bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2020–10–18
39 papers selected by
Viktor Korolchuk, Newcastle University
  1. The GATOR-Rag GTPase pathway inhibits mTORC1 activation by lysosome-derived amino acids.
  2. Inositol requiring enzyme 1 alpha (IRE1a) links palmitate-induced mTOR activation and lipotoxicity in Hepatocytes.
  3. Inhibition of class I PI3K enhances chaperone-mediated autophagy.
  4. Ciliary localization of folliculin mediated via a kinesin-2-binding motif is required for its functions in mTOR regulation and tumor suppression.
  5. SSH1 impedes SQSTM1/p62 flux and MAPT/Tau clearance independent of CFL (cofilin) activation.
  6. Selective autophagy as a therapeutic target for neurological diseases.
  7. Mediators of mitophagy that regulate mitochondrial quality control play crucial role in diverse pathophysiology.
  8. Lyn kinase regulates egress of flaviviruses in autophagosome-derived organelles.
  9. Acute effects of fatty acids on autophagy in NPY neurones.
  10. Oxidative Damage and Antioxidant Defense in Ferroptosis.
  11. Autophagy and liver cancer.
  12. Atg8-mediated super-assembly of Atg40 induces local ER remodeling in reticulophagy.
  13. LRRK2 and the Endolysosomal System in Parkinson's Disease.
  14. Sulfur depletion induces autophagy through Ecl1 family genes in fission yeast.
  15. The Impact of Mitochondrial Deficiencies in Neuromuscular Diseases.
  16. The lysosomal membrane - export of metabolites and beyond.
  17. Oxygen Glucose Deprivation Induced Prosurvival Autophagy Is Insufficient to Rescue Endothelial Function.
  18. Autophagy and Heat-Shock Response Impair Stress Granule Assembly during Cellular Senescence.
  19. The promise of mTOR as a therapeutic target pathway in idiopathic pulmonary fibrosis.
  20. BNIP3L/Nix-induced mitochondrial fission, mitophagy, and impaired myocyte glucose uptake are abrogated by PRKA/PKA phosphorylation.
  21. Parallel global profiling of plant TOR dynamics reveals a conserved role for LARP1 in translation.
  22. HIPK2 Is Required for Midbody Remnant Removal Through Autophagy-Mediated Degradation.
  23. Exenatide improves random-pattern skin flap survival via TFE3 mediated autophagy augment.
  24. ALS-Related Mutant SOD1 Aggregates Interfere with Mitophagy by Sequestering the Autophagy Receptor Optineurin.
  25. Sanqi Oral Solution Ameliorates Renal Ischemia/Reperfusion Injury via Reducing Apoptosis and Enhancing Autophagy: Involvement of ERK/mTOR Pathways.
  26. Cathepsin D deficiency in mammary epithelium transiently stalls breast cancer by interference with mTORC1 signaling.
  27. EXO70D isoforms mediate selective autophagic degradation of type-A ARR proteins to regulate cytokinin sensitivity.
  28. PE homeostasis rebalanced through mitochondria-ER lipid exchange prevents retinal degeneration in Drosophila.
  29. Chlorin A-mediated photodynamic therapy induced apoptosis in human cholangiocarcinoma cells via impaired autophagy flux.
  30. The Ccr4-Not complex regulates TORC1 signaling and mitochondrial metabolism by promoting vacuole V-ATPase activity.
  31. Kahweol activates the Nrf2/HO-1 pathway by decreasing Keap1 expression independently of p62 and autophagy pathways.
  32. mTORC1/2 signaling is downregulated by amino acid-free culture of mouse preimplantation embryos and is only partially restored by amino acid re-addition.
  33. Depletion of Adipocyte Becn1 Leads to Lipodystrophy and Metabolic Dysregulation.
  34. Neuronal AMPK coordinates mitochondrial energy sensing and hypoxia resistance in C. elegans.
  35. Autophagy in Human Diseases.
  36. HSP70 interacts with Rheb, inhibiting mTORC1 signaling.
  37. The Chlamydia effector CT622/TaiP targets a nonautophagy related function of ATG16L1.
  38. Upregulation of Parkin Accelerates Osteoblastic Differentiation of Bone Marrow-Derived Mesenchymal Stem Cells and Bone Regeneration by Enhancing Autophagy and β-Catenin Signaling.
  39. Intimate Relations-Mitochondria and Ageing.
  1. Science. 2020 Oct 16. 370(6514): 351-356
    The GATOR-Rag GTPase pathway inhibits mTORC1 activation by lysosome-derived amino acids.
    Geoffrey G Hesketh, Fotini Papazotos, Judy Pawling, Dushyandi Rajendran, James D R Knight, Sebastien Martinez, Mikko Taipale, Daniel Schramek, James W Dennis, Anne-Claude Gingras.
      The mechanistic target of rapamycin complex 1 (mTORC1) couples nutrient sufficiency to cell growth. mTORC1 is activated by exogenously acquired amino acids sensed through the GATOR-Rag guanosine triphosphatase (GTPase) pathway, or by amino acids derived through lysosomal degradation of protein by a poorly defined mechanism. Here, we revealed that amino acids derived from the degradation of protein (acquired through oncogenic Ras-driven macropinocytosis) activate mTORC1 by a Rag GTPase-independent mechanism. mTORC1 stimulation through this pathway required the HOPS complex and was negatively regulated by activation of the GATOR-Rag GTPase pathway. Therefore, distinct but functionally coordinated pathways control mTORC1 activity on late endocytic organelles in response to distinct sources of amino acids.
    DOI:  https://doi.org/10.1126/science.aaz0863
  2. Am J Physiol Cell Physiol. 2020 Oct 14.
    Inositol requiring enzyme 1 alpha (IRE1a) links palmitate-induced mTOR activation and lipotoxicity in Hepatocytes.
    Yingli Chen, Alexandra Griffiths, Jun Wang, Tingting Zhang, Qing Song, Zhenyuan Song.
      Hepatic lipotoxicity, hepatocyte dysfunction/cell death induced by saturated fatty acids (SFA), plays a central role in the pathogenesis of non-alcoholic fatty liver disease (NAFLD); however, the underlying mechanisms remain unclear. Palmitate is the most abundant SFA in the circulation. In this study, via a small-scale screening of chemical inhibitors using AML12 hepatocytes, we identified mTOR complex 1 (mTORC1) to be a culprit in palmitate-induced cell death in hepatocytes in that mTOR inhibition is protective against palmitate-induced cell death. The protective effects of mTORC1 inhibition are independent of autophagy induction as autophagy inhibition failed to ablate the mTORC1 inhibitor-conferred protection. We have previously reported that the endonuclease activity of inositol-requiring enzyme 1a (IRE1a), one of three canonical signaling pathways of endoplasmic reticulum (ER) stress, was implicated in palmitate-induced cell death in hepatocytes. The continuous mechanistic investigation in this study revealed that IRE1α is a downstream target of mTORC1 activation upon palmitate exposure and the inhibition of either its endonuclease activity or kinase activity protected against the lipotoxic effect of palmitate. Our research further uncovered that protein palmitoylation is potentially involved in palmitate-induced mTORC1 activation and lipotoxicity in hepatocytes. 2-bromopalmitate, a protein palmitoylation inhibitor, ameliorated palmitate-triggered mTORC1 activation, concomitant with prevention of lipotoxicity in hepatocytes. Collectively, our data have identified that mTORC1 and ER stress are coordinately implicated in hepatocyte cell death in response to palmitate exposure and suggests that this pathway may potentially serve as a therapeutic target for the treatment of NAFLD as well as other metabolic disorders involving lipotoxicity.
    Keywords:  ER stress; IRE1alpha; Lipotoxicity; Palmitate; mTORC1
    DOI:  https://doi.org/10.1152/ajpcell.00165.2020
  3. J Cell Biol. 2020 Dec 07. pii: e202001031. [Epub ahead of print]219(12):
    Inhibition of class I PI3K enhances chaperone-mediated autophagy.
    S Joseph Endicott, Zachary J Ziemba, Logan J Beckmann, Dennis N Boynton, Richard A Miller.
      Chaperone-mediated autophagy (CMA) is the most selective form of lysosomal proteolysis, where individual peptides, recognized by a consensus motif, are translocated directly across the lysosomal membrane. CMA regulates the abundance of many disease-related proteins, with causative roles in neoplasia, neurodegeneration, hepatosteatosis, and other pathologies relevant to human health and aging. At the lysosomal membrane, CMA is inhibited by Akt-dependent phosphorylation of the CMA regulator GFAP. The INS-PI3K-PDPK1 pathway regulates Akt, but its role in CMA is unclear. Here, we report that inhibition of class I PI3K or PDPK1 activates CMA. In contrast, selective inhibition of class III PI3Ks does not activate CMA. Isolated liver lysosomes from mice treated with either of two orally bioavailable class I PI3K inhibitors, pictilisib or buparlisib, display elevated CMA activity, and decreased phosphorylation of lysosomal GFAP, with no change in macroautophagy. The findings of this study represent an important first step in repurposing class I PI3K inhibitors to modulate CMA in vivo.
    DOI:  https://doi.org/10.1083/jcb.202001031
  4. FEBS Lett. 2020 Oct 16.
    Ciliary localization of folliculin mediated via a kinesin-2-binding motif is required for its functions in mTOR regulation and tumor suppression.
    Yunlong Zhang, Ying Liu, Yu Dai, Yazhe Ren, Guangsen Bao, Bo Ai, Yu Jiang.
      Folliculin (FLCN) is a tumor suppressor protein involved in many cellular processes, including cell signaling, apoptosis and autophagy. In ciliated cells, FLCN localizes to primary cilia and controls mTORC1 signaling in response to flow stress. Here, we show that the ciliary localization of FLCN requires its interaction with kinesin-2, the motor protein for anterograde intraflagellar transport. FLCN binds to kinesin-2 through a loop region in the middle of the protein. Single point mutations within this region of FLCN disrupt its kinesin-2 binding and ciliary entry. The mutants lose the ability to suppress the abnormal mTORC1/2 signaling activities and anchorage-independent growth of FLCN-deficient tumor cells. These observations suggest that ciliary localization of FLCN is essential for its function as a tumor suppressor.
    Keywords:  FLCN; cilium; kinesin-2; mTORC1; mTORC2
    DOI:  https://doi.org/10.1002/1873-3468.13959
  5. Autophagy. 2020 Oct 12. 1-22
    SSH1 impedes SQSTM1/p62 flux and MAPT/Tau clearance independent of CFL (cofilin) activation.
    Cenxiao Fang, Jung-A A Woo, Tian Liu, Xingyu Zhao, Sara Cazzaro, Yan Yan, Jenet Matlack, Teresa Kee, Patrick LePochat, David E Kang.
      Accumulation of toxic protein assemblies and damaged mitochondria are key features of neurodegenerative diseases, which arise in large part from clearance defects in the Macroautophagy/autophagy-lysosome system. The autophagy cargo receptor SQSTM1/p62 plays a major role in the clearance of ubiquitinated cargo through Ser403 phosphorylation by multiple kinases. However, no phosphatase is known to physiologically dephosphorylate SQSTM1 on this activating residue. RNAi-mediated knockdown and overexpression experiments using genetically encoded fluorescent reporters and defined mutant constructs in cell lines, primary neurons, and brains show that SSH1, the canonical CFL (cofilin) phosphatase, mediates the dephosphorylation of phospho-Ser403-SQSTM1, thereby impairing SQSTM1 flux and phospho-MAPT/tau clearance. The inhibitory action of SSH1 on SQSTM1 is fully dependent on SQSTM1 Ser403 phosphorylation status and is separable from SSH1-mediated CFL activation. These findings reveal a unique action of SSH1 on SQSTM1 independent of CFL and implicate an inhibitory role of SSH1 in SQSTM1-mediated clearance of autophagic cargo, including phospho-MAPT/tau. Abbreviations: AAV: adeno-associated virus; Aβ42O: amyloid β1-42 oligomers; AD: Alzheimer disease; CA3: cornu Ammonis 3; CSNK2/CK2: casein kinase 2; FCCP: 2-[2-[4-(trifluoromethoxy)phenyl]hydrazinylidene]-propanedinitrile; FTLD: frontotemporal lobar degeneration; GFP: green fluorescent protein; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; SQSTM1/p62: sequestosome-1; PLA: proximity ligation assay; RFP: red fluorescent protein; RIPA: radioimmunoprecipitation assay; shRNA: short hairpin RNA; siRNA: small interfering RNA; Ser403: Serine403; SSH1: slingshot protein phosphatase 1; TBK1: TANK-binding kinase 1; ULK: unc-51 like kinase 1.
    Keywords:  Autophagy; CFL (cofilin); MAP1LC3/LC3; MAPT/tau; SQSTM1/p62; SSH1; mitochondria; tauopathy; ubiquitin
    DOI:  https://doi.org/10.1080/15548627.2020.1816663
  6. Cell Mol Life Sci. 2020 Oct 16.
    Selective autophagy as a therapeutic target for neurological diseases.
    Weilin Xu, Umut Ocak, Liansheng Gao, Sheng Tu, Cameron J Lenahan, Jianmin Zhang, Anwen Shao.
      The neurological diseases primarily include acute injuries, chronic neurodegeneration, and others (e.g., infectious diseases of the central nervous system). Autophagy is a housekeeping process responsible for the bulk degradation of misfolded protein aggregates and damaged organelles through the lysosomal machinery. Recent studies have suggested that autophagy, particularly selective autophagy, such as mitophagy, pexophagy, ER-phagy, ribophagy, lipophagy, etc., is closely implicated in neurological diseases. These forms of selective autophagy are controlled by a group of important proteins, including PTEN-induced kinase 1 (PINK1), Parkin, p62, optineurin (OPTN), neighbor of BRCA1 gene 1 (NBR1), and nuclear fragile X mental retardation-interacting protein 1 (NUFIP1). This review highlights the characteristics and underlying mechanisms of different types of selective autophagy, and their implications in various forms of neurological diseases.
    Keywords:  Alzheimer’s disease; Autophagy receptor; Macroautophagy; Neuroprotection; Parkinson’s disease; Stroke
    DOI:  https://doi.org/10.1007/s00018-020-03667-9
  7. Cell Biol Toxicol. 2020 Oct 17.
    Mediators of mitophagy that regulate mitochondrial quality control play crucial role in diverse pathophysiology.
    Rudranil De, Somnath Mazumder, Uday Bandyopadhyay.
      Mitochondria are double membrane-bound cellular work-horses constantly functioning to regulate vital aspects of cellular metabolism, bioenergetics, proliferation and death. Biogenesis, homeostasis and regulated turnover of mitochondria are stringently regulated to meet the bioenergetic requirements. Diverse external and internal stimuli including oxidative stress, diseases, xenobiotics and even age profoundly affect mitochondrial integrity. Damaged mitochondria need immediate segregation and selective culling to maintain physiological homeostasis. Mitophagy is a specialised form of macroautophagy that constantly checks mitochondrial quality followed by elimination of rogue mitochondria by lysosomal targeting through multiple pathways tightly regulated and activated in context-specific manners. Mitophagy is implicated in diverse oxidative stress-associated metabolic, proliferating and degenerative disorders owing to the centrality of mitopathology in diseases as well as the common mandate to eliminate damaged mitochondria for restoring physiological homeostasis. With improved health care and growing demand for precision medicine, specifically targeting the keystone factors in pathogenesis, more exploratory studies are focused on mitochondrial quality control as underlying guardian of cellular pathophysiology. In this context, mitophagy emerged as a promising area to focus biomedical research for identifying novel therapeutic targets against diseases linked with physiological redox perturbation. The present review provides a comprehensive account of the recent developments on mitophagy along with precise discussion on its impact on major diseases and possibilities of therapeutic modulation.
    Keywords:  Autophagy; Mitochondrial apoptosis; Mitochondrial disease; Mitochondrial quality control; Mitophagy; Oxidative stress
    DOI:  https://doi.org/10.1007/s10565-020-09561-1
  8. Nat Commun. 2020 10 15. 11(1): 5189
    Lyn kinase regulates egress of flaviviruses in autophagosome-derived organelles.
    Ming Yuan Li, Trupti Shivaprasad Naik, Lewis Yu Lam Siu, Oreste Acuto, Eric Spooner, Peigang Wang, Xiaohan Yang, Yongping Lin, Roberto Bruzzone, Joseph Ashour, Matthew J Evans, Sumana Sanyal.
      Among the various host cellular processes that are hijacked by flaviviruses, few mechanisms have been described with regard to viral egress. Here we investigate how flaviviruses exploit Src family kinases (SFKs) for exit from infected cells. We identify Lyn as a critical component for secretion of Dengue and Zika infectious particles and their corresponding virus like particles (VLPs). Pharmacological inhibition or genetic depletion of the SFKs, Lyn in particular, block virus secretion. Lyn-/- cells are impaired in virus release and are rescued when reconstituted with wild-type Lyn, but not a kinase- or palmitoylation-deficient Lyn mutant. We establish that virus particles are secreted in two distinct populations - one as free virions and the other enclosed within membranes. Lyn is critical for the latter, which consists of proteolytically processed, infectious virus progenies within autophagosome-derived vesicles. This process depends on Ulk1, Rab GTPases and SNARE complexes implicated in secretory but not degradative autophagy and occur with significantly faster kinetics than the conventional secretory pathway. Our study reveals a previously undiscovered Lyn-dependent exit route of flaviviruses in LC3+ secretory organelles that enables them to evade circulating antibodies and might affect tissue tropism.
    DOI:  https://doi.org/10.1038/s41467-020-19028-w
  9. J Neuroendocrinol. 2020 Oct;32(10): e12900
    Acute effects of fatty acids on autophagy in NPY neurones.
    Andressa Reginato, Beatriz Piatezzi Siqueira, Josiane Érica Miyamoto, Mariana Portovedo, Suleyma de Oliveira Costa, Thaís de Fante, Hosana Gomes Rodrigues, Letícia Martins Ignácio-Souza, Márcio Alberto Torsoni, Adriana Souza Torsoni, Hervé Le Stunff, Denise D Belsham, Marciane Milanski.
      High-fat diet (HFD) feeding is deleterious to hypothalamic tissue, leading to inflammation and lipotoxicity, as well as contributing to central insulin resistance. Autophagy is a process that restores cellular homeostasis by degrading malfunctioning organelles and proteins. Chronic HFD-feeding down-regulates hypothalamic autophagy. However, the effects of short-term HFD-feeding and the saturated fatty acid palmitate (PA) on hypothalamic autophagy and in neurones that express neuropeptide Y (NPY) and agouti-related peptide remains unknown. Therefore, we assessed hypothalamic autophagy after 1 and 3 days of HFD-feeding. We also injected PA i.c.v and analysed the modulation of autophagy in hypothalamic tissue. Both interventions resulted in changes in autophagy-related gene profiles without significant differences in protein content of p62 and LC3B-II, markers of the autophagy pathway. When we assessed native NPY neurones in brain slices from PA-treated animals, we observed increased levels of Atg7 and LC3B protein in response to PA treatment, indicating the induction of autophagy. We then tested the direct effects of fatty acids using the immortalised hypothalamic NPY-expressing neuronal cell model mHypoE-46. We found that PA, but not palmitoleate (PO) (a monounsaturated fatty acid), was able to induce autophagy. Co-treatment with PA and PO was able to block the PA-mediated induction of autophagy, as assessed by flow cytometry. When the de novo ceramide synthesis pathway was blocked with myriocin pre-treatment, we observed a decrease in PA-mediated induction of autophagy, although there was no change with the toll-like receptor 4 inhibitor, TAK-242. Taken together, these findings provide evidence that saturated and unsaturated fatty acids can differentially regulate hypothalamic autophagy and that ceramide synthesis may be an important mediator of those effects. Understanding the mechanisms by which dietary fats affect autophagy in neurones involved in the control of energy homeostasis will provide potential new pathways for targeting and containing the obesity epidemic.
    Keywords:  autophagy; hypothalamus; lipids; obesity; palmitate; palmitoleate
    DOI:  https://doi.org/10.1111/jne.12900
  10. Front Cell Dev Biol. 2020 ;8 586578
    Oxidative Damage and Antioxidant Defense in Ferroptosis.
    Feimei Kuang, Jiao Liu, Daolin Tang, Rui Kang.
      Many new types of regulated cell death have been recently implicated in human health and disease. These regulated cell deaths have different morphological, genetic, biochemical, and functional hallmarks. Ferroptosis was originally described as a carcinogenic RAS-dependent non-apoptotic cell death, and is now defined as a type of regulated necrosis characterized by iron accumulation, lipid peroxidation, and the release of damage-associated molecular patterns (DAMPs). Multiple oxidative and antioxidant systems, acting together autophagy machinery, shape the process of lipid peroxidation during ferroptosis. In particular, the production of reactive oxygen species (ROS) that depends on the activity of nicotinamide adenine dinucleotide phosphate (NADPH) oxidases (NOXs) and the mitochondrial respiratory chain promotes lipid peroxidation by lipoxygenase (ALOX) or cytochrome P450 reductase (POR). In contrast, the glutathione (GSH), coenzyme Q10 (CoQ10), and tetrahydrobiopterin (BH4) system limits oxidative damage during ferroptosis. These antioxidant processes are further transcriptionally regulated by nuclear factor, erythroid 2-like 2 (NFE2L2/NRF2), whereas membrane repair during ferroptotic damage requires the activation of endosomal sorting complexes required for transport (ESCRT)-III. A further understanding of the process and function of ferroptosis may provide precise treatment strategies for disease.
    Keywords:  ROS; antioxidant; cell death; ferroptosis; redox
    DOI:  https://doi.org/10.3389/fcell.2020.586578
  11. Clin Mol Hepatol. 2020 Oct;26(4): 606-617
    Autophagy and liver cancer.
    Xiaojuan Chao, Hui Qian, Shaogui Wang, Sam Fulte, Wen-Xing Ding.
      Autophagy is a highly conserved catabolic process that degrades cytosolic proteins and organelles via formation of autophagosomes that fuse with lysosomes to form autolysosomes, whereby autophagic cargos are degraded. Numerous studies have demonstrated that autophagy plays a critical role in the regulation of liver physiology and homeostasis, and impaired autophagy leads to the pathogenesis of various liver diseases such as viral hepatitis, alcohol associated liver diseases (AALD), non-alcoholic fatty liver diseases (NAFLD), and liver cancer. Recent evidence indicates that autophagy may play a dual role in liver cancer: inhibiting early tumor initiation while promoting progression and malignancy of already formed liver tumors. In this review, we summarized the progress of current understanding of how hepatic viral infection, alcohol consumption and diet-induced fatty liver diseases impair hepatic autophagy. We also discussed how impaired autophagy promotes liver tumorigenesis, and paradoxically how autophagy is required to promote the malignancy and progression of liver cancer. Understanding the molecular mechanisms underlying how autophagy differentially affects liver cancer development and progression may help to design better therapeutic strategies for prevention and treatment of liver cancer.
    Keywords:  Alcohol; Nrf2; TFEB; mTOR; p62
    DOI:  https://doi.org/10.3350/cmh.2020.0169
  12. Autophagy. 2020 Oct 10. 1-2
    Atg8-mediated super-assembly of Atg40 induces local ER remodeling in reticulophagy.
    Keisuke Mochida, Hitoshi Nakatogawa.
      Reticulophagy (or ER-phagy) is a type of selective autophagy that targets the endoplasmic reticulum (ER). In the process of reticulophagy, part of the ER is fragmented and packed within autophagosomes. However, the underlying mechanism that induces this local remodeling of ER subdomains was poorly understood. Our recent study showed that in the budding yeast Saccharomyces cerevisiae the reticulophagy receptor Atg40 plays an important role in ER remodeling beyond its role as a tether between the ER and the phagophore [1]. Atg40 has an ability to generate positive membrane curvature through the reticulon-like domain and locally forms a super assemblage though its binding to Atg8 at ER-phagophore contacts. These Atg40 assemblages cause folding of the ER subdomains to allow them to be efficiently packed into autophagosomes. Furthermore, our structural analysis identified an evolutionarily conserved short helix that assists strong Atg8-binding of reticulophagy receptors.
    Keywords:  Atg40; Atg8; endoplasmic reticulum; reticulophagy
    DOI:  https://doi.org/10.1080/15548627.2020.1831801
  13. J Parkinsons Dis. 2020 Oct 02.
    LRRK2 and the Endolysosomal System in Parkinson's Disease.
    Madalynn L Erb, Darren J Moore.
      Mutations in leucine-rich repeat kinase 2 (LRRK2) cause autosomal dominant familial Parkinson's disease (PD), with pathogenic mutations enhancing LRRK2 kinase activity. There is a growing body of evidence indicating that LRRK2 contributes to neuronal damage and pathology both in familial and sporadic PD, making it of particular interest for understanding the molecular pathways that underlie PD. Although LRRK2 has been extensively studied to date, our understanding of the seemingly diverse functions of LRRK2 throughout the cell remains incomplete. In this review, we discuss the functions of LRRK2 within the endolysosomal pathway. Endocytosis, vesicle trafficking pathways, and lysosomal degradation are commonly disrupted in many neurodegenerative diseases, including PD. Additionally, many PD-linked gene products function in these intersecting pathways, suggesting an important role for the endolysosomal system in maintaining protein homeostasis and neuronal health in PD. LRRK2 activity can regulate synaptic vesicle endocytosis, lysosomal function, Golgi network maintenance and sorting, vesicular trafficking and autophagy, with alterations in LRRK2 kinase activity serving to disrupt or regulate these pathways depending on the distinct cell type or model system. LRRK2 is critically regulated by at least two proteins in the endolysosomal pathway, Rab29 and VPS35, which may serve as master regulators of LRRK2 kinase activity. Investigating the function and regulation of LRRK2 in the endolysosomal pathway in diverse PD models, especially in vivo models, will provide critical insight into the cellular and molecular pathophysiological mechanisms driving PD and whether LRRK2 represents a viable drug target for disease-modification in familial and sporadic PD.
    Keywords:  Leucine-rich repeat kinase 2; Parkinson’s disease; endocytosis; lysosomes; trans-Golgi network; vesicular trafficking
    DOI:  https://doi.org/10.3233/JPD-202138
  14. Genes Cells. 2020 Oct 16.
    Sulfur depletion induces autophagy through Ecl1 family genes in fission yeast.
    Takafumi Shimasaki, Keisuke Okamoto, Hokuto Ohtsuka, Hirofumi Aiba.
      Autophagy is an intracellular degradation system widely conserved among various species. Autophagy is induced by the depletion of various nutrients, and this degradation mechanism is essential for adaptation to such conditions. In this study, we demonstrated that sulfur depletion induces autophagy in the fission yeast Schizosaccharomyces pombe. Based on the finding that autophagy induced by sulfur depletion was completely abolished in a mutant in which the ecl1, ecl2, and ecl3 genes were deleted (Δecls), we report that these three genes are essential for the induction of autophagy by sulfur depletion. Furthermore, autophagy-defective mutant cells exhibited poor growth and short lifespan (compared with wild-type cells) under the sulfur-depleted condition. These results indicated that the mechanism of autophagy is necessary for the appropriate adaptation to sulfur depletion.
    Keywords:   Schizosaccharomyces pombe ; Ecl1 family genes; autophagy; chronological lifespan; sulfur depletion
    DOI:  https://doi.org/10.1111/gtc.12815
  15. Antioxidants (Basel). 2020 Oct 09. pii: E964. [Epub ahead of print]9(10):
    The Impact of Mitochondrial Deficiencies in Neuromuscular Diseases.
    Judith Cantó-Santos, Josep M Grau-Junyent, Glòria Garrabou.
      Neuromuscular diseases (NMDs) are a heterogeneous group of acquired or inherited rare disorders caused by injury or dysfunction of the anterior horn cells of the spinal cord (lower motor neurons), peripheral nerves, neuromuscular junctions, or skeletal muscles leading to muscle weakness and waste. Unfortunately, most of them entail serious or even fatal consequences. The prevalence rates among NMDs range between 1 and 10 per 100,000 population, but their rarity and diversity pose difficulties for healthcare and research. Some molecular hallmarks are being explored to elucidate the mechanisms triggering disease, to set the path for further advances. In fact, in the present review we outline the metabolic alterations of NMDs, mainly focusing on the role of mitochondria. The aim of the review is to discuss the mechanisms underlying energy production, oxidative stress generation, cell signaling, autophagy, and inflammation triggered or conditioned by the mitochondria. Briefly, increased levels of inflammation have been linked to reactive oxygen species (ROS) accumulation, which is key in mitochondrial genomic instability and mitochondrial respiratory chain (MRC) dysfunction. ROS burst, impaired autophagy, and increased inflammation are observed in many NMDs. Increasing knowledge of the etiology of NMDs will help to develop better diagnosis and treatments, eventually reducing the health and economic burden of NMDs for patients and healthcare systems.
    Keywords:  damage-associated molecular patterns (DAMPs); mitochondrial respiratory chain (MRC); mitophagy; neuromuscular diseases (NMDs); oxidative stress; reactive oxygen species (ROS)
    DOI:  https://doi.org/10.3390/antiox9100964
  16. FEBS J. 2020 Oct 17.
    The lysosomal membrane - export of metabolites and beyond.
    Sönke Rudnik, Markus Damme.
      Lysosomes are degradative organelles in eukaryotic cells mediating the hydrolytic catabolism of various macromolecules to small basic building blocks. These low molecular weight metabolites are transported across the lysosomal membrane and re-used in the cytoplasm and other organelles for biosynthetic pathways. Even though in the past 20 years our understanding of the lysosomal membrane regarding various transporters, other integral- and peripheral-membrane proteins, the lipid composition but also its turnover has greatly improved, there are still many unresolved questions concerning key aspects of the function of the lysosomal membrane. These include a possible function of lysosomes as a cellular storage compartment, yet unidentified transporters mediating the export e.g. of various amino acids, mechanisms mediating the transport of lysosomal membrane proteins from the Golgi apparatus to lysosomes, and the turnover of lysosomal membrane proteins. We here review the current knowledge about the lysosomal membrane and identify some of the open questions that need to be solved in the future for a comprehensive and complete understanding of how lysosomes communicate with other organelles, cellular processes, and pathways.
    Keywords:  Accessory subunits; Lysosomal Membrane; Lysosomal Storage Diseases; Transporter
    DOI:  https://doi.org/10.1111/febs.15602
  17. Front Physiol. 2020 ;11 533683
    Oxygen Glucose Deprivation Induced Prosurvival Autophagy Is Insufficient to Rescue Endothelial Function.
    Venkateswaran Natarajan, Tania Mah, Chen Peishi, Shu Yi Tan, Ritu Chawla, Thiruma Valavan Arumugam, Adaikalavan Ramasamy, Karthik Mallilankaraman.
      Endothelial dysfunction, referring to a disturbance in the vascular homeostasis, has been implicated in many disease conditions including ischemic/reperfusion injury and atherosclerosis. Endothelial mitochondria have been increasingly recognized as a regulator of calcium homeostasis which has implications in the execution of diverse cellular events and energy production. The mitochondrial calcium uniporter complex through which calcium enters the mitochondria is composed of several proteins, including the pore-forming subunit MCU and its regulators MCUR1, MICU1, and MICU2. Mitochondrial calcium overload leads to opening of MPTP (mitochondrial permeability transition pore) and results in apoptotic cell death. Whereas, blockage of calcium entry into the mitochondria results in reduced ATP production thereby activates AMPK-mediated pro-survival autophagy. Here, we investigated the expression of mitochondrial calcium uniporter complex components (MCU, MCUR1, MICU1, and MICU2), induction of autophagy and apoptotic cell death in endothelial cells in response to oxygen-glucose deprivation. Human pulmonary microvascular endothelial cells (HPMVECs) were subjected to oxygen-glucose deprivation (OGD) at 3-h timepoints up to 12 h. Interestingly, except MCUR1 which was significantly downregulated, all other components of the uniporter (MCU, MICU1, and MICU2) remained unchanged. MCUR1 downregulation has been shown to activate AMPK mediated pro-survival autophagy. Similarly, MCUR1 downregulation in response to OGD resulted in AMPK phosphorylation and LC3 processing indicating the activation of pro-survival autophagy. Despite the activation of autophagy, OGD induced Caspase-mediated apoptotic cell death. Blockade of autophagy did not reduce OGD-induced apoptotic cell death whereas serum starvation conferred enough cellular and functional protection. In conclusion, the autophagic flux induced by MCUR1 downregulation in response to OGD is insufficient in protecting endothelial cells from undergoing apoptotic cell death and requires enhancement of autophagic flux by additional means such as serum starvation.
    Keywords:  MCUR1; apoptotic cell death; autophagy; endothelial dysfunction; oxygen-glucose deprivation
    DOI:  https://doi.org/10.3389/fphys.2020.533683
  18. Mech Ageing Dev. 2020 Oct 10. pii: S0047-6374(20)30178-0. [Epub ahead of print] 111382
    Autophagy and Heat-Shock Response Impair Stress Granule Assembly during Cellular Senescence.
    Amr Omer, Devang Patel, Julian Lucas Moran, Xian Jin Lian, Sergio Di Marco, Imed-Eddine Gallouzi.
      Stress granules (SGs) are membraneless organelles formed in response to insult. These granules are related to pathological granules found in age-related neurogenerative diseases such as Parkinson's and Alzheimer's. Previously, we demonstrated that senescent cells, which accumulate with age, exposed to chronic oxidative stress, are unable to form SGs. Here, we show that the inability of senescent cells to form SGs correlates with an upregulation in both the heat-shock response and autophagy pathways, both of which are well-established promoters of SG disassembly. Our data also reveals that the knockdown of HSP70 and ATG5, important components of the heat-shock response and autophagy pathways, respectively, restores the number of SGs formed in senescent cells exposed to chronic oxidative stress. Surprisingly, under these conditions, the depletion of HSP70 or ATG5 did not affect the clearance of these SGs during their recovery from chronic stress. These data reveal that senescent cells possess a unique heat-shock and autophagy-dependent ability to impair the formation of SGs in response to chronic stress, thereby expanding the existing understanding of SG dynamics in senescent cells and their potential contribution to age-related neurodegenerative diseases.
    Keywords:  Ageing; Cellular Senescence; Molecular Biology; Oxidative Stress; Stress Granules
    DOI:  https://doi.org/10.1016/j.mad.2020.111382
  19. Eur Respir Rev. 2020 Sep 30. pii: 200269. [Epub ahead of print]29(157):
    The promise of mTOR as a therapeutic target pathway in idiopathic pulmonary fibrosis.
    Manuela Platé, Delphine Guillotin, Rachel C Chambers.
      Idiopathic pulmonary fibrosis (IPF) is characterised by the progressive deposition of excessive extracellular matrix proteins within the lung parenchyma and represents the most rapidly progressive and fatal of all fibrotic conditions. Current anti-fibrotic drugs approved for the treatment of IPF fail to halt disease progression and have significant side-effect profiles. Therefore, there remains a pressing need to develop novel therapeutic strategies for IPF. Mammalian target of rapamycin (mTOR) forms the catalytic subunit of two complexes, mTORC1 and mTORC2. mTORC1 acts as critical cellular sensor which integrates intracellular and extracellular signals to reciprocally regulate a variety of anabolic and catabolic processes. The emerging evidence for a critical role for mTORC1 in influencing extracellular matrix production, metabolism, autophagy and senescence in the setting of IPF highlights this axis as a novel therapeutic target with the potential to impact multiple IPF pathomechanisms.
    DOI:  https://doi.org/10.1183/16000617.0269-2020
  20. Autophagy. 2020 Oct 12. 1-16
    BNIP3L/Nix-induced mitochondrial fission, mitophagy, and impaired myocyte glucose uptake are abrogated by PRKA/PKA phosphorylation.
    Simone C da Silva Rosa, Matthew D Martens, Jared T Field, Lucas Nguyen, Stephanie M Kereliuk, Yan Hai, Donald Chapman, William Diehl-Jones, Michel Aliani, Adrian R West, James Thliveris, Saeid Ghavami, Christof Rampitsch, Vernon W Dolinsky, Joseph W Gordon.
      Lipotoxicity is a form of cellular stress caused by the accumulation of lipids resulting in mitochondrial dysfunction and insulin resistance in muscle. Previously, we demonstrated that the mitophagy receptor BNIP3L/Nix is responsive to lipotoxicity and accumulates in response to a high-fat (HF) feeding. To provide a better understanding of this observation, we undertook gene expression array and shot-gun metabolomics studies in soleus muscle from rodents on an HF diet. Interestingly, we observed a modest reduction in several autophagy-related genes. Moreover, we observed alterations in the fatty acyl composition of cardiolipins and phosphatidic acids. Given the reported roles of these phospholipids and BNIP3L in mitochondrial dynamics, we investigated aberrant mitochondrial turnover as a mechanism of impaired myocyte insulin signaling. In a series of gain-of-function and loss-of-function experiments in rodent and human myotubes, we demonstrate that BNIP3L accumulation triggers mitochondrial depolarization, calcium-dependent activation of DNM1L/DRP1, and mitophagy. In addition, BNIP3L can inhibit insulin signaling through activation of MTOR-RPS6KB/p70S6 kinase inhibition of IRS1, which is contingent on phosphatidic acids and RHEB. Finally, we demonstrate that BNIP3L-induced mitophagy and impaired glucose uptake can be reversed by direct phosphorylation of BNIP3L by PRKA/PKA, leading to the translocation of BNIP3L from the mitochondria and sarcoplasmic reticulum to the cytosol. These findings provide insight into the role of BNIP3L, mitochondrial turnover, and impaired myocyte insulin signaling during an overfed state when overall autophagy-related gene expression is reduced. Furthermore, our data suggest a mechanism by which exercise or pharmacological activation of PRKA may overcome myocyte insulin resistance. Abbreviations: BCL2: B cell leukemia/lymphoma 2; BNIP3L/Nix: BCL2/adenovirus E1B interacting protein 3-like; DNM1L/DRP1: dynamin 1-like; FUNDC1: FUN14 domain containing 1; IRS1: insulin receptor substrate 1; MAP1LC3A/LC3: microtubule-associated protein 1 light chain 3 alpha; MFN1: mitofusin 1; MFN2: mitofusin 2; MTOR: mechanistic target of rapamycin kinase; OPA1: OPA1 mitochondrial dynamin like GTPase; PDE4i: phosphodiesterase 4 inhibitor; PLD1: phospholipase D1; PLD6: phospholipase D family member 6; PRKA/PKA: protein kinase, AMP-activated; PRKCD/PKCδ: protein kinase C, delta; PRKCQ/PKCθ: protein kinase C, theta; RHEB: Ras homolog enriched in brain; RPS6KB/p70S6K: ribosomal protein S6 kinase; SQSTM1/p62: sequestosome 1; YWHAB/14-3-3β: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein beta.
    Keywords:  Insulin signaling; MTOR; Nix; PKA; mitochondria; mitophagy; muscle
    DOI:  https://doi.org/10.1080/15548627.2020.1821548
  21. Elife. 2020 Oct 15. pii: e58795. [Epub ahead of print]9
    Parallel global profiling of plant TOR dynamics reveals a conserved role for LARP1 in translation.
    M Regina Scarpin, Samuel Leiboff, Jacob Oliver Brunkard.
      TARGET OF RAPAMYCIN (TOR) is a protein kinase that coordinates eukaryotic metabolism. In mammals, TOR specifically promotes translation of ribosomal protein mRNAs when amino acids are available to support protein synthesis. The mechanisms controlling translation downstream from TOR remain contested, however, and are largely unexplored in plants. To define these mechanisms in plants, we globally profiled the plant TOR-regulated transcriptome, translatome, proteome, and phosphoproteome. We found that TOR regulates ribosome biogenesis in plants at multiple levels, but through mechanisms that do not directly depend on 5' oligopyrimidine tract motifs (5'TOPs) found in mammalian ribosomal protein mRNAs. We then show that the TOR-LARP1-5'TOP signaling axis is conserved in plants and regulates expression of a core set of eukaryotic 5'TOP mRNAs, as well as new, plant-specific 5'TOP mRNAs. Our study illuminates ancestral roles of the TOR-LARP1-5'TOP metabolic regulatory network and provides evolutionary context for ongoing debates about the molecular function of LARP1.
    Keywords:  A. thaliana; cell biology; plant biology
    DOI:  https://doi.org/10.7554/eLife.58795
  22. Front Cell Dev Biol. 2020 ;8 572094
    HIPK2 Is Required for Midbody Remnant Removal Through Autophagy-Mediated Degradation.
    Francesca Sardina, Laura Monteonofrio, Manuela Ferrara, Fiorenza Magi, Silvia Soddu, Cinzia Rinaldo.
      At the end of abscission, the residual midbody forms the so-called midbody remnant (MBR), a platform affecting cell fate with emerging key role in differentiation, development, and tumorigenicity. Depending on cell type and pathophysiological context, MBRs undergo different outcomes: they can be retained, released, internalized by nearby cells, or removed through autophagy-mediated degradation. Although mechanisms underlying MBR formation, positioning, and processing have been recently identified, their regulation is still largely unknown. Here, we report that the multifunctional kinase HIPK2 regulates MBR processing contributing to MBR removal. In the process of studying the role of HIPK2 in abscission, we observed that, in addition to cytokinesis failure, HIPK2 depletion leads to significant accumulation of MBRs. In particular, we detected comparable accumulation of MBRs after HIPK2 depletion or treatment with the autophagic inhibitor chloroquine. In contrast, single depletion of the two independent HIPK2 abscission targets, extrachromosomal histone H2B and severing enzyme Spastin, only marginally increased MBR retention, suggesting that MBR accumulation is not just linked to cytokinesis failure. We found that HIPK2 depletion leads to (i) increased levels of CEP55, a key effector of both midbody formation and MBR degradation; (ii) decreased levels of the selective autophagy receptors NBR1 and p62/SQSTM1; and (iii) impaired autophagic flux. These data suggest that HIPK2 contributes to MBR processing by regulating its autophagy-mediated degradation.
    Keywords:  HIPK2; abscission; autophagy; midbody remnants; nbr1
    DOI:  https://doi.org/10.3389/fcell.2020.572094
  23. J Cell Physiol. 2020 Oct 12.
    Exenatide improves random-pattern skin flap survival via TFE3 mediated autophagy augment.
    Jiafeng Li, Huanwen Chen, Junsheng Lou, Guodong Bao, Chenyu Wu, Zhiling Lou, Xingyu Wang, Jian Ding, Zhijie Li, Jian Xiao, Huazi Xu, Weiyang Gao, Kailiang Zhou.
      Random-pattern skin flaps are widely applied to rebuild and restore soft-tissue damage in reconstructive surgery; however, ischemia and subsequent ischemia-reperfusion injury lead to flap necrosis and are major complications. Exenatide, a glucagon-like peptide-1 analog, exerts therapeutic benefits for diabetic wounds, cardiac injury, and nonalcoholic fatty liver disease. Furthermore, Exenatide is a known activator of autophagy, which is a complex process of subcellular degradation that may enhance the viability of random skin flaps. In this study, we explored whether exenatide can improve skin flap survival. Our results showed that exenatide augments autophagy, increases flap viability, enhances angiogenesis, reduces oxidative stress, and alleviates pyroptosis. Coadministration of exenatide with 3-methyladenine and chloroquine, potent inhibitors of autophagy, reversed the beneficial effects, suggesting that the therapeutic benefits of exenatide for skin flaps are due largely to autophagy activation. Mechanistically, we identified that exenatide enhanced activation and nuclear translocation of TFE3, which leads to autophagy activation. Furthermore, we found that exenatide activates the AMPK-SKP2-CARM1 and AMPK-mTOR signaling pathways, which likely lead to exenatide's effects on activating TFE3. Overall, our findings suggest that exenatide may be a potent therapy to prevent flap necrosis, and we also reveal novel mechanistic insight into exenatide's effect on flap survival.
    Keywords:  TFE3; autophagy; exenatide; pyroptosis; random-pattern skin flaps
    DOI:  https://doi.org/10.1002/jcp.30102
  24. Int J Mol Sci. 2020 Oct 13. pii: E7525. [Epub ahead of print]21(20):
    ALS-Related Mutant SOD1 Aggregates Interfere with Mitophagy by Sequestering the Autophagy Receptor Optineurin.
    Yeong Jin Tak, Ju-Hwang Park, Hyangshuk Rhim, Seongman Kang.
      Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by the progressive demise of motor neurons. One of the causes of familial ALS is the mutation of the gene encoding superoxide dismutase 1 (SOD1), which leads to abnormal protein aggregates. How SOD1 aggregation drives ALS is still poorly understood. Recently, ALS pathogenesis has been functionally implicated in mitophagy, specifically the clearance of damaged mitochondria. Here, to understand this mechanism, we investigated the relationship between the mitophagy receptor optineurin and SOD1 aggregates. We found that mutant SOD1 (mSOD1) proteins associate with and then sequester optineurin, which is required to form the mitophagosomes, to aggregates in N2a cells. Optineurin recruitment into mSOD1 aggregates resulted in a reduced mitophagy flux. Furthermore, we observed that an exogenous augmentation of optineurin alleviated the cellular cytotoxicity induced by mSOD1. Taken together, these studies demonstrate that ALS-linked mutations in SOD1 interfere with the mitophagy process through optineurin sequestration, suggesting that the accumulation of damaged mitochondria may play a crucial role in the pathophysiological mechanisms contributing to ALS.
    Keywords:  amyotrophic lateral sclerosis (ALS); mitophagy; optineurin (OPTN); superoxide dismutase 1 (SOD1)
    DOI:  https://doi.org/10.3390/ijms21207525
  25. Front Pharmacol. 2020 ;11 537147
    Sanqi Oral Solution Ameliorates Renal Ischemia/Reperfusion Injury via Reducing Apoptosis and Enhancing Autophagy: Involvement of ERK/mTOR Pathways.
    Ruimin Tian, Pinchao Wang, Lihua Huang, Chuang Li, Zhaoyu Lu, Zhisheng Lu, Aijun Wu, Kun Bao, Wei Mao, Qingming Huang, Peng Xu.
      Ischemia-reperfusion (I/R) induced acute kidney injury (AKI) is a significant health problem with high morbidity and mortality, yet prophylaxis strategies and effective drugs are limited. Sanqi oral solution (SQ) is a formulated medicine widely used in clinical settings to treat various renal diseases via enriching qi and activating blood circulation while its role on I/R-AKI remains unclear. Herein, by establishing rat I/R-AKI models, we intended to investigate the effect of SQ on the prevention of I/R-AKI and explore its underlying mechanisms. We demonstrated that SQ treatment significantly attenuated renal dysfunction of I/R-AKI, alleviated histological damages, inhibited renal apoptosis, and enhanced autophagy. Further investigation proved that SQ could significantly inhibit the activation of ERK and mTOR signaling pathways. Moreover, its renoprotective effect can be abolished by autophagy inhibitor 3-methyladenine (3-MA). Collectively, our results suggest that SQ exerts renoprotective effects on renal I/R injury via reducing apoptosis and enhancing autophagy, which are associated with regulating ERK/mTOR pathways.
    Keywords:  Radix Astragali; Radix Notoginseng; acute kidney injury (AKI); apoptosis; autophagy; extracellular signal-regulated kinase (ERK); mammalian target of rapamycin (mTOR); renal ischemia-reperfusion (I/R)
    DOI:  https://doi.org/10.3389/fphar.2020.537147
  26. Nat Commun. 2020 10 12. 11(1): 5133
    Cathepsin D deficiency in mammary epithelium transiently stalls breast cancer by interference with mTORC1 signaling.
    Stephanie Ketterer, Julia Mitschke, Anett Ketscher, Manuel Schlimpert, Wilfried Reichardt, Natascha Baeuerle, Maria Elena Hess, Patrick Metzger, Melanie Boerries, Christoph Peters, Bernd Kammerer, Tilman Brummer, Florian Steinberg, Thomas Reinheckel.
      Cathepsin D (CTSD) is a lysosomal protease and a marker of poor prognosis in breast cancer. However, the cells responsible for this association and the function of CTSD in cancer are still incompletely understood. By using a conditional CTSD knockout mouse crossed to the transgenic MMTV-PyMT breast cancer model we demonstrate that CTSD deficiency in the mammary epithelium, but not in myeloid cells, blocked tumor development in a cell-autonomous manner. We show that lack of CTSD impaired mechanistic Target of Rapamycin Complex 1 (mTORC1) signaling and induced reversible cellular quiescence. In line, CTSD-deficient tumors started to grow with a two-month delay and quiescent Ctsd-/- tumor cells re-started proliferation upon long-term culture. This was accompanied by rewiring of oncogenic gene expression and signaling pathways, while mTORC1 signaling remained permanently disabled in CTSD-deficient cells. Together, these studies reveal a tumor cell-autonomous effect of CTSD deficiency, and establish a pivotal role of this protease in the cellular response to oncogenic stimuli.
    DOI:  https://doi.org/10.1038/s41467-020-18935-2
  27. Proc Natl Acad Sci U S A. 2020 Oct 13. pii: 202013161. [Epub ahead of print]
    EXO70D isoforms mediate selective autophagic degradation of type-A ARR proteins to regulate cytokinin sensitivity.
    Atiako Kwame Acheampong, Carly Shanks, Chia-Yi Cheng, G Eric Schaller, Yasin Dagdas, Joseph J Kieber.
      The phytohormone cytokinin influences many aspects of plant growth and development, several of which also involve the cellular process of autophagy, including leaf senescence, nutrient remobilization, and developmental transitions. The Arabidopsis type-A response regulators (type-A ARR) are negative regulators of cytokinin signaling that are transcriptionally induced in response to cytokinin. Here, we describe a mechanistic link between cytokinin signaling and autophagy, demonstrating that plants modulate cytokinin sensitivity through autophagic regulation of type-A ARR proteins. Type-A ARR proteins were degraded by autophagy in an AUTOPHAGY-RELATED (ATG)5-dependent manner, and this degradation is promoted by phosphorylation on a conserved aspartate in the receiver domain of the type-A ARRs. EXO70D family members interacted with type-A ARR proteins, likely in a phosphorylation-dependent manner, and recruited them to autophagosomes via interaction of the EXO70D AIM with the core autophagy protein, ATG8. Consistently, loss-of-function exo70D1,2,3 mutants exhibited compromised targeting of type-A ARRs to autophagic vesicles, have elevated levels of type-A ARR proteins, and are hyposensitive to cytokinin. Disruption of both type-A ARRs and EXO70D1,2,3 compromised survival in carbon-deficient conditions, suggesting interaction between autophagy and cytokinin responsiveness in response to stress. These results indicate that the EXO70D proteins act as selective autophagy receptors to target type-A ARR cargos for autophagic degradation, demonstrating modulation of cytokinin signaling by selective autophagy.
    Keywords:  carbon starvation; concanamycin A; cytokinin signaling; selective autophagy
    DOI:  https://doi.org/10.1073/pnas.2013161117
  28. PLoS Genet. 2020 Oct 16. 16(10): e1009070
    PE homeostasis rebalanced through mitochondria-ER lipid exchange prevents retinal degeneration in Drosophila.
    Haifang Zhao, Tao Wang.
      The major glycerophospholipid phosphatidylethanolamine (PE) in the nervous system is essential for neural development and function. There are two major PE synthesis pathways, the CDP-ethanolamine pathway in the endoplasmic reticulum (ER) and the phosphatidylserine decarboxylase (PSD) pathway in mitochondria. However, the role played by mitochondrial PE synthesis in maintaining cellular PE homeostasis is unknown. Here, we show that Drosophila pect (phosphoethanolamine cytidylyltransferase) mutants lacking the CDP-ethanolamine pathway, exhibited alterations in phospholipid composition, defective phototransduction, and retinal degeneration. Induction of the PSD pathway fully restored levels and composition of cellular PE, thus rescued the retinal degeneration and defective visual responses in pect mutants. Disrupting lipid exchange between mitochondria and ER blocked the ability of PSD to rescue pect mutant phenotypes. These findings provide direct evidence that the synthesis of PE in mitochondria contributes to cellular PE homeostasis, and suggest the induction of mitochondrial PE synthesis as a promising therapeutic approach for disorders associated with PE deficiency.
    DOI:  https://doi.org/10.1371/journal.pgen.1009070
  29. Am J Transl Res. 2020 ;12(9): 5080-5094
    Chlorin A-mediated photodynamic therapy induced apoptosis in human cholangiocarcinoma cells via impaired autophagy flux.
    Chongxin He, Jie Xia, Yinghua Gao, Zhilong Chen, Xinjian Wan.
       BACKGROUND: Photodynamic therapy (PDT) is a promising strategy for multiple cancers. Chlorin e6 and its derivative 131-[2'-(2-pyridyl)ethylamine] Chlorin e6 (Chlorin A) are effective photosensitizers, although their cytotoxic mechanisms have not yet been fully characterized.
    METHODS: Cell viability and apoptosis were evaluated by CCK8 assay, TUNEL assay, and Annexin V/PI staining. The expression levels of different proteins were analyzed by Western blot analysis and immunofluorescence. The crosstalk between autophagy, endoplasmic reticulum stress (ERS), and mitochondrial dysfunction was investigated using reactive oxygen species (ROS) scavenger N-acetyl cysteine (NAC), PERK inhibitor GSK2606414, autophagy inhibitor 3-MA, and mitochondrial stabilizer elamipretide. Furthermore, the extent of ROS production, lysosomal damage, autophagy flux, and mitochondrial membrane potential (MMP) were tracked using established probes. An in vivo xenograft model of cholangiocarcinoma (CCA) was established in BALB/c-nude mice by inoculation with EGI-1 cells, and Chlorin A was administered topically or intravenously, followed by light irradiation.
    RESULTS: Chlorin A-PDT decreased the viability of CCA cells and induced apoptosis. Intriguingly, Chlorin A-PDT promoted autophagy via activation of ROS-induced ERS-related PERK/p-eif2α/CHOP axis, and blocked the ensuing autophagy flux by lysosomal damage. The PERK inhibitor GSK2606414 and NAC alleviated apoptosis and autophagy induced by Chlorin A-PDT. Furthermore, mitochondrial dysfunction aggravated ERS, and stabilizing the mitochondria reduced both apoptosis and autophagy. Finally, Chlorin A-PDT significantly reduced tumor growth in vivo.
    CONCLUSIONS: Chlorin A-PDT induced apoptosis in CCA cells by initiating autophagy and impaired the autophagy flux via ROS-mediated ERS and lysosomal damage.
    Keywords:  Chlorin; PDT; ROS; autophagy; endoplasmic reticulum stress
  30. PLoS Genet. 2020 Oct 16. 16(10): e1009046
    The Ccr4-Not complex regulates TORC1 signaling and mitochondrial metabolism by promoting vacuole V-ATPase activity.
    Hongfeng Chen, P Winston Miller, Daniel L Johnson, R Nicholas Laribee.
      The Ccr4-Not complex functions as an effector of multiple signaling pathways that control gene transcription and mRNA turnover. Consequently, Ccr4-Not contributes to a diverse array of processes, which includes a significant role in cell metabolism. Yet a mechanistic understanding of how it contributes to metabolism is lacking. Herein, we provide evidence that Ccr4-Not activates nutrient signaling through the essential target of rapamycin complex 1 (TORC1) pathway. Ccr4-Not disruption reduces global TORC1 signaling, and it also upregulates expression of the cell wall integrity (CWI) pathway terminal kinase Mpk1. Although CWI signaling represses TORC1 signaling, we find that Ccr4-Not loss inhibits TORC1 independently of CWI activation. Instead, we demonstrate that Ccr4-Not promotes the function of the vacuole V-ATPase, which interacts with the Gtr1 GTPase-containing EGO complex to stimulate TORC1 in response to nutrient sufficiency. Bypassing the V-ATPase requirement in TORC1 activation using a constitutively active Gtr1 mutant fully restores TORC1 signaling in Ccr4-Not deficient cells. Transcriptome analysis and functional studies revealed that loss of the Ccr4 subunit activates the TORC1 repressed retrograde signaling pathway to upregulate mitochondrial activity. Blocking this mitochondrial upregulation in Ccr4-Not deficient cells further represses TORC1 signaling, and it causes synergistic deficiencies in mitochondrial-dependent metabolism. These data support a model whereby Ccr4-Not loss impairs V-ATPase dependent TORC1 activation that forces cells to enhance mitochondrial metabolism to sustain a minimal level of TORC1 signaling necessary for cell growth and proliferation. Therefore, Ccr4-Not plays an integral role in nutrient signaling and cell metabolism by promoting V-ATPase dependent TORC1 activation.
    DOI:  https://doi.org/10.1371/journal.pgen.1009046
  31. PLoS One. 2020 ;15(10): e0240478
    Kahweol activates the Nrf2/HO-1 pathway by decreasing Keap1 expression independently of p62 and autophagy pathways.
    Hye-Young Seo, So-Hee Lee, Ji-Ha Lee, Jae Seok Hwang, Mi Kyung Kim, Byoung Kuk Jang.
      Kahweol is a diterpene found in coffee beans and unfiltered coffee drinks. Several studies have demonstrated that kahweol induces the nuclear factor erythroid-2 related factor 2/ hemeoxygenase-1 (Nrf2/HO-1) pathway; however, the mechanisms involved are currently unknown. Kelch-like ECH-associated protein 1 (Keap1) is a major regulator of Nrf2 expression and is degraded mostly by autophagy. The p62 protein enhances binding to Keap1 and contributes to the activation of Nrf2. Here, we examined the role of Keap1 regulation in the effect of kahweol on the Nrf2/HO-1 pathway in hepatocytes. In AML12 cells and primary mouse hepatocytes, kahweol increased the levels of Nrf2 and HO-1 protein without increasing expression of the Nrf2 mRNA. In addition, kahweol reduced Keap1 protein levels significantly without decreasing Keap1 mRNA levels. Although regulation of the Keap1-Nrf2-pathway by p62-dependent autophagy is well known, we confirmed here that the reduction of Keap1 protein levels by kahweol does not involve p62-dependent autophagy degradation or ubiquitination. In conclusion, kahweol increases the expression of Nrf2 in hepatocytes by inhibiting translation of the Keap1 mRNA.
    DOI:  https://doi.org/10.1371/journal.pone.0240478
  32. Am J Physiol Cell Physiol. 2020 Oct 14.
    mTORC1/2 signaling is downregulated by amino acid-free culture of mouse preimplantation embryos and is only partially restored by amino acid re-addition.
    Radu C Zamfirescu, Margot L Day, Michael B Morris.
      Development of the mammalian preimplantation embryo is influenced by autocrine/paracrine factors and availability of nutrients. Deficiencies of these during in vitro culture reduce the success of assisted reproductive technologies. The mTORC1 pathway integrates external and internal signals, including those by amino acids (AAs), to promote normal preimplantation development. For this reason, AAs are often included in embryo culture media. In this study, we examined how withdrawal and addition of AAs to culture media modulate mTORC1 pathway activity compared to its activity in mouse embryos developed in vivo. Phosphorylation of signalling components downstream of mTORC1, namely p70S6K, RPS6 and 4E-BP1, and that of Akt, which lies upstream of mTORC1, changed significantly across stages of embryos developed in vivo. For freshly isolated blastocysts placed in vitro, the absence of AAs in culture medium, even for a few hours, decreased mTORC1 signalling, which could only be partially restored by their addition. Long-term culture of early embryos to blastocysts in the absence of AAs decreased mTORC1 signalling to a greater extent and again this could only be partially restored by their inclusion. This failure to fully restore is probably due to decreased PI3K/Akt/mTORC2 signalling in culture, as indicated by decreased P-AktS473. mTORC2 lies upstream of mTORC1 and is insensitive to AAs, and its reduced activity probably results from loss of maternal/autocrine factors. These data highlight reduced mTORC1/2 signalling activity correlating with compromised development in vitro and show that addition of AAs can only partially offset these effects.
    Keywords:  Akt; Preimplantation embryo; amino acids; mTOR; proline
    DOI:  https://doi.org/10.1152/ajpcell.00385.2020
  33. Diabetes. 2020 Oct 12. pii: db191239. [Epub ahead of print]
    Depletion of Adipocyte Becn1 Leads to Lipodystrophy and Metabolic Dysregulation.
    Young Jin, Yul Ji, Yaechan Song, Sung Sik Choe, Yong Geun Jeon, Heeju Na, Tae Wook Nam, Hye Jeong Kim, Hahn Nahmgoong, Sung Min Kim, Jae-Woo Kim, Ki Taek Nam, Je Kyung Seong, Daehee Hwang, Chan Bae Park, In Hye Lee, Jae Bum Kim, Han-Woong Lee.
      Becn1/Beclin-1 is a core component of the class III phosphatidylinositol 3-kinase required for autophagosome formation and vesicular trafficking. Although Becn1 has been implicated in numerous diseases such as cancer, aging, and neurodegenerative disease, the role of Becn1 in white adipose tissue and related metabolic diseases remains elusive. Here we show that adipocyte-specific Becn1 knockout mice develop severe lipodystrophy, leading to adipose tissue inflammation, hepatic steatosis, insulin resistance. Ablation of Becn1 in adipocytes stimulates programmed cell death in a cell-autonomous manner, accompanied by elevated ER stress gene expression. Furthermore, we observed that Becn1 depletion sensitized mature adipocytes to ER stress, leading to accelerated cell death. Taken together, these data suggest that adipocyte Becn1 would serve as a crucial player for adipocyte survival and adipose tissue homeostasis.
    DOI:  https://doi.org/10.2337/db19-1239
  34. FASEB J. 2020 Oct 15.
    Neuronal AMPK coordinates mitochondrial energy sensing and hypoxia resistance in C. elegans.
    Brandon J Berry, Aksana Baldzizhar, Tyrone O Nieves, Andrew P Wojtovich.
      Organisms adapt to their environment through coordinated changes in mitochondrial function and metabolism. The mitochondrial protonmotive force (PMF) is an electrochemical gradient that powers ATP synthesis and adjusts metabolism to energetic demands via cellular signaling. It is unknown how or where transient PMF changes are sensed and signaled due to the lack of precise spatiotemporal control in vivo. We addressed this by expressing a light-activated proton pump in mitochondria to spatiotemporally "turn off" mitochondrial function through PMF dissipation in tissues with light. We applied our construct-mitochondria-OFF (mtOFF)-to understand how metabolic status impacts hypoxia resistance, a response that relies on mitochondrial function. Activation of mtOFF induced starvation-like behavior mediated by AMP-activated protein kinase (AMPK). We found prophylactic mtOFF activation increased survival following hypoxia, and that protection relied on neuronal AMPK. Our study links spatiotemporal control of mitochondrial PMF to cellular metabolic changes that mediate behavior and stress resistance.
    Keywords:  anoxia; metabolism; optogenetics; uncoupling
    DOI:  https://doi.org/10.1096/fj.202001150RR
  35. N Engl J Med. 2020 Oct 15. 383(16): 1564-1576
    Autophagy in Human Diseases.
    Noboru Mizushima, Beth Levine.
      
    DOI:  https://doi.org/10.1056/NEJMra2022774
  36. Biochem Biophys Res Commun. 2020 Oct 12. pii: S0006-291X(20)31442-X. [Epub ahead of print]
    HSP70 interacts with Rheb, inhibiting mTORC1 signaling.
    Hyang Hwa Ryu, Sang Hoon Ha.
      The small GTPase Rheb binds and activates mTORC1, which plays a pivotal role in diverse cellular physiologies. To increase our understanding of how Rheb regulates mTORC1 signaling, we set out to identify Rheb binding proteins using shotgun proteomics approaches. In this study, we characterized HSP70, one of the identified proteins, as a new Rheb binding protein. The present study showed that Rheb forms a complex with HSP70 in intact cells. Interestingly, the binding of Rheb to mTORC1 was abolished by HSP70. Furthermore, the stability of Rheb is dramatically decreased by HSP70, and this degradation is proteasome-dependent. As a result, Rheb-dependent mTORC1 activation was decreased by HSP70. Taken together, HSP70 dissociates Rheb from mTORC1 and induces proteasome-dependent degradation, leading to the inhibition of mTORC1 signaling. Our findings suggest that HSP70 is a negative regulator of mTORC1 signaling via interaction with Rheb.
    Keywords:  HSP70; Negative regulation; Rheb; mTORC1
    DOI:  https://doi.org/10.1016/j.bbrc.2020.07.053
  37. Proc Natl Acad Sci U S A. 2020 Oct 14. pii: 202005389. [Epub ahead of print]
    The Chlamydia effector CT622/TaiP targets a nonautophagy related function of ATG16L1.
    Daniel Hamaoui, Mathilde M Cossé, Jagan Mohan, Alf Håkon Lystad, Thomas Wollert, Agathe Subtil.
      The obligate intracellular bacteria Chlamydia trachomatis, the causative agent of trachoma and sexually transmitted diseases, multiply in a vacuolar compartment, the inclusion. From this niche, they secrete "effector" proteins, that modify cellular activities to enable bacterial survival and proliferation. Here, we show that the host autophagy-related protein 16-1 (ATG16L1) restricts inclusion growth and that this effect is counteracted by the secretion of the bacterial effector CT622/TaiP (translocated ATG16L1 interacting protein). ATG16L1 is mostly known for its role in the lipidation of the human homologs of ATG8 (i.e., LC3 and homologs) on double membranes during autophagy as well as on single membranes during LC3-associated phagocytosis and other LC3-lipidation events. Unexpectedly, the LC3-lipidation-related functions of ATG16L1 are not required for restricting inclusion development. We show that the carboxyl-terminal domain of TaiP exposes a mimic of an eukaryotic ATG16L1-binding motif that binds to ATG16L1's WD40 domain. By doing so, TaiP prevents ATG16L1 interaction with the integral membrane protein TMEM59 and allows the rerouting of Rab6-positive compartments toward the inclusion. The discovery that one bacterial effector evolved to target ATG16L1's engagement in intracellular traffic rather than in LC3 lipidation brings this "secondary" activity of ATG16L1 in full light and emphasizes its importance for maintaining host cell homeostasis.
    Keywords:  ATG16L1; Chlamydia trachomatis; autophagy; host-pathogen interactions; intracellular traffic
    DOI:  https://doi.org/10.1073/pnas.2005389117
  38. Front Cell Dev Biol. 2020 ;8 576104
    Upregulation of Parkin Accelerates Osteoblastic Differentiation of Bone Marrow-Derived Mesenchymal Stem Cells and Bone Regeneration by Enhancing Autophagy and β-Catenin Signaling.
    Wei Zhang, Weiduo Hou, Mo Chen, Erman Chen, Deting Xue, Chenyi Ye, Weixu Li, Zhijun Pan.
      Osteogenic differentiation of bone marrow-derived mesenchymal stem cells (BMSCs) plays a key role in bone formation. Parkin, an E3 ubiquitin ligase, related to Parkinson's disease and aging. Previous studies have indicated that Parkinson's disease have a higher risk of osteoporotic fracture. To investigate the effects and underlying mechanism of Parkin in the osteogenic differentiation of BMSCs, osteogenic differentiation was analyzed following upregulation or downregulation of Parkin. We found that Parkin was increased during differentiation. Parkin overexpression enhanced osteo-specific markers, and downregulation of Parkin mitigated osteo-specific markers. Moreover, upregulation of Parkin promoted β-catenin expression and autophagy and vice versa. The upregulation of β-catenin enhanced autophagy, and the activation of autophagy also increased the expression of β-catenin in Parkin-downregulated BMSCs. Parkin-overexpressed cell sheets accelerated bone healing in a tibial fracture model. Based on these results, we concluded that Parkin meditates osteoblastic differentiation of BMSCs via β-catenin and autophagy signaling.
    Keywords:  Parkin; autophagy; beta-Catenin; osteogenic differentiation; stem cells
    DOI:  https://doi.org/10.3389/fcell.2020.576104
  39. Int J Mol Sci. 2020 Oct 14. pii: E7580. [Epub ahead of print]21(20):
    Intimate Relations-Mitochondria and Ageing.
    Michael Webb, Dionisia P Sideris.
      Mitochondrial dysfunction is associated with ageing, but the detailed causal relationship between the two is still unclear. We review the major phenomenological manifestations of mitochondrial age-related dysfunction including biochemical, regulatory and energetic features. We conclude that the complexity of these processes and their inter-relationships are still not fully understood and at this point it seems unlikely that a single linear cause and effect relationship between any specific aspect of mitochondrial biology and ageing can be established in either direction.
    Keywords:  ROS; ageing; energetics; gene regulation; mitochondria
    DOI:  https://doi.org/10.3390/ijms21207580
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