bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2019–11–10
nineteen papers selected by
Viktor Korolchuk, Newcastle University
  1. Regulation of lysosome integrity and lysophagy by the ubiquitin-conjugating enzyme UBE2QL1.
  2. Mitochondrial Perturbations Couple mTORC2 to Autophagy in C. elegans.
  3. TRIM32 acts both as a substrate and a positive regulator of p62/SQSTM1 impaired in a muscular dystrophy disease.
  4. Ubiquitin and Receptor Dependent Mitophagy Pathways and Their Implication in Neurodegeneration.
  5. Dysregulation of TFEB contributes to Manganese-induced Autophagic Failure and Mitochondrial Dysfunction in Astrocytes.
  6. Anabolic SIRT4 exerts retrograde control over TORC1 signalling by glutamine sparing in the mitochondria.
  7. Lipid signalling drives proteolytic rewiring of mitochondria by YME1L.
  8. PTK2/FAK regulates UPS impairment via SQSTM1/p62 phosphorylation in TARDBP/TDP-43 proteinopathies.
  9. The lysosomal membrane protein LAMP-2 is dispensable for PINK1/Parkin-mediated mitophagy.
  10. Negative Regulator of Ubiquitin-Like Protein 1 modulates the autophagy-lysosomal pathway via p62 to facilitate the extracellular release of tau following proteasome impairment.
  11. ON THE RELEVANCE OF PRECISION AUTOPHAGY FLUX CONTROL IN VIVO - POINTS OF DEPARTURE FOR CLINICAL TRANSLATION.
  12. STYK1 promotes autophagy through enhancing the assembly of autophagy-specific class III phosphatidylinositol 3-kinase complex I.
  13. Negative regulation of autophagy by UBA6-BIRC6-mediated ubiquitination of LC3.
  14. Autophagosome-lysosome fusion.
  15. Cryo-EM Structure of the Human FLCN-FNIP2-Rag-Ragulator Complex.
  16. The many functions of ESCRTs.
  17. SQSTM-1/p62 potentiates HTLV-1 Tax-mediated NF-κB activation through its ubiquitin binding function.
  18. A Double Negative Feedback Loop between mTORC1 and AMPK Kinases Guarantees Precise Autophagy Induction upon Cellular Stress.
  19. TFEB drives PGC-1α expression in adipocytes to protect against diet-induced metabolic dysfunction.
  1. Autophagy. 2019 Nov 06. 1-2
    Regulation of lysosome integrity and lysophagy by the ubiquitin-conjugating enzyme UBE2QL1.
    Bojana Kravic, Christian Behrends, Hemmo Meyer.
      Lysosomal membrane permeabilization or full rupture of lysosomes is a common and severe stress condition that is relevant for degenerative disease, infection and cancer. Cells respond with extensive ubiquitination of damaged lysosomes, which triggers selective macroautophagy/autophagy of the whole organelle, termed lysophagy. We screened an siRNA library targeting human E2-conjugating enzymes and identified UBE2QL1 as critical for efficient lysosome ubiquitination after chemically-induced lysosomal damage. UBE2QL1 translocates to lysosomes upon damage and associates with autophagy regulators. Loss of UBE2QL1-mediated ubiquitination reduces association of the autophagy receptor SQSTM1/p62 and the LC3-decorated phagophore, and prevents recruitment of the ubiquitin-targeted AAA-ATPase VCP/p97 that facilitates lysophagy. Even in unchallenged cells, UBE2QL1 depletion leads to MTOR dissociation and TFEB activation, and mutation of the homolog UBC-25 destabilizes lysosomes in C. elegans, indicating that UBE2QL1 is critical for maintaining lysosome integrity in addition to lysophagy.
    Keywords:  Lysophagy; lysosomal membrane permeabilization; neurodegeneration; stress response; ubiquitin
    DOI:  https://doi.org/10.1080/15548627.2019.1687217
  2. Cell Rep. 2019 Nov 05. pii: S2211-1247(19)31269-0. [Epub ahead of print]29(6): 1399-1409.e5
    Mitochondrial Perturbations Couple mTORC2 to Autophagy in C. elegans.
    Helena Aspernig, Thomas Heimbucher, Wenjing Qi, Dipak Gangurde, Sedric Curic, Yijian Yan, Erika Donner von Gromoff, Ralf Baumeister, Antje Thien.
      Autophagy is stimulated by stress conditions and needs to be precisely tuned to ensure cellular homeostasis and organismal development and health. The kinase mechanistic target of rapamycin (mTOR) forms the enzymatic core of the highly conserved mTOR complexes mTORC1 and mTORC2. mTORC1 is a key inhibitor of autophagy, yet the function of mTORC2 in autophagy is controversial. We here show that inactivation of mTORC2 and its direct target serum- and glucocorticoid-inducible kinase 1 (SGK-1) potently induces autophagy and the autophagic degradation of mitochondria in C. elegans. Enhanced autophagy in mTORC2- or SGK-1-deficient animals contributes to their developmental and reproductive defects and is independent of the canonical SGK-1 effector DAF-16/FOXO. Importantly, we find that inactivation of mTORC2-SGK-1 signaling impairs mitochondrial homeostasis and triggers an increased release of mitochondria-derived reactive oxygen species (mtROS) to induce autophagy. Thus, mitochondrial stress couples reduced mTORC2 activity to enhanced autophagic turnover.
    Keywords:  ROS; SGK-1; autophagy; mTOR; mTORC2; mammalian target of rapamycin; mitochondria; mitophagy; reactive oxygen species; serum glucocorticoid-regulated kinase 1
    DOI:  https://doi.org/10.1016/j.celrep.2019.09.072
  3. J Cell Sci. 2019 Nov 04. pii: jcs.236596. [Epub ahead of print]
    TRIM32 acts both as a substrate and a positive regulator of p62/SQSTM1 impaired in a muscular dystrophy disease.
    Katrine Stange Overå, Juncal Garcia Garcia, Zambarlal Bhujabal, Ashish Jain, Aud Øvervatn, Kenneth Bowitz Larsen, Vojo Deretic, Terje Johansen, Trond Lamark, Eva Sjøttem.
      The tripartite motif (TRIM) proteins constitute a family of ubiquitin E3 ligases involved in a multitude of cellular processes, including protein homeostasis and autophagy. TRIM32 is characterized by six protein-protein interaction domains termed NHL, in which various point mutations are associated with limb-girdle-muscular dystrophy 2H (LGMD2H). We show that TRIM32 is an autophagy substrate. Lysosomal degradation of TRIM32 was dependent on ATG7 and blocked by knock out of the five autophagy receptors p62/SQSTM1, NBR1, NDP52, TAX1BP1 and OPTN pointing towards degradation by selective autophagy. p62/SQSTM1 directed TRIM32 to lysosomal degradation, while TRIM32 mono-ubiquitylated p62/SQSTM1 on lysine residues involved in regulation of p62/SQSTM1 activity. Loss of TRIM32 impaired p62/SQSTM1 sequestration, while reintroduction of TRIM32 facilitated p62/SQSTM1 dot formation and its autophagic degradation. The TRIM32LGMD2H disease mutant was unable to undergo autophagic degradation and to mono-ubiquitylate p62/SQSTM1, and its reintroduction into the TRIM32 KO cells did not affect p62/SQSTM1 dot formation. In light of the important roles of autophagy and p62/SQSTM1 in muscle cell proteostasis, our results point towards impaired TRIM32 mediated regulation of p62/SQSTM1 activity as a pathological mechanisms in LGMD2H.
    Keywords:  AUTOPHAGY; BBS11; LGMD2H; P62/SQSTM1; TRIM32; UBIQUITYLATION
    DOI:  https://doi.org/10.1242/jcs.236596
  4. J Mol Biol. 2019 Nov 02. pii: S0022-2836(19)30611-4. [Epub ahead of print]
    Ubiquitin and Receptor Dependent Mitophagy Pathways and Their Implication in Neurodegeneration.
    Lauren E Fritsch, M Elyse Moore, Shireen A Sarraf, Alicia M Pickrell.
      Selective autophagy of mitochondria, or mitophagy, refers to the specific removal and degradation of damaged or surplus mitochondria via targeting to the lysosome for destruction. Disruptions in this homeostatic process may contribute to disease. The identification of diverse mitophagic pathways and how selectivity for each of these pathways is conferred is just beginning to be understood. The removal of both damaged and healthy mitochondria under disease and physiological conditions is controlled by either ubiquitin-dependent or receptor-dependent mechanisms. In this review, we will discuss the known types of mitophagy observed in mammals, recent findings related to PINK1/Parkin-mediated mitophagy (which is the most well-studied form of mitophagy), discuss the implications of defective mitophagy to neurodegenerative processes, and unanswered questions inspiring future research that would enhance our understanding of mitochondrial quality control.
    Keywords:  ATG8; BNIP3L/Nix; PINK1/Parkin; autophagosome; mitochondria; ubiquitin
    DOI:  https://doi.org/10.1016/j.jmb.2019.10.015
  5. Autophagy. 2019 Nov 05.
    Dysregulation of TFEB contributes to Manganese-induced Autophagic Failure and Mitochondrial Dysfunction in Astrocytes.
    Ziyan Zhang, Jingqi Yan, Aaron B Bowman, Miles R Bryan, Rajat Singh, Michael Aschner.
      Epidemiological and clinical studies have long shown that exposure to high levels of heavy metals are associated with increased risks of neurodegenerative diseases. It is widely accepted that autophagic dysfunction is involved in pathogenesis of various neurodegenerative disorders; however, the role of heavy metals in regulation of macroautophagy/autophagy is unclear. Here, we show that manganese (Mn) induces a decline in nuclear localization of TFEB (transcription factor EB), a master regulator of the autophagy-lysosome pathway, leading to autophagic dysfunction in astrocytes of mouse striatum. We further show that Mn exposure suppresses autophagic-lysosomal degradation of mitochondria and induces accumulation of unhealthy mitochondria. Activation of autophagy by rapamycin or TFEB overexpression ameliorates Mn-induced mitochondrial respiratory dysfunction and reactive oxygen species (ROS) generation in astrocytes, suggesting a causal relation between autophagic failure and mitochondrial dysfunction in Mn toxicity. Taken together, our data demonstrate that Mn inhibits TFEB activity, leading to impaired autophagy that is causally related to mitochondrial dysfunction in astrocytes. These findings reveal a previously unappreciated role for Mn in dysregulation of autophagy and identify TFEB as a potential therapeutic target to mitigate Mn toxicity.
    Keywords:  TFEB; astrocytes; autophagy; manganese toxicity; mitochondrial dysfunction; rapamycin
    DOI:  https://doi.org/10.1080/15548627.2019.1688488
  6. Mol Cell Biol. 2019 Nov 04. pii: MCB.00212-19. [Epub ahead of print]
    Anabolic SIRT4 exerts retrograde control over TORC1 signalling by glutamine sparing in the mitochondria.
    Eisha Shaw, Manasi Talwadekar, Zeenat Rashida, Nitya Mohan, Aishwarya Acharya, Subhash Khatri, Sunil Laxman, Ullas Kolthur-Seetharam.
      Anabolic and catabolic signalling mediated via mTOR and AMPK have to be intrinsically coupled to mitochondrial functions for maintaining homeostasis and mitigate cellular/organismal stress. Although, glutamine is known to activate mTOR, if/how differential mitochondrial utilization of glutamine impinges on mTOR signalling is less explored. Mitochondrial SIRT4, which unlike other sirtuins is induced in a fed state, is known to inhibit catabolic signalling/pathways through AMPK-PGC1α/SIRT1-PPARα axis and negatively regulate glutamine metabolism via TCA cycle. However, physiological significance of SIRT4 functions during a fed state is still unknown. Here, we establish SIRT4 as key anabolic factor that activates TORC1 signalling and regulates lipogenesis, autophagy and cell proliferation. Mechanistically, we demonstrate that the ability of SIRT4 to inhibit anaplerotic conversion of glutamine to α-ketoglutarate potentiates TORC1. Interestingly, we also show that mitochondrial glutamine sparing or utilization is critical for differentially regulating TORC1 under fed and fasted conditions. Moreover, we conclusively show that differential expression of SIRT4 during fed and fasted states is vital for coupling mitochondrial energetics and glutamine utilization with anabolic pathways. These significant findings also illustrate that SIRT4 integrates nutrient inputs with mitochondrial retrograde signals to maintain a balance between anabolic and catabolic pathways.
    DOI:  https://doi.org/10.1128/MCB.00212-19
  7. Nature. 2019 Nov 06.
    Lipid signalling drives proteolytic rewiring of mitochondria by YME1L.
    Thomas MacVicar, Yohsuke Ohba, Hendrik Nolte, Fiona Carola Mayer, Takashi Tatsuta, Hans-Georg Sprenger, Barbara Lindner, Yue Zhao, Jiahui Li, Christiane Bruns, Marcus Krüger, Markus Habich, Jan Riemer, Robin Schwarzer, Manolis Pasparakis, Sinika Henschke, Jens C Brüning, Nicola Zamboni, Thomas Langer.
      Reprogramming of mitochondria provides cells with the metabolic flexibility required to adapt to various developmental transitions such as stem cell activation or immune cell reprogramming, and to respond to environmental challenges such as those encountered under hypoxic conditions or during tumorigenesis1-3. Here we show that the i-AAA protease YME1L rewires the proteome of pre-existing mitochondria in response to hypoxia or nutrient starvation. Inhibition of mTORC1 induces a lipid signalling cascade via the phosphatidic acid phosphatase LIPIN1, which decreases phosphatidylethanolamine levels in mitochondrial membranes and promotes proteolysis. YME1L degrades mitochondrial protein translocases, lipid transfer proteins and metabolic enzymes to acutely limit mitochondrial biogenesis and support cell growth. YME1L-mediated mitochondrial reshaping supports the growth of pancreatic ductal adenocarcinoma (PDAC) cells as spheroids or xenografts. Similar changes to the mitochondrial proteome occur in the tumour tissues of patients with PDAC, suggesting that YME1L is relevant to the pathophysiology of these tumours. Our results identify the mTORC1-LIPIN1-YME1L axis as a post-translational regulator of mitochondrial proteostasis at the interface between metabolism and mitochondrial dynamics.
    DOI:  https://doi.org/10.1038/s41586-019-1738-6
  8. Autophagy. 2019 Nov 05. 1-17
    PTK2/FAK regulates UPS impairment via SQSTM1/p62 phosphorylation in TARDBP/TDP-43 proteinopathies.
    Shinrye Lee, Yu-Mi Jeon, Sun Joo Cha, Seyeon Kim, Younghwi Kwon, Myungjin Jo, You-Na Jang, Seongsoo Lee, Jaekwang Kim, Sang Ryong Kim, Kea Joo Lee, Sung Bae Lee, Kiyoung Kim, Hyung-Jun Kim.
      TARDBP/TDP-43 (TAR DNA binding protein) proteinopathies are a common feature in a variety of neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration (FTLD), and Alzheimer disease (AD). However, the molecular mechanisms underlying TARDBP-induced neurotoxicity are largely unknown. In this study, we demonstrated that TARDBP proteinopathies induce impairment in the ubiquitin proteasome system (UPS), as evidenced by an accumulation of ubiquitinated proteins and a reduction in proteasome activity in neuronal cells. Through kinase inhibitor screening, we identified PTK2/FAK (PTK2 protein tyrosine kinase 2) as a suppressor of neurotoxicity induced by UPS impairment. Importantly, PTK2 inhibition significantly reduced ubiquitin aggregates and attenuated TARDBP-induced cytotoxicity in a Drosophila model of TARDBP proteinopathies. We further identified that phosphorylation of SQSTM1/p62 (sequestosome 1) at S403 (p-SQSTM1 [S403]), a key component in the autophagic degradation of poly-ubiquitinated proteins, is increased upon TARDBP overexpression and is dependent on the activation of PTK2 in neuronal cells. Moreover, expressing a non-phosphorylated form of SQSTM1 (SQSTM1S403A) significantly repressed the accumulation of insoluble poly-ubiquitinated proteins and neurotoxicity induced by TARDBP overexpression in neuronal cells. In addition, TBK1 (TANK binding kinase 1), a kinase that phosphorylates S403 of SQSTM1, was found to be involved in the PTK2-mediated phosphorylation of SQSTM1. Taken together, our data suggest that the PTK2-TBK1-SQSTM1 axis plays a critical role in the pathogenesis of TARDBP by regulating neurotoxicity induced by UPS impairment. Therefore, targeting the PTK2-TBK1-SQSTM1 axis may represent a novel therapeutic intervention for neurodegenerative diseases with TARDBP proteinopathies.Abbreviations: ALP: macroautophagy/autophagy lysosomal pathway; ALS: amyotrophic lateral sclerosis; ATXN2: ataxin 2; BafA1: bafilomycin A1; cCASP3: cleaved caspase 3; CSNK2: casein kinase 2; FTLD: frontotemporal lobar degeneration; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; OPTN: optineurin; PTK2/FAK: PTK2 protein tyrosine kinase 2; SQSTM1/p62: sequestosome 1; TARDBP/TDP-43: TAR DNA binding protein; TBK1: TANK binding kinase 1; ULK1: unc-51 like autophagy activating kinase 1; UPS: ubiquitin-proteasome system.
    Keywords:  Amyotrophic lateral sclerosis; PTK2/FAK; SQSTM1/p62; TARDBP/TDP-43; ubiquitin-proteasome system
    DOI:  https://doi.org/10.1080/15548627.2019.1686729
  9. FEBS Lett. 2019 Nov 06.
    The lysosomal membrane protein LAMP-2 is dispensable for PINK1/Parkin-mediated mitophagy.
    Xuemei Liu, Xinyi Liao, Xiyun Rao, Bin Wang, Jun Zhang, Ge Xu, Xuejun Jiang, Xia Qin, Chengzhi Chen, Zhen Zou.
      Selective autophagy for elimination of aberrant mitochondria, termed mitophagy, can be regulated by the kinase PINK1 and the ubiquitin ligase Parkin. The lysosome-associated membrane protein 2 (LAMP-2) plays diverse functions in non-selective autophagy, chaperone-mediated autophagy and selective autophagy for the degradation of RNA/DNA. Here, we investigated whether LAMP-2 plays important roles during PINK1/Parkin-mediated mitophagy. Our results clearly show that knockdown of LAMP-2 does not cause defects in mitophagy in HeLa cells stably expressing Parkin, indicating that LAMP-2 is dispensable for PINK1/Parkin-mediated mitophagy. Our study is the first to determine the potential role of LAMP-2 in PINK1/Parkin-mediated mitophagy, thereby helping us gain more insights into the sophisticated process of mitophagy.
    Keywords:  LAMP-2; PINK1; Parkin; mitochondria; mitophagy
    DOI:  https://doi.org/10.1002/1873-3468.13663
  10. Hum Mol Genet. 2019 Nov 06. pii: ddz255. [Epub ahead of print]
    Negative Regulator of Ubiquitin-Like Protein 1 modulates the autophagy-lysosomal pathway via p62 to facilitate the extracellular release of tau following proteasome impairment.
    Rosellina Guarascio, Dervis Salih, Marina Yasvoina, Frances A Edwards, Michael E Cheetham, Jacqueline van der Spuy.
      Negative Regulator of Ubiquitin-Like Protein 1 (NUB1) and its longer isoform NUB1L are ubiquitin-like (UBL)/ubiquitin-associated (UBA) proteins that facilitate the targeting of proteasomal substrates, including tau, synphilin-1 and huntingtin. Previous data revealed that NUB1 also mediated a reduction in tau phosphorylation and aggregation following proteasome inhibition, suggesting a switch in NUB1 function from targeted proteasomal degradation to a role in autophagy. Here, we delineate the mechanisms of this switch and show that NUB1 interacted specifically with p62 and induced an increase in p62 levels in a manner facilitated by inhibition of the proteasome. NUB1 moreover increased autophagosomes and the recruitment of lysosomes to aggresomes following proteasome inhibition. Autophagy flux assays revealed that NUB1 affected the autophagy-lysosomal pathway primarily via the UBA domain. NUB1 localized to cytosolic inclusions with pathological forms of tau, as well as LAMP1 and p62 in the hippocampal neurons of tauopathy mice. Finally, NUB1 facilitated the extracellular release of tau following proteasome inhibition. This study thus shows that NUB1 plays a role in regulating the autophagy-lysosomal pathway when the ubiquitin proteasome system is compromised, thus contributing to the mechanisms targeting the removal of aggregation-prone proteins upon proteasomal impairment.
    DOI:  https://doi.org/10.1093/hmg/ddz255
  11. Autophagy. 2019 Nov 03.
    ON THE RELEVANCE OF PRECISION AUTOPHAGY FLUX CONTROL IN VIVO - POINTS OF DEPARTURE FOR CLINICAL TRANSLATION.
    Ben Loos, Daniel J Klionsky, Andre du Toit, Jan-Hendrik S Hofmeyr.
      Macroautophagy (which we will call autophagy hereafter) is a critical intracellular bulk degradation system that is active at basal rates in eukaryotic cells. This process is embedded in the homeostasis of nutrient availability and cellular metabolic demands, degrading primarily long-lived proteins and some organelles, preserving cell viability. Autophagy is perturbed in many pathological conditions, and its manipulation to either enhance or inhibit this pathway therapeutically has received considerable attention. Although better probes are being developed for a more precise readout of autophagic activity in vitro and increasingly in vivo, many questions remain. These center in particular around the accurate measurement of autophagic flux and its translation from the in vitro to the in vivo environment as well as its application in the clinic. In this review, we highlight some of the key aspects that appear to contribute to stumbling blocks on the road towards clinical translation and discuss points of departure for reaching some of the desired goals. We discuss techniques that may be well aligned with achieving the desired spatiotemporal resolution to gather data on autophagic flux in a multi-scale fashion, so as to better apply the existing tools that are based on single-cell analysis and to use them in the living organism. We assess how current techniques may be used for the establishment of autophagic flux standards or reference points and consider strategies for a conceptual approach on titrating autophagy inducers based on their effect on autophagic flux and potency to achieve a favorable protein degradation rate. Finally, we discuss potential solutions for inherent controls for autophagy analysis that are accessible, so as to better discern systemic and tissue-specific autophagic flux in future clinical applications.
    DOI:  https://doi.org/10.1080/15548627.2019.1687211
  12. Autophagy. 2019 Nov 07. 1-21
    STYK1 promotes autophagy through enhancing the assembly of autophagy-specific class III phosphatidylinositol 3-kinase complex I.
    Cefan Zhou, Xuehong Qian, Miao Hu, Rui Zhang, Nanxi Liu, Yuan Huang, Jing Yang, Juan Zhang, Hua Bai, Yuyan Yang, Yefu Wang, Declan Ali, Marek Michalak, Xing-Zhen Chen, Jingfeng Tang.
      Macroautophagy/autophagy plays key roles in development, oncogenesis, and cardiovascular and metabolic diseases. Autophagy-specific class III phosphatidylinositol 3-kinase complex I (PtdIns3K-C1) is essential for autophagosome formation. However, the regulation of this complex formation requires further investigation. Here, we discovered that STYK1 (serine/threonine/tyrosine kinase 1), a member of the receptor tyrosine kinases (RTKs) family, is a new upstream regulator of autophagy. We discovered that STYK1 facilitated autophagosome formation in human cells and zebrafish, which was characterized by elevated LC3-II and lowered SQSTM1/p62 levels and increased puncta formation by several marker proteins, such as ATG14, WIPI1, and ZFYVE1. Moreover, we observed that STYK1 directly binds to the PtdIns3K-C1 complex as a homodimer. The binding with this complex was promoted by Tyr191 phosphorylation, by means of which the kinase activity of STYK1 was elevated. We also demonstrated that STYK1 elevated the serine phosphorylation of BECN1, thereby decreasing the interaction between BECN1 and BCL2. Furthermore, we found that STYK1 preferentially facilitated the assembly of the PtdIns3K-C1 complex and was required for PtdIns3K-C1 complex kinase activity. Taken together, our findings provide new insights into autophagy induction and reveal evidence of novel crosstalk between the components of RTK signaling and autophagy.Abbreviations: AICAR: 5-aminoimidazole-4-carboxamide ribonucleotide; AMPK: adenosine 5'-monophosphate (AMP)-activated protein kinase; ATG: autophagy related; ATP: adenosine triphosphate; BCL2: BCL2 apoptosis regulator; BECN1: beclin 1; Bre A: brefeldin A; Co-IP: co-immunoprecipitation; CRISPR: clustered regularly interspaced short palindromic repeats; DAPI: 4',6-diamidino-2-phenylindole; EBSS: Earle's balanced salt solution; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; GSEA: gene set enrichment analysis; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; MAPK8/JNK1: mitogen-activated protein kinase 8; mRFP: monomeric red fluorescent protein; MTOR: mechanistic target of rapamycin kinase; MTT: 3-(4,5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; PIK3R4: phosphoinositide-3-kinase regulatory subunit 4; qRT-PCR: quantitative reverse transcription PCR; RACK1: receptor for activated C kinase 1; RUBCN: rubicon autophagy regulator; siRNA: small interfering RNA; SQSTM1: sequestosome 1; STYK1/NOK: serine/threonine/tyrosine kinase 1; TCGA: The Cancer Genome Atlas; Ub: ubiquitin; ULK1: unc-51 like autophagy activating kinase 1; UVRAG: UV radiation resistance associated; WIPI1: WD repeat domain, phosphoinositide interacting 1; ZFYVE1: zinc finger FYVE-type containing 1.
    Keywords:  ATG14-BECN1-PIK3C3 complex; BCL2; STYK1; Tyr191; autophagy; dimerization
    DOI:  https://doi.org/10.1080/15548627.2019.1687212
  13. Elife. 2019 Nov 06. pii: e50034. [Epub ahead of print]8
    Negative regulation of autophagy by UBA6-BIRC6-mediated ubiquitination of LC3.
    Rui Jia, Juan S Bonifacino.
      Although the process of autophagy has been extensively studied, the mechanisms that regulate it remain insufficiently understood. To identify novel autophagy regulators, we performed a whole-genome CRISPR/Cas9 knockout screen in H4 human neuroglioma cells expressing endogenous LC3B tagged with a tandem of GFP and mCherry. Using this methodology, we identified the ubiquitin-activating enzyme UBA6 and the hybrid ubiquitin-conjugating enzyme/ubiquitin ligase BIRC6 as autophagy regulators. We found that these enzymes cooperate to monoubiquitinate LC3B, targeting it for proteasomal degradation. Knockout of UBA6 or BIRC6 increased autophagic flux under conditions of nutrient deprivation or protein synthesis inhibition. Moreover, UBA6 or BIRC6 depletion decreased the formation of aggresome-like induced structures in H4 cells, and α-synuclein aggregates in rat hippocampal neurons. These findings demonstrate that UBA6 and BIRC6 negatively regulate autophagy by limiting the availability of LC3B. Inhibition of UBA6/BIRC6 could be used to enhance autophagic clearance of protein aggregates in neurodegenerative disorders.
    Keywords:  cell biology; human; rat
    DOI:  https://doi.org/10.7554/eLife.50034
  14. J Mol Biol. 2019 Nov 01. pii: S0022-2836(19)30624-2. [Epub ahead of print]
    Autophagosome-lysosome fusion.
    Péter Lőrincz, Gábor Juhász.
      Macroautophagy is a conserved catabolic process observed in all eukaryotic cells, during which selected cellular components are transported to and broken down within lysosomes. The process starts with the capture of unnecessary material into autophagosomes, which is followed by autophagosome-lysosome fusion to generate autolysosomes that degrade the cargo. In the past quarter-century, our knowledge about autophagosome formation almost exponentially increased, while the later steps were much less studied. This fortunately changed in the past few years, with more and more publications focusing on the fate of the completed autophagosome. In this review we aspire to summarize the current knowledge about the molecular mechanisms of autophagosome-lysosome fusion.
    Keywords:  autophagosome; autophagy; fusion; lysosome; vesicle tethering
    DOI:  https://doi.org/10.1016/j.jmb.2019.10.028
  15. Cell. 2019 Nov 05. pii: S0092-8674(19)31213-9. [Epub ahead of print]
    Cryo-EM Structure of the Human FLCN-FNIP2-Rag-Ragulator Complex.
    Kuang Shen, Kacper B Rogala, Hui-Ting Chou, Rick K Huang, Zhiheng Yu, David M Sabatini.
      mTORC1 controls anabolic and catabolic processes in response to nutrients through the Rag GTPase heterodimer, which is regulated by multiple upstream protein complexes. One such regulator, FLCN-FNIP2, is a GTPase activating protein (GAP) for RagC/D, but despite its important role, how it activates the Rag GTPase heterodimer remains unknown. We used cryo-EM to determine the structure of FLCN-FNIP2 in a complex with the Rag GTPases and Ragulator. FLCN-FNIP2 adopts an extended conformation with two pairs of heterodimerized domains. The Longin domains heterodimerize and contact both nucleotide binding domains of the Rag heterodimer, while the DENN domains interact at the distal end of the structure. Biochemical analyses reveal a conserved arginine on FLCN as the catalytic arginine finger and lead us to interpret our structure as an on-pathway intermediate. These data reveal features of a GAP-GTPase interaction and the structure of a critical component of the nutrient-sensing mTORC1 pathway.
    DOI:  https://doi.org/10.1016/j.cell.2019.10.036
  16. Nat Rev Mol Cell Biol. 2019 Nov 08.
    The many functions of ESCRTs.
    Marina Vietri, Maja Radulovic, Harald Stenmark.
      Cellular membranes can form two principally different involutions, which either exclude or contain cytosol. The 'classical' budding reactions, such as those occurring during endocytosis or formation of exocytic vesicles, involve proteins that assemble on the cytosol-excluding face of the bud neck. Inverse membrane involution occurs in a wide range of cellular processes, supporting cytokinesis, endosome maturation, autophagy, membrane repair and many other processes. Such inverse membrane remodelling is mediated by a heteromultimeric protein machinery known as endosomal sorting complex required for transport (ESCRT). ESCRT proteins assemble on the cytosolic (or nucleoplasmic) face of the neck of the forming involution and cooperate with the ATPase VPS4 to drive membrane scission or sealing. Here, we review similarities and differences of various ESCRT-dependent processes, with special emphasis on mechanisms of ESCRT recruitment.
    DOI:  https://doi.org/10.1038/s41580-019-0177-4
  17. Sci Rep. 2019 Nov 05. 9(1): 16014
    SQSTM-1/p62 potentiates HTLV-1 Tax-mediated NF-κB activation through its ubiquitin binding function.
    Aurélien Schwob, Elodie Teruel, Louise Dubuisson, Florence Lormières, Pauline Verlhac, Yakubu Princely Abudu, Janelle Gauthier, Marie Naoumenko, Fanny-Meï Cloarec-Ung, Mathias Faure, Terje Johansen, Hélène Dutartre, Renaud Mahieux, Chloé Journo.
      The NF-κB pathway is constitutively activated in adult T cell leukemia, an aggressive malignancy caused by Human T Leukemia Virus type 1 (HTLV-1). The viral oncoprotein Tax triggers this constitutive activation by interacting with the ubiquitin-rich IKK complex. We previously demonstrated that Optineurin and TAX1BP1, two members of the ubiquitin-binding, Sequestosome-1 (SQSTM-1/p62)-like selective autophagy receptor family, are involved in Tax-mediated NF-κB signaling. Here, using a proximity-dependent biotinylation approach (BioID), we identify p62 as a new candidate partner of Tax and confirm the interaction in infected T cells. We then demonstrate that p62 knock-out in MEF cells as well as p62 knock-down in HEK293T cells significantly reduces Tax-mediated NF-κB activity. We further show that although p62 knock-down does not alter NF-κB activation in Jurkat T cells nor in infected T cells, p62 does potentiate Tax-mediated NF-κB activity upon over-expression in Jurkat T cells. We next show that p62 associates with the Tax/IKK signalosome in cells, and identify the 170-206 domain of p62 as sufficient for the direct, ubiquitin-independent interaction with Tax. However, we observe that this domain is dispensable for modulating Tax activity in cells, and functional analysis of p62 mutants indicates that p62 could potentiate Tax activity in cells by facilitating the association of ubiquitin chains with the Tax/IKK signalosome. Altogether, our results identify p62 as a new ubiquitin-dependent modulator of Tax activity on NF-κB, further highlighting the importance of ubiquitin in the signaling activity of the viral Tax oncoprotein.
    DOI:  https://doi.org/10.1038/s41598-019-52408-x
  18. Int J Mol Sci. 2019 Nov 07. pii: E5543. [Epub ahead of print]20(22):
    A Double Negative Feedback Loop between mTORC1 and AMPK Kinases Guarantees Precise Autophagy Induction upon Cellular Stress.
    Marianna Holczer, Bence Hajdú, Tamás Lőrincz, András Szarka, Gábor Bánhegyi, Orsolya Kapuy.
      Cellular homeostasis is controlled by an evolutionary conserved cellular digestive process called autophagy. This mechanism is tightly regulated by the two sensor elements called mTORC1 and AMPK. mTORC1 is one of the master regulators of proteostasis, while AMPK maintains cellular energy homeostasis. AMPK is able to promote autophagy by phosphorylating ULK1, the key inducer of autophagosome formation, while mTORC1 downregulates the self-eating process via ULK1 under nutrient rich conditions. We claim that the feedback loops of the AMPK-mTORC1-ULK1 regulatory triangle guarantee the appropriate response mechanism when nutrient and/or energy supply changes. In our opinion, there is an essential double negative feedback loop between mTORC1 and AMPK. Namely, not only does AMPK downregulate mTORC1, but mTORC1 also inhibits AMPK and this inhibition is required to keep AMPK inactive at physiological conditions. The aim of the present study was to explore the dynamical characteristic of AMPK regulation upon various cellular stress events. We approached our scientific analysis from a systems biology perspective by incorporating both theoretical and molecular biological techniques. In this study, we confirmed that AMPK is essential to promote autophagy, but is not sufficient to maintain it. AMPK activation is followed by ULK1 induction, where protein has a key role in keeping autophagy active. ULK1-controlled autophagy is always preceded by AMPK activation. With both ULK1 depletion and mTORC1 hyper-activation (i.e., TSC1/2 downregulation), we demonstrate that a double negative feedback loop between AMPK and mTORC1 is crucial for the proper dynamic features of the control network. Our computer simulations have further proved the dynamical characteristic of AMPK-mTORC1-ULK1 controlled cellular nutrient sensing.
    Keywords:  AMPK; autophagy; double negative feedback; mTOR; systems biology
    DOI:  https://doi.org/10.3390/ijms20225543
  19. Sci Signal. 2019 Nov 05. pii: eaau2281. [Epub ahead of print]12(606):
    TFEB drives PGC-1α expression in adipocytes to protect against diet-induced metabolic dysfunction.
    Trent D Evans, Xiangyu Zhang, Se-Jin Jeong, Anyuan He, Eric Song, Somashubhra Bhattacharya, Karyn B Holloway, Irfan J Lodhi, Babak Razani.
      TFEB is a basic helix-loop-helix transcription factor that confers protection against metabolic diseases such as atherosclerosis by targeting a network of genes involved in autophagy-lysosomal biogenesis and lipid catabolism. In this study, we sought to characterize the role of TFEB in adipocyte and adipose tissue physiology and evaluate the therapeutic potential of adipocyte-specific TFEB overexpression in obesity. We demonstrated that mice with adipocyte-specific TFEB overexpression (Adipo-TFEB) were protected from diet-induced obesity, insulin resistance, and metabolic sequelae. Adipo-TFEB mice were lean primarily through increased metabolic rate, suggesting a role for adipose tissue browning and enhanced nonshivering thermogenesis in fat. Transcriptional characterization revealed that TFEB targeted genes involved in adipose tissue browning rather than those involved in autophagy. One such gene encoded PGC-1α, an established target of TFEB that promotes adipocyte browning. To dissect the role of PGC-1α in mediating the downstream effects of TFEB overexpression, we generated mice with adipocyte-specific PGC-1α deficiency and TFEB overexpression. Without PGC-1α, the ability of TFEB overexpression to brown adipose tissue and to elicit beneficial metabolic effects was blunted. Overall, these data implicate TFEB as a PGC-1α-dependent regulator of adipocyte browning and suggest its therapeutic potential in treating metabolic disease.
    DOI:  https://doi.org/10.1126/scisignal.aau2281
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