bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2020‒01‒05
nine papers selected by
Viktor Korolchuk
Newcastle University


  1. Cell. 2019 Dec 21. pii: S0092-8674(19)31331-5. [Epub ahead of print]
    Schütter M, Giavalisco P, Brodesser S, Graef M.
      Autophagy is a conserved catabolic homeostasis process central for cellular and organismal health. During autophagy, small single-membrane phagophores rapidly expand into large double-membrane autophagosomes to encapsulate diverse cargoes for degradation. It is thought that autophagic membranes are mainly derived from preformed organelle membranes. Instead, here we delineate a pathway that expands the phagophore membrane by localized phospholipid synthesis. Specifically, we find that the conserved acyl-CoA synthetase Faa1 accumulates on nucleated phagophores and locally activates fatty acids (FAs) required for phagophore elongation and autophagy. Strikingly, using isotopic FA tracing, we directly show that Faa1 channels activated FAs into the synthesis of phospholipids and promotes their assembly into autophagic membranes. Indeed, the first committed steps of de novo phospholipid synthesis at the ER, which forms stable contacts with nascent autophagosomes, are essential for autophagy. Together, our work illuminates how cells spatially tune synthesis and flux of phospholipids for autophagosome biogenesis during autophagy.
    Keywords:  Acyl-CoA synthetase; autophagosome biogenesis; autophagy; de novo phospholipid synthesis; endoplasmic reticulum; fatty acid metabolism; membrane composition; membrane contact site; phagophore expansion; phospholipids
    DOI:  https://doi.org/10.1016/j.cell.2019.12.005
  2. J Mol Biol. 2019 Dec 27. pii: S0022-2836(19)30745-4. [Epub ahead of print]
    Djajadikerta A, Keshri S, Pavel M, Prestil R, Ryan L, Rubinsztein DC.
      Autophagy is a major, conserved cellular pathway by which cells deliver cytoplasmic contents to lysosomes for degradation. Genetic studies have revealed extensive links between autophagy and neurodegenerative disease, and disruptions to autophagy may contribute to pathology in some cases. Autophagy degrades many of the toxic, aggregate-prone proteins responsible for disease, including mutant huntingtin (mHTT), alpha-synuclein (α-syn), tau and others, raising the possibility that autophagy upregulation may help to reduce levels of toxic protein species and thereby alleviate disease. This review examines autophagy induction as a potential therapy in several neurodegenerative diseases - Alzheimer's disease, Parkinson's disease, polyglutamine diseases, and amyotrophic lateral sclerosis. Evidence in cells and in vivo demonstrates promising results in many disease models, in which autophagy upregulation is able to reduce the levels of toxic proteins, ameliorate signs of disease, and delay disease progression. However, effective therapeutic use of autophagy induction requires a detailed knowledge of how the disease affects the autophagy-lysosome pathway, as activating autophagy when the pathway cannot go to completion (e.g. when lysosomal degradation is impaired) may instead exacerbate disease in some cases. Investigating the interactions between autophagy and disease pathogenesis is thus a critical area for further research.
    Keywords:  Alzheimer’s disease; Parkinson’s disease; amyotrophic lateral sclerosis; lysosome; polyglutamine diseases
    DOI:  https://doi.org/10.1016/j.jmb.2019.12.035
  3. Neuron. 2019 Dec 23. pii: S0896-6273(19)31045-1. [Epub ahead of print]
    Fox LM, Kim K, Johnson CW, Chen S, Croce KR, Victor MB, Eenjes E, Bosco JR, Randolph LK, Dragatsis I, Dragich JM, Yoo AS, Yamamoto A.
      Despite being an autosomal dominant disorder caused by a known coding mutation in the gene HTT, Huntington's disease (HD) patients with similar trinucleotide repeat mutations can have an age of onset that varies by decades. One likely contributing factor is the genetic heterogeneity of patients that might modify their vulnerability to disease. We report that although the heterozygous depletion of the autophagy adaptor protein Alfy/Wdfy3 has no consequence in control mice, it significantly accelerates age of onset and progression of HD pathogenesis. Alfy is required in the adult brain for the autophagy-dependent clearance of proteinaceous deposits, and its depletion in mice and neurons derived from patient fibroblasts accelerates the aberrant accumulation of this pathological hallmark shared across adult-onset neurodegenerative diseases. These findings indicate that selectively compromising the ability to eliminate aggregated proteins is a pathogenic driver, and the selective elimination of aggregates may confer disease resistance.
    Keywords:  Alfy; Huntington's disease; Wdfy3; autophagy; direct conversion; mice; neurodegeneration; patient fibroblasts; proteinopathy; selective autophagy
    DOI:  https://doi.org/10.1016/j.neuron.2019.12.003
  4. J Mol Biol. 2019 Dec 27. pii: S0022-2836(19)30746-6. [Epub ahead of print]
    Welz PS, Benitah SA.
      The mammalian circadian clockwork has evolved as a timing system that allows the daily environmental changes to be anticipated, so that behavior and tissue physiology can be adjusted accordingly. The circadian clock synchronizes the function of all cells within tissues in order to temporally separate preclusive and potentially harmful physiologic processes, and to establish a coherent temporal organismal physiology. Thus, proper functioning of the circadian clockwork is essential for maintaining cellular and tissue homeostasis. Importantly, aging reduces the robustness of the circadian clock, resulting in disturbed sleep-wake cycles, a lowered capacity to synchronize circadian rhythms in peripheral tissues and reprogramming of the circadian clock output at the molecular function levels. These circadian clock-dependent behavioral and molecular changes in turn further accelerate the process of aging. Here we review the current knowledge about how aging affects the circadian clock, how the functional decline of the circadian clock affects aging and how the circadian clock machinery and the molecular processes that underlie aging are intertwined.
    Keywords:  SIRT1; circadian reprogramming; deregulated nutrient sensing; mTOR; mitochondrial dysfunction; stem cell exhaustion; tissue homeostasis
    DOI:  https://doi.org/10.1016/j.jmb.2019.12.036
  5. Nat Commun. 2020 Jan 03. 11(1): 88
    Moskal N, Riccio V, Bashkurov M, Taddese R, Datti A, Lewis PN, Angus McQuibban G.
      The accumulation of damaged mitochondria causes the death of dopaminergic neurons. The Parkin-mediated mitophagy pathway functions to remove these mitochondria from cells. Targeting this pathway represents a therapeutic strategy for several neurodegenerative diseases, most notably Parkinson's disease. We describe a discovery pipeline to identify small molecules that increase Parkin recruitment to damaged mitochondria and ensuing mitophagy. We show that ROCK inhibitors promote the activity of this pathway by increasing the recruitment of HK2, a positive regulator of Parkin, to mitochondria. This leads to the increased targeting of mitochondria to lysosomes and removal of damaged mitochondria from cells. Furthermore, ROCK inhibitors demonstrate neuroprotective effects in flies subjected to paraquat, a parkinsonian toxin that induces mitochondrial damage. Importantly, parkin and rok are required for these effects, revealing a signaling axis which controls Parkin-mediated mitophagy that may be exploited for the development of Parkinson's disease therapeutics.
    DOI:  https://doi.org/10.1038/s41467-019-13781-3
  6. J Mater Chem B. 2020 Jan 02.
    Guo S, Sun Y, Geng X, Yang R, Xiao L, Qu L, Li Z.
      Lysosomes are crucial dynamic organelles which play key roles in different cellular processes such as autophagy, endocytosis and phagocytosis. Thus, long-term and real-time lysosomal imaging is desirable and essential to understand the dynamics and biological functions of lysosomes. Herein, ultra-stable carbon dots (CDs) which have shown many advantages such as pH-independence, high water solubility, good photostability and high biocompatibility for lysosome labeling and long-term tracking were synthesized using a one-pot pyrolysis method via microwave irradiation. Compared with the commercial lysosome probe (LysoTracker™ Deep Red), the fluorescent CDs show superior resistance to photobleaching and the HeLa cells were stably labeled by CDs for over 48 h. In addition, the CDs could stain lysosomes in different cell lines with high specificity and track lysosomal movements. Furthermore, the CDs could stain not only lysosomes in living cells, but also lysosomes in drug-induced apoptotic cells and fixed cells, suggesting that they are suitable for lysosomal tracking under both physiological and toxicological processes. All these excellent properties could be attributable to the ultrastability of CDs, which can be employed for constructing nanoplatforms for other applications such as drug carriers and signal guiders in biological processes. This study provides not only a strategy to synthesize green fluorescent CDs for tracking lysosomes, but also a promising candidate for drug loading and signal guidance of biological processes.
    DOI:  https://doi.org/10.1039/c9tb02043h
  7. Cerebellum. 2020 Jan 02.
    Wardman JH, Henriksen EE, Marthaler AG, Nielsen JE, Nielsen TT.
      Spinocerebellar ataxia type 2 (SCA2), a rare polyglutamine neurodegenerative disorder caused by a CAG repeat expansion in the ataxin-2 gene, exhibits common cellular phenotypes with other neurodegenerative disorders, including oxidative stress and mitochondrial dysfunction. Here, we show that SCA2 patient cells exhibit higher levels of caspase-8- and caspase-9-mediated apoptotic activation than control cells, cellular phenotypes that we find to be exacerbated by reactive oxygen species (ROS) and inhibition of autophagy. We also suggest that oligomerization of mutant ataxin-2 protein is likely to be the cause of the observed cellular phenotypes by causing inhibition of autophagy and by inducing ROS generation. Finally, we show that removal of ataxin-2 oligomers, either by increasing autophagic clearance or by oligomer dissolution, appears to alleviate the cellular phenotypes. Our results suggest that oligomerized ataxin-2 and oxidative stress affect autophagic clearance in SCA2 cells, contributing to the pathophysiology, and that activation of autophagy or clearance of oligomers may prove to be effective therapeutic strategies.
    Keywords:  Ataxia; Autophagy; Neurodegenerative disease; Polyglutamine disease
    DOI:  https://doi.org/10.1007/s12311-019-01092-8
  8. Autophagy. 2019 Dec 29. 1-14
    Zhang Y, Hu B, Li Y, Deng T, Xu Y, Lei J, Zhou J.
      Macroautophagy/autophagy is a host natural defense response. Viruses have developed various strategies to subvert autophagy during their life cycle. Recently, we revealed that autophagy was activated by binding of Avibirnavirus to cells. In the present study, we report the inhibition of autophagy initiated by PIK3C3/VPS34 via the PDPK1-dependent AKT-MTOR pathway. Autophagy detection revealed that viral protein VP3 triggered inhibition of autophagy at the early stage of Avibirnavirus replication. Subsequent interaction analysis showed that the CC1 domain of VP3 disassociated PIK3C3-BECN1 complex by direct interaction with BECN1 and blocked autophagosome formation, while the CC3 domain of VP3 disrupted PIK3C3-PDPK1 complex via directly binding to PIK3C3 and inhibited both formation and maturation of autophagosome. Furthermore, we found that PDPK1 activated AKT-MTOR pathway for suppressing autophagy via binding to AKT. Finally, we proved that CC3 domain was critical for role of VP3 in regulating replication of Avibirnavirus through autophagy. Taken together, our study identified that Avibirnavirus VP3 links PIK3C3-PDPK1 complex to AKT-MTOR pathway and inhibits autophagy, a critical step for controlling virus replication.Abbreviations: ATG14/Barkor: autophagy related 14; BECN1: beclin 1; CC: coiled-coil; ER: endoplasmic reticulum; hpi: hours post-infection; IBDV: infectious bursal disease virus; IP: co-immunoprecipitation; mAb: monoclonal antibody; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MOI: multiplicity of infection; MTOR: mechanistic target of rapamycin kinase; PDPK1: 3-phosphoinositid-dependent protein kinase-1; PIK3C3/VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PtdIns3K: phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; SQSTM1: sequestosome 1; vBCL2: viral BCL2 apoptosis regulator.
    Keywords:  AKT-MTOR; Avibirnavirus VP3; CC domain; PIK3C3-BECN1; autophagy
    DOI:  https://doi.org/10.1080/15548627.2019.1704118
  9. Nat Commun. 2020 Jan 02. 11(1): 37
    He D, Wu H, Xiang J, Ruan X, Peng P, Ruan Y, Chen YG, Wang Y, Yu Q, Zhang H, Habib SL, De Pinho RA, Liu H, Li B.
      Nutrients are absorbed solely by the intestinal villi. Aging of this organ causes malabsorption and associated illnesses, yet its aging mechanisms remain unclear. Here, we show that aging-caused intestinal villus structural and functional decline is regulated by mTORC1, a sensor of nutrients and growth factors, which is highly activated in intestinal stem and progenitor cells in geriatric mice. These aging phenotypes are recapitulated in intestinal stem cell-specific Tsc1 knockout mice. Mechanistically, mTORC1 activation increases protein synthesis of MKK6 and augments activation of the p38 MAPK-p53 pathway, leading to decreases in the number and activity of intestinal stem cells as well as villus size and density. Targeting p38 MAPK or p53 prevents or rescues ISC and villus aging and nutrient absorption defects. These findings reveal that mTORC1 drives aging by augmenting a prominent stress response pathway in gut stem cells and identify p38 MAPK as an anti-aging target downstream of mTORC1.
    DOI:  https://doi.org/10.1038/s41467-019-13911-x