bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2019–09–22
fourteen papers selected by
Viktor Korolchuk, Newcastle University
  1. TBK1 Limits mTORC1 by Promoting Phosphorylation of Raptor Ser877.
  2. The Paf1 complex transcriptionally regulates the mitochondrial-anchored protein Atg32 leading to activation of mitophagy.
  3. Atp6ap2 deletion causes extensive vacuolation that consumes the insulin content of pancreatic β cells.
  4. A critical role of VMP1 in lipoprotein secretion.
  5. The secret life of degradative lysosomes in axons: delivery from the soma, enzymatic activity, and local autophagic clearance.
  6. How bacteria can block xenophagy: an insight from Salmonella.
  7. The ubiquitin E2 enzyme UBE2QL1 mediates lysophagy.
  8. Weak membrane interactions allow rheb to activate mTORC1 signaling without major lysosome enrichment.
  9. α-Ketoglutarate links p53 to cell fate during tumour suppression.
  10. Endogenous nicotinamide riboside metabolism protects against diet-induced liver damage.
  11. Chemotherapy-induced senescent cancer cells engulf other cells to enhance their survival.
  12. How Sweet It Is: Small-Molecule Inhibitors of mTORC1 Glucose Sensing.
  13. NPC1 regulates ER contacts with endocytic organelles to mediate cholesterol egress.
  14. Insulin-induced de novo lipid synthesis occurs mainly via mTOR-dependent regulation of proteostasis of SREBP-1c.
  1. Sci Rep. 2019 Sep 17. 9(1): 13470
    TBK1 Limits mTORC1 by Promoting Phosphorylation of Raptor Ser877.
    Ricardo J Antonia, Johnny Castillo, Laura E Herring, D Stephen Serafin, Pengda Liu, Lee M Graves, Albert S Baldwin, Robert S Hagan.
      While best known for its role in the innate immune system, the TANK-binding kinase 1 (TBK1) is now known to play a role in modulating cellular growth and autophagy. One of the major ways that TBK1 accomplishes this task is by modulating the mechanistic Target of Rapamycin (mTOR), a master regulator that when activated promotes cell growth and inhibits autophagy. However, whether TBK1 promotes or inhibits mTOR activity is highly cell type and context dependent. To further understand the mechanism whereby TBK1 regulates mTOR, we tested the hypothesis that TBK1 phosphorylates a key component of the mTOR complex 1 (mTORC1), Raptor. Using kinase assays coupled with mass spectrometry, we mapped the position of the TBK1 dependent phosphorylation sites on Raptor in vitro. Among the sites identified in vitro, we found that TBK1 promotes Raptor Ser877 phosphorylation in cells both basally and in response to pathogen-associated molecules known to induce TBK1 activity. The levels of Raptor Ser877 phosphorylation were inversely correlated with the levels of mTOR activity. Expression of a mutant Raptor that could not be phosphorylated at Ser877 led to an increase in mTORC1 activity. We conclude that TBK1 limits mTORC1 activity by promoting Raptor Ser877 phosphorylation.
    DOI:  https://doi.org/10.1038/s41598-019-49707-8
  2. Autophagy. 2019 Sep 19. 1-14
    The Paf1 complex transcriptionally regulates the mitochondrial-anchored protein Atg32 leading to activation of mitophagy.
    Liangde Zheng, Wen-Jie Shu, Yu-Min Li, Muriel Mari, Chaojun Yan, Dehe Wang, Zhao-Hong Yin, Wei Jiang, Yu Zhou, Koji Okamoto, Fulvio Reggiori, Daniel J Klionsky, Zhiyin Song, Hai-Ning Du.
      Mitophagy is a critical process that safeguards mitochondrial quality control in order to maintain proper cellular homeostasis. Although the mitochondrial-anchored receptor Atg32-mediated cargo-recognition system has been well characterized to be essential for this process, the signaling pathway modulating its expression as a contribution of governing the mitophagy process remains largely unknown. Here, bioinformatics analyses of epigenetic or transcriptional regulators modulating gene expression allow us to identify the Paf1 complex (the polymerase-associated factor 1 complex, Paf1C) as a transcriptional repressor of ATG genes. We show that Paf1C suppresses glucose starvation-induced autophagy, but does not affect nitrogen starvation- or rapamycin-induced autophagy. Moreover, we show that Paf1C specifically regulates mitophagy through modulating ATG32 expression. Deletion of the genes encoding two core subunits of Paf1C, Paf1 and Ctr9, increases ATG32 and ATG11 expression and facilitates mitophagy activity. Although Paf1C is required for many histone modifications and gene activation, we show that Paf1C regulates mitophagy independent of its positive regulatory role in other processes. More importantly, we also demonstrate the mitophagic role of PAF1C in mammals. Overall, we conclude that Paf1C maintains mitophagy at a low level through binding the promoter of the ATG32 gene in glucose-rich conditions. Dissociation of Paf1C from ATG32 leads to the increased expression of this gene, and mitophagy induction upon glucose starvation. Thus, we uncover a new role of Paf1C in modulating the mitophagy process at the transcriptional level. Abbreviations: AMPK: AMP-activated protein kinase; ATP5F1A: ATP synthase F1 subunit alpha; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CCCP: chlorophenylhydrazone; DFP: chelator deferiprone; GFP: green fluorescent protein; H2B-Ub1: H2B monoubiquitination; HSPD1/HSP60: heat shock protein family D (Hsp60) member 1; KD: kinase dead; OPTN, optineurin; Paf1: polymerase-associated factor 1; PINK1: PTEN induced kinase 1; PRKN/Parkin: parkin RBR E3 ubiquitin protein ligase; RT-qPCR: real-time quantitative PCR; SD-N: synthetic dropout without nitrogen base; TIMM23: translocase of inner mitochondrial membrane 23; TOMM20: translocase of outer mitochondrial membrane 20; WT: wild-type; YPD: yeast extract peptone dextrose; YPL: yeast extract peptone lactate.
    Keywords:  Atg32; Paf1 complex; glucose starvation; mitophagy; transcription
    DOI:  https://doi.org/10.1080/15548627.2019.1668228
  3. Proc Natl Acad Sci U S A. 2019 Sep 16. pii: 201903678. [Epub ahead of print]
    Atp6ap2 deletion causes extensive vacuolation that consumes the insulin content of pancreatic β cells.
    Katrina J Binger, Martin Neukam, Sudhir Gopal Tattikota, Fatimunnisa Qadri, Dmytro Puchkov, Diana M Willmes, Sabrina Wurmsee, Sabrina Geisberger, Ralf Dechend, Klemens Raile, Thomas Kurth, Genevieve Nguyen, Matthew N Poy, Michele Solimena, Dominik N Muller, Andreas L Birkenfeld.
      Pancreatic β cells store insulin within secretory granules which undergo exocytosis upon elevation of blood glucose levels. Crinophagy and autophagy are instead responsible to deliver damaged or old granules to acidic lysosomes for intracellular degradation. However, excessive consumption of insulin granules can impair β cell function and cause diabetes. Atp6ap2 is an essential accessory component of the vacuolar ATPase required for lysosomal degradative functions and autophagy. Here, we show that Cre recombinase-mediated conditional deletion of Atp6ap2 in mouse β cells causes a dramatic accumulation of large, multigranular vacuoles in the cytoplasm, with reduction of insulin content and compromised glucose homeostasis. Loss of insulin stores and gigantic vacuoles were also observed in cultured insulinoma INS-1 cells upon CRISPR/Cas9-mediated removal of Atp6ap2. Remarkably, these phenotypic alterations could not be attributed to a deficiency in autophagy or acidification of lysosomes. Together, these data indicate that Atp6ap2 is critical for regulating the stored insulin pool and that a balanced regulation of granule turnover is key to maintaining β cell function and diabetes prevention.
    Keywords:  (pro)renin receptor; autophagy; diabetes; vacuolar H+ ATPase
    DOI:  https://doi.org/10.1073/pnas.1903678116
  4. Elife. 2019 Sep 17. pii: e48834. [Epub ahead of print]8
    A critical role of VMP1 in lipoprotein secretion.
    Hideaki Morishita, Yan G Zhao, Norito Tamura, Taki Nishimura, Yuki Kanda, Yuriko Sakamaki, Mitsuyo Okazaki, Dongfang Li, Noboru Mizushima.
      Lipoproteins are lipid-protein complexes that are primarily generated and secreted from the intestine, liver, and visceral endoderm and delivered to peripheral tissues. Lipoproteins, which are assembled in the endoplasmic reticulum (ER) membrane, are released into the ER lumen for secretion, but its mechanism remains largely unknown. Here, we show that the release of lipoproteins from the ER membrane requires VMP1, an ER transmembrane protein essential for autophagy and certain types of secretion. Loss of vmp1, but not other autophagy-related genes, in zebrafish causes lipoprotein accumulation in the intestine and liver. Vmp1 deficiency in mice also leads to lipid accumulation in the visceral endoderm and intestine. In VMP1-depleted cells, neutral lipids accumulate within lipid bilayers of the ER membrane, thus affecting lipoprotein secretion. These results suggest that VMP1 is important for the release of lipoproteins from the ER membrane to the ER lumen in addition to its previously known functions.
    Keywords:  VMP1; autophagy-related gene; cell biology; endoplasmic reticulum; human; lipoprotein; mouse; zebrafish
    DOI:  https://doi.org/10.7554/eLife.48834
  5. Autophagy. 2019 Sep 19.
    The secret life of degradative lysosomes in axons: delivery from the soma, enzymatic activity, and local autophagic clearance.
    Tamar Farfel-Becker, Joseph C Roney, Xiu-Tang Cheng, Sunan Li, Sean R Cuddy, Zu-Hang Sheng.
      Lysosomal degradation of protein aggregates and damaged organelles is essential for maintaining cellular homeostasis. This process in neurons is challenging due to their highly polarized architecture. While enzymatically active degradative lysosomes are enriched in the cell body, their trafficking and degradation capacity in axons remain elusive. We recently characterized the axonal delivery of degradative lysosomes by applying a set of fluorescent probes that selectively label active forms of lysosomal hydrolases on cortical neurons in microfluidic devices. We revealed that soma-derived degradative lysosomes rapidly influx into distal axons and target to autophagosomes and Parkinson disease-related SNCA/α-synuclein cargos for local degradation. Disrupting axon-targeted delivery of degradative lysosomes induces axonal autophagic stress. We demonstrate that the axon is an active compartment for local degradation, establishing a foundation for future investigations into axonal lysosome trafficking and functionality in neurodegenerative diseases and lysosomal storage disorders associated with axonal pathology and macroautophagy/autophagy stress.
    Keywords:  active lysosomal hydrolase; autophagic stress; autophagosome; axonal transport; cathepsin; degradative lysosome; lysosomal trafficking; α-synuclein
    DOI:  https://doi.org/10.1080/15548627.2019.1669869
  6. Autophagy. 2019 Sep 18. 1-2
    How bacteria can block xenophagy: an insight from Salmonella.
    Xin Wen, Daniel J Klionsky.
      Xenophagy, a unique type of selective macroautophagy/autophagy, targets invading pathogens as part of the host immune response. In order to survive within the host, bacteria have established various self-defense mechanisms. In a recent paper from Feng Shao's lab, the Salmonella effector protein SopF has been demonstrated to block xenophagy by interrupting the vacuolar type H+-translocating (v-) ATPase-ATG16L1 axis, which is important for antibacterial autophagy initiation. SopF can specifically ADP-ribosylate Gln124 on ATP6V0C, a v-ATPase component, thus influencing recruitment of ATG16L1 onto the bacteria-containing vacuole within the host cytosol. Abbreviations: ATG: autophagy-related; S. Typhimurium: Salmonella enterica serovar Typhimurium; T3SS: type III secretion system.
    Keywords:  ATG16L1; autophagy; lysosome; stress; v-ATPase
    DOI:  https://doi.org/10.1080/15548627.2019.1666580
  7. EMBO Rep. 2019 Sep 15. e49104
    The ubiquitin E2 enzyme UBE2QL1 mediates lysophagy.
    Noboru Mizushima.
      Although damaged lysosomes with ruptured membranes can be repaired, these dangerous organelles are also selectively eliminated by autophagic degradation termed lysophagy. This process is initiated by ubiquitination of lysosomal proteins. In this issue of EMBO Reports, Koerver et al [1] identify the E2 enzyme UBE2QL1 that catalyzes ubiquitination of damaged lysosomes. Without this enzyme, the clearance of ruptured lysosomes is compromised not only upon lysosomal damage but also under normal conditions, revealing its adaptive and constitutive functions.
    DOI:  https://doi.org/10.15252/embr.201949104
  8. Mol Biol Cell. 2019 Sep 18. mbcE19030146
    Weak membrane interactions allow rheb to activate mTORC1 signaling without major lysosome enrichment.
    Brittany Angarola, Shawn M Ferguson.
      Stable localization of the Rheb GTPase to lysosomes is thought to be required for activation of mTORC1 signaling. However, the lysosome targeting mechanisms for Rheb remain unclear. We therefore investigated the relationship between Rheb subcellular localization and mTORC1 activation. Surprisingly, we found that Rheb was undetectable at lysosomes. Nonetheless, functional assays in knockout human cells revealed that farnesylation of the C-terminal CaaX motif on Rheb was essential for Rheb-dependent mTORC1 activation. Although farnesylated Rheb exhibited partial endoplasmic reticulum localization, constitutively targeting Rheb to ER membranes did not support mTORC1 activation. Further systematic analysis of Rheb lipidation revealed that weak, non-selective, membrane interactions support Rheb-dependent mTORC1 activation without the need for a specific lysosome targeting motif. Collectively, these results argue against stable interactions of Rheb with lysosomes and instead that transient membrane interactions optimally allow Rheb to activate mTORC1 signaling. [Media: see text].
    DOI:  https://doi.org/10.1091/mbc.E19-03-0146
  9. Nature. 2019 Sep 18.
    α-Ketoglutarate links p53 to cell fate during tumour suppression.
    John P Morris, Jossie J Yashinskie, Richard Koche, Rohit Chandwani, Sha Tian, Chi-Chao Chen, Timour Baslan, Zoran S Marinkovic, Francisco J Sánchez-Rivera, Steven D Leach, Carlos Carmona-Fontaine, Craig B Thompson, Lydia W S Finley, Scott W Lowe.
      The tumour suppressor TP53 is mutated in the majority of human cancers, and in over 70% of pancreatic ductal adenocarcinoma (PDAC)1,2. Wild-type p53 accumulates in response to cellular stress, and regulates gene expression to alter cell fate and prevent tumour development2. Wild-type p53 is also known to modulate cellular metabolic pathways3, although p53-dependent metabolic alterations that constrain cancer progression remain poorly understood. Here we find that p53 remodels cancer-cell metabolism to enforce changes in chromatin and gene expression that favour a premalignant cell fate. Restoring p53 function in cancer cells derived from KRAS-mutant mouse models of PDAC leads to the accumulation of α-ketoglutarate (αKG, also known as 2-oxoglutarate), a metabolite that also serves as an obligate substrate for a subset of chromatin-modifying enzymes. p53 induces transcriptional programs that are characteristic of premalignant differentiation, and this effect can be partially recapitulated by the addition of cell-permeable αKG. Increased levels of the αKG-dependent chromatin modification 5-hydroxymethylcytosine (5hmC) accompany the tumour-cell differentiation that is triggered by p53, whereas decreased 5hmC characterizes the transition from premalignant to de-differentiated malignant lesions that is associated with mutations in Trp53. Enforcing the accumulation of αKG in p53-deficient PDAC cells through the inhibition of oxoglutarate dehydrogenase-an enzyme of the tricarboxylic acid cycle-specifically results in increased 5hmC, tumour-cell differentiation and decreased tumour-cell fitness. Conversely, increasing the intracellular levels of succinate (a competitive inhibitor of αKG-dependent dioxygenases) blunts p53-driven tumour suppression. These data suggest that αKG is an effector of p53-mediated tumour suppression, and that the accumulation of αKG in p53-deficient tumours can drive tumour-cell differentiation and antagonize malignant progression.
    DOI:  https://doi.org/10.1038/s41586-019-1577-5
  10. Nat Commun. 2019 Sep 20. 10(1): 4291
    Endogenous nicotinamide riboside metabolism protects against diet-induced liver damage.
    Audrey Sambeat, Joanna Ratajczak, Magali Joffraud, José L Sanchez-Garcia, Maria P Giner, Armand Valsesia, Judith Giroud-Gerbetant, Miriam Valera-Alberni, Angelique Cercillieux, Marie Boutant, Sameer S Kulkarni, Sofia Moco, Carles Canto.
      Supplementation with the NAD+ precursor nicotinamide riboside (NR) ameliorates and prevents a broad array of metabolic and aging disorders in mice. However, little is known about the physiological role of endogenous NR metabolism. We have previously shown that NR kinase 1 (NRK1) is rate-limiting and essential for NR-induced NAD+ synthesis in hepatic cells. To understand the relevance of hepatic NR metabolism, we generated whole body and liver-specific NRK1 knockout mice. Here, we show that NRK1 deficiency leads to decreased gluconeogenic potential and impaired mitochondrial function. Upon high-fat feeding, NRK1 deficient mice develop glucose intolerance, insulin resistance and hepatosteatosis. Furthermore, they are more susceptible to diet-induced liver DNA damage, due to compromised PARP1 activity. Our results demonstrate that endogenous NR metabolism is critical to sustain hepatic NAD+ levels and hinder diet-induced metabolic damage, highlighting the relevance of NRK1 as a therapeutic target for metabolic disorders.
    DOI:  https://doi.org/10.1038/s41467-019-12262-x
  11. J Cell Biol. 2019 Sep 17. pii: jcb.201904051. [Epub ahead of print]
    Chemotherapy-induced senescent cancer cells engulf other cells to enhance their survival.
    Crystal A Tonnessen-Murray, Wesley D Frey, Sonia G Rao, Ashkan Shahbandi, Nathan A Ungerleider, Joy O Olayiwola, Lucas B Murray, Benjamin T Vinson, Douglas B Chrisey, Christopher J Lord, James G Jackson.
      In chemotherapy-treated breast cancer, wild-type p53 preferentially induces senescence over apoptosis, resulting in a persisting cell population constituting residual disease that drives relapse and poor patient survival via the senescence-associated secretory phenotype. Understanding the properties of tumor cells that allow survival after chemotherapy treatment is paramount. Using time-lapse and confocal microscopy to observe interactions of cells in treated tumors, we show here that chemotherapy-induced senescent cells frequently engulf both neighboring senescent or nonsenescent tumor cells at a remarkable frequency. Engulfed cells are processed through the lysosome and broken down, and cells that have engulfed others obtain a survival advantage. Gene expression analysis showed a marked up-regulation of conserved macrophage-like program of engulfment in chemotherapy-induced senescent cell lines and tumors. Our data suggest compelling explanations for how senescent cells persist in dormancy, how they manage the metabolically expensive process of cytokine production that drives relapse in those tumors that respond the worst, and a function for their expanded lysosomal compartment.
    DOI:  https://doi.org/10.1083/jcb.201904051
  12. Cell Chem Biol. 2019 Sep 19. pii: S2451-9456(19)30275-2. [Epub ahead of print]26(9): 1195-1196
    How Sweet It Is: Small-Molecule Inhibitors of mTORC1 Glucose Sensing.
    Junbing Zhang, Liron Bar-Peled.
      In this issue of Cell Chemical Biology, Kang et al. (2019) describe the use of a high-throughput cell-based screen to identify chemical scaffolds that selectively inhibit mTORC1 nutrient sensing. Chemical proteomic-based target identification reveals class I glucose transporters as direct targets for these inhibitors, linking glucose sensing with mTORC1 regulation.
    DOI:  https://doi.org/10.1016/j.chembiol.2019.09.001
  13. Nat Commun. 2019 Sep 19. 10(1): 4276
    NPC1 regulates ER contacts with endocytic organelles to mediate cholesterol egress.
    D Höglinger, T Burgoyne, E Sanchez-Heras, P Hartwig, A Colaco, J Newton, C E Futter, S Spiegel, F M Platt, E R Eden.
      Transport of dietary cholesterol from endocytic organelles to the endoplasmic reticulum (ER) is essential for cholesterol homoeostasis, but the mechanism and regulation of this transport remains poorly defined. Membrane contact sites (MCS), microdomains of close membrane apposition, are gaining attention as important platforms for non-vesicular, inter-organellar communication. Here we investigate the impact of ER-endocytic organelle MCS on cholesterol transport. We report a role for Niemann-Pick type C protein 1 (NPC1) in tethering ER-endocytic organelle MCS where it interacts with the ER-localised sterol transport protein Gramd1b to regulate cholesterol egress. We show that artificially tethering MCS rescues the cholesterol accumulation that characterises NPC1-deficient cells, consistent with direct lysosome to ER cholesterol transport across MCS. Finally, we identify an expanded population of lysosome-mitochondria MCS in cells depleted of NPC1 or Gramd1b that is dependent on the late endosomal sterol-binding protein STARD3, likely underlying the mitochondrial cholesterol accumulation in NPC1-deficient cells.
    DOI:  https://doi.org/10.1038/s41467-019-12152-2
  14. Mol Cell Biochem. 2019 Sep 20.
    Insulin-induced de novo lipid synthesis occurs mainly via mTOR-dependent regulation of proteostasis of SREBP-1c.
    Qingming Dong, Gipsy Majumdar, Robert N O'Meally, Robert N Cole, Marshall B Elam, Rajendra Raghow.
      Insulin stimulates de novo lipid synthesis in the liver and in cultured hepatocytes via its ability to activate sterol regulatory element-binding protein 1c (SREBP-1c). Although PI3K-AKT-mTORC1-p70S6K-signaling kinases are known to drive feed-forward expression of SREBP-1c, the identity of the phosphorylated amino acid residue(s) putatively involved in insulin-stimulated de novo lipogenesis remains elusive. We obtained in silico and mass spectrometry evidence, that was combined with siRNA strategies, to discover that insulin-induced phosphorylation of serine 418, serine 419, and serine 422 in rat SREBP-1c was most likely mediated by p70S6 kinase. Here, for the first time, we show that insulin-induced phosphorylation of these 3 serine residues mainly impinged on the mechanisms of proteostasis of both full-length and mature SREBP-1c in the McArdle-RH7777 hepatoma cells. Consistent with this conclusion, nascent SREBP-1c, substituted with phosphomimetic aspartic acid residues at these 3 sites, was resistant to proteasomal degradation. As a consequence, endoplasmic reticulum to Golgi migration and proteolytic maturation of pSREBP-1c was significantly enhanced which led to increased accumulation of mature nSREBP-1c, even in the absence of insulin. Remarkably, aspartic acid substitutions at S418, S419 and S422 also protected the nascent SREBP-1c from ubiquitin-mediated proteasome degradation thus increasing its steady-state levels and transactivation potential in the nucleus. These complementary effects of p70S6K-mediated phosphorylation on proteostasis of pSREBP-1c were necessary and sufficient to account for insulin's ability to enhance transcription of genes controlling de novo lipogenesis in hepatocytes.
    Keywords:  Mass spectrometry; Mechanistic target of rapamycin (mTOR); Phosphorylation; Proteasome degradation; SREBP-1c; Ubiquitin
    DOI:  https://doi.org/10.1007/s11010-019-03625-5
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