bims-auttor 2020-12-13 papers

bims-auttor

Biomed News

on Autophagy and mTOR

Issue of 2020‒12‒13
23 papers selected by
Viktor Korolchuk, Newcastle University

SIRT1 - a new mammalian substrate of nuclear autophagy.
Aberrant mitochondrial morphology and function associated with impaired mitophagy and DNM1L-MAPK/ERK signaling are found in aged mutant Parkinsonian LRRK2R1441G mice.
PINK1 phosphorylates ubiquitin predominantly in astrocytes.
When lipid homeostasis runs havoc: lipotoxicity links lysosomal dysfunction to autophagy.
Direct lysosome-based autophagy of lipid droplets in hepatocytes.
Pontin arginine methylation by CARM1 is crucial for epigenetic regulation of autophagy.
The conformational and mutational landscape of the ubiquitin-like marker for autophagosome formation in cancer.
Inositol Polyphosphate Multikinase Inhibits Liquid-Liquid Phase Separation of TFEB to Negatively Regulate Autophagy Activity.
Autophagy Is Required for Maturation of Surfactant-Containing Lamellar Bodies in the Lung and Swim Bladder.
Transcription factor EB agonists from natural products for treating human diseases with impaired autophagy-lysosome pathway.
RNF186 regulates EFNB1 (ephrin B1)-EPHB2-induced autophagy in the colonic epithelial cells for the maintenance of intestinal homeostasis.
Autophagy alleviates hypoxia-induced blood-brain barrier injury via regulation of CLDN5 (claudin 5).
Architecture of the Tuberous Sclerosis Protein Complex.
Caveolin-1 in autophagy: a potential therapeutic target in atherosclerosis.
Autophagy repurposes cells during paligenosis.
REV-ERBα alters circadian rhythms by modulating mTOR signaling.
Out of Phase: How IPMK Inhibits TFEB.
A genome-wide RNA interference screen disentangles the Golgi tropism of LC3.
The BAD-BAX-caspase-3 cascade modulates synaptic vesicle pools via autophagy.
A Conformational Change in the N Terminus of SLC38A9 Signals mTORC1 Activation.
Regulation of Beclin 1-Mediated Autophagy by Oncogenic Tyrosine Kinases.
TFEB/Mitf links impaired nuclear import to autophagolysosomal dysfunction in C9-ALS.
ATM plays antioxidant, boosting mitophagy via denitrosylation.

Autophagy. 2020 Dec 08.

SIRT1 - a new mammalian substrate of nuclear autophagy.

Lu Wang, Caiyue Xu, Terje Johansen, Shelley L Berger, Zhixun Dou.

  Macroautophagic/autophagic degradation of nuclear components (or nuclear autophagy) is a poorly understood area in autophagy research. We previously reported the nuclear lamina protein LMNB1 (lamin B1) as a nuclear autophagy substrate in primary human cells, stimulating the investigation of nuclear autophagy in the mammalian system. We recently reported the sirtuin protein SIRT1 as a new selective substrate of nuclear autophagy in senescence and aging. Upon senescence of primary human cells, SIRT1 degradation is mediated by a direct nuclear SIRT1-LC3 interaction, followed by nucleus-to-cytoplasm shuttling of SIRT1 and autophagosome-lysosome degradation. In vivo, SIRT1 is downregulated by lysosomes in hematopoietic and immune organs upon natural aging in mice and in aged human T cells. Our study identified another substrate of nuclear autophagy and suggests a new strategy to promote SIRT1-mediated health benefits by suppressing its autophagic degradation.

Keywords:  Aging; SIRT1; nuclear autophagy; senescence; sirtuin

DOI:  https://doi.org/10.1080/15548627.2020.1860541
Autophagy. 2020 Dec 10. 1-25

Aberrant mitochondrial morphology and function associated with impaired mitophagy and DNM1L-MAPK/ERK signaling are found in aged mutant Parkinsonian LRRK2R1441G mice.

Huifang Liu, Philip Wing-Lok Ho, Chi-Ting Leung, Shirley Yin-Yu Pang, Eunice Eun Seo Chang, Zoe Yuen-Kiu Choi, Michelle Hiu-Wai Kung, David Boyer Ramsden, Shu-Leong Ho.

  Mitochondrial dysfunction causes energy deficiency and nigrostriatal neurodegeneration which is integral to the pathogenesis of Parkinson disease (PD). Clearance of defective mitochondria involves fission and ubiquitin-dependent degradation via mitophagy to maintain energy homeostasis. We hypothesize that LRRK2 (leucine-rich repeat kinase 2) mutation disrupts mitochondrial turnover causing accumulation of defective mitochondria in aging brain. We found more ubiquitinated mitochondria with aberrant morphology associated with impaired function in aged (but not young) LRRK2R1441G knockin mutant mouse striatum compared to wild-type (WT) controls. LRRK2R1441G mutant mouse embryonic fibroblasts (MEFs) exhibited reduced MAP1LC3/LC3 activation indicating impaired macroautophagy/autophagy. Mutant MEFs under FCCP-induced (mitochondrial uncoupler) stress showed increased LC3-aggregates demonstrating impaired mitophagy. Using a novel flow cytometry assay to quantify mitophagic rates in MEFs expressing photoactivatable mito-PAmCherry, we found significantly slower mitochondria clearance in mutant cells. Specific LRRK2 kinase inhibition using GNE-7915 did not alleviate impaired mitochondrial clearance suggesting a lack of direct relationship to increased kinase activity alone. DNM1L/Drp1 knockdown in MEFs slowed mitochondrial clearance indicating that DNM1L is a prerequisite for mitophagy. DNM1L knockdown in slowing mitochondrial clearance was less pronounced in mutant MEFs, indicating preexisting impaired DNM1L activation. DNM1L knockdown disrupted mitochondrial network which was more evident in mutant MEFs. DNM1L-Ser616 and MAPK/ERK phosphorylation which mediate mitochondrial fission and downstream mitophagic processes was apparent in WT using FCCP-induced stress but not mutant MEFs, despite similar total MAPK/ERK and DNM1L levels. In conclusion, aberrant mitochondria morphology and dysfunction associated with impaired mitophagy and DNM1L-MAPK/ERK signaling are found in mutant LRRK2 MEFs and mouse brain. Abbreviations: ATP: adenosine triphosphate; BAX: BCL2-associated X protein; CDK1: cyclin-dependent kinase 1; CDK5: cyclin-dependent kinase 5; CQ: chloroquine; CSF: cerebrospinal fluid; DNM1L/DRP1: dynamin 1-like; ELISA: enzyme-linked immunosorbent assay; FACS: fluorescence-activated cell sorting; FCCP: carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; LAMP2A: lysosomal-associated membrane protein 2A; LRRK2: leucine-rich repeat kinase 2; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MAPK1/ERK2: mitogen-activated protein kinase 1; MEF: mouse embryonic fibroblast; MFN1: mitofusin 1; MMP: mitochondrial membrane potential; PAmCherry: photoactivatable-mCherry; PD: Parkinson disease; PINK1: PTEN induced putative kinase 1; PRKN/PARKIN: parkin RBR E3 ubiquitin protein ligase; RAB10: RAB10, member RAS oncogene family; RAF: v-raf-leukemia oncogene; SNCA: synuclein, alpha; TEM: transmission electron microscopy; VDAC: voltage-dependent anion channel; WT: wild type; SQSTM1/p62: sequestosome 1.

Keywords:  Aging; Dnm1l/DRP1; SQSTM1/p62; knockin mice; macroautophagy; mitochondria dysfunction; mitochondrial fission; mitophagy; parkinson disease; ubiquitination

DOI:  https://doi.org/10.1080/15548627.2020.1850008
NPJ Parkinsons Dis. 2019 Dec 11. 5(1): 29

PINK1 phosphorylates ubiquitin predominantly in astrocytes.

Sandeep K Barodia, Laura J McMeekin, Rose B Creed, Elijah K Quinones, Rita M Cowell, Matthew S Goldberg.

Loss-of-function mutations in PINK1 are causally linked to recessively inherited Parkinson's disease (PD), with marked loss of dopaminergic neurons in the substantia nigra that are required for normal movement. PINK1 is a nuclear-encoded mitochondrial-targeted kinase that phosphorylates a conserved serine at amino acid 65 (pS65) in ubiquitin as well as Parkin, another gene with loss-of-function mutations linked to recessive parkinsonism. The steady-state levels of PINK1 protein are very low, even in cells that express PINK1, because PINK1 is normally targeted for degradation after mitochondrial import by a process that is dependent upon mitochondrial membrane potential. Dissipation of the mitochondrial membrane potential with ionophores, such as CCCP and valinomycin, causes the accumulation of PINK1 on the outer mitochondrial membrane, a marked increase of pS65-ubiquitin and the recruitment of Parkin, which targets dysfunctional mitochondria for degradation by autophagy. While the high penetrance of PINK1 mutations establish its critical function for maintaining neurons, the activity of PINK1 in primary neurons has been difficult to detect. Mounting evidence implicates non-neuronal cells, including astrocytes and microglia, in the pathogenesis of both idiopathic and inherited PD. Herein we used both western analysis and immunofluorescence of pS65-ubiquitin to directly compare the activity of PINK1 in primary neurons, astrocytes, microglia, and oligodendrocyte progenitor cells cultured from the brains of wild-type (WT) and PINK1 knockout (KO) rat pups. Our findings that PINK1-dependent ubiquitin phosphorylation is predominantly in astrocytes supports increased priority for research on the function of PINK1 in astrocytes and the contribution of astrocyte dysfunction to PD pathogenesis.

DOI: https://doi.org/10.1038/s41531-019-0101-9
Matrix Biol. 2020 Dec 05. pii: S0945-053X(20)30115-3. [Epub ahead of print]

When lipid homeostasis runs havoc: lipotoxicity links lysosomal dysfunction to autophagy.

Irmgard Tegeder, Donat Kögel.

  Autophagy is one of the major cellular degradation pathways, which prevents accumulation of cellular wastes including "hazardous" material such as oxidized proteins and lipids and allows removal of aggregates and dysfunctional organelles. Hence, autophagy is meant to preserve cell survival, and is mostly protective. However, autophagy may trigger a feedforward, exaggerated cycle in which cells continue to degrade proteins and organelles, finally leading to autophagy-dependent cell death (ADCD), a process that can be initiated with lysosomotropic detergents, which are protonated within the lysosome and cause a permeabilization of the membrane. Such drugs may be useful to combat cancer. In some paradigms of ADCD, there is evidence that the cellular fate is determined by the integrity of lysosomal membranes, transporters, enzymes and ion gradients. Detergent-like effects of lysosomotropic drugs can over-activate autophagy. A disruption of the lysosomal membrane barrier with leakage of lysosomal enzymes or lipids may trigger a vicious cycle via proteases and accumulation of lipids, which impair the functions of the plasma - and organelle membranes. This review summarizes the current evidence for a crosstalk between lysosomal dysfunction and autophagy and the lysosomal events, which progress toward ADCD with a focus on the role of sphingolipids and cholesterol as cargo and as regulators of ADCD.

Keywords:  Lysosomal leak; cell death; ceramides; cholesterol; sphingolipids

DOI:  https://doi.org/10.1016/j.matbio.2020.11.005
Proc Natl Acad Sci U S A. 2020 Dec 07. pii: 202011442. [Epub ahead of print]

Direct lysosome-based autophagy of lipid droplets in hepatocytes.

Ryan J Schulze, Eugene W Krueger, Shaun G Weller, Katherine M Johnson, Carol A Casey, Micah B Schott, Mark A McNiven.

  Hepatocytes metabolize energy-rich cytoplasmic lipid droplets (LDs) in the lysosome-directed process of autophagy. An organelle-selective form of this process (macrolipophagy) results in the engulfment of LDs within double-membrane delimited structures (autophagosomes) before lysosomal fusion. Whether this is an exclusive autophagic mechanism used by hepatocytes to catabolize LDs is unclear. It is also unknown whether lysosomes alone might be sufficient to mediate LD turnover in the absence of an autophagosomal intermediate. We performed live-cell microscopy of hepatocytes to monitor the dynamic interactions between lysosomes and LDs in real-time. We additionally used a fluorescent variant of the LD-specific protein (PLIN2) that exhibits altered fluorescence in response to LD interactions with the lysosome. We find that mammalian lysosomes and LDs undergo interactions during which proteins and lipids can be transferred from LDs directly into lysosomes. Electron microscopy (EM) of primary hepatocytes or hepatocyte-derived cell lines supports the existence of these interactions. It reveals a dramatic process whereby the lipid contents of the LD can be "extruded" directly into the lysosomal lumen under nutrient-limited conditions. Significantly, these interactions are not affected by perturbations to crucial components of the canonical macroautophagy machinery and can occur in the absence of double-membrane lipoautophagosomes. These findings implicate the existence of an autophagic mechanism used by mammalian cells for the direct transfer of LD components into the lysosome for breakdown. This process further emphasizes the critical role of lysosomes in hepatic LD catabolism and provides insights into the mechanisms underlying lipid homeostasis in the liver.

Keywords:  hepatocyte; lipid droplet; lipolysis; lysosome; microautophagy

DOI:  https://doi.org/10.1073/pnas.2011442117
Nat Commun. 2020 12 08. 11(1): 6297

Pontin arginine methylation by CARM1 is crucial for epigenetic regulation of autophagy.

Young Suk Yu, Hijai R Shin, Dongha Kim, Seon Ah Baek, Seon Ah Choi, Hyejin Ahn, Amen Shamim, Jeonghwan Kim, Ik Soo Kim, Kyeong Kyu Kim, Kyoung-Jae Won, Sung Hee Baek.

Autophagy is a catabolic process through which cytoplasmic components are degraded and recycled in response to various stresses including starvation. Recently, transcriptional and epigenetic regulations of autophagy have emerged as essential mechanisms for maintaining homeostasis. Here, we identify that coactivator-associated arginine methyltransferase 1 (CARM1) methylates Pontin chromatin-remodeling factor under glucose starvation, and methylated Pontin binds Forkhead Box O 3a (FOXO3a). Genome-wide analyses and biochemical studies reveal that methylated Pontin functions as a platform for recruiting Tip60 histone acetyltransferase with increased H4 acetylation and subsequent activation of autophagy genes regulated by FOXO3a. Surprisingly, CARM1-Pontin-FOXO3a signaling axis can work in the distal regions and activate autophagy genes through enhancer activation. Together, our findings provide a signaling axis of CARM1-Pontin-FOXO3a and further expand the role of CARM1 in nuclear regulation of autophagy.

DOI: https://doi.org/10.1038/s41467-020-20080-9
Autophagy. 2020 Dec 11. 1-24

The conformational and mutational landscape of the ubiquitin-like marker for autophagosome formation in cancer.

Burcu Aykac Fas, Emiliano Maiani, Valentina Sora, Mukesh Kumar, Maliha Mashkoor, Matteo Lambrughi, Matteo Tiberti, Elena Papaleo.

  Macroautophagy/autophagy is a cellular process to recycle damaged cellular components, and its modulation can be exploited for disease treatments. A key autophagy player is the ubiquitin-like protein MAP1LC3B/LC3B. Mutations and changes in MAP1LC3B expression occur in cancer samples. However, the investigation of the effects of these mutations on MAP1LC3B protein structure is still missing. Despite many LC3B structures that have been solved, a comprehensive study, including dynamics, has not yet been undertaken. To address this knowledge gap, we assessed nine physical models for biomolecular simulations for their capabilities to describe the structural ensemble of MAP1LC3B. With the resulting MAP1LC3B structural ensembles, we characterized the impact of 26 missense mutations from pan-cancer studies with different approaches, and we experimentally validated our prediction for six variants using cellular assays. Our findings shed light on damaging or neutral mutations in MAP1LC3B, providing an atlas of its modifications in cancer. In particular, P32Q mutation was found detrimental for protein stability with a propensity to aggregation. In a broader context, our framework can be applied to assess the pathogenicity of protein mutations or to prioritize variants for experimental studies, allowing to comprehensively account for different aspects that mutational events alter in terms of protein structure and function. Abbreviations: ATG: autophagy-related; Cα: alpha carbon; CG: coarse-grained; CHARMM: Chemistry at Harvard macromolecular mechanics; CONAN: contact analysis; FUNDC1: FUN14 domain containing 1; FYCO1: FYVE and coiled-coil domain containing 1; GABARAP: GABA type A receptor-associated protein; GROMACS: Groningen machine for chemical simulations; HP: hydrophobic pocket; LIR: LC3 interacting region; MAP1LC3B/LC3B microtubule associated protein 1 light chain 3 B; MD: molecular dynamics; OPTN: optineurin; OSF: open software foundation; PE: phosphatidylethanolamine, PLEKHM1: pleckstrin homology domain-containing family M 1; PSN: protein structure network; PTM: post-translational modification; SA: structural alphabet; SLiM: short linear motif; SQSTM1/p62: sequestosome 1; WT: wild-type.

Keywords:  Autophagy; MAP1LC3B; cancer mutations; molecular dynamics; protein structure network; structural alphabets

DOI:  https://doi.org/10.1080/15548627.2020.1847443
Dev Cell. 2020 Dec 07. pii: S1534-5807(20)30800-5. [Epub ahead of print]55(5): 588-602.e7

Inositol Polyphosphate Multikinase Inhibits Liquid-Liquid Phase Separation of TFEB to Negatively Regulate Autophagy Activity.

Di Chen, Zheng Wang, Yan G Zhao, Hui Zheng, Hongyu Zhao, Nan Liu, Hong Zhang.

  Liquid-liquid phase separation (LLPS) compartmentalizes transcriptional condensates for gene expression, but little is known about how this process is controlled. Here, we showed that depletion of IPMK, encoding inositol polyphosphate multikinase, promotes autophagy and lysosomal function and biogenesis in a TFEB-dependent manner. Cytoplasmic-nuclear trafficking of TFEB, a well-characterized mechanism by which diverse signaling pathways regulate TFEB activity, is not evidently altered by IPMK depletion. We demonstrated that nuclear TFEB forms distinct puncta that colocalize with the Mediator complex and with mRNAs of target lysosomal genes. TFEB undergoes LLPS in vitro. IPMK directly interacts with and inhibits LLPS of TFEB and also dissolves TFEB condensates. Depletion of IPMK increases the number of nuclear TFEB puncta and the co-localization of TFEB with Mediator and mRNAs of target genes. Our study reveals that nuclear-localized IPMK acts as a chaperone to inhibit LLPS of TFEB to negatively control its transcriptional activity.

Keywords:  IPMK; TFEB; autophagy; lysosome; phase separation

DOI:  https://doi.org/10.1016/j.devcel.2020.10.010
Cell Rep. 2020 Dec 08. pii: S2211-1247(20)31466-2. [Epub ahead of print]33(10): 108477

Autophagy Is Required for Maturation of Surfactant-Containing Lamellar Bodies in the Lung and Swim Bladder.

Hideaki Morishita, Yuki Kanda, Takeshi Kaizuka, Haruka Chino, Kazuki Nakao, Yoshimi Miki, Yoshitaka Taketomi, Jun-Lin Guan, Makoto Murakami, Atsu Aiba, Noboru Mizushima.

  Autophagy is an intracellular degradation system, but its physiological functions in vertebrates are not yet fully understood. Here, we show that autophagy is required for inflation of air-filled organs: zebrafish swim bladder and mouse lung. In wild-type zebrafish swim bladder and mouse lung type II pulmonary epithelial cells, autophagosomes are formed and frequently fuse with lamellar bodies. The lamellar body is a lysosome-related organelle that stores a phospholipid-containing surfactant complex that lines the air-liquid interface and reduces surface tension. We find that autophagy is critical for maturation of the lamellar body. Accordingly, atg-deficient zebrafish fail to maintain their position in the water, and type-II-pneumocyte-specific Fip200-deficient mice show neonatal lethality with respiratory failure. Autophagy suppression does not affect synthesis of the surfactant phospholipid, suggesting that autophagy supplies lipids and membranes to lamellar bodies. These results demonstrate an evolutionarily conserved role of autophagy in lamellar body maturation.

Keywords:  autophagy; autophagy-related gene; lamellar body; lung; lysosome-related organelle; surfactant; swim bladder

DOI:  https://doi.org/10.1016/j.celrep.2020.108477
Chin Med. 2020 Nov 23. 15(1): 123

Transcription factor EB agonists from natural products for treating human diseases with impaired autophagy-lysosome pathway.

Jie Xu, Xiao-Qi Zhang, Zaijun Zhang.

  Autophagy is a highly conserved degradation process for long-lived intracellular proteins and organelles mediated by lysosomes. Deficits in the autophagy-lysosome pathway (ALP) have been linked to a variety of human diseases, including neurodegenerative diseases, lysosomal storage disorders, and cancers. Transcription factor EB (TFEB) has been identified as a major regulator of autophagy and lysosomal biogenesis. Increasing evidence has demonstrated that TFEB activation can promote the clearance of toxic protein aggregates and regulate cellular metabolism. Traditional Chinese medicine (TCM)-derived natural products as important sources for drug discovery have been widely used for the treatment of various diseases associated with ALP dysfunction. Herein, we review (1) the regulation of TFEB and ALP; (2) TFEB and ALP dysregulation in human diseases; (3) TFEB activators from natural products and their potential uses.

Keywords:  Autophagy; Autophagy-lysosome pathway; Natural products; TFEB; TFEB agonists

DOI:  https://doi.org/10.1186/s13020-020-00402-1
Autophagy. 2020 Dec 06.

RNF186 regulates EFNB1 (ephrin B1)-EPHB2-induced autophagy in the colonic epithelial cells for the maintenance of intestinal homeostasis.

Huazhi Zhang, Zhihui Cui, Du Cheng, Yanyun Du, Xiaoli Guo, Ru Gao, Jianwen Chen, Wanwei Sun, Ruirui He, Xiaojian Ma, Qianwen Peng, Bradley N Martin, Wei Yan, Yueguang Rong, Chenhui Wang.

  Although genome-wide association studies have identified the gene RNF186 encoding an E3 ubiquitin-protein ligase as conferring susceptibility to ulcerative colitis, the exact function of this protein remains unclear. In the present study, we demonstrate an important role for RNF186 in macroautophagy/autophagy activation in colonic epithelial cells and intestinal homeostasis. Mechanistically, RNF186 acts as an E3 ubiquitin-protein ligase for EPHB2 and regulates the ubiquitination of EPHB2. Upon stimulation by ligand EFNB1 (ephrin B1), EPHB2 is ubiquitinated by RNF186 at Lys892, and further recruits MAP1LC3B for autophagy. Compared to control mice, rnf186-/- and ephb2-/- mice have a more severe phenotype in the DSS-induced colitis model, which is due to a defect in autophagy in colon epithelial cells. More importantly, treatment with ephrin-B1-Fc recombinant protein effectively relieves DSS-induced mouse colitis, which suggests that ephrin-B1-Fc may be a potential therapy for human inflammatory bowel diseases.

Keywords:  Autophagy; EPHB2; RNF186; ephrin B1; ulcerative colitis

DOI:  https://doi.org/10.1080/15548627.2020.1851496
Autophagy. 2020 Dec 07. 1-20

Autophagy alleviates hypoxia-induced blood-brain barrier injury via regulation of CLDN5 (claudin 5).

Zhenguo Yang, Panpan Lin, Bing Chen, Xiaoqi Zhang, Wei Xiao, Shuilong Wu, Chunnian Huang, Du Feng, Wenqing Zhang, Jingjing Zhang.

  Blood-brain barrier (BBB) disruption is a key event in triggering secondary damage to the central nervous system (CNS) under stroke, and is frequently associated with abnormal macroautophagy/autophagy in brain microvascular endothelial cells (BMECs). However, the underlying mechanism of autophagy in maintaining BBB integrity remains unclear. Here we report that in BMECs of patients suffering stroke, CLDN5 (claudin 5) abnormally aggregates in the cytosol accompanied by autophagy activation. In vivo zebrafish and in vitro cell studies reveal that BBB breakdown is partially caused by CAV1 (caveolin 1)-mediated redistribution of membranous CLDN5 into the cytosol under hypoxia. Meanwhile, autophagy is activated and contributes mainly to the degradation of CAV1 and aggregated CLDN5 in the cytosol of BMECs, therefore alleviating BBB breakdown. Blockage of autophagy by genetic methods or chemicals aggravates cytosolic aggregation of CLDN5, resulting in severer BBB impairment. These data demonstrate that autophagy functions in the protection of BBB integrity by regulating CLDN5 redistribution and provide a potential therapeutic strategy for BBB disorder-related cerebrovascular disease. Abbreviations: BBB: blood-brain barrier; BECN1: beclin 1; BMEC: brain microvascular endothelial cell; CAV1: caveolin 1; CCA: common carotid artery; CLDN5: claudin 5; CNS: central nervous system; CQ: chloroquine; HIF1A: hypoxia inducible factor 1 subunit alpha; MCAO: middle cerebral artery occlusion-reperfusion; OCLN: occludin; ROS: reactive oxygen species; STED: stimulated emission depletion; TEER: trans-endothelial electrical resistance; TEM: transmission electron microscopy; TJ: tight junction; TJP1: tight junction protein 1; UPS: ubiquitin-proteasome system.

Keywords:  Autophagy; blood-brain barrier; claudin 5; hypoxia; zebrafish

DOI:  https://doi.org/10.1080/15548627.2020.1851897
J Mol Biol. 2020 Dec 08. pii: S0022-2836(20)30668-9. [Epub ahead of print] 166743

Architecture of the Tuberous Sclerosis Protein Complex.

Kailash Ramlaul, Wencheng Fu, Hua Li, Natàlia de Martin Garrido, Lin He, Manjari Trivedi, Wei Cui, Christopher H S Aylett, Geng Wu.

  The Tuberous Sclerosis Complex (TSC) protein complex (TSCC), comprising TSC1, TSC2, and TBC1D7, is widely recognised as a key integration hub for cell growth and intracellular stress signals upstream of the mammalian target of rapamycin complex 1 (mTORC1). The TSCC negatively regulates mTORC1 by acting as a GTPase-activating protein (GAP) towards the small GTPase Rheb. Both human TSC1 and TSC2 are important tumour suppressors, and mutations in them underlie the disease tuberous sclerosis. We used single-particle cryo-EM to reveal the organisation and architecture of the complete human TSCC. We show that TSCC forms an elongated scorpion-like structure, consisting of a central "body", with a "pincer" and a "tail" at the respective ends. The "body" is composed of a flexible TSC2 HEAT repeat dimer, along the surface of which runs the TSC1 coiled-coil backbone, breaking the symmetry of the dimer. Each end of the body is structurally distinct, representing the N- and C-termini of TSC1; a "pincer" is formed by the highly flexible N-terminal TSC1 core domains and a barbed "tail" makes up the TSC1 coiled-coil-TBC1D7 junction. The TSC2 GAP domain is found abutting the centre of the body on each side of the dimerisation interface, poised to bind a pair of Rheb molecules at a similar separation to the pair in activated mTORC1. Our architectural dissection reveals the mode of association and topology of the complex, casts light on the recruitment of Rheb to the TSCC, and also hints at functional higher order oligomerisation, which has previously been predicted to be important for Rheb-signalling suppression.

Keywords:  Cryo-EM; Hamartin; RapGAP; Tuberin; Tuberous sclerosis complex

DOI:  https://doi.org/10.1016/j.jmb.2020.166743
Clin Chim Acta. 2020 Dec 03. pii: S0009-8981(20)30553-2. [Epub ahead of print]

Caveolin-1 in autophagy: a potential therapeutic target in atherosclerosis.

Kai Hou, Shuai Li, Meng Zhang, Xuping Qin.

  Caveolin-1 is considered an important pathophysiological factor in atherosclerosis development. Previous studies indicate that caveolin-1 exhibits a pathogenic capacity in atherosclerosis via the regulation of membrane trafficking, cholesterol metabolism and cellular signal transduction. Accumulating evidence shows that autophagy activation influences the progression and development of atherosclerosis in multiple ways, including cholesterol metabolism, inflammatory responses and lipid transcytosis. However, how caveolin-1 is involved in autophagy activation in atherosclerosis remains unclear, and the precise mechanisms of caveolin-1 on autophagic flux in atherosclerosis need to be further investigated. Clarifying the roles and mechanisms of caveolin-1 in the regulation of autophagy activation is of great importance, contributing to the ability to manipulate caveolin-1 as a novel therapeutic approach for atherosclerosis. In this review, we summarize the understanding of the molecular structure, biological roles and biochemical functions of caveolin-1 to date and discuss the roles and mechanisms of caveolin-1 in autophagy activation. The emphasis on the potential of caveolin-1 to be a novel therapeutic target in atherosclerosis and understanding its precise functions and exact mechanisms in autophagic flux will provide evidence for future experimental research and aid in the development of novel therapeutic strategies for atherosclerosis.

Keywords:  Atherosclerosis; Autophagy; Caveolin-1; Inflammatory response; Lipid metabolism

DOI:  https://doi.org/10.1016/j.cca.2020.11.020
Autophagy. 2020 Dec 07. 1-2

Autophagy repurposes cells during paligenosis.

Zhi-Feng Miao, Charles J Cho, Zhen-Ning Wang, Jason C Mills.

  Differentiated cells have evolved paligenosis, a conserved program to return to a stem or progenitor state and reenter the cell cycle to fuel tissue repair. Paligenosis comprises three sequential stages: 1) quenching of MTORC1 activity with induction of massive macroautophagy/autophagy that remodels differentiated cell architecture; 2) induced expression of progenitor/repair-associated genes; 3) MTORC1 reactivation with cell cycle reentry. Here, we summarize work showing that evolutionarily conserved genes - Ddit4 and Ifrd1 - are critical regulators of paligenosis. DDIT4 suppresses MTORC1 function to induce lysosomes and autophagosomes in paligenosis stage 1. As DDIT4 decreases during paligenosis, TRP53 continues MTORC1 suppression until cells are licensed to reenter the cell cycle by IFRD1 suppression of TRP53. Cells with DNA damage maintain TRP53 until either the damage is repaired, or they undergo apoptosis. The concept of paligenosis and identification of paligenosis-dedicated genes may provide new angles to harness tissue regeneration and specifically target tumor cells.

Keywords:  Acinar-ductal metaplasia (ADM); dedifferentiation; progenitor cell; regeneration; spasmolytic polypeptide-expressing metaplasia (SPEM); tumorigenesis

DOI:  https://doi.org/10.1080/15548627.2020.1857080
Mol Cell Endocrinol. 2020 Dec 04. pii: S0303-7207(20)30410-X. [Epub ahead of print] 111108

REV-ERBα alters circadian rhythms by modulating mTOR signaling.

Dadon-Freiberg Maayan, Nava Chapnik, Oren Froy.

  REV-ERBα is a nuclear receptor that inhibits Bmal1 transcription as part of the circadian clock molecular mechanism. Mammalian target of rapamycin (mTOR) complex 1 (mTORC1) is a master regulator of cell and whole-body energy homeostasis, that serves as an important link between metabolism and circadian clock, in part, by regulating BMAL1 activity. While the connection of REV-ERBα to the circadian clock molecular mechanism is well characterized, the interaction between mTORC1, REV-ERBα and the circadian clock machinery is not very clear. We used leucine and rapamycin to modulate mTORC1 activation and evaluate this effect on circadian rhythms. In the liver, mTORC1 was inhibited by leucine. REV-ERBα overexpression activated the mTORC1 signaling pathway via transcription inhibition of mTORC1 inhibitor, Tsc1, antagonizing the effect of leucine, while its silencing downregulated mTORC1 signaling. Activation of mTORC1 led to increased levels of BMAL1 phosphorylation. Activation as well as inhibition of mTORC1 led to altered circadian rhythms in mouse muscle. Inhibition of liver mTORC1 by leucine or rapamycin led to low-amplitude circadian rhythms. In summary, our study shows that leucine inhibits liver mTORC1 pathway leading to dampened circadian rhythms. REV-ERBα activates the mTORC1 pathway, leading to phosphorylation of the clock protein BMAL1.

Keywords:  REV-ERB; circadian; clock; leucine; liver; mTOR

DOI:  https://doi.org/10.1016/j.mce.2020.111108
Dev Cell. 2020 Dec 07. pii: S1534-5807(20)30880-7. [Epub ahead of print]55(5): 517-519

Out of Phase: How IPMK Inhibits TFEB.

Luca Ferrari, Sascha Martens.

The expression of autophagy and lysosomal genes is coordinated by the transcription factor EB (TFEB). In this issue of Developmental Cell, Chen et al. identify an evolutionary conserved mode of TFEB regulation, which entails the inhibition of TFEB phase separation in the nucleus by inositol polyphosphate multikinase.

DOI: https://doi.org/10.1016/j.devcel.2020.11.005
Autophagy. 2020 Dec 10.

A genome-wide RNA interference screen disentangles the Golgi tropism of LC3.

Giulia Cerrato, Oliver Kepp, Allan Sauvat, Guido Kroemer.

  Oleate, the most abundantly occurring cis-unsaturated fatty acid, has the particularity to induce the accumulation of MAP1LC3B/LC3 (microtubule associated protein 1 light chain 3 beta) at the trans-Golgi apparatus. A genome-wide RNA interference screen designed to identify the mechanisms of this LC3 redistribution led to the identification of a BECN1-PIK3C3-independent pathway that, however, requires the ATG12-ATG5 and ATG7-dependent conjugation system, and several genes/proteins involved in endoplasmic reticulum (ER)-to-Golgi anterograde protein transport, as well as the unfolded protein response, including the integrated stress response that results in the phosphorylation of EIF2A/eIF2α (eukaryotic translation initiation factor 2A). Functional experiments revealed that oleate blocks conventional protein secretion, stalling the process at the level of the trans-Golgi network. Oleate-induced blockade of protein secretion occurred even after depletion of ATG5, suggesting that it does not rely on the recruitment of LC3 to the Golgi apparatus (which does require ATG5). Rather, it appears that oleate and other pharmacological inhibitors of protein secretion with a similar mode of action provoke a perturbation of the trans-Golgi compartment that secondarily results in the local enrichment of LC3.

Keywords:  autophagy; fatty acids; oleate; protein secretion; unfolded protein response

DOI:  https://doi.org/10.1080/15548627.2020.1861836
J Neurosci. 2020 Dec 10. pii: JN-RM-0969-20. [Epub ahead of print]

The BAD-BAX-caspase-3 cascade modulates synaptic vesicle pools via autophagy.

Qinhua Gu, Song Jiao, Kaizheng Duan, Ya-Xian Wang, Ronald S Petralia, Zheng Li.

The BAD-BAX-caspase-3 cascade is a canonical apoptosis pathway. Macroautophagy ('autophagy' hereinafter) is a process by which organelles and aggregated proteins are delivered to lysosomes for degradation. Here, we report a new function of the BAD-BAX-caspase-3 cascade and autophagy in the control of synaptic vesicle pools. We found that in hippocampal neurons of male mice, the BAD-BAX-caspase-3 pathway regulates autophagy, which in turn limits the size of synaptic vesicle pools and influences the kinetics of activity-induced depletion and recovery of synaptic vesicle pools. Moreover, the caspase-autophagy pathway is engaged by fear conditioning to facilitate associative fear learning and memory. This work identifies a new mechanism for controlling synaptic vesicle pools, and a novel, non-apoptotic, presynaptic function of the BAD-BAX-caspase-3 cascade.SIGNIFICANCE STATEMENT:Despite the importance of synaptic vesicles for neurons, little is known about how the size of synaptic vesicle pools is maintained under basal conditions and regulated by neural activity. This study identifies a new mechanism for the control of synaptic vesicle pools, and a new, non-apoptotic function of the BAD-BAX-caspase-3 pathway in presynaptic terminals. Additionally, it indicates that autophagy is not only a homeostatic mechanism to maintain the integrity of cells and tissues, but also a process engaged by neural activity to regulate synaptic vesicle pools for optimal synaptic responses, learning, and memory.

DOI: https://doi.org/10.1523/JNEUROSCI.0969-20.2020
Structure. 2020 Dec 07. pii: S0969-2126(20)30426-3. [Epub ahead of print]

A Conformational Change in the N Terminus of SLC38A9 Signals mTORC1 Activation.

Hsiang-Ting Lei, Xuelang Mu, Johan Hattne, Tamir Gonen.

  mTORC1 is a central hub that integrates environmental cues, such as cellular stresses and nutrient availability to modulate metabolism and cellular responses. Recently, SLC38A9, a lysosomal amino acid transporter, emerged as a sensor for luminal arginine and as an activator of mTORC1. The amino acid-mediated activation of mTORC1 is regulated by the N-terminal domain of SLC38A9. Here, we determined the crystal structure of zebrafish SLC38A9 (drSLC38A9) and found the N-terminal fragment inserted deep within the transporter, bound in the substrate-binding pocket where normally arginine would bind. This represents a significant conformational change of the N-terminal domain (N-plug) when compared with our recent arginine-bound structure of drSLC38A9. We propose a ball-and-chain model for mTORC1 activation, where N-plug insertion and Rag GTPase binding with SLC38A9 is regulated by luminal arginine levels. This work provides important insights into nutrient sensing by SLC38A9 to activate the mTORC1 pathways in response to dietary amino acids.

Keywords:  SLC38A9; arginine transport; crystallography; mTORC1

DOI:  https://doi.org/10.1016/j.str.2020.11.014
Int J Mol Sci. 2020 Dec 03. pii: E9210. [Epub ahead of print]21(23):

Regulation of Beclin 1-Mediated Autophagy by Oncogenic Tyrosine Kinases.

Silvia Vega-Rubín-de-Celis, Lisa Kinch, Samuel Peña-Llopis.

  Beclin 1 is a major regulator of autophagy, and it is a core component of the class III PI3K complexes. Beclin 1 is a highly conserved protein and its function is regulated in a number of ways, including post-translational modifications. Several studies indicate that receptor and non-receptor tyrosine kinases regulate autophagy activity in cancer, and some suggest the importance of Beclin 1 tyrosine phosphorylation in this process. Here we summarize the current knowledge of the mechanism whereby some oncogenic tyrosine kinases regulate autophagy through Beclin 1.

Keywords:  Beclin 1; autophagy; cancer; tyrosine kinases

DOI:  https://doi.org/10.3390/ijms21239210
Elife. 2020 Dec 10. pii: e59419. [Epub ahead of print]9

TFEB/Mitf links impaired nuclear import to autophagolysosomal dysfunction in C9-ALS.

Kathleen M Cunningham, Kirstin Maulding, Kai Ruan, Mumine Senturk, Jonathan C Grima, Hyun Sung, Zhongyuan Zuo, Helen Song, Junli Gao, Sandeep Dubey, Jeffrey D Rothstein, Ke Zhang, Hugo J Bellen, Thomas E Lloyd.

  Disrupted nucleocytoplasmic transport (NCT) has been implicated in neurodegenerative disease pathogenesis; however, the mechanisms by which disrupted NCT causes neurodegeneration remain unclear. In a Drosophila screen, we identified ref(2)P/p62, a key regulator of autophagy, as a potent suppressor of neurodegeneration caused by the GGGGCC hexanucleotide repeat expansion (G4C2 HRE) in C9orf72 that causes amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). We found that p62 is increased and forms ubiquitinated aggregates due to decreased autophagic cargo degradation. Immunofluorescence and electron microscopy of Drosophila tissues demonstrate an accumulation of lysosome-like organelles that precedes neurodegeneration. These phenotypes are partially caused by cytoplasmic mislocalization of Mitf/TFEB, a key transcriptional regulator of autophagolysosomal function. Additionally, TFEB is mislocalized and downregulated in human cells expressing GGGGCC repeats and in C9-ALS patient motor cortex. Our data suggest that the C9orf72-HRE impairs Mitf/TFEB nuclear import, thereby disrupting autophagy and exacerbating proteostasis defects in C9-ALS/FTD.

Keywords:  D. melanogaster; cell biology; neuroscience

DOI:  https://doi.org/10.7554/eLife.59419
Autophagy. 2020 Dec 08.

ATM plays antioxidant, boosting mitophagy via denitrosylation.

Claudia Cirotti, Giuseppe Filomeni.

  Mitophagy is a selective process aimed at removing damaged or burned-out mitochondria; it is activated upon different stimuli and plays a fundamental role in preventing overproduction of reactive oxygen species (ROS) that might be generated by dysfunctional mitochondria. From this angle, mitophagy can be considered a fully-fledged antioxidant process. Such a surrogate antioxidant function is recently emerging, being shared among many molecular pathways and players that are usually not included among - and, formally, do not directly act as - antioxidants. ATM (ataxia telangiectasia mutated) is a prototype of this class of "neglected" antioxidants. In spite of its well-known role in DNA damage response, many phenotypes of ataxia telangiectasia (A-T) patients are, indeed, related to chronic oxidative stress, arguing for an additional antioxidant role of ATM. In a recent study, we discovered the mechanism through which ATM exerts antioxidant activity. In particular, we provided evidence that this involves ADH5/GSNOR (alcohol dehydrogenase 5 (class III), chi polypeptide), which, in turn, sustains mitophagy via PARK2 denitrosylation, and protects the cell from detrimental effects due to ROS.

Keywords:   S-nitrosylation; ADH5; ATM; DNA damage; GSNOR; T cell; hydrogen peroxide; mitophagy; nitric oxide; oxidative stress

DOI:  https://doi.org/10.1080/15548627.2020.1860490