (PINK1) gene have been linked to an early-onset autosomal recessive form of familial Parkinson's disease (PD). PINK1, a mitochondrial serine/threonine-protein kinase, plays an important role in clearing defective mitochondria by mitophagy - the selective removal of mitochondria through autophagy. Evidence suggests that alteration of the PINK1 pathway contributes to the pathogenesis of PD, but the mechanisms by which the PINK1 pathway regulates mitochondrial quality control through mitophagy remain unclear. Human telomerase reverse transcriptase (hTERT) is a catalytic subunit of telomerase that functions in telomere maintenance as well as several non-telomeric activities. For example, hTERT has been associated with cellular immortalization, cell growth control, and mitochondrial regulation. We determined that hTERT negatively regulates the cleavage and cytosolic processing of PINK1 and enhances its mitochondrial localization by inhibiting mitochondrial processing peptidase β (MPPβ). Consequently, hTERT promotes mitophagy following carbonyl cyanide m-chlorophenylhydrazone (CCCP)-induced mitochondrial dysfunction and improves the function of damaged mitochondria by modulating PINK1. These findings suggest that hTERT positively regulates PINK1 function, leading to increased mitophagy following mitochondrial damage.
    DOI:  https://doi.org/10.1038/s41419-020-2641-7
  39. J Cell Biol. 2020 Jul 06. pii: e201911047. [Epub ahead of print]219(7):
    ULK complex organization in autophagy by a C-shaped FIP200 N-terminal domain dimer.
    Xiaoshan Shi, Adam L Yokom, Chunxin Wang, Lindsey N Young, Richard J Youle, James H Hurley.
      The autophagy-initiating human ULK complex consists of the kinase ULK1/2, FIP200, ATG13, and ATG101. Hydrogen-deuterium exchange mass spectrometry was used to map their mutual interactions. The N-terminal 640 residues (NTD) of FIP200 interact with the C-terminal IDR of ATG13. Mutations in these regions abolish their interaction. Negative stain EM and multiangle light scattering showed that FIP200 is a dimer, while a single molecule each of the other subunits is present. The FIP200NTD is flexible in the absence of ATG13, but in its presence adopts the shape of the letter C ∼20 nm across. The ULK1 EAT domain interacts loosely with the NTD dimer, while the ATG13:ATG101 HORMA dimer does not contact the NTD. Cryo-EM of the NTD dimer revealed a structural similarity to the scaffold domain of TBK1, suggesting an evolutionary similarity between the autophagy-initiating TBK1 kinase and the ULK1 kinase complex.
    DOI:  https://doi.org/10.1083/jcb.201911047
  40. Am J Hypertens. 2020 Apr 06. pii: hpaa058. [Epub ahead of print]
    Mitophagy in Hypertension-Associated Premature Vascular Aging.
    Zachary J Schreckenberger, Camilla F Wenceslau, Bina Joe, Cameron G McCarthy.
      Hypertension has been described as a condition of premature vascular aging, relative to actual chronological age. In fact, many factors that contribute to the deterioration of vascular function as we age are accelerated and exacerbated in hypertension. Nonetheless, the precise mechanisms that underlie the aged phenotype of arteries from hypertensive patients and animals remain elusive. Classically, the aged phenotype is the buildup of cellular debris and dysfunctional organelles. One means by which this can occur is insufficient degradation and cellular recycling. Mitophagy is the selective catabolism of damaged mitochondria. Mitochondria are organelles that contribute importantly to the determination of cellular age via their production of reactive oxygen species (ROS; Harman's free radical theory of aging). Therefore, the accumulation of dysfunctional and ROS-producing mitochondria could contribute to the acceleration of vascular age in hypertension. This review will address and critically evaluate the current literature on mitophagy in vascular physiology and hypertension.
    Keywords:  blood pressure; hypertension; mitophagy; premature vascular aging
    DOI:  https://doi.org/10.1093/ajh/hpaa058
  41. Autophagy. 2020 Jun 09. 1-21
    Atg21 organizes Atg8 lipidation at the contact of the vacuole with the phagophore.
    Lena Munzel, Piotr Neumann, Florian B Otto, Roswitha Krick, Janina Metje-Sprink, Benjamin Kroppen, Narain Karedla, Jörg Enderlein, Michael Meinecke, Ralf Ficner, Michael Thumm.
      Coupling of Atg8 to phosphatidylethanolamine is crucial for the expansion of the crescent-shaped phagophore during cargo engulfment. Atg21, a PtdIns3P-binding beta-propeller protein, scaffolds Atg8 and its E3-like complex Atg12-Atg5-Atg16 during lipidation. The crystal structure of Atg21, in complex with the Atg16 coiled-coil domain, showed its binding at the bottom side of the Atg21 beta-propeller. Our structure allowed detailed analyses of the complex formation of Atg21 with Atg16 and uncovered the orientation of the Atg16 coiled-coil domain with respect to the membrane. We further found that Atg21 was restricted to the phagophore edge, near the vacuole, known as the vacuole isolation membrane contact site (VICS). We identified a specialized vacuolar subdomain at the VICS, typical of organellar contact sites, where the membrane protein Vph1 was excluded, while Vac8 was concentrated. Furthermore, Vac8 was required for VICS formation. Our results support a specialized organellar contact involved in controlling phagophore elongation.
    Keywords:  Atg16; Atg21; Atg8 lipidation; VICS; organellar contact site; phagophore elongation
    DOI:  https://doi.org/10.1080/15548627.2020.1766332
  42. Front Genet. 2020 ;11 519
    GTR1 Affects Nitrogen Consumption and TORC1 Activity in Saccharomyces cerevisiae Under Fermentation Conditions.
    Jennifer Molinet, Francisco Salinas, José Manuel Guillamón, Claudio Martínez.
      The TORC1 pathway coordinates cell growth in response to nitrogen availability present in the medium, regulating genes related to nitrogen transport and metabolism. Therefore, the adaptation of Saccharomyces cerevisiae to changes in nitrogen availability implies variations in the activity of this signaling pathway. In this sense, variations in nitrogen detection and signaling pathway are one of the main causes of differences in nitrogen assimilation during alcoholic fermentation. Previously, we demonstrated that allelic variants in the GTR1 gene underlying differences in ammonium and amino acids consumption between Wine/European (WE) and West African (WA) strains impact the expression of nitrogen transporters. The GTR1 gene encodes a GTPase that participates in the EGO complex responsible for TORC1 activation in response to amino acids availability. In this work, we assessed the role of the GTR1 gene on nitrogen consumption under fermentation conditions, using a high sugar concentration medium with nitrogen limitation and in the context of the WE and WA genetic backgrounds. The gtr1Δ mutant presented a reduced TORC1 activity and increased expression levels of nitrogen transporters, which in turn favored ammonium consumption, but decreased amino acid assimilation. Furthermore, to identify the SNPs responsible for differences in nitrogen consumption during alcoholic fermentation, we studied the polymorphisms present in the GTR1 gene. We carried out swapping experiments for the promoter and coding regions of GTR1 between the WE and WA strains. We observed that polymorphisms in the coding region of the WA GTR1 gene are relevant for TORC1 activity. Altogether, our results highlight the role of the GTR1 gene on nitrogen consumption in S. cerevisiae under fermentation conditions.
    Keywords:  GTR1 gene; Saccharomyces cerevisiae; TORC1 pathway; allelic diversity; wine fermentation
    DOI:  https://doi.org/10.3389/fgene.2020.00519
  43. Oxid Med Cell Longev. 2020 ;2020 7156579
    Autophagy Induced by ROS Aggravates Testis Oxidative Damage in Diabetes via Breaking the Feedforward Loop Linking p62 and Nrf2.
    Yuanyuan Tian, Wei Song, Dongsheng Xu, Xiao Chen, Xiaojiao Li, Yuguang Zhao.
      Testicular dysfunction due to hyperglycemia is the main cause of infertility in diabetic men. Over the years, in order to solve this growing problem, a lot of research has been done and a variety of treatments have been created, but so far, there is no safe, effective, and practical method to prevent male infertility caused by diabetes. In this review, we emphasize the male infertility mechanism caused by diabetes from the effects of oxidative stress and autophagy on the function of testes via the PI3K/Akt/mTOR signaling pathway, and we highlight that oxidative stress-induced autophagy breaks the feedforward loop linking Nrf2 and p62 and promotes oxidative damage in diabetic testes.
    DOI:  https://doi.org/10.1155/2020/7156579
  44. J Theor Biol. 2020 Jun 06. pii: S0022-5193(20)30215-0. [Epub ahead of print] 110360
    Crosstalk dynamics between the circadian clock and the mTORC1 pathway.
    José G Guerrero-Morín, Moisés Santillán.
      Crosstalk between the circadian clock clockwork and cellular metabolic regulatory networks is crucial to ensure an adequate response of an organism to the day/night cycle. mTOR (mammalian/mechanistic target of rapamycin) is a master growth regulator and sensor of nutrient status, which is part of the mTOR complex 1 (mTORC1). While the circadian clock confers rhythmicity to the mTOR protein by regulating its degradation rate, mTORC1 activity diminishes period and augments amplitude of circadian oscillations at the cellular level by a currently unknown mechanism. Here, we develop a mathematical deterministic DAE (differential-algebraic equation) model, to explore the possible interactions that allow mTORC1 to display such regulation of the core circadian clock. Our results suggest that mTORC1 is capable of regulating amplitude by exerting translational control on core the clock protein BMAL1, and that period-tuning is achieved by controlling post-translational localization of BMAL1. Since, in our model, mTORC1 control of BMAL1 localization greatly diminishes the ability of the clock to oscillate, and regulation of BMAL1 translation reduces this effect, our results also suggest that both levels of regulation must be present to ensure the robustness of oscillations. Together, the above results emphasize the importance of the influence of mTORC1 on the circadian rhythms.
    DOI:  https://doi.org/10.1016/j.jtbi.2020.110360
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