bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2019‒05‒19
twelve papers selected by
Viktor Korolchuk
Newcastle University


  1. J Mol Biol. 2019 May 10. pii: S0022-2836(19)30265-7. [Epub ahead of print]
    Kirkin V.
      Autophagy, self-eating, is a pivotal catabolic mechanism that ensures homeostasis and survival of the cell in the face of stressors as different as starvation, infection, or protein misfolding. The importance of the research in this field was recognized by the general public after the Nobel Prize for Physiology or Medicine was awarded in 2016 to Yoshinori Ohsumi for discoveries of the mechanisms of autophagy using yeast as a model organism. One of the seminal findings of Ohsumi was on the role ubiquitin-like proteins (UBLs) - Atg5, Atg12, and Atg8 - play in the formation of the double-membrane vesicle autophagosome, which is the functional unit of autophagy. Subsequent work by several groups demonstrated that, like the founding member of the UBL family ubiquitin, these small but versatile protein and lipid modifiers interact with a plethora of proteins, which either directly regulate autophagosome formation, e.g., components of the Atg1/ULK1 complex, or are involved in cargo recognition, e.g., Atg19 and p62/SQSTM1. By tethering the cargo to the UBLs present on the forming autophagosome, the latter proteins were proposed to effectively act as selective autophagy receptors (SARs). The discovery of the SARs brought a breakthrough in the autophagy field, supplying the mechanistic underpinning for the formation of an autophagosome selectively around the cytosolic cargo, i.e. a protein aggregate, a mitochondrion, or a cytosolic bacterium. In this historical overview, I highlight key steps that the research into selective autophagy has been taking over the past 20 years. I comment on their significance and discuss current challenges in developing more detailed knowledge of the mechanisms of selective autophagy. I will conclude by introducing the new directions that this dynamic research field is taking into its third decade.
    Keywords:  Atg12; Atg5; Atg8; GABARAP; LC3; SAR; SLR; UBL; selective autophagy
    DOI:  https://doi.org/10.1016/j.jmb.2019.05.010
  2. J Genet Genomics. 2019 Apr 21. pii: S1673-8527(19)30066-9. [Epub ahead of print]
    Yan Y, Wang H, Wei C, Xiang Y, Liang X, Phang CW, Jiao R.
      Autophagy has been evolved as one of the adaptive cellular processes in response to stresses such as nutrient deprivation. Various cellular cargos such as damaged organelles and protein aggregates can be selectively degraded through autophagy. Recently, the lipid storage organelle, lipid droplet (LD), has been reported to be the cargo of starvation-induced autophagy. However, it remains largely unknown how the autophagy machinery recognizes the LDs and whether it can selectively degrade LDs. In this study, we show that Drosophila histone deacetylase 6 (dHDAC6), a key regulator of selective autophagy, is required for the LD turnover in the hepatocyte-like oenocytes in response to starvation. HDAC6 regulates LD turnover via p62/SQSTM1 (sequestosome 1)-mediated aggresome formation, suggesting that the selective autophagy machinery is required for LD recognition and degradation. Furthermore, our results show that the loss of dHDAC6 causes steatosis in response to starvation. Our findings suggest that there is a potential link between selective autophagy and susceptible predisposition to lipid metabolism associated diseases in stress conditions.
    Keywords:  Drosophila; HDAC6; Lipid droplets; Metabolic adaption; Selective autophagy; p62/SQSTM1
    DOI:  https://doi.org/10.1016/j.jgg.2019.03.008
  3. J Cell Biochem. 2019 May 12.
    Hua R, Wei H, Liu C, Shi Z, Xing Y.
      OBJECTIVES: The sequential reactivation of mechanistic target of rapamycin (mTOR) inhibited autophagic flux in neurons exposed to oxygen-glucose deprivation/reperfusion (OGD/R), which was characterized by reduction of autophagosome formation and restriction of autolysosome degradation. However, its detailed molecular mechanism was still unknown. In this study, we further explore the existing form of mTOR and its suppression on the transcriptional levels of related mRNA from neurons exposed to ischemia-reperfusion injury.METHODS: The OGD/R or middle cerebral artery occlusion/reperfusion (MCAO/R)-treated neurons was used to simulate ischemia/reperfusion injury . Autophagy flux was monitored by means of microtubule-associated protein 1 light chain 3 (LC3) and p62. The reactivation of mTOR was determined by phosphorylation of ribosomal protein S6 kinase 1 (S6K1). Then the inhibitors of mTOR were used to confirm its existence form. Finally, the mRNA transcription levels were analyzed to observe the negative regulation of mTOR.
    RESULTS: The sequential phosphorylation of mTOR contributed to the neuronal autophagy flux blocking. mTOR was re-phosphorylated and existed as mTOR complex 1 (mTORC1), which was supported by phosphorylation of S6K1 at Thr 389 in neurons. In addition, the phosphorylation of S6K1 was decreased roughly by applying mTORC1 inhibitors, rapamycin and torin 1. However, the administration of mTORC1/2 inhibitor PP242 could recover the phosphorylation of S6K1, which suggested that mTORC2 was involved in the regulation of mTORC1 activity. In paralleling with reactivation of mTORC1, related mRNA transcription was repressed in neurons under ischemia-reperfusion exposure in vivo and in vitro. The mRNA expression levels of LC3, Stx17, Vamp8, Snap29, Lamp2a, and Lamp2b were decreased in neurons after reperfusion, comparing with ischemia-treated neurons.
    CONCLUSIONS: The reactivated mTORC1 could suppress the transcription levels of related mRNA, such as LC3, Stx17, Vamp8, Snap29, Lamp2a, and Lamp2b. The research will expand the horizons that mTOR would negatively regulate autophagy at transcription and post-translation levels in neurons suffering ischemia-reperfusion injury.
    Keywords:  autophagy; ischemia; mTOR; reperfusion
    DOI:  https://doi.org/10.1002/jcb.28865
  4. Life Sci Alliance. 2019 Jun;pii: e201900340. [Epub ahead of print]2(3):
    Kohno S, Shiozaki Y, Keenan AL, Miyazaki-Anzai S, Miyazaki M.
      Autophagy is a conserved system that adapts to nutrient starvation, after which proteins and organelles are degraded to recycle amino acids in response to starvation. Recently, the ER was added to the list of targets of autophagic degradation. Autophagic degradation pathways of bulk ER and the specific proteins sorted through the ER are considered key mechanisms in maintaining ER homeostasis. Four ER-resident proteins (FAM134B, CCPG1, SEC62, and RTN3) have been identified as ER-resident cargo receptors, which contain LC3-interacting regions. In this study, we identified an N-terminal-truncated isoform of FAM134B (FAM134B-2) that contributes to starvation-induced ER-related autophagy. Hepatic FAM134B-2 but not full-length FAM134B (FAM134B-1) is expressed in a fed state. Starvation drastically induces FAM134B-2 but no other ER-resident cargo receptors through transcriptional activation by C/EBPβ. C/EBPβ overexpression increases FAM134B-2 recruitment into autophagosomes and lysosomal degradation. FAM134B-2 regulates lysosomal degradation of ER-retained secretory proteins such as ApoCIII. This study demonstrates that the C/EBPβ-FAM134B-2 axis regulates starvation-induced selective ER-phagy.
    DOI:  https://doi.org/10.26508/lsa.201900340
  5. J Genet Genomics. 2019 Apr 23. pii: S1673-8527(19)30065-7. [Epub ahead of print]
    Bhattacharjee A, Szabó Á, Csizmadia T, Laczkó-Dobos H, Juhász G.
      Autophagy is a lysosome-dependent intracellular degradation pathway that has been implicated in the pathogenesis of various human diseases, either positively or negatively impacting disease outcomes depending on the specific context. The majority of medical conditions including cancer, neurodegenerative diseases, infections and immune system disorders and inflammatory bowel disease could probably benefit from therapeutic modulation of the autophagy machinery. Drosophila represents an excellent model animal to study disease mechanisms thanks to its sophisticated genetic toolkit, and the conservation of human disease genes and autophagic processes. Here, we provide an overview of the various autophagy pathways observed both in flies and human cells (macroautophagy, microautophagy and chaperone-mediated autophagy), and discuss Drosophila models of the above-mentioned diseases where fly research has already helped to understand how defects in autophagy genes and pathways contribute to the relevant pathomechanisms.
    Keywords:  Alzheimer's disease; Autophagy; Cancer; Drosophila; Inflammatory bowel disease; Neurodegeneration; Parkinson's disease
    DOI:  https://doi.org/10.1016/j.jgg.2019.03.007
  6. Autophagy. 2019 May 14.
    Texada MJ, Malita A, Rewitz K.
      Steroid hormones are made from cholesterol and are essential for many developmental processes and disease conditions. The production of these hormones is nutrient dependent and tightly controlled by mechanisms that involve delivery of the precursor molecule cholesterol stored in lipid droplets (LDs). Recent studies have implicated macroautophagy/autophagy, a process regulated by nutrition, in the degradation of LDs and the mobilization of stored lipids. We recently identified an autophagy-dependent mechanism that regulates steroid production via effects on cholesterol trafficking. Through gain- and loss-of-function studies in Drosophila, we found that essential autophagy-related (Atg) genes are required in steroidogenic cells for normal steroid production. Inhibition of autophagy in these cells by knockdown of Atg genes causes strong accumulation of cholesterol in LDs and reduces steroid production, resembling effects seen in some lipid storage disorders and steroid-dependent cancer conditions. This autophagy-dependent steroid hormone regulation (ASHR) process is regulated by the wts-yki/Warts-Yorkie tumor-suppressor pathway downstream of nutrition, coupling nutrient intake with steroid-dependent developmental growth. This mechanism potentially contributes to the development of certain cancers and lipid-storage disorder, and thus may be of great therapeutic relevance.
    Keywords:  ; Autophagy; Cholesterol; Ecdysone; Endocrine; Nutrition; Steroid; Warts
    DOI:  https://doi.org/10.1080/15548627.2019.1617608
  7. Science. 2019 05 17. pii: eaau0159. [Epub ahead of print]364(6441):
    Lee YR, Chen M, Lee JD, Zhang J, Lin SY, Fu TM, Chen H, Ishikawa T, Chiang SY, Katon J, Zhang Y, Shulga YV, Bester AC, Fung J, Monteleone E, Wan L, Shen C, Hsu CH, Papa A, Clohessy JG, Teruya-Feldstein J, Jain S, Wu H, Matesic L, Chen RH, Wei W, Pandolfi PP.
      Activation of tumor suppressors for the treatment of human cancer has been a long sought, yet elusive, strategy. PTEN is a critical tumor suppressive phosphatase that is active in its dimer configuration at the plasma membrane. Polyubiquitination by the ubiquitin E3 ligase WWP1 (WW domain-containing ubiquitin E3 ligase 1) suppressed the dimerization, membrane recruitment, and function of PTEN. Either genetic ablation or pharmacological inhibition of WWP1 triggered PTEN reactivation and unleashed tumor suppressive activity. WWP1 appears to be a direct MYC (MYC proto-oncogene) target gene and was critical for MYC-driven tumorigenesis. We identified indole-3-carbinol, a compound found in cruciferous vegetables, as a natural and potent WWP1 inhibitor. Thus, our findings unravel a potential therapeutic strategy for cancer prevention and treatment through PTEN reactivation.
    DOI:  https://doi.org/10.1126/science.aau0159
  8. Nutr Res Rev. 2019 May 17. 1-9
    Cao Y, Liu S, Liu K, Abbasi IHR, Cai C, Yao J.
      Some amino acids (AA) act through several signalling pathways and mechanisms to mediate the control of gene expression at the translation level, and the regulation occurs, specifically, on the initiation and the signalling pathways for translation. The translation of mRNA to protein synthesis proceeds through the steps of initiation and elongation, and AA act as important feed-forward activators that are involved in many pathways, such as the sensing and the transportation of AA by cells, in these steps in many tissues of mammals. For the translation, phosphorylation of eukaryotic translation initiation factor 2α (eIF2α) is a critical molecule that controls the translation initiation and its functions can be regulated by some AA. Another control point in the mRNA binding step in the translation initiation is at the regulation by mammalian target of rapamycin, which requires a change of phosphorylation status of ribosomal protein S6. In fact, the change of phosphorylation status of ribosomal protein S6 might be involved in global protein synthesis. The present review summarises recent work on the molecular mechanisms of the regulation of protein synthesis by AA and highlights new findings.
    Keywords:   4EBP1 inhibitory 4E-binding protein-1; AA amino acid; Arg arginine; GCN2 general control nonderepressible 2; Ile isoleucine; Leu leucine; MAP4K3 mitogen-activated protein kinase 3; Met methionine; Rag Ras-related GTP-binding protein; Rheb Ras homologue enriched in brain; S6K1 S6 kinase 1; TSC tuberous sclerosis complex; Thr threonine; Trp tryptophan; Val valine; Vps34 vacuolar protein sorting 34; eEF eukaryotic translation elongation factor; eIF eukaryotic initiation factor; mTOR mammalian target of rapamycin; mTORC1 mammalian target of rapamycin complex 1; mTORC2 mammalian target of rapamycin complex 2; Amino acids; Mammalian target of rapamycin (mTOR); Protein synthesis; eEF2; eIF2
    DOI:  https://doi.org/10.1017/S0954422419000052
  9. Hepatology. 2019 May 16.
    Ni HM, Chao X, Yang H, Deng F, Wang S, Bai Q, Qian H, Cui Y, Cui W, Shi Y, Zong WX, Wang Z, Yang L, Ding WX.
      Autophagy is a lysosomal degradation pathway that degrades cytoplasmic proteins and organelles. Absence of autophagy in hepatocytes has been linked to promoting liver injury and tumorigenesis, however the mechanisms behind why a lack of autophagy induces these complications is not fully understood. The role of mammalian target of rapamycin (mTOR) in impaired autophagy-induced liver pathogenesis and tumorigenesis was investigated by using liver-specific Atg5 knockout (L-Atg5 KO) mice, L-Atg5/mTOR, and L-Atg5/Raptor double knockout (DKO) mice. At two months of age, we found that deletion of mTOR or Raptor in L-Atg5 KO mice attenuated hepatomegaly, cell death and inflammation but not fibrosis. Surprisingly, at six months of age, L-Atg5/mTOR DKO and L-Atg5/Raptor DKO mice also had increased hepatic inflammation, fibrosis, and liver injury, similar to the L-Atg5 KO mice. Moreover, more than 50% of L-Atg5/mTOR DKO and L-Atg5/Raptor DKO mice already developed spontaneous tumors but none of the L-Atg5 KO mice had developed any tumors at six months of age. At nine months of age, all L-Atg5/mTOR DKO and L-Atg5/Raptor DKO had developed liver tumors. Mechanistically, L-Atg5/mTOR DKO and L-Atg5/Raptor DKO mice had deceased levels of hepatic ubiquitinated proteins and persistent Nrf2 activation but had increased Akt activation compared with L-Atg5 KO mice. In conclusion, loss of mTOR signaling attenuates the liver pathogenesis in mice with impaired-hepatic autophagy but paradoxically promotes tumorigenesis in mice at a relatively young age. Therefore, the balance of mTOR is critical in regulating the liver pathogenesis and tumorigenesis in mice with impaired hepatic autophagy. This article is protected by copyright. All rights reserved.
    Keywords:  Atg5; Nrf2; Raptor; ductular reaction; fibrosis; inflammation
    DOI:  https://doi.org/10.1002/hep.30770
  10. J Mol Biol. 2019 May 14. pii: S0022-2836(19)30279-7. [Epub ahead of print]
    Wilkinson S.
      The endoplasmic reticulum (ER) is a fundamental organelle in cellular metabolism and signal transduction. It is subject to complex, dynamic sculpting of morphology and composition. Degradation of ER content has an important role to play here. Indeed, a major emerging player in ER turnover is ER-phagy, the degradation of ER fragments by selective autophagy, particularly macroautophagy. This article proposes a number of unifying principles of ER-phagy mechanism, and compares these with other selective autophagy pathways. A perspective on the likely roles of ER-phagy in determining cell fate is provided. Emerging related forms of intracellular catabolism of the ER or contents, including ER-phagy by microautophagy and selective ER protein removal via the lysosome, are outlined for comparison. Unresolved questions regarding the mechanism of ER-phagy, and its significance in cellular and organismal health, are put forward. This review concludes with a perspective on how this fundamental knowledge might inform future clinical developments.
    Keywords:  CCPG1; FAM134B; RTN3L; SEC62; TEX264
    DOI:  https://doi.org/10.1016/j.jmb.2019.05.012
  11. Nature. 2019 May 15.
    Lieber T, Jeedigunta SP, Palozzi JM, Lehmann R, Hurd TR.
      Mitochondria contain their own genomes that, unlike nuclear genomes, are inherited only in the maternal line. Owing to a high mutation rate and low levels of recombination of mitrochondrial DNA (mtDNA), special selection mechanisms exist in the female germline to prevent the accumulation of deleterious mutations1-5. However, the molecular mechanisms that underpin selection are poorly understood6. Here we visualize germline selection in Drosophila using an allele-specific fluorescent in situ-hybridization approach to distinguish wild-type from mutant mtDNA. Selection first manifests in the early stages of Drosophila oogenesis, triggered by reduction of the pro-fusion protein Mitofusin. This leads to the physical separation of mitochondrial genomes into different mitochondrial fragments, which prevents the mixing of genomes and their products and thereby reduces complementation. Once fragmented, mitochondria that contain mutant genomes are less able to produce ATP, which marks them for selection through a process that requires the mitophagy proteins Atg1 and BNIP3. A reduction in Atg1 or BNIP3 decreases the amount of wild-type mtDNA, which suggests a link between mitochondrial turnover and mtDNA replication. Fragmentation is not only necessary for selection in germline tissues, but is also sufficient to induce selection in somatic tissues in which selection is normally absent. We postulate that there is a generalizable mechanism for selection against deleterious mtDNA mutations, which may enable the development of strategies for the treatment of mtDNA disorders.
    DOI:  https://doi.org/10.1038/s41586-019-1213-4
  12. Cell Death Dis. 2019 May 15. 10(6): 376
    Slobodnyuk K, Radic N, Ivanova S, Llado A, Trempolec N, Zorzano A, Nebreda AR.
      Apoptosis and senescence are two mutually exclusive cell fate programs that can be activated by stress. The factors that instruct cells to enter into senescence or apoptosis are not fully understood, but both programs can be regulated by the stress kinase p38α. Using an inducible system that specifically activates this pathway, we show that sustained p38α activation suffices to trigger massive autophagosome formation and to enhance the basal autophagic flux. This requires the concurrent effect of increased mitochondrial reactive oxygen species production and the phosphorylation of the ULK1 kinase on Ser-555 by p38α. Moreover, we demonstrate that macroautophagy induction by p38α signaling determines that cancer cells preferentially enter senescence instead of undergoing apoptosis. In agreement with these results, we present evidence that the induction of autophagy by p38α protects cancer cells from chemotherapy-induced apoptosis by promoting senescence. Our results identify a new mechanism of p38α-regulated basal autophagy that controls the fate of cancer cells in response to stress.
    DOI:  https://doi.org/10.1038/s41419-019-1607-0