bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2019–03–10
thirteen papers selected by
Viktor Korolchuk, Newcastle University
  1. Phosphorylation of Syntaxin 17 by TBK1 Controls Autophagy Initiation.
  2. Autophagy induction via STING trafficking is a primordial function of the cGAS pathway.
  3. Regulation of the proline regulatory axis and autophagy modulates stemness in TP73/p73 deficient cancer stem-like cells.
  4. TRAPPC11 functions in autophagy by recruiting ATG2B-WIPI4/WDR45 to preautophagosomal membranes.
  5. Autophagy requires Tip20 in Saccharomyces cerevisiae.
  6. Evidence for a Role for Sestrin1 in Mediating Leucine-Induced Activation of mTORC1 in Skeletal Muscle.
  7. Disruption of mitochondrial dynamics affects behaviour and lifespan in Caenorhabditis elegans.
  8. Autophagy in cardiomyopathies.
  9. Human Fis1 regulates mitochondrial dynamics through inhibition of the fusion machinery.
  10. Combination of ERK and autophagy inhibition as a treatment approach for pancreatic cancer.
  11. Recent advances in understanding of amino acid signaling to mTORC1 activation.
  12. Overexpression of Mitochondrial Ligases Reverses Rotenone-Induced Effects in a Drosophila Model of Parkinson's Disease.
  13. Nicotinamide adenine dinucleotide emerges as a therapeutic target in aging and ischemic conditions.
  1. Dev Cell. 2019 Feb 27. pii: S1534-5807(19)30055-3. [Epub ahead of print]
    Phosphorylation of Syntaxin 17 by TBK1 Controls Autophagy Initiation.
    Suresh Kumar, Yuexi Gu, Yakubu Princely Abudu, Jack-Ansgar Bruun, Ashish Jain, Farzin Farzam, Michal Mudd, Jan Haug Anonsen, Tor Erik Rusten, Gary Kasof, Nicholas Ktistakis, Keith A Lidke, Terje Johansen, Vojo Deretic.
      Syntaxin 17 (Stx17) has been implicated in autophagosome-lysosome fusion. Here, we report that Stx17 functions in assembly of protein complexes during autophagy initiation. Stx17 is phosphorylated by TBK1 whereby phospho-Stx17 controls the formation of the ATG13+FIP200+ mammalian pre-autophagosomal structure (mPAS) in response to induction of autophagy. TBK1 phosphorylates Stx17 at S202. During autophagy induction, Stx17pS202 transfers from the Golgi, where its steady-state pools localize, to the ATG13+FIP200+ mPAS. Stx17pS202 was in complexes with ATG13 and FIP200, whereas its non-phosphorylatable mutant Stx17S202A was not. Stx17 or TBK1 knockouts blocked ATG13 and FIP200 puncta formation. Stx17 or TBK1 knockouts reduced the formation of ATG13 protein complexes with FIP200 and ULK1. Endogenous Stx17pS202 colocalized with LC3B following induction of autophagy. Stx17 knockout diminished LC3 response and reduced sequestration of the prototypical bulk autophagy cargo lactate dehydrogenase. We conclude that Stx17 is a TBK1 substrate and that together they orchestrate assembly of mPAS.
    Keywords:  TBK1; ULK1; autophagy; pre-autophagosomal structure
    DOI:  https://doi.org/10.1016/j.devcel.2019.01.027
  2. Nature. 2019 Mar 06.
    Autophagy induction via STING trafficking is a primordial function of the cGAS pathway.
    Xiang Gui, Hui Yang, Tuo Li, Xiaojun Tan, Peiqing Shi, Minghao Li, Fenghe Du, Zhijian J Chen.
      Cyclic GMP-AMP (cGAMP) synthase (cGAS) detects infections or tissue damage by binding to microbial or self DNA in the cytoplasm1. Upon binding DNA, cGAS produces cGAMP that binds to and activates the adaptor protein STING, which then activates the kinases IKK and TBK1 to induce interferons and other cytokines2-6. Here we report that STING also activates autophagy through a mechanism that is independent of TBK1 activation and interferon induction. Upon binding cGAMP, STING translocates to the endoplasmic reticulum-Golgi intermediate compartment (ERGIC) and the Golgi in a process that is dependent on the COP-II complex and ARF GTPases. STING-containing ERGIC serves as a membrane source for LC3 lipidation, which is a key step in autophagosome biogenesis. cGAMP induced LC3 lipidation through a pathway that is dependent on WIPI2 and ATG5 but independent of the ULK and VPS34-beclin kinase complexes. Furthermore, we show that cGAMP-induced autophagy is important for the clearance of DNA and viruses in the cytosol. Interestingly, STING from the sea anemone Nematostella vectensis induces autophagy but not interferons in response to stimulation by cGAMP, which suggests that induction of autophagy is a primordial function of the cGAS-STING pathway.
    DOI:  https://doi.org/10.1038/s41586-019-1006-9
  3. Autophagy. 2019 Mar 08. 1-3
    Regulation of the proline regulatory axis and autophagy modulates stemness in TP73/p73 deficient cancer stem-like cells.
    Tanveer Sharif, Emma Martell, Cathleen Dai, Sheila K Singh, Shashi Gujar.
      Cancer stem-like cells (CSLCs) reside as a small population within tumors, which mostly contain a larger population of differentiated cells. With their unique self-renewing abilities, CSLCs remain refractory to various therapeutic interventions, which otherwise kill differentiated cancer cells, and thus are a major culprit behind cancer treatment failures and cancer relapse. Recently, the process of macroautophagy/autophagy has emerged as a potential therapeutic target for eliminating CSLCs, as autophagic homeostasis has been discovered to play an important role in the growth of cancer and normal stem cells, and is required for the maintenance of the non-differentiated state of CSLCs. Our current work now shows that the so-called 'tumor suppressor' TP73/p73 plays an unconventional role in CSLC biology, and positively regulates the growth and stemness of CSLCs through the modulation of autophagy. Our data show that TP73/p73 deficiency, promotes autophagy in CSLCs by activating the autophagy machinery involving AMPK-TSC-MTOR signaling. Mechanistically, TP73/p73 deficiency-induced autophagy occurs as a result of reduced ATP levels resulting from the metabolic perturbations within the proline regulatory axis. Collectively, these findings unveil novel therapeutically-relevant implications for autophagy in the TP73/p73-dependent regulation of stemness within CSLCs.
    Keywords:  Autophagy; TP73/p73; brain tumor-initiating cells; cancer stem cells; glutamine; metabolism; proline-regulatory axis; tumor suppressors
    DOI:  https://doi.org/10.1080/15548627.2019.1586321
  4. Traffic. 2019 Mar 07.
    TRAPPC11 functions in autophagy by recruiting ATG2B-WIPI4/WDR45 to preautophagosomal membranes.
    Daniela Stanga, Qingchuan Zhao, Miroslav P Milev, Djenann Saint-Dic, Cecilia Jimenez-Mallebrera, Michael Sacher.
      TRAPPC11 has been implicated in membrane traffic and lipid-linked oligosaccharide synthesis, and mutations in TRAPPC11 result in neuromuscular and developmental phenotypes. Here, we show that TRAPPC11 has a role upstream of autophagosome formation during macroautophagy. Upon TRAPPC11 depletion, LC3-positive membranes accumulate prior to, and fail to be cleared during, starvation. A proximity biotinylation assay identified ATG2B and its binding partner WIPI4/WDR45 as TRAPPC11 interactors. TRAPPC11 depletion phenocopies that of ATG2 and WIPI4 and recruitment of both proteins to membranes is defective upon reduction of TRAPPC11. We find that a portion of TRAPPC11 and other TRAPP III proteins localize to isolation membranes. Fibroblasts from a patient with TRAPPC11 mutations failed to recruit ATG2B-WIPI4, suggesting that this interaction is physiologically relevant. Since ATG2B-WIPI4 is required for isolation membrane expansion, our study suggests that TRAPPC11 plays a role in this process. We propose a model whereby the TRAPP III complex participates in the formation and expansion of the isolation membrane at several steps. This article is protected by copyright. All rights reserved.
    DOI:  https://doi.org/10.1111/tra.12640
  5. J Biosci. 2019 Mar;pii: 17. [Epub ahead of print]44(1):
    Autophagy requires Tip20 in Saccharomyces cerevisiae.
    Lei Chen, Chunling Zhang, Yuancun Liang, Aixin Liu, Hansong Dong, Shenshen Zou.
      Autophagy is a highly conserved intracellular degradation pathway in eukaryotic cells that responds to environmental changes. Genetic analyses have shown that more than 40 autophagy-related genes (ATG) are directly involved in this process in fungi. In addition to Atg proteins, most vesicle transport regulators are also essential for each step of autophagy. The present study showed that one Endoplasmic Reticulum protein in Saccharomyces cerevisiae, Tip20, which controls Golgi-to-ER retrograde transport, was also required for starvation-induced autophagy under high temperature stress. In tip20 conditional mutant yeast, the transport of Atg8 was impaired during starvation, resulting in multiple Atg8 puncta dispersed outside the vacuole that could not be transported to the pre-autophagosomal structure/phagophore assembly site (PAS). Several Atg8 puncta were trapped in ER exit sites (ERES). Moreover, the GFP-Atg8 protease protection assay indicated that Tip20 functions before autophagosome closure. Furthermore, genetic studies showed that Tip20 functions downstream of Atg5 and upstream of Atg1, Atg9 and Atg14 in the autophagy pathway. The present data show that Tip20, as a vesicle transport regulator, has novel roles in autophagy.
  6. Am J Physiol Endocrinol Metab. 2019 Mar 05.
    Evidence for a Role for Sestrin1 in Mediating Leucine-Induced Activation of mTORC1 in Skeletal Muscle.
    Dandan Xu, Kevin L Shimkus, Holly A Lacko, Lydia Kutzler, Leonard S Jefferson, Scot R Kimball.
      Previous studies established that leucine stimulates protein synthesis in skeletal muscle to the same extent as a complete mixture of amino acids, and the effect occurs through activation of the mechanistic target of rapamycin in complex 1 (mTORC1). Recent studies using cells in culture showed that the Sestrins bind leucine and are required for leucine-dependent activation of mTORC1. However, the role they play in mediating leucine-dependent activation of the kinase in vivohas been questioned because the dissociation constant of Sestrin2 for leucine is well below circulating and intramuscular levels of the amino acid. The goal of the present study was to compare expression of the Sestrins in skeletal muscle to other tissues, and to assess their relative role in mediating activation of mTORC1 by leucine. The results show that the relative expression of the Sestrin proteins varies widely among tissues, and that in skeletal muscle Sestrin1 expression is higher than Sestrin3 while Sestrin2 expression is markedly lower. Analysis of the dissociation constants of the Sestrins for leucine as assessed by leucine-induced dissociation of the Sestrin•GATOR2 complex revealed that Sestrin1 has the highest affinity for leucine and that Sestrin3 has the lowest affinity. In agreement with the dissociation constants calculated using cells in culture, oral leucine administration promotes disassembly of the Sestrin1•GATOR2 complex, but not the Sestrin2 or Sestrin3•GATOR2 complex. Overall, the results presented herein are consistent with a model in which leucine-induced activation of mTORC1 in skeletal muscle in vivooccurs primarily through release of Sestrin1 from GATOR2.
    Keywords:  Sestrin; leucine; mTOR; skeletal muscle
    DOI:  https://doi.org/10.1152/ajpendo.00522.2018
  7. Cell Mol Life Sci. 2019 Mar 06.
    Disruption of mitochondrial dynamics affects behaviour and lifespan in Caenorhabditis elegans.
    Joseph J Byrne, Ming S Soh, Gursimran Chandhok, Tarika Vijayaraghavan, Jean-Sébastien Teoh, Simon Crawford, Ansa E Cobham, Nethmi M B Yapa, Christen K Mirth, Brent Neumann.
      Mitochondria are essential components of eukaryotic cells, carrying out critical physiological processes that include energy production and calcium buffering. Consequently, mitochondrial dysfunction is associated with a range of human diseases. Fundamental to their function is the ability to transition through fission and fusion states, which is regulated by several GTPases. Here, we have developed new methods for the non-subjective quantification of mitochondrial morphology in muscle and neuronal cells of Caenorhabditis elegans. Using these techniques, we uncover surprising tissue-specific differences in mitochondrial morphology when fusion or fission proteins are absent. From ultrastructural analysis, we reveal a novel role for the fusion protein FZO-1/mitofusin 2 in regulating the structure of the inner mitochondrial membrane. Moreover, we have determined the influence of the individual mitochondrial fission (DRP-1/DRP1) and fusion (FZO-1/mitofusin 1,2; EAT-3/OPA1) proteins on animal behaviour and lifespan. We show that loss of these mitochondrial fusion or fission regulators induced age-dependent and progressive deficits in animal movement, as well as in muscle and neuronal function. Our results reveal that disruption of fusion induces more profound defects than lack of fission on animal behaviour and tissue function, and imply that while fusion is required throughout life, fission is more important later in life likely to combat ageing-associated stressors. Furthermore, our data demonstrate that mitochondrial function is not strictly dependent on morphology, with no correlation found between morphological changes and behavioural defects. Surprisingly, we find that disruption of either mitochondrial fission or fusion significantly reduces median lifespan, but maximal lifespan is unchanged, demonstrating that mitochondrial dynamics play an important role in limiting variance in longevity across isogenic populations. Overall, our study provides important new insights into the central role of mitochondrial dynamics in maintaining organismal health.
    Keywords:  Caenorhabditis elegans; DRP-1; DRP1; EAT-3; FZO-1; Mitochondria; Mitochondrial dynamics; Mitofusin 1; Mitofusin 2; OPA1; Transmission electron microscopy
    DOI:  https://doi.org/10.1007/s00018-019-03024-5
  8. Biochim Biophys Acta Mol Cell Res. 2019 Feb 06. pii: S0167-4889(18)30496-8. [Epub ahead of print]
    Autophagy in cardiomyopathies.
    Antonia T L Zech, Sonia R Singh, Saskia Schlossarek, Lucie Carrier.
      Autophagy (greek auto: self; phagein: eating) is a highly conserved process within eukaryotes that degrades long-lived proteins and organelles within lysosomes. Its accurate and constant operation in basal conditions ensures cellular homeostasis by degrading damaged cellular components and thereby acting not only as a quality control but as well as an energy supplier. An increasing body of evidence indicates a major role of autophagy in the regulation of cardiac homeostasis and function. In this review, we describe the different forms of mammalian autophagy, their regulations and monitoring with a specific emphasis on the heart. Furthermore, we address the role of autophagy in several forms of cardiomyopathy and the options for therapy.
    Keywords:  Autophagosome; Autophagy; Cardiomyopathy; Heart; Lysosome
    DOI:  https://doi.org/10.1016/j.bbamcr.2019.01.013
  9. EMBO J. 2019 Mar 06. pii: e99748. [Epub ahead of print]
    Human Fis1 regulates mitochondrial dynamics through inhibition of the fusion machinery.
    Rong Yu, Shao-Bo Jin, Urban Lendahl, Monica Nistér, Jian Zhao.
      Mitochondrial dynamics is important for life. At center stage for mitochondrial dynamics, the balance between mitochondrial fission and fusion is a set of dynamin-related GTPases that drive mitochondrial fission and fusion. Fission is executed by the GTPases Drp1 and Dyn2, whereas the GTPases Mfn1, Mfn2, and OPA1 promote fusion. Recruitment of Drp1 to mitochondria is a critical step in fission. In yeast, Fis1p recruits the Drp1 homolog Dnm1p to mitochondria through Mdv1p and Caf4p, but whether human Fis1 (hFis1) promotes fission through a similar mechanism as in yeast is not established. Here, we show that hFis1-mediated mitochondrial fragmentation occurs in the absence of Drp1 and Dyn2, suggesting that they are dispensable for hFis1 function. hFis1 instead binds to Mfn1, Mfn2, and OPA1 and inhibits their GTPase activity, thus blocking the fusion machinery. Consistent with this, disruption of the fusion machinery in Drp1-/- cells phenocopies the fragmentation phenotype induced by hFis1 overexpression. In sum, our data suggest a novel role for hFis1 as an inhibitor of the fusion machinery, revealing an important functional evolutionary divergence between yeast and mammalian Fis1 proteins.
    Keywords:  Drp1; OPA1; hFis1; mitochondrial dynamics; mitofusins
    DOI:  https://doi.org/10.15252/embj.201899748
  10. Nat Med. 2019 Mar 04.
    Combination of ERK and autophagy inhibition as a treatment approach for pancreatic cancer.
    Kirsten L Bryant, Clint A Stalnecker, Daniel Zeitouni, Jennifer E Klomp, Sen Peng, Andrey P Tikunov, Venugopal Gunda, Mariaelena Pierobon, Andrew M Waters, Samuel D George, Garima Tomar, Björn Papke, G Aaron Hobbs, Liang Yan, Tikvah K Hayes, J Nathaniel Diehl, Gennifer D Goode, Nina V Chaika, Yingxue Wang, Guo-Fang Zhang, Agnieszka K Witkiewicz, Erik S Knudsen, Emanuel F Petricoin, Pankaj K Singh, Jeffrey M Macdonald, Nhan L Tran, Costas A Lyssiotis, Haoqiang Ying, Alec C Kimmelman, Adrienne D Cox, Channing J Der.
      Pancreatic ductal adenocarcinoma (PDAC) is characterized by KRAS- and autophagy-dependent tumorigenic growth, but the role of KRAS in supporting autophagy has not been established. We show that, to our surprise, suppression of KRAS increased autophagic flux, as did pharmacological inhibition of its effector ERK MAPK. Furthermore, we demonstrate that either KRAS suppression or ERK inhibition decreased both glycolytic and mitochondrial functions. We speculated that ERK inhibition might thus enhance PDAC dependence on autophagy, in part by impairing other KRAS- or ERK-driven metabolic processes. Accordingly, we found that the autophagy inhibitor chloroquine and genetic or pharmacologic inhibition of specific autophagy regulators synergistically enhanced the ability of ERK inhibitors to mediate antitumor activity in KRAS-driven PDAC. We conclude that combinations of pharmacologic inhibitors that concurrently block both ERK MAPK and autophagic processes that are upregulated in response to ERK inhibition may be effective treatments for PDAC.
    DOI:  https://doi.org/10.1038/s41591-019-0368-8
  11. Front Biosci (Landmark Ed). 2019 Mar 01. 24 971-982
    Recent advances in understanding of amino acid signaling to mTORC1 activation.
    Yu Zhuang, Xiang-Xiang Wang, Jieyu He, Shanping He, Yulong Yin.
      The mechanistic target of rapamycin complex 1 (mTORC1) is a master controller of cell growth and metabolism which integrates diverse bio-signaling inputs to coordinate various fundamental biological processes. Amino acids, especially leucine, arginine and glutamine, signal to mTORC1 activation. Classically, Rag GTPases play a crucial role in amino acids-induced mTORC1 activation in the lysosome and Golgi apparatus. More recently, multiple amino acid sensors have been identified and most of them indirectly associate with Rag GTPases. As a result, the mechanistic details on how amino acids are sensed and activate mTORC1 are rapidly evolving. This review discusses current understanding of mTORC1 activation and provides a brief and up-to-date narrative on the progress of amino acid sensors regulating mTORC1 activation.
  12. Front Neurosci. 2019 ;13 94
    Overexpression of Mitochondrial Ligases Reverses Rotenone-Induced Effects in a Drosophila Model of Parkinson's Disease.
    Bartosz Doktór, Milena Damulewicz, Elzbieta Pyza.
      Mul1 and Park are two major mitochondrial ligases responsible for mitophagy. Damaged mitochondria that cannot be removed are a source of an increased level of free radicals, which in turn can destructively affect other cell organelles as well as entire cells. One of the toxins that damages mitochondria is rotenone, a neurotoxin that after exposure displays symptoms typical of Parkinson's disease. In the present study, we showed that overexpressing genes encoding mitochondrial ligases protects neurons during treatment with rotenone. Drosophila strains with overexpressed mul1 or park show a significantly reduced degeneration of dopaminergic neurons, as well as normal motor activity during exposure to rotenone. In the nervous system, rotenone affected synaptic proteins, including Synapsin, Synaptotagmin and Disk Large1, as well as the structure of synaptic vesicles, while high levels of Mul1 or Park suppressed degenerative events at synapses. We concluded that increased levels of mitochondrial ligases are neuroprotective and could be considered in developing new therapies for Parkinson's disease.
    Keywords:  apoptosis; autophagy; mul1; neurodegeneration; park; synapses
    DOI:  https://doi.org/10.3389/fnins.2019.00094
  13. Biogerontology. 2019 Mar 05.
    Nicotinamide adenine dinucleotide emerges as a therapeutic target in aging and ischemic conditions.
    Leila Hosseini, Manouchehr S Vafaee, Javad Mahmoudi, Reza Badalzadeh.
      Nicotinamide adenine dinucleotide (NAD+) has been described as central coenzyme of redox reactions and is a key regulator of stress resistance and longevity. Aging is a multifactorial and irreversible process that is characterized by a gradual diminution in physiological functions in an organism over time, leading to development of age-associated pathologies and eventually increasing the probability of death. Ischemia is the lack of nutritive blood flow that causes damage and mortality that mostly occurs in various organs during aging. During the process of aging and related ischemic conditions, NAD+ levels decline and lead to nuclear and mitochondrial dysfunctions, resulting in age-related pathologies. The majority of studies have shown that restoring of NAD+ using supplementation with intermediates such as nicotinamide mononucleotide and nicotinamide riboside can be a valuable strategy for recovery of ischemic injury and age-associated defects. This review summarizes the molecular mechanisms responsible for the reduction in NAD+ levels during ischemic disorders and aging, as well as a particular focus is given to the recent progress in the understanding of NAD+ precursor's effects on aging and ischemia.
    Keywords:  Aging; Ischemic disorders; Longevity; Mitochondria; Nicotinamide adenine dinucleotide; Nicotinamide mononucleotide
    DOI:  https://doi.org/10.1007/s10522-019-09805-6
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