bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2021–08–15
twenty-six papers selected by
Viktor Korolchuk, Newcastle University
  1. AMPK-activated ULK1 phosphorylates PIKFYVE to drive formation of PtdIns5P-containing autophagosomes during glucose starvation.
  2. An AMPK-ULK1-PIKFYVE signaling axis for PtdIns5P-dependent autophagy regulation upon glucose starvation.
  3. Lipotoxicity-induced STING1 activation stimulates MTORC1 and restricts hepatic lipophagy.
  4. TRIM44 links the UPS to SQSTM1/p62-dependent aggrephagy and removing misfolded proteins.
  5. Delineating the lipidated Atg8 structure for unveiling its hidden activity in autophagy.
  6. A DRP-1 dependent autophagy process facilitates rebuilding of the mitochondrial network and modulates adaptation capacity in response to acute heat stress during C. elegans development.
  7. Structural and biochemical advances on the recruitment of the autophagy-initiating ULK and TBK1 complexes by autophagy receptor NDP52.
  8. MTORC1-dependent crinophagy regulates glucagon content in pancreatic α-cells.
  9. Lamin regulates the dietary restriction response via the mTOR pathway in Caenorhabditis elegans.
  10. The Hippo kinase LATS2 impairs pancreatic β-cell survival in diabetes through the mTORC1-autophagy axis.
  11. Mitochondrial fission, integrity and completion of mitophagy require separable functions of Vps13D in Drosophila neurons.
  12. Strain induced mechanoresponse depends on cell contractility and BAG3-mediated autophagy.
  13. The Role of NCOA4-Mediated Ferritinophagy in Ferroptosis.
  14. Inborn errors of autophagy and infectious diseases.
  15. ORF3a-Mediated Incomplete Autophagy Facilitates Severe Acute Respiratory Syndrome Coronavirus-2 Replication.
  16. Natural compounds modulate the autophagy with potential implication of stroke.
  17. Glycans in autophagy, endocytosis and lysosomal functions.
  18. BioID reveals an ATG9A interaction with ATG13-ATG101 in the degradation of p62/SQSTM1-ubiquitin clusters.
  19. A conserved ATG2 binding site in WIPI4 and yeast Hsv2 is disrupted by mutations causing β-propeller protein-associated neurodegeneration.
  20. The zinc finger/RING domain protein Unkempt regulates cognitive flexibility.
  21. NDP52 Protects against Myocardial Infarction-Provoked Cardiac Anomalies through Promoting Autophagosome-Lysosome Fusion via Recruiting TBK1 and RAB7.
  22. Sustained intracellular calcium rise mediates neuronal mitophagy in models of autosomal dominant optic atrophy.
  23. Sestrins regulate muscle stem cell metabolic homeostasis.
  24. Dynamics of autophagy and ubiquitin proteasome system coordination and interplay in skeletal muscle atrophy.
  25. Two parallel pathways connect glutamine metabolism and mTORC1 activity to regulate glutamoptosis.
  26. New insights into mitophagy and stem cells.
  1. Autophagy. 2021 Aug 12. 1-2
    AMPK-activated ULK1 phosphorylates PIKFYVE to drive formation of PtdIns5P-containing autophagosomes during glucose starvation.
    Cansu Karabiyik, David C Rubinsztein.
      The induction of macroautophagy/autophagy upon glucose deprivation can occur independently of the PIK3C3/VPS34 complex. Recently, we described a non-canonical signaling pathway involving the kinases AMPK, ULK1 and PIKFYVE that are induced during glucose starvation, leading to the formation of PtdIns5P-containing autophagosomes, resulting in increased autophagy flux and clearance of autophagy substrates. In this cascade, the activation of AMPK leads to ULK1 phosphorylation. ULK1 then phosphorylates PIKFYVE at S1548, leading to its activation and increased PtdIns5P formation, which enables the recruitment of machinery required for autophagosome biogenesis.
    Keywords:  AMPK; Autophagy; PIKFYVE; Ptdins5P; ULK1; glucose starvation
    DOI:  https://doi.org/10.1080/15548627.2021.1961409
  2. Autophagy. 2021 Aug 09. 1-2
    An AMPK-ULK1-PIKFYVE signaling axis for PtdIns5P-dependent autophagy regulation upon glucose starvation.
    Ying Yang, Daniel J Klionsky.
      Glucose deprivation induces macroautophagy/autophagy primarily through AMPK activation. However, little is known about the exact mechanism of this signaling. A recent study from Dr. David C. Rubinsztein's lab showed that ULK1 is activated by AMPK upon glucose starvation, resulting in the phosphorylation of the lipid kinase PIKFYVE on S1548. The activated PIKFYVE consequently enhances the formation of phosphatidylinositol-5-phosphate (PtdIns5P)-containing autophagosomes, and therefore drives autophagy upregulation. The novel discovery of how ULK1 regulates the non-canonical autophagy signaling (PtdIns5P-dependent autophagy), not only expands our knowledge of autophagy, but also sheds light on therapeutic strategies for curing human disorders, where glucose-induced starvation can play an important role.
    Keywords:  Lipid kinase; lysosome; non-canonical autophagy; phosphoinositides; stress
    DOI:  https://doi.org/10.1080/15548627.2021.1959240
  3. Autophagy. 2021 Aug 12. 1-17
    Lipotoxicity-induced STING1 activation stimulates MTORC1 and restricts hepatic lipophagy.
    Kunpeng Liu, Dongbo Qiu, Xue Liang, Yingqi Huang, Yao Wang, Xin Jia, Kun Li, Jingyuan Zhao, Cong Du, Xiusheng Qiu, Jun Cui, Zhendong Xiao, Yunfei Qin, Qi Zhang.
      Lipid accumulation often leads to lipotoxic injuries to hepatocytes, which can cause nonalcoholic steatohepatitis. The association of inflammation with lipid accumulation in liver tissue has been studied for decades; however, key mechanisms have been identified only recently. In particular, it is still unknown how hepatic inflammation regulates lipid metabolism in hepatocytes. Herein, we found that PA treatment or direct stimulation of STING1 promoted, whereas STING1 deficiency impaired, MTORC1 activation, suggesting that STING1 is involved in PA-induced MTORC1 activation. Mechanistic studies revealed that STING1 interacted with several components of the MTORC1 complex and played an important role in the complex formation of MTORC1 under PA treatment. The involvement of STING1 in MTORC1 activation was dependent on SQSTM1, a key regulator of the MTORC1 pathway. In SQSTM1-deficient cells, the interaction of STING1 with the components of MTORC1 was weak. Furthermore, the impaired activity of MTORC1 via rapamycin treatment or STING1 deficiency decreased the numbers of LDs in cells. PA treatment inhibited lipophagy, which was not observed in STING1-deficient cells or rapamycin-treated cells. Restoration of MTORC1 activity via treatment with amino acids blocked lipophagy and LDs degradation. Finally, increased MTORC1 activation concomitant with STING1 activation was observed in liver tissues of nonalcoholic fatty liver disease patients, which provided clinical evidence for the involvement of STING1 in MTORC1 activation. In summary, we identified a novel regulatory loop of STING1-MTORC1 and explain how hepatic inflammation regulates lipid accumulation. Our findings may facilitate the development of new strategies for clinical treatment of hepatic steatosis.Abbreviations: AA: amino acid; ACTB: actin beta; cGAMP: cyclic GMP-AMP; CGAS: cyclic GMP-AMP synthase; DEPTOR: DEP domain containing MTOR interacting protein; EIF4EBP1: eukaryotic translation initiation factor 4E binding protein 1; FFAs: free fatty acids; GFP: green fluorescent protein; HFD: high-fat diet; HT-DNA: herring testis DNA; IL1B: interleukin 1 beta; LAMP1: lysosomal associated membrane protein 1; LDs: lipid droplets; MAP1LC3: microtubule associated protein 1 light chain 3; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; MEFs: mouse embryonic fibroblasts; MLST8: MTOR associated protein, LST8 homolog; MT-ND1: mitochondrially encoded NADH: ubiquinone oxidoreductase core subunit 1; mtDNA: mitochondrial DNA; MTOR: mechanistic target of rapamycin kinase; MTORC1: MTOR complex 1; NAFL: nonalcoholic fatty liver; NAFLD: nonalcoholic fatty liver disease; NASH: nonalcoholic steatohepatitis; NPCs: non-parenchymal cells; PA: palmitic acid; PLIN2: perilipin 2; RD: regular diet; RELA: RELA proto-oncogene, NF-kB subunit; RPS6: ribosomal protein S6; RPS6KB1: ribosomal protein S6 kinase B1; RPTOR: regulatory associated protein of MTOR complex 1; RRAGA: Ras related GTP binding A; RRAGC: Ras related GTP binding C; SQSTM1: sequestosome 1; STING1: stimulator of interferon response cGAMP interactor 1; TBK1: TANK binding kinase 1; TGs: triglycerides; TREX1: three prime repair exonuclease 1.
    Keywords:  Lipophagy; MTORC1; NAFLD; STING1; TBK1
    DOI:  https://doi.org/10.1080/15548627.2021.1961072
  4. Autophagy. 2021 Aug 12. 1-16
    TRIM44 links the UPS to SQSTM1/p62-dependent aggrephagy and removing misfolded proteins.
    Lin Lyu, Zheng Chen, Nami McCarty.
      Until recently, the ubiquitin-proteasome system (UPS) and macroautophagy/autophagy were considered to be two independent systems that target proteins for degradation by proteasomes or via lysosomes, respectively. Here, we report that TRIM44 (tripartite motif containing 44) is a novel link that connects the UPS system with the autophagy degradation pathway. Suppressing the UPS degradation pathway leads to TRIM44 upregulation, which further promotes aggregated protein clearance through the binding of K48 ubiquitin chains on proteins. TRIM44 expression activates autophagy via promoting SQSTM1/p62 oligomerization, which rapidly increases the rate of aggregate protein removal. Overall, our data reveal that TRIM44 is a newly identified link between the UPS system and the autophagy pathway. Delineating the cross-talk between these two degradation pathways may reveal new mechanisms of targeting aggregate-prone diseases, such as cancer and neurodegenerative disease.Abbreviations: 3-MA: 3-methyladenine; ACTB: actin beta; ATG5: autophagy related 5; BB: B-box domain; BECN1: beclin1; BM: bone marrow; CC: coiled-coil domain; CFTR: cystic fibrosis transmembrane conductance regulator; CON: control; CQ: chloroquine; DOX: doxycycline; DSP: dithiobis(succinimidly propionate); ER: endoplasmic reticulum; FI: fluorescence intensity; FL: full length; HIF1A/HIF-1#x3B1;: hypoxia inducible factor 1 subunit alpha; HSC: hematopoietic stem cells; HTT: huntingtin; KD: knockdown; KD-CON: knockdown construct control; MM: multiple myeloma; MTOR: mechanistic target of rapamycin kinase; NP-40: nonidet P-40; NFE2L2/NRF2: nuclear factor, erythroid 2 like 2; OE: overexpression; OE-CON: overexpression construct control; PARP: poly (ADP-ribose) polymerase; SDS: sodium dodecyl sulfate; SQSTM1/p62: sequestosome 1; Tet-on: tetracycline; TRIM44: tripartite motif containing 44; UPS: ubiquitin-proteasome system; ZF: zinc-finger.
    Keywords:  Aggregates; TRIM44; autophagy; deubiquitinase; misfolded proteins; protein homeostasis; ubiquitin-proteasome system
    DOI:  https://doi.org/10.1080/15548627.2021.1956105
  5. Autophagy. 2021 Aug 12. 1-2
    Delineating the lipidated Atg8 structure for unveiling its hidden activity in autophagy.
    Tatsuro Maruyama, Nobuo N Noda.
      Atg8 has attracted attention as a central factor in autophagosome biogenesis for a long time. However, the molecular activities of Atg8 on the phagophore membranes as the physiologically functional lipidated form remain enigmatic. In our recent study, we unveiled the hidden physicochemical activity of lipidated Atg8 toward the membrane. Structural analysis revealed that lipidated Atg8 adopts a preferred orientation on the membrane, contacting the membrane using aromatic residues and at the same time exposing cargo binding pockets to the solvent, enabling this small protein to perturb and transform membranes while recognizing autophagic cargos. The membrane perturbation activity was shown to be essential for efficient autophagosome biogenesis, yet questions on the mechanistic roles of Atg8 remain open.
    Keywords:  Atg8; GUV; NMR; autophagosome; autophagy; lipidation; membrane perturbation; vacuolar morphology
    DOI:  https://doi.org/10.1080/15548627.2021.1961075
  6. Autophagy. 2021 Aug 12. 1-2
    A DRP-1 dependent autophagy process facilitates rebuilding of the mitochondrial network and modulates adaptation capacity in response to acute heat stress during C. elegans development.
    Yanfang Chen, Emmanuel Culetto, Renaud Legouis.
      Temperature variations induce stressful conditions that challenge the ability of organisms to maintain cell homeostasis. The intensity and duration of heat stress affect cell response very differently, ranging from a beneficial effect - hormesis - to necrotic cell death. There is a strong interplay between the cell response to heat shock and macroautophagy/autophagy, which is induced to cope with stress. Using Caenorhabditis elegans, we developed a new paradigm to study adaptation to acute non-lethal heat-stress (aHS) during development. We found that aHS results in transient fragmentation of mitochondria, decreased cellular respiration, and delayed development. Moreover, an active autophagy flux associated with mitophagy events is triggered in many tissues, enables the rebuilding of the mitochondrial network and modulates the adaptive plasticity of the development, showing that the autophagic response is protective for C. elegans. Using genetic and cellular approaches, we showed that mitochondria are a major site for autophagosome biogenesis in the epidermis, under both standard and heat-stress conditions. We determined that DRP-1 (Dynamin-Related Protein 1) involved in mitochondrial fission, is an important player for the autophagy process and the adaptation to aHS. Our study suggests that DRP-1 is involved in coordinating mitochondrial fission and autophagosome biogenesis during stress.
    Keywords:  Autophagy; C. elegans; DRP-1; development plasticity; heat shock; mitochondria
    DOI:  https://doi.org/10.1080/15548627.2021.1953821
  7. Sci Adv. 2021 Aug;pii: eabi6582. [Epub ahead of print]7(33):
    Structural and biochemical advances on the recruitment of the autophagy-initiating ULK and TBK1 complexes by autophagy receptor NDP52.
    Tao Fu, Mingfang Zhang, Zixuan Zhou, Ping Wu, Chao Peng, Yingli Wang, Xinyu Gong, Ying Li, Yaru Wang, Xiaolong Xu, Miao Li, Liqiang Shen, Lifeng Pan.
      The recruitment of Unc-51-like kinase and TANK-binding kinase 1 complexes is essential for Nuclear dot protein 52-mediated selective autophagy and relies on the specific association of NDP52, RB1-inducible coiled-coil protein 1, and Nak-associated protein 1 (5-azacytidine-induced protein 2, AZI2). However, the underlying molecular mechanism remains elusive. Here, we find that except for the NDP52 SKIP carboxyl homology (SKICH)/RB1CC1 coiled-coil interaction, the LC3-interacting region of NDP52 can directly interact with the RB1CC1 Claw domain, as that of NAP1 FIP200-binding region (FIR). The determined crystal structures of NDP52 SKICH/RB1CC1 complex, NAP1 FIR/RB1CC1 complex, and the related NAP1 FIR/Gamma-aminobutyric acid receptor-associated protein complex not only elucidate the molecular bases underpinning the interactions of RB1CC1 with NDP52 and NAP1 but also reveal that RB1CC1 Claw and Autophagy-related protein 8 family proteins are competitive in binding to NAP1 and NDP52. Overall, our findings provide mechanistic insights into the interactions of NDP52, NAP1 with RB1CC1 and ATG8 family proteins.
    DOI:  https://doi.org/10.1126/sciadv.abi6582
  8. Autophagy. 2021 Aug 12. 1-2
    MTORC1-dependent crinophagy regulates glucagon content in pancreatic α-cells.
    Sangam Rajak, Paul M Yen, Rohit A Sinha.
      Hormone synthesis and secretion is a highly regulated process governed by metabolic cues. Although peptide hormone action is largely governed by the rate of its synthesis and secretion by endocrine cells, and the levels of its receptors on the target cells, intracellular degradation of the hormone-containing secretory vesicles by lysosomes (crinophagy) adds an additional layer of regulation. In our recent study, we uncovered the regulatory mechanism governing the crinophagic turnover of GCG (glucagon), a glycoprotein hormone secreted by pancreatic α-cells. Our results showed that inhibition of MTORC1 induces crinophagy-mediated degradation of glucagon and decreases its secretion in response to hypoglycemia. Furthermore, we demonstrated that crinophagy-regulated glucagon turnover does not involve macroautophagy. These results suggest that modulation of crinophagy may serve as a novel therapeutic strategy to regulate hormone secretion in endocrine and metabolic pathologies.
    Keywords:  Autophagy; MTORC1; crinophagy; diabetes; glucagon; lysosomes; rapamycin
    DOI:  https://doi.org/10.1080/15548627.2021.1961074
  9. J Cell Sci. 2021 Aug 12. pii: jcs.258428. [Epub ahead of print]
    Lamin regulates the dietary restriction response via the mTOR pathway in Caenorhabditis elegans.
    Chayki Charar, Sally Metsuyanim-Cohen, Daniel Z Bar.
      Animals subjected to dietary restriction (DR) have reduced body size, low fecundity, slower development, lower fat content and longer life span. We identified lamin as a regulator of multiple dietary restriction phenotypes. Downregulation of lmn-1, the single Caenorhabditis elegans lamin gene, increased animal size and fat content, specifically in DR animals. The LMN-1 protein acts in the mTOR pathway, upstream to RAPTOR and S6K, key component and target of mTOR complex 1 (mTORC1), respectively. DR excludes the mTORC1 activator RAGC-1 from the nucleus. Downregulation of lmn-1 restores RAGC-1 to the nucleus, a necessary step for the activation of the mTOR pathway. These findings further link lamin to metabolic regulation.
    Keywords:  Caenorhabditis elegans; Dietary restriction; Lamin; mTOR
    DOI:  https://doi.org/10.1242/jcs.258428
  10. Nat Commun. 2021 Aug 13. 12(1): 4928
    The Hippo kinase LATS2 impairs pancreatic β-cell survival in diabetes through the mTORC1-autophagy axis.
    Ting Yuan, Karthika Annamalai, Shruti Naik, Blaz Lupse, Shirin Geravandi, Anasua Pal, Aleksandra Dobrowolski, Jaee Ghawali, Marina Ruhlandt, Kanaka Durga Devi Gorrepati, Zahra Azizi, Dae-Sik Lim, Kathrin Maedler, Amin Ardestani.
      Diabetes results from a decline in functional pancreatic β-cells, but the molecular mechanisms underlying the pathological β-cell failure are poorly understood. Here we report that large-tumor suppressor 2 (LATS2), a core component of the Hippo signaling pathway, is activated under diabetic conditions and induces β-cell apoptosis and impaired function. LATS2 deficiency in β-cells and primary isolated human islets as well as β-cell specific LATS2 ablation in mice improves β-cell viability, insulin secretion and β-cell mass and ameliorates diabetes development. LATS2 activates mechanistic target of rapamycin complex 1 (mTORC1), a physiological suppressor of autophagy, in β-cells and genetic and pharmacological inhibition of mTORC1 counteracts the pro-apoptotic action of activated LATS2. We further show a direct interplay between Hippo and autophagy, in which LATS2 is an autophagy substrate. On the other hand, LATS2 regulates β-cell apoptosis triggered by impaired autophagy suggesting an existence of a stress-sensitive multicomponent cellular loop coordinating β-cell compensation and survival. Our data reveal an important role for LATS2 in pancreatic β-cell turnover and suggest LATS2 as a potential therapeutic target to improve pancreatic β-cell survival and function in diabetes.
    DOI:  https://doi.org/10.1038/s41467-021-25145-x
  11. PLoS Genet. 2021 Aug 12. 17(8): e1009731
    Mitochondrial fission, integrity and completion of mitophagy require separable functions of Vps13D in Drosophila neurons.
    Ryan Insolera, Péter Lőrincz, Alec J Wishnie, Gábor Juhász, Catherine A Collins.
      A healthy population of mitochondria, maintained by proper fission, fusion, and degradation, is critical for the long-term survival and function of neurons. Here, our discovery of mitophagy intermediates in fission-impaired Drosophila neurons brings new perspective into the relationship between mitochondrial fission and mitophagy. Neurons lacking either the ataxia disease gene Vps13D or the dynamin related protein Drp1 contain enlarged mitochondria that are engaged with autophagy machinery and also lack matrix components. Reporter assays combined with genetic studies imply that mitophagy both initiates and is completed in Drp1 impaired neurons, but fails to complete in Vps13D impaired neurons, which accumulate compromised mitochondria within stalled mito-phagophores. Our findings imply that in fission-defective neurons, mitophagy becomes induced, and that the lipid channel containing protein Vps13D has separable functions in mitochondrial fission and phagophore elongation.
    DOI:  https://doi.org/10.1371/journal.pgen.1009731
  12. Mol Biol Cell. 2021 Aug 11. mbcE21050254
    Strain induced mechanoresponse depends on cell contractility and BAG3-mediated autophagy.
    Lukas Lövenich, Georg Dreissen, Christina Hoffmann, Jens Konrad, Ronald Springer, Jörg Höhfeld, Rudolf Merkel, Bernd Hoffmann.
      Basically all mammalian tissues are constantly exposed to a variety of environmental mechanical signals. Depending on the signal strength, mechanics intervenes in a multitude of cellular processes and is thus capable to induce simple cellular adaptations but also complex differentiation processes and even apoptosis. The underlying recognition typically depends on mechanosensitive proteins, which most often sense the mechanical signal for the induction of a cellular signaling cascade by changing their protein conformation. However, the fate of mechanosensors after mechanical stress application is still poorly understood and it remains unclear whether protein degradation pathways affect the mechanosensitivity of cells. Here, we show that cyclic stretch induces autophagosome formation in a time-dependent manner. Formation depends on the cochaperone BAG3 and thus likely involves BAG3-mediated chaperone-assisted selective autophagy. Furthermore, we demonstrate that strain-induced cell reorientation is clearly delayed upon inhibition of autophagy, suggesting a bidirectional crosstalk between mechanotransduction and autophagic degradation. The strength of the observed delay depends on stable adhesion structures and stress fiber formation in a RhoA-dependent manner.
    DOI:  https://doi.org/10.1091/mbc.E21-05-0254
  13. Adv Exp Med Biol. 2021 ;1301 41-57
    The Role of NCOA4-Mediated Ferritinophagy in Ferroptosis.
    Naiara Santana-Codina, Ajami Gikandi, Joseph D Mancias.
      Nuclear receptor coactivator 4 (NCOA4) is a selective cargo receptor that mediates the autophagic degradation of ferritin, the cytosolic iron storage complex, in a process known as ferritinophagy. NCOA4-mediated ferritinophagy is required to maintain intracellular and systemic iron homeostasis and thereby iron-dependent physiologic processes such as erythropoiesis. Given this role of ferritinophagy in regulating iron homeostasis, modulating NCOA4-mediated ferritinophagic flux alters sensitivity to ferroptosis, a non-apoptotic iron-dependent form of cell death triggered by peroxidation of polyunsaturated fatty acids (PUFAs). A role for ferroptosis has been established in the pathophysiology of cancer and neurodegeneration; however, the importance of ferritinophagy in these pathologies remains largely unknown. Here, we review the available evidence on biochemical regulation of NCOA4-mediated ferritinophagy and its role in modulating sensitivity to innate and induced ferroptosis in neurodegenerative diseases and cancer. Finally, we evaluate the potential of modulating ferritinophagy in combination with ferroptosis inducers as a therapeutic strategy.
    Keywords:  Autophagy; Cancer; Ferritin; Ferritinophagy; NCOA4; Neurodegeneration
    DOI:  https://doi.org/10.1007/978-3-030-62026-4_4
  14. Curr Opin Immunol. 2021 Aug 06. pii: S0952-7915(21)00092-3. [Epub ahead of print]72 272-276
    Inborn errors of autophagy and infectious diseases.
    Ira Kd Sabli, Vanessa Sancho-Shimizu.
      Autophagy is a fundamental component of cell-autonomous immunity, targeting intracellular pathogens including viruses and cytosolic bacteria to lysosomes for degradation. Genetic mutations in components of the autophagy pathway result in autoinflammatory and neurodegenerative disorders. We focus on recent developments through the newly discovered inborn errors of autophagy strictly predisposing to severe viral infections. These feature mutations in TBK1, ATG4A, MAP1LC3B2, and ATG7, leading to herpes encephalitis, recurrent lymphocytic meningitis, and paralytic poliomyelitis. We highlight how this enhances our understanding of autophagy mechanisms and its role in human viral disease. As we better understand the contribution of these genes to disease, we can aim to develop targeted therapies for enhanced infection control.
    DOI:  https://doi.org/10.1016/j.coi.2021.07.005
  15. Front Cell Dev Biol. 2021 ;9 716208
    ORF3a-Mediated Incomplete Autophagy Facilitates Severe Acute Respiratory Syndrome Coronavirus-2 Replication.
    Yafei Qu, Xin Wang, Yunkai Zhu, Weili Wang, Yuyan Wang, Gaowei Hu, Chengrong Liu, Jingjiao Li, Shanhui Ren, Maggie Z X Xiao, Zhenshan Liu, Chunxia Wang, Joyce Fu, Yucai Zhang, Ping Li, Rong Zhang, Qiming Liang.
      Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the causative agent for the coronavirus disease 2019 (COVID-19) pandemic and there is an urgent need to understand the cellular response to SARS-CoV-2 infection. Beclin 1 is an essential scaffold autophagy protein that forms two distinct subcomplexes with modulators Atg14 and UVRAG, responsible for autophagosome formation and maturation, respectively. In the present study, we found that SARS-CoV-2 infection triggers an incomplete autophagy response, elevated autophagosome formation but impaired autophagosome maturation, and declined autophagy by genetic knockout of essential autophagic genes reduces SARS-CoV-2 replication efficiency. By screening 26 viral proteins of SARS-CoV-2, we demonstrated that expression of ORF3a alone is sufficient to induce incomplete autophagy. Mechanistically, SARS-CoV-2 ORF3a interacts with autophagy regulator UVRAG to facilitate PI3KC3-C1 (Beclin-1-Vps34-Atg14) but selectively inhibit PI3KC3-C2 (Beclin-1-Vps34-UVRAG). Interestingly, although SARS-CoV ORF3a shares 72.7% amino acid identity with the SARS-CoV-2 ORF3a, the former had no effect on cellular autophagy response. Thus, our findings provide the mechanistic evidence of possible takeover of host autophagy machinery by ORF3a to facilitate SARS-CoV-2 replication and raise the possibility of targeting the autophagic pathway for the treatment of COVID-19.
    Keywords:  COVID-19; ORF3a; SARS-CoV-2; UVRAG; autophagy
    DOI:  https://doi.org/10.3389/fcell.2021.716208
  16. Acta Pharm Sin B. 2021 Jul;11(7): 1708-1720
    Natural compounds modulate the autophagy with potential implication of stroke.
    Anil Ahsan, Mengru Liu, Yanrong Zheng, Wenping Yan, Lin Pan, Yue Li, Shijia Ma, Xingxian Zhang, Ming Cao, Zhanxun Wu, Weiwei Hu, Zhong Chen, Xiangnan Zhang.
      Stroke is considered a leading cause of mortality and neurological disability, which puts a huge burden on individuals and the community. To date, effective therapy for stroke has been limited by its complex pathological mechanisms. Autophagy refers to an intracellular degrading process with the involvement of lysosomes. Autophagy plays a critical role in maintaining the homeostasis and survival of cells by eliminating damaged or non-essential cellular constituents. Increasing evidence support that autophagy protects neuronal cells from ischemic injury. However, under certain circumstances, autophagy activation induces cell death and aggravates ischemic brain injury. Diverse naturally derived compounds have been found to modulate autophagy and exert neuroprotection against stroke. In the present work, we have reviewed recent advances in naturally derived compounds that regulate autophagy and discussed their potential application in stroke treatment.
    Keywords:  AD, Alzheimer's disease; ALS, amyotrophic lateral sclerosis; AMPK, 5′-adenosine monophosphate-activated protein kinase; ATF6, activating transcription factor 6; ATG, autophagy related genes; Autophagy; BCL-2, B-cell lymphoma 2; BNIP3L, BCL2/adenovirus; COPII, coat protein complex II; Cerebral ischemia; ER, endoplasmic reticulum; FOXO, forkhead box O; FUNDC1, FUN14 domain containing 1; GPCR, G-protein coupled receptor; HD, Huntington's disease; IPC, ischemic preconditioning; IRE1, inositol-requiring enzyme 1; JNK, c-Jun N-terminal kinase; LAMP, lysosomal-associated membrane protein; LC3, light chain 3; LKB1, liver kinase B1; Lysosomal activation; Mitochondria; Mitophagy; Natural compounds; Neurological disorders; Neuroprotection; OGD/R, oxygen and glucose deprivation-reperfusion; PD, Parkinson's disease; PERK, protein kinase R (PKR)-like endoplasmic reticulum kinase; PI3K, phosphatidylinositol 3-kinase; ROS, reactive oxygen species; SQSTM1, sequestosome 1; TFEB, transcription factor EB; TIGAR, TP53-induced glycolysis and apoptosis regulator; ULK, Unc-51- like kinase; Uro-A, urolithin A; eIF2a, eukaryotic translation-initiation factor 2; mTOR, mechanistic target of rapamycin; ΔΨm, mitochondrial membrane potential
    DOI:  https://doi.org/10.1016/j.apsb.2020.10.018
  17. Glycoconj J. 2021 Aug 14.
    Glycans in autophagy, endocytosis and lysosomal functions.
    Fulvio Reggiori, Hans-Joachim Gabius, Massimo Aureli, Winfried Römer, Sandro Sonnino, Eeva-Liisa Eskelinen.
      Glycans have been shown to function as versatile molecular signals in cells. This prompted us to look at their roles in endocytosis, endolysosomal system and autophagy. We start by introducing the cell biological aspects of these pathways, the concept of the sugar code, and provide an overview on the role of glycans in the targeting of lysosomal proteins and in lysosomal functions. Moreover, we review evidence on the regulation of endocytosis and autophagy by glycans. Finally, we discuss the emerging concept that cytosolic exposure of luminal glycans, and their detection by endogenous lectins, provides a mechanism for the surveillance of the integrity of the endolysosomal compartments, and serves their eventual repair or disposal.
    Keywords:  Endolysosomal system; Glycoconjugates; Glycolipids; Glycoproteins; Lectins; Sugar code
    DOI:  https://doi.org/10.1007/s10719-021-10007-x
  18. EMBO Rep. 2021 Aug 09. e51136
    BioID reveals an ATG9A interaction with ATG13-ATG101 in the degradation of p62/SQSTM1-ubiquitin clusters.
    Ashari R Kannangara, Daniel M Poole, Colten M McEwan, Joshua C Youngs, Vajira K Weerasekara, Alex M Thornock, Misael T Lazaro, Eranga R Balasooriya, Laura M Oh, Erik J Soderblom, Jonathan J Lee, Daniel L Simmons, Joshua L Andersen.
      ATG9A, the only multi-pass transmembrane protein among core ATG proteins, is an essential regulator of autophagy, yet its regulatory mechanisms and network of interactions are poorly understood. Through quantitative BioID proteomics, we identify a network of ATG9A interactions that includes members of the ULK1 complex and regulators of membrane fusion and vesicle trafficking, including the TRAPP, EARP, GARP, exocyst, AP-1, and AP-4 complexes. These interactions mark pathways of ATG9A trafficking through ER, Golgi, and endosomal systems. In exploring these data, we find that ATG9A interacts with components of the ULK1 complex, particularly ATG13 and ATG101. Using knockout/reconstitution and split-mVenus approaches to capture the ATG13-ATG101 dimer, we find that ATG9A interacts with ATG13-ATG101 independently of ULK1. Deletion of ATG13 or ATG101 causes a shift in ATG9A distribution, resulting in an aberrant accumulation of ATG9A at stalled clusters of p62/SQSTM1 and ubiquitin, which can be rescued by an ULK1 binding-deficient mutant of ATG13. Together, these data reveal ATG9A interactions in vesicle-trafficking and autophagy pathways, including a role for an ULK1-independent ATG13 complex in regulating ATG9A.
    Keywords:  ATG13; ATG9A; BioID; autophagy; p62
    DOI:  https://doi.org/10.15252/embr.202051136
  19. Hum Mol Genet. 2021 Aug 09. pii: ddab225. [Epub ahead of print]
    A conserved ATG2 binding site in WIPI4 and yeast Hsv2 is disrupted by mutations causing β-propeller protein-associated neurodegeneration.
    Miranda Bueno-Arribas, Irene Blanca, Celia Cruz-Cuevas, Ricardo Escalante, María-Angeles Navas, Olivier Vincent.
      PROPPINs are phosphoinositide-binding β-propeller proteins that mediate membrane recruitment of other proteins and are involved in different membrane remodeling processes. The main role of PROPPINs is their function in autophagy, where they act at different steps in phagophore formation. The human PROPPIN WIPI4 (WDR45) forms a complex with ATG2 involved in phagophore elongation, and mutations in this gene cause β-propeller protein-associated neurodegeneration (BPAN). The yeast functional counterpart of WIPI4 is Atg18, although its closest sequence homolog is another member of the PROPPIN family, Hsv2, whose function remains largely undefined. Here, we provide evidence that Hsv2, like WIPI4 and Atg18, interact with Atg2. We show that Hsv2 and a pool of Atg2 colocalize on endosomes under basal conditions, and at the pre-autophagosomal structure (PAS) upon autophagy induction. We further show that Hsv2 drives the recruitment of Atg2 to endosomes while Atg2 mediates Hsv2 recruitment to the PAS. HSV2 overexpression results in mis-sorting and secretion of carboxypeptidase CPY, suggesting that the endosomal function of this protein is related to the endosome-to-Golgi recycling pathway. Furthermore, we show that the Atg2 binding site is conserved in Hsv2 and WIPI4 but not in Atg18. Notably, two WIPI4 residues involved in ATG2 binding are mutated in patients with BPAN and there is a correlation between the inhibitory effect of these mutations on ATG2 binding and the severity of the disease.
    DOI:  https://doi.org/10.1093/hmg/ddab225
  20. Sci Rep. 2021 Aug 11. 11(1): 16299
    The zinc finger/RING domain protein Unkempt regulates cognitive flexibility.
    Elin Vinsland, Pranetha Baskaran, Simeon R Mihaylov, Carl Hobbs, Hannah Wood, Ihssane Bouybayoune, Kriti Shah, Corinne Houart, Andrew R Tee, Jernej Murn, Cathy Fernandes, Joseph M Bateman.
      Correct orchestration of nervous system development is a profound challenge that involves coordination of complex molecular and cellular processes. Mechanistic target of rapamycin (mTOR) signaling is a key regulator of nervous system development and synaptic function. The mTOR kinase is a hub for sensing inputs including growth factor signaling, nutrients and energy levels. Activation of mTOR signaling causes diseases with severe neurological manifestations, such as tuberous sclerosis complex and focal cortical dysplasia. However, the molecular mechanisms by which mTOR signaling regulates nervous system development and function are poorly understood. Unkempt is a conserved zinc finger/RING domain protein that regulates neurogenesis downstream of mTOR signaling in Drosophila. Unkempt also directly interacts with the mTOR complex I component Raptor. Here we describe the generation and characterisation of mice with a conditional knockout of Unkempt (UnkcKO) in the nervous system. Loss of Unkempt reduces Raptor protein levels in the embryonic nervous system but does not affect downstream mTORC1 targets. We also show that nervous system development occurs normally in UnkcKO mice. However, we find that Unkempt is expressed in the adult cerebellum and hippocampus and behavioural analyses show that UnkcKO mice have improved memory formation and cognitive flexibility to re-learn. Further understanding of the role of Unkempt in the nervous system will provide novel mechanistic insight into the role of mTOR signaling in learning and memory.
    DOI:  https://doi.org/10.1038/s41598-021-95286-y
  21. Antioxid Redox Signal. 2021 Aug 12.
    NDP52 Protects against Myocardial Infarction-Provoked Cardiac Anomalies through Promoting Autophagosome-Lysosome Fusion via Recruiting TBK1 and RAB7.
    Mingming Sun, Wenjing Zhang, Yaguang Bi, Haixia Xu, Miyesaier Abudureyimu, Hu Peng, Yingmei Zhang, Jun Ren.
       AIMS: Acute myocardial infarction (MI), caused by acute coronary artery obstruction, is a common cardiovascular event leading to mortality. Nuclear dot protein 52 (NDP52) is an essential selective autophagy adaptor, although its function in MI is still obscure. This study was designed to examine the function of NDP52 in MI and the associated mechanisms.
    RESULTS: Our results revealed that MI challenge overtly impaired myocardial geometry and systolic function, along with cardiomyocyte apoptosis, myocardial interstitial fibrosis, and mitochondrial damage, and NDP52 nullified such devastating responses. Further studies showed the blockade of mitochondrial clearance is related to MI-induced buildup of damaged mitochondria. Mechanistic approaches depicted that 7-day MI induced abnormal mitophagy flux, resulting in poor lysosomal clearance of injured mitochondria. NDP52 promoted mitophagy flux through recruitment of RAB7 and TBK1. Upon protein colocalization, TBK1 phosphorylated RAB7, in line with the finding that chloroquine or a TBK1 inhibitor reversed NDP52-dependent beneficial responses.
    INNOVATION: This study denoted a novel mechanism that NDP52 promotes cardioprotection against ischemic heart diseases through interaction with TBK1 and RAB7, leading to RAB7 phosphorylation, induction of mitophagy to clear ischemia-induced impaired mitochondria, thus preventing cardiomyocyte apoptosis in MI.
    CONCLUSION: Our results indicate that NDP52 promotes autophagic flux and clears damaged mitochondria to diminish ROS and cell death in a TBK1/RAB7-dependent manner and thus limits MI induced injury.
    DOI:  https://doi.org/10.1089/ars.2020.8253
  22. Cell Death Differ. 2021 Aug 13.
    Sustained intracellular calcium rise mediates neuronal mitophagy in models of autosomal dominant optic atrophy.
    Marta Zaninello, Konstantinos Palikaras, Aggeliki Sotiriou, Nektarios Tavernarakis, Luca Scorrano.
      Mitochondrial dysfunction and mitophagy are often hallmarks of neurodegenerative diseases such as autosomal dominant optic atrophy (ADOA) caused by mutations in the key mitochondrial dynamics protein optic atrophy 1 (Opa1). However, the second messengers linking mitochondrial dysfunction to initiation of mitophagy remain poorly characterized. Here, we show in mammalian and nematode neurons that Opa1 mutations trigger Ca2+-dependent mitophagy. Deletion or expression of mutated Opa1 in mouse retinal ganglion cells and Caenorhabditis elegans motor neurons lead to mitochondrial dysfunction, increased cytosolic Ca2+ levels, and decreased axonal mitochondrial density. Chelation of Ca2+ restores mitochondrial density in neuronal processes, neuronal function, and viability. Mechanistically, sustained Ca2+ levels activate calcineurin and AMPK, placed in the same genetic pathway regulating axonal mitochondrial density. Our data reveal that mitophagy in ADOA depends on Ca2+-calcineurin-AMPK signaling cascade.
    DOI:  https://doi.org/10.1038/s41418-021-00847-3
  23. Stem Cell Reports. 2021 Jul 29. pii: S2213-6711(21)00380-5. [Epub ahead of print]
    Sestrins regulate muscle stem cell metabolic homeostasis.
    Benjamin A Yang, Jesus Castor-Macias, Paula Fraczek, Ashley Cornett, Lemuel A Brown, Myungjin Kim, Susan V Brooks, Isabelle M A Lombaert, Jun Hee Lee, Carlos A Aguilar.
      The health and homeostasis of skeletal muscle are preserved by a population of tissue-resident muscle stem cells (MuSCs) that maintain a state of mitotic and metabolic quiescence in adult tissues. The capacity of MuSCs to preserve the quiescent state declines with aging and metabolic insults, promoting premature activation and stem cell exhaustion. Sestrins are a class of stress-inducible proteins that act as antioxidants and inhibit the activation of the mammalian target of rapamycin complex 1 (mTORC1) signaling complex. Despite these pivotal roles, the role of Sestrins has not been explored in adult stem cells. We show that SESTRIN1,2 loss results in hyperactivation of the mTORC1 complex, increased propensity to enter the cell cycle, and shifts in metabolic flux. Aged SESTRIN1,2 knockout mice exhibited loss of MuSCs and a reduced ability to regenerate injured muscle. These findings demonstrate that Sestrins help maintain metabolic pathways in MuSCs that protect quiescence against aging.
    Keywords:  RNA sequencing; aging; mTORC1; metabolism; oxidative stress; reactive oxygen species; regeneration; satellite cells
    DOI:  https://doi.org/10.1016/j.stemcr.2021.07.014
  24. Curr Mol Pharmacol. 2021 Aug 06.
    Dynamics of autophagy and ubiquitin proteasome system coordination and interplay in skeletal muscle atrophy.
    Ajay Singh, Aarti Yadav, Jatin Phogat, Rajesh Dabur.
      Skeletal muscles are considered the largest reservoirs of the protein pool in the body and are critical for the maintenances of body homeostasis. Skeletal muscle atrophy is supported by various physiopathological conditions that lead to loss of muscle mass and contractile capacity of the skeletal muscle. Lysosomal mediated autophagy and ubiquitin-proteasomal system (UPS) concede the major intracellular systems of muscle protein degradation that result in the loss of mass and strength. Both systems recognize ubiquitination as a signal of degradation through different mechanisms, a sign of dynamic interplay between systems. Hence, growing shreds of evidence suggest the interdependency of autophagy and UPS in the progression of skeletal muscle atrophy under various pathological conditions. Therefore, understanding the molecular dynamics as well associated factors responsible for their interdependency is a necessity for the new therapeutic insights to counteract the muscle loss. Based on current literature, the present review summarizes the factors interplay in between the autophagy and UPS in favor of enhanced proteolysis of skeletal muscle and how they affect the anabolic signaling pathways under various conditions of skeletal muscle atrophy.
    Keywords:  Skeletal muscle atrophy; autophagosome-lysosome system; mitophagy; myostatin and ubiquitination; ubiquitin-proteasomal system
    DOI:  https://doi.org/10.2174/1874467214666210806163851
  25. Nat Commun. 2021 08 10. 12(1): 4814
    Two parallel pathways connect glutamine metabolism and mTORC1 activity to regulate glutamoptosis.
    Clément Bodineau, Mercedes Tomé, Sarah Courtois, Ana S H Costa, Marco Sciacovelli, Benoit Rousseau, Elodie Richard, Pierre Vacher, Carlos Parejo-Pérez, Emilie Bessede, Christine Varon, Pierre Soubeyran, Christian Frezza, Piedad Del Socorro Murdoch, Victor H Villar, Raúl V Durán.
      Glutamoptosis is the induction of apoptotic cell death as a consequence of the aberrant activation of glutaminolysis and mTORC1 signaling during nutritional imbalance in proliferating cells. The role of the bioenergetic sensor AMPK during glutamoptosis is not defined yet. Here, we show that AMPK reactivation blocks both the glutamine-dependent activation of mTORC1 and glutamoptosis in vitro and in vivo. We also show that glutamine is used for asparagine synthesis and the GABA shunt to produce ATP and to inhibit AMPK, independently of glutaminolysis. Overall, our results indicate that glutamine metabolism is connected with mTORC1 activation through two parallel pathways: an acute alpha-ketoglutarate-dependent pathway; and a secondary ATP/AMPK-dependent pathway. This dual metabolic connection between glutamine and mTORC1 must be considered for the future design of therapeutic strategies to prevent cell growth in diseases such as cancer.
    DOI:  https://doi.org/10.1038/s41467-021-25079-4
  26. Stem Cell Res Ther. 2021 Aug 11. 12(1): 452
    New insights into mitophagy and stem cells.
    Qingyin Lin, Jiaqi Chen, Lifang Gu, Xingang Dan, Cheng Zhang, Yanzhou Yang.
      Mitophagy is a specific autophagic phenomenon in which damaged or redundant mitochondria are selectively cleared by autophagic lysosomes. A decrease in mitophagy can accelerate the aging process. Mitophagy is related to health and longevity and is the key to protecting stem cells from metabolic stress damage. Mitophagy decreases the metabolic level of stem cells by clearing active mitochondria, so mitophagy is becoming increasingly necessary to maintain the regenerative capacity of old stem cells. Stem cell senescence is the core problem of tissue aging, and tissue aging occurs not only in stem cells but also in transport amplifying cell chambers and the stem cell environment. The loss of the autophagic ability of stem cells can cause the accumulation of mitochondria and the activation of the metabolic state as well as damage the self-renewal ability and regeneration potential of stem cells. However, the claim remains controversial. Mitophagy is an important survival strategy against nutrient deficiency and starvation, and mitochondrial function and integrity may affect the viability, proliferation and differentiation potential, and longevity of normal stem cells. Mitophagy can affect the health and longevity of the human body, so the number of studies in this field has increased, but the mechanism by which mitophagy participates in stem cell development is still not fully understood. This review describes the potential significance of mitophagy in stem cell developmental processes, such as self-renewal, differentiation and aging. Through this work, we discovered the role and mechanism of mitophagy in different types of stem cells, identified novel targets for killing cancer stem cells and curing cancer, and provided new insights for future research in this field.
    Keywords:  Autophagy; Cancer stem cells; Mitochondria; Mitophagy; Stem cells
    DOI:  https://doi.org/10.1186/s13287-021-02520-5
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