bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2019‒10‒06
fourteen papers selected by
Viktor Korolchuk
Newcastle University


  1. Mol Cell. 2019 Sep 21. pii: S1097-2765(19)30690-2. [Epub ahead of print]
    Kirkin V, Rogov VV.
      The clearance of surplus, broken, or dangerous components is key for maintaining cellular homeostasis. The failure to remove protein aggregates, damaged organelles, or intracellular pathogens leads to diseases, including neurodegeneration, cancer, and infectious diseases. Autophagy is the evolutionarily conserved pathway that sequesters cytoplasmic components in specialized vesicles, autophagosomes, which transport the cargo to the degradative compartments (vacuoles or lysosomes). Research during the past few decades has elucidated how autophagosomes engulf their substrates selectively. This type of autophagy involves a growing number of selective autophagy receptors (SARs) (e.g., Atg19 in yeasts, p62/SQSTM1 in mammals), which bind to the cargo and simultaneously engage components of the core autophagic machinery via direct interaction with the ubiquitin-like proteins (UBLs) of the Atg8/LC3/GABARAP family and adaptors, Atg11 (in yeasts) or FIP200 (in mammals). In this Review, we critically discuss the biology of the SARs with special emphasis on their interactions with UBLs.
    Keywords:  GABARAP; LC3; LDS; LIR; Mitophagy; SAR; SLR; UBL; UDS; autophagy
    DOI:  https://doi.org/10.1016/j.molcel.2019.09.005
  2. J Biol Chem. 2019 Oct 04. pii: jbc.AC119.010671. [Epub ahead of print]
    Lear TB, Lockwood KC, Ouyang Y, Evankovich JW, Larsen MB, Lin B, Liu Y, Chen BB.
      Nutrient sensing is a critical cellular process controlling metabolism and signaling. mTOR complex 1 (mTORC1) is the primary signaling hub for nutrient sensing and, when activated, stimulates anabolic processes while decreasing autophagic flux. mTORC1 receives nutrient status signals from intracellular amino acid sensors. One of these sensors, Sestrin-2, functions as an intracellular sensor of cytosolic leucine and inhibitor of mTORC1 activity. Genetic studies of Sestrin-2 have confirmed its critical role in regulating mTORC1 activity, especially in the case of leucine starvation. Sestrin-2 is known to be transcriptionally controlled by several mechanisms; however, the post-translational proteolytic regulation of Sestrin-2 remains unclear. Here, we explored how Sestrin-2 is regulated through the ubiquitin proteasome system. Using an unbiased screening approach of an siRNA library targeting ubiquitin E3 ligases, we identified a RING-type E3 ligase, ring finger protein 186 (RNF186), that critically mediates the Sestrin-2 ubiquitination and degradation. We observed that RNF186 and Sestrin-2 bind each other through distinct C-terminal motifs and that Lys-13 in Sestrin-2 is a putative ubiquitin-acceptor site. RNF186 knockdown increased Sestrin-2 protein levels and decreased mTORC1 activation. These results reveal a new mechanism of E3-ligase control of mTORC1 activity through the RNF186-Sestrin-2 axis, suggesting that RNF186 inhibition may be potential strategy to increase levels of the mTORC1 inhibitor Sestrin-2.
    Keywords:  E3 ubiquitin ligase; SESN2; autophagy; high-throughput screening (HTS); mammalian target of rapamycin (mTOR); nutrient sensing; ring finger protein 186 (RNF186); ubiquitylation (ubiquitination)
    DOI:  https://doi.org/10.1074/jbc.AC119.010671
  3. Proc Natl Acad Sci U S A. 2019 Sep 30. pii: 201913212. [Epub ahead of print]
    Castillo-Quan JI, Tain LS, Kinghorn KJ, Li L, Grönke S, Hinze Y, Blackwell TK, Bjedov I, Partridge L.
      Increasing life expectancy is causing the prevalence of age-related diseases to rise, and there is an urgent need for new strategies to improve health at older ages. Reduced activity of insulin/insulin-like growth factor signaling (IIS) and mechanistic target of rapamycin (mTOR) nutrient-sensing signaling network can extend lifespan and improve health during aging in diverse organisms. However, the extensive feedback in this network and adverse side effects of inhibition imply that simultaneous targeting of specific effectors in the network may most effectively combat the effects of aging. We show that the mitogen-activated protein kinase kinase (MEK) inhibitor trametinib, the mTOR complex 1 (mTORC1) inhibitor rapamycin, and the glycogen synthase kinase-3 (GSK-3) inhibitor lithium act additively to increase longevity in Drosophila Remarkably, the triple drug combination increased lifespan by 48%. Furthermore, the combination of lithium with rapamycin cancelled the latter's effects on lipid metabolism. In conclusion, a polypharmacology approach of combining established, prolongevity drug inhibitors of specific nodes may be the most effective way to target the nutrient-sensing network to improve late-life health.
    Keywords:  aging; lithium; polypharmacology; rapamycin; trametinib
    DOI:  https://doi.org/10.1073/pnas.1913212116
  4. Cell Rep. 2019 Oct 01. pii: S2211-1247(19)31147-7. [Epub ahead of print]29(1): 225-235.e5
    Sarraf SA, Sideris DP, Giagtzoglou N, Ni L, Kankel MW, Sen A, Bochicchio LE, Huang CH, Nussenzweig SC, Worley SH, Morton PD, Artavanis-Tsakonas S, Youle RJ, Pickrell AM.
      PINK1 and Parkin are established mediators of mitophagy, the selective removal of damaged mitochondria by autophagy. PINK1 and Parkin have been proposed to act as tumor suppressors, as loss-of-function mutations are correlated with enhanced tumorigenesis. However, it is unclear how PINK1 and Parkin act in coordination during mitophagy to influence the cell cycle. Here we show that PINK1 and Parkin genetically interact with proteins involved in cell cycle regulation, and loss of PINK1 and Parkin accelerates cell growth. PINK1- and Parkin-mediated activation of TBK1 at the mitochondria during mitophagy leads to a block in mitosis due to the sequestration of TBK1 from its physiological role at centrosomes during mitosis. Our study supports a diverse role for the far-reaching, regulatory effects of mitochondrial quality control in cellular homeostasis and demonstrates that the PINK1/Parkin pathway genetically interacts with the cell cycle, providing a framework for understanding the molecular basis linking PINK1 and Parkin to mitosis.
    Keywords:  ATM; PINK1; Parkin; TBK1; cell cycle; centrosome; ik2; mitophagy; mitosis; tank binding kinase 1
    DOI:  https://doi.org/10.1016/j.celrep.2019.08.085
  5. Cell Rep. 2019 Oct 01. pii: S2211-1247(19)31146-5. [Epub ahead of print]29(1): 236-248.e3
    Yu D, Tomasiewicz JL, Yang SE, Miller BR, Wakai MH, Sherman DS, Cummings NE, Baar EL, Brinkman JA, Syed FA, Lamming DW.
      Calorie restriction (CR) extends the healthspan and lifespan of diverse species. In mammals, a broadly conserved metabolic effect of CR is improved insulin sensitivity, which may mediate the beneficial effects of a CR diet. This model has been challenged by the identification of interventions that extend lifespan and healthspan yet promote insulin resistance. These include rapamycin, which extends mouse lifespan yet induces insulin resistance by disrupting mTORC2 (mechanistic target of rapamycin complex 2). Here, we induce insulin resistance by genetically disrupting adipose mTORC2 via tissue-specific deletion of the mTORC2 component Rictor (AQ-RKO). Loss of adipose mTORC2 blunts the metabolic adaptation to CR and prevents whole-body sensitization to insulin. Despite this, AQ-RKO mice subject to CR experience the same increase in fitness and lifespan on a CR diet as wild-type mice. We conclude that the CR-induced improvement in insulin sensitivity is dispensable for the effects of CR on fitness and longevity.
    Keywords:  Rictor; adipose; calorie restriction; fitness; frailty; healthspan; insulin sensitivity; lifespan; lipogenesis; mTORC2
    DOI:  https://doi.org/10.1016/j.celrep.2019.08.084
  6. Front Cell Dev Biol. 2019 ;7 192
    Schmeisser K, Parker JA.
      Autophagy as a ubiquitous catabolic process causes degradation of cytoplasmic components and is generally considered to have beneficial effects on health and lifespan. In contrast, inefficient autophagy has been linked with detrimental effects on the organism and various diseases, such as Parkinson's disease. Previous research, however, showed that this paradigm is far from being black and white. For instance, it has been reported that increased levels of autophagy during development can be harmful, but become advantageous in the aging cell or organism, causing enhanced healthspan and even longevity. The antagonistic pleiotropy hypothesis postulates that genes, which control various traits in an organism, can be fitness-promoting in early life, but subsequently trigger aging processes later. Autophagy is controlled by the mechanistic target of rapamycin (mTOR), a key player of nutrient sensing and signaling and classic example of a pleiotropic gene. mTOR acts upstream of transcription factors such as FOXO, NRF, and TFEB, controlling protein synthesis, degradation, and cellular growth, thereby regulating fertility as well as aging. Here, we review recent findings about the pleiotropic role of autophagy during development and aging, examine the upstream factors, and contemplate specific mechanisms leading to disease, especially neurodegeneration.
    Keywords:  C. elegans; aging; autophagy; genetics; pleiotropy
    DOI:  https://doi.org/10.3389/fcell.2019.00192
  7. Elife. 2019 Oct 03. pii: e46380. [Epub ahead of print]8
    Zhao X, Nedvetsky P, Stanchi F, Vion AC, Popp O, Zühlke K, Dittmar G, Klussmann E, Gerhardt H.
      The cAMP-dependent protein kinase A (PKA) regulates various cellular functions in health and disease. In endothelial cells PKA activity promotes vessel maturation and limits tip cell formation. Here, we used a chemical genetic screen to identify endothelial-specific direct substrates of PKA in human umbilical vein endothelial cells (HUVEC) that may mediate these effects. Amongst several candidates, we identified ATG16L1, a regulator of autophagy, as novel target of PKA. Biochemical validation, mass spectrometry and peptide spot arrays revealed that PKA phosphorylates ATG16L1α at Ser268 and ATG16L1β at Ser269, driving phosphorylation-dependent degradation of ATG16L1 protein. Reducing PKA activity increased ATG16L1 protein levels and endothelial autophagy. Mouse in vivo genetics and pharmacological experiments demonstrated that autophagy inhibition partially rescues vascular hypersprouting caused by PKA deficiency. Together these results indicate that endothelial PKA activity mediates a critical switch from active sprouting to quiescence in part through phosphorylation of ATG16L1, which in turn reduces endothelial autophagy.
    Keywords:  biochemistry; cell biology; chemical biology; human; mouse
    DOI:  https://doi.org/10.7554/eLife.46380
  8. Cell Metab. 2019 Oct 01. pii: S1550-4131(19)30502-9. [Epub ahead of print]30(4): 630-655
    Lautrup S, Sinclair DA, Mattson MP, Fang EF.
      NAD+ is a pivotal metabolite involved in cellular bioenergetics, genomic stability, mitochondrial homeostasis, adaptive stress responses, and cell survival. Multiple NAD+-dependent enzymes are involved in synaptic plasticity and neuronal stress resistance. Here, we review emerging findings that reveal key roles for NAD+ and related metabolites in the adaptation of neurons to a wide range of physiological stressors and in counteracting processes in neurodegenerative diseases, such as those occurring in Alzheimer's, Parkinson's, and Huntington diseases, and amyotrophic lateral sclerosis. Advances in understanding the molecular and cellular mechanisms of NAD+-based neuronal resilience will lead to novel approaches for facilitating healthy brain aging and for the treatment of a range of neurological disorders.
    Keywords:  Alzheimer’s disease; NAD+; Parkinson’s disease; brain aging; mitochondria; mitophagy; neurodegeneration; neuronal plasticity; sirtuins
    DOI:  https://doi.org/10.1016/j.cmet.2019.09.001
  9. Mol Cell. 2019 Oct 03. pii: S1097-2765(19)30688-4. [Epub ahead of print]76(1): 5-7
    Green DR.
      A decline in polyamine levels with age has been implicated in the pathophysiology of aging, and nutritional supplementation of spermidine can reduce age-related pathology and increase lifespan in a number of different organisms. In this issue of Molecular Cell, Zhang and colleagues provide a mechanistic link between polyamines, autophagy, and aging.
    DOI:  https://doi.org/10.1016/j.molcel.2019.09.003
  10. Sci Rep. 2019 Oct 02. 9(1): 14167
    Krichel C, Möckel C, Schillinger O, Huesgen PF, Sticht H, Strodel B, Weiergräber OH, Willbold D, Neudecker P.
      (Macro-)autophagy is a compartmental degradation pathway conserved from yeast to mammals. The yeast protein Atg8 mediates membrane tethering/hemifusion and cargo recruitment and is essential for autophagy. The human MAP1LC3/GABARAP family proteins show high sequence identity with Atg8, but MAP1LC3C is distinguished by a conspicuous amino-terminal extension with unknown functional significance. We have determined the high-resolution three-dimensional structure and measured the backbone dynamics of MAP1LC3C by NMR spectroscopy. From Ser18 to Ala120, MAP1LC3C forms an α-helix followed by the ubiquitin-like tertiary fold with two hydrophobic binding pockets used by MAP1LC3/GABARAP proteins to recognize targets presenting LC3-interacting regions (LIRs). Unlike other MAP1LC3/GABARAP proteins, the amino-terminal region of MAP1LC3C does not form a stable helix α1 but a "sticky arm" consisting of a polyproline II motif on a flexible linker. Ser18 at the interface between this linker and the structural core can be phosphorylated in vitro by protein kinase A, which causes additional conformational heterogeneity as monitored by NMR spectroscopy and molecular dynamics simulations, including changes in the LIR-binding interface. Based on these results we propose that the amino-terminal polyproline II motif mediates specific interactions with the microtubule cytoskeleton and that Ser18 phosphorylation modulates the interplay of MAP1LC3C with its various target proteins.
    DOI:  https://doi.org/10.1038/s41598-019-48155-8
  11. Int J Mol Sci. 2019 Sep 27. pii: E4804. [Epub ahead of print]20(19):
    Kozhevnikova OS, Telegina DV, Tyumentsev MA, Kolosova NG.
      Age-related macular degeneration (AMD) is one of the main causes of vision impairment in the elderly. Autophagy is the process of delivery of cytoplasmic components into lysosomes for cleavage; its age-related malfunction may contribute to AMD. Here we showed that the development of AMD-like retinopathy in OXYS rats is accompanied by retinal transcriptome changes affecting genes involved in autophagy. These genes are associated with kinase activity, immune processes, and FoxO, mTOR, PI3K-AKT, MAPK, AMPK, and neurotrophin pathways at preclinical and manifestation stages, as well as vesicle transport and processes in lysosomes at the progression stage. We demonstrated a reduced response to autophagy modulation (inhibition or induction) in the OXYS retina at age 16 months: expression of genes Atg5, Atg7, Becn1, Nbr1, Map1lc3b, p62, and Gabarapl1 differed between OXYS and Wistar (control) rats. The impaired reactivity of autophagy was confirmed by a decreased number of autophagosomes under the conditions of blocked autophagosome-lysosomal fusion according to immunohistochemical analysis and transmission electron microscopy. Thus, the development of AMD signs occurs against the background of changes in the expression of autophagy-related genes and a decrease in autophagy reactivity: the ability to enhance autophagic flux in response to stress.
    Keywords:  age-related macular degeneration; autophagy; chloroquine; fasting; retina; retinal pigment epithelium; transcriptome
    DOI:  https://doi.org/10.3390/ijms20194804
  12. Cardiovasc Res. 2019 Oct 04. pii: cvz251. [Epub ahead of print]
    Oka SI, Chin A, Park JY, Ikeda S, Mizushima W, Ralda G, Zhai P, Tong M, Byun J, Tang F, Einaga Y, Huang CY, Kashihara T, Zhao M, Nah J, Tian B, Hirabayashi Y, Yodoi J, Sadoshima J.
      AIMS: Thioredoxin 1 (Trx1) is an evolutionarily conserved oxidoreductase that cleaves disulfide bonds in oxidized substrate proteins such as mechanistic target of rapamycin (mTOR) and maintains nuclear-encoded mitochondrial gene expression. The cardioprotective effect of Trx1 has been demonstrated via cardiac-specific overexpression of Trx1 and dominant negative Trx1. However, the pathophysiological role of endogenous Trx1 has not been defined with a loss-of-function model. To address this, we have generated cardiac-specific Trx1 knockout (Trx1cKO) mice.METHODS AND RESULTS: Trx1cKO mice were viable but died with a median survival age of 25.5 days. They developed heart failure, evidenced by contractile dysfunction, hypertrophy, and increased fibrosis and apoptotic cell death. Multiple markers consistently indicated increased oxidative stress and RNA-sequencing revealed downregulation of genes involved in energy production in Trx1cKO mice. Mitochondrial morphological abnormality was evident in these mice. Although heterozygous Trx1cKO mice did not show any significant baseline phenotype, pressure-overload-induced cardiac dysfunction and downregulation of metabolic genes were exacerbated in these mice. mTOR was more oxidized and phosphorylation of mTOR substrates such as S6K and 4EBP1 was impaired in Trx1cKO mice. In cultured cardiomyocytes, Trx1 knockdown inhibited mitochondrial respiration and metabolic gene promoter activity, suggesting that Trx1 maintains mitochondrial function in a cell autonomous manner. Importantly, mTOR-C1483F, an oxidation resistant mutation, prevented Trx1 knockdown-induced mTOR oxidation and inhibition and attenuated suppression of metabolic gene promoter activity.
    CONCLUSION(S): Endogenous Trx1 is essential for maintaining cardiac function and metabolism, partly through mTOR regulation via Cys1483.
    TRANSLATIONAL PERSPECTIVE: Although cell protective effects of Trx1 have been demonstrated previously, the in vivo function and the direct target of endogenous Trx1 remain to be elucidated. Using cardiac-specific Trx1 KO mice, this study demonstrates that endogenous Trx1 plays an essential role in maintaining cardiac function and redox homeostasis and confers stress resistance to the heart. The salutary effect of Trx1 in the heart is primarily mediated through reduction of mTOR in vivo.
    Keywords:  Heart; Redox; Thioredoxin-1(Trx1); mechanistic target of rapamycin (mTOR); metabolism
    DOI:  https://doi.org/10.1093/cvr/cvz251
  13. J Cell Physiol. 2019 Oct 02.
    Ashrafizadeh M, Ahmadi Z, Farkhondeh T, Samarghandian S.
      Autophagy is considered as an important mechanism for maintaining homeostasis and responsible for the degradation of superfluous or potentially toxic components and organelles. Autophagy impairment is associated with a number of pathological conditions, such as aging, neurological disorders, cancer, and infection. Autophagy also plays a significant role in cancer chemotherapy. The multiple cancer drugs have been notably developed with the strategy of autophagy modulation. Statins, 3-hydroxy-3-methyl-glutaryl-CoA inhibitors, are known due to their efficacy in decreasing low-density lipoprotein and extensively used for the management of cardiovascular diseases. Statins have other therapeutic and biological activities, such as antioxidant, anti-inflammatory, antitumor, and neuroprotective known as pleiotropic effects. It seems that statins are capable of targeting various signaling pathways in the induction of their great pharmacological effects. At the present study, we demonstrate the therapeutic effects of statins mediated via autophagy regulation.
    Keywords:  autophagy; cancer therapy; cardiovascular disease; programmed cell death; statins; therapeutic effect
    DOI:  https://doi.org/10.1002/jcp.29227
  14. Sci Adv. 2019 Sep;5(9): eaax8164
    Zhang T, Péli-Gulli MP, Zhang Z, Tang X, Ye J, De Virgilio C, Ding J.
      The Rag/Gtr GTPases serve as a central module in the nutrient-sensing signaling network upstream of TORC1. In yeast, the anchoring of Gtr1-Gtr2 to membranes depends on the Ego1-Ego2-Ego3 ternary complex (EGO-TC), resulting in an EGO-TC-Gtr1-Gtr2 complex (EGOC). EGO-TC and human Ragulator share no obvious sequence similarities and also differ in their composition with respect to the number of known subunits, which raises the question of how the EGO-TC fulfills its function in recruiting Gtr1-Gtr2. Here, we report the structure of EGOC, in which Ego1 wraps around Ego2, Ego3, and Gtr1-Gtr2. In addition, Ego3 interacts with Gtr1-Gtr2 to stabilize the complex. The functional roles of key residues involved in the assembly are validated by in vivo assays. Our structural and functional data combined demonstrate that EGOC and Ragulator-Rag complex are structurally conserved and that EGO-TC is essential and sufficient to recruit Gtr1-Gtr2 to membranes to ensure appropriate TORC1 signaling.
    DOI:  https://doi.org/10.1126/sciadv.aax8164