bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2019–07–14
nine papers selected by
Viktor Korolchuk, Newcastle University
  1. Covalent targeting of the vacuolar H+-ATPase activates autophagy via mTORC1 inhibition.
  2. Diverse Cellular Roles of Autophagy.
  3. Quality Control in Neurons: Mitophagy and Other Selective Autophagy Mechanisms.
  4. The L-type amino acid transporter LAT1 inhibits osteoclastogenesis and maintains bone homeostasis through the mTORC1 pathway.
  5. Myocardial hypothermia increases autophagic flux, mitochondrial mass and myocardial function after ischemia-reperfusion injury.
  6. PINK1 Content in Mitochondria is Regulated by ER-Associated Degradation.
  7. LC3-positive structures are prominent in autophagy-deficient cells.
  8. Outstanding Questions in Mitophagy: What we Do and Do Not Know.
  9. Autophagy links MTOR and GABA signaling in the brain.
  1. Nat Chem Biol. 2019 Jul 08.
    Covalent targeting of the vacuolar H+-ATPase activates autophagy via mTORC1 inhibition.
    Clive Yik-Sham Chung, Hijai R Shin, Charles A Berdan, Breanna Ford, Carl C Ward, James A Olzmann, Roberto Zoncu, Daniel K Nomura.
      Autophagy is a lysosomal degradation pathway that eliminates aggregated proteins and damaged organelles to maintain cellular homeostasis. A major route for activating autophagy involves inhibition of the mTORC1 kinase, but current mTORC1-targeting compounds do not allow complete and selective mTORC1 blockade. Here, we have coupled screening of a covalent ligand library with activity-based protein profiling to discover EN6, a small-molecule in vivo activator of autophagy that covalently targets cysteine 277 in the ATP6V1A subunit of the lysosomal v-ATPase, which activates mTORC1 via the Rag guanosine triphosphatases. EN6-mediated ATP6V1A modification decouples the v-ATPase from the Rags, leading to inhibition of mTORC1 signaling, increased lysosomal acidification and activation of autophagy. Consistently, EN6 clears TDP-43 aggregates, a causative agent in frontotemporal dementia, in a lysosome-dependent manner. Our results provide insight into how the v-ATPase regulates mTORC1, and reveal a unique approach for enhancing cellular clearance based on covalent inhibition of lysosomal mTORC1 signaling.
    DOI:  https://doi.org/10.1038/s41589-019-0308-4
  2. Annu Rev Cell Dev Biol. 2019 Jul 05.
    Diverse Cellular Roles of Autophagy.
    Hideaki Morishita, Noboru Mizushima.
      Macroautophagy is an intracellular degradation system that delivers diverse cytoplasmic materials to lysosomes via autophagosomes. Recent advances have enabled identification of several selective autophagy substrates and receptors, greatly expanding our understanding of the cellular functions of autophagy. In this review, we describe the diverse cellular functions of macroautophagy, including its essential contribution to metabolic adaptation and cellular homeostasis. We also discuss emerging findings on the mechanisms and functions of various types of selective autophagy. Expected final online publication date for the Annual Review of Cell and Developmental Biology Volume 35 is October 7, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    DOI:  https://doi.org/10.1146/annurev-cellbio-100818-125300
  3. J Mol Biol. 2019 Jul 08. pii: S0022-2836(19)30428-0. [Epub ahead of print]
    Quality Control in Neurons: Mitophagy and Other Selective Autophagy Mechanisms.
    Chantell S Evans, Erika L F Holzbaur.
      The cargo-specific removal of organelles via selective autophagy is important to maintain neuronal homeostasis. Genetic studies indicate that deficits in these pathways are implicated in neurodegenerative diseases, including Parkinson's and Amyotrophic lateral sclerosis. Here, we review our current understanding of the pathways that regulate mitochondrial quality control, and compare these mechanisms to those regulating ER and the clearance of protein aggregates. Research suggests that there are multiple mechanisms regulating the degradation of specific cargos, such as dysfunctional organelles and protein aggregates. These mechanisms are critical for neuronal health, as neurons are uniquely vulnerable to impairment in organelle quality control pathways due to their morphology, size, polarity and postmitotic nature. We highlight the consequences of dysregulation of selective autophagy in neurons, and discuss current challenges in correlating noncongruent findings from in vitro and in vivo systems.
    Keywords:  ER-phagy; Mitochondrial quality control; Mitophagy; Neurodegeneration; Selective autophagy
    DOI:  https://doi.org/10.1016/j.jmb.2019.06.031
  4. Sci Signal. 2019 Jul 09. pii: eaaw3921. [Epub ahead of print]12(589):
    The L-type amino acid transporter LAT1 inhibits osteoclastogenesis and maintains bone homeostasis through the mTORC1 pathway.
    Kakeru Ozaki, Takanori Yamada, Tetsuhiro Horie, Atsushi Ishizaki, Manami Hiraiwa, Takashi Iezaki, Gyujin Park, Kazuya Fukasawa, Hikari Kamada, Kazuya Tokumura, Mei Motono, Katsuyuki Kaneda, Kazuma Ogawa, Hiroki Ochi, Shingo Sato, Yasuhiro Kobayashi, Yun-Bo Shi, Peter M Taylor, Eiichi Hinoi.
      L-type amino acid transporter 1 (LAT1), which is encoded by solute carrier transporter 7a5 (Slc7a5), plays a crucial role in amino acid sensing and signaling in specific cell types, contributing to the pathogenesis of cancer and neurological disorders. Amino acid substrates of LAT1 have a beneficial effect on bone health directly and indirectly, suggesting a potential role for LAT1 in bone homeostasis. Here, we identified LAT1 in osteoclasts as important for bone homeostasis. Slc7a5 expression was substantially reduced in osteoclasts in a mouse model of ovariectomy-induced osteoporosis. The osteoclast-specific deletion of Slc7a5 in mice led to osteoclast activation and bone loss in vivo, and Slc7a5 deficiency increased osteoclastogenesis in vitro. Loss of Slc7a5 impaired activation of the mechanistic target of rapamycin complex 1 (mTORC1) pathway in osteoclasts, whereas genetic activation of mTORC1 corrected the enhanced osteoclastogenesis and bone loss in Slc7a5-deficient mice. Last, Slc7a5 deficiency increased the expression of nuclear factor of activated T cells, cytoplasmic 1 (Nfatc1) and the nuclear accumulation of NFATc1, a master regulator of osteoclast function, possibly through the canonical nuclear factor κB pathway and the Akt-glycogen synthase kinase 3β signaling axis, respectively. These findings suggest that the LAT1-mTORC1 axis plays a pivotal role in bone resorption and bone homeostasis by modulating NFATc1 in osteoclasts, thereby providing a molecular connection between amino acid intake and skeletal integrity.
    DOI:  https://doi.org/10.1126/scisignal.aaw3921
  5. Sci Rep. 2019 Jul 10. 9(1): 10001
    Myocardial hypothermia increases autophagic flux, mitochondrial mass and myocardial function after ischemia-reperfusion injury.
    Stefanie Marek-Iannucci, Amandine Thomas, Jean Hou, Annunziata Crupi, Jon Sin, David J Taylor, Lawrence S Czer, Fardad Esmailian, Robert M Mentzer, Allen M Andres, Roberta A Gottlieb.
      Animal studies have demonstrated beneficial effects of therapeutic hypothermia on myocardial function, yet exact mechanisms remain unclear. Impaired autophagy leads to heart failure and mitophagy is important for mitigating ischemia/reperfusion injury. This study aims to investigate whether the beneficial effects of therapeutic hypothermia are due to preserved autophagy and mitophagy. Under general anesthesia, the left anterior descending coronary artery of 19 female farm pigs was occluded for 90 minutes with consecutive reperfusion. 30 minutes after reperfusion, we performed pericardial irrigation with warm or cold saline for 60 minutes. Myocardial tissue analysis was performed one and four weeks after infarction. Therapeutic hypothermia induced a significant increase in autophagic flux, mitophagy, mitochondrial mass and function in the myocardium after infarction. Cell stress, apoptosis, inflammation as well as fibrosis were reduced, with significant preservation of systolic and diastolic function four weeks post infarction. We found similar biochemical changes in human samples undergoing open chest surgery under hypothermic conditions when compared to the warm. These results suggest that autophagic flux and mitophagy are important mechanisms implicated in cardiomyocyte recovery after myocardial infarction under hypothermic conditions. New therapeutic strategies targeting these pathways directly could lead to improvements in prevention of heart failure.
    DOI:  https://doi.org/10.1038/s41598-019-46452-w
  6. J Neurosci. 2019 Jul 12. pii: 1691-18. [Epub ahead of print]
    PINK1 Content in Mitochondria is Regulated by ER-Associated Degradation.
    Cristina Guardia-Laguarta, Yuhui Liu, Knut H Lauritzen, Hediye Erdjument-Bromage, Brittany Martin, Theresa C Swayne, Xuejun Jiang, Serge Przedborski.
      Maintaining a pool of functional mitochondria requires degradation of damaged ones within the cell. PINK1 is critical in this quality-control process: loss of mitochondrial membrane potential causes PINK1 to accumulate on the mitochondrial surface, triggering mitophagy. However, little is known about how PINK1 is regulated. Recently, we showed that PINK1 content is kept low in healthy mitochondria by continuous ubiquitination and proteasomal degradation of its mature form via a mechanism inconsistent with the proposed N-end rule process. Using both human female and monkey cell lines, here, we now demonstrate that once generated within the mitochondria, 52-kDa PINK1 adopts a mitochondrial topology most consistent with it being at the mitochondrial-endoplasmic reticulum (ER) interface. From this particular submitochondrial location, PINK1 interacts with components of the ER-associated degradation pathway, such as the E3 ligases gp78 and HRD1, which cooperate to catalyze PINK1 ubiquitination. The valosin-containing protein and its cofactor, UFD1, then target ubiquitinated PINK1 for proteasomal degradation. Our data show that PINK1 in healthy mitochondria is negatively regulated via an interplay between mitochondria and ER, and shed light on how this mitochondrial protein gains access to the proteasome.SIGNIFICANCE STATEMENTRegulation of mitochondrial content of PINK1, a contributor to mitophagy, is an important area of research. Recently, we found that PINK1 content is kept low in healthy mitochondria by continuous ubiquitination and proteasomal degradation. We now extend and refine this novel finding by showing that PINK1 localizes at the mitochondrial-endoplasmic reticulum (ER) interface, from where it interacts with the ER-associated degradation machinery, which catalyzes its ubiquitination and transfer to the proteasome. Thus, these data show that PINK1 in healthy mitochondria is negatively regulated via a mitochondria and ER interplay, and how this mitochondrial protein gains access to the proteasome.
    DOI:  https://doi.org/10.1523/JNEUROSCI.1691-18.2019
  7. Sci Rep. 2019 Jul 12. 9(1): 10147
    LC3-positive structures are prominent in autophagy-deficient cells.
    Gautam Runwal, Eleanna Stamatakou, Farah H Siddiqi, Claudia Puri, Ye Zhu, David C Rubinsztein.
      Autophagy is an evolutionarily conserved process across eukaryotes that degrades cargoes like aggregate-prone proteins, pathogens, damaged organelles and macromolecules via delivery to lysosomes. The process involves the formation of double-membraned autophagosomes that engulf the cargoes destined for degradation, sometimes with the help of autophagy receptors like p62, which are themselves autophagy substrates. LC3-II, a standard marker for autophagosomes, is generated by the conjugation of cytosolic LC3-I to phosphatidylethanolamine (PE) on the surface of nascent autophagosomes. As LC3-II is relatively specifically associated with autophagosomes and autolysosomes (in the absence of conditions stimulating LC3-associated phagocytosis), quantification of LC3-positive puncta is considered as a gold-standard assay for assessing the numbers of autophagosomes in cells. Here we find that the endogenous LC3-positive puncta become larger in cells where autophagosome formation is abrogated, and are prominent even when LC3-II is not formed. This occurs even with transient and incomplete inhibition of autophagosome biogenesis. This phenomenon is due to LC3-I sequestration to p62 aggregates, which accumulate when autophagy is impaired. This observation questions the reliability of LC3-immunofluorescence assays in cells with compromised autophagy.
    DOI:  https://doi.org/10.1038/s41598-019-46657-z
  8. J Mol Biol. 2019 Jul 09. pii: S0022-2836(19)30429-2. [Epub ahead of print]
    Outstanding Questions in Mitophagy: What we Do and Do Not Know.
    Lambert Montava-Garriga, Ian G Ganley.
      The elimination of mitochondria via autophagy, termed mitophagy, is an evolutionarily conserved mechanism for mitochondrial quality control and homeostasis. Mitophagy, therefore, has an important contribution to cell function and integrity, which extends to the whole organism for development and survival. Research in mitophagy has boomed in recent years and it is becoming clear that mitophagy is a complex and multi-factorial cellular response that depends on tissue, energetic, stress and signalling contexts. Yet we know very little of its physiological regulation and the direct contribution of mitophagy to pathologies like neurodegenerative diseases. In this review, we aim to discuss the outstanding questions (and questions outstanding) in the field and reflect on our current understanding of mitophagy, the current challenges and the future directions to take.
    Keywords:  Autophagosome; Autophagy; Metabolism; Mitochondria; Mitophagy; Neurodegeneration; Parkinson's disease; Ubiquitylation; mito-QC
    DOI:  https://doi.org/10.1016/j.jmb.2019.06.032
  9. Autophagy. 2019 Jul 07. 1-2
    Autophagy links MTOR and GABA signaling in the brain.
    Kelvin K Hui, Motomasa Tanaka.
      The disruption of MTOR-regulated macroautophagy/autophagy was previously shown to cause autistic-like abnormalities; however, the underlying molecular defects remained largely unresolved. In a recent study, we demonstrated that autophagy deficiency induced by conditional Atg7 deletion in either forebrain GABAergic inhibitory or excitatory neurons leads to a similar set of autistic-like behavioral abnormalities even when induced following the peak period of synaptic pruning during postnatal neurodevelopment. Our proteomic analysis and molecular dissection further revealed a mechanism in which the GABAA receptor trafficking function of GABARAP (gamma-aminobutyric acid receptor associated protein) family proteins was compromised as they became sequestered by SQSTM1/p62-positive aggregates formed due to autophagy deficiency. Our discovery of autophagy as a link between MTOR and GABA signaling may have implications not limited to neurodevelopmental and neuropsychiatric disorders, but could potentially be involved in other human pathologies such as cancer and diabetes in which both pathways are implicated.
    Keywords:  Autism spectrum disorder (ASD); GABA receptor trafficking; MTOR hyperactivation; excitatory-inhibitory imbalance (E-I imbalance); protein aggregation
    DOI:  https://doi.org/10.1080/15548627.2019.1637643
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