1
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Zou T, Xie R, Huang S, Lu D, Liu J. Potential role of modulating autophagy levels in sensorineural hearing loss. Biochem Pharmacol 2024; 222:116115. [PMID: 38460910 DOI: 10.1016/j.bcp.2024.116115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/20/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
In recent years, extensive research has been conducted on the pathogenesis of sensorineural hearing loss (SNHL). Apoptosis and necrosis have been identified to play important roles in hearing loss, but they cannot account for all hearing loss. Autophagy, a cellular process responsible for cell self-degradation and reutilization, has emerged as a significant factor contributing to hearing loss, particularly in cases of autophagy deficiency. Autophagy plays a crucial role in maintaining cell health by exerting cytoprotective and metabolically homeostatic effects in organisms. Consequently, modulating autophagy levels can profoundly impact the survival, death, and regeneration of cells in the inner ear, including hair cells (HCs) and spiral ganglion neurons (SGNs). Abnormal mitochondrial autophagy has been demonstrated in animal models of SNHL. These findings indicate the profound significance of comprehending autophagy while suggesting that our perspective on this cellular process holds promise for advancing the treatment of SNHL. Thus, this review aims to clarify the pathogenic mechanisms of SNHL and the role of autophagy in the developmental processes of various cochlear structures, including the greater epithelial ridge (GER), SGNs, and the ribbon synapse. The pathogenic mechanisms of age-related hearing loss (ARHL), also known as presbycusis, and the latest research on autophagy are also discussed. Furthermore, we underscore recent findings on the modulation of autophagy in SNHL induced by ototoxic drugs. Additionally, we suggest further research that might illuminate the complete potential of autophagy in addressing SNHL, ultimately leading to the formulation of pioneering therapeutic strategies and approaches for the treatment of deafness.
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Affiliation(s)
- Ting Zou
- Department of Otorhinolaryngology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Renwei Xie
- Department of Otorhinolaryngology, Renhe Hospital, Baoshan District, Shanghai, China
| | - Sihan Huang
- Department of Otorhinolaryngology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Dingkun Lu
- Cardiac Arrhythmia Center, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jun Liu
- Department of Otorhinolaryngology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
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2
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Zhu Q, Combs ME, Bowles DE, Gross RT, Mendiola Pla M, Mack CP, Taylor JM. GRAF1 Acts as a Downstream Mediator of Parkin to Regulate Mitophagy in Cardiomyocytes. Cells 2024; 13:448. [PMID: 38474413 PMCID: PMC10930636 DOI: 10.3390/cells13050448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
Cardiomyocytes rely on proper mitochondrial homeostasis to maintain contractility and achieve optimal cardiac performance. Mitochondrial homeostasis is controlled by mitochondrial fission, fusion, and mitochondrial autophagy (mitophagy). Mitophagy plays a particularly important role in promoting the degradation of dysfunctional mitochondria in terminally differentiated cells. However, the precise mechanisms by which this is achieved in cardiomyocytes remain opaque. Our study identifies GRAF1 as an important mediator in PINK1-Parkin pathway-dependent mitophagy. Depletion of GRAF1 (Arhgap26) in cardiomyocytes results in actin remodeling defects, suboptimal mitochondria clustering, and clearance. Mechanistically, GRAF1 promotes Parkin-LC3 complex formation and directs autophagosomes to damaged mitochondria. Herein, we found that these functions are regulated, at least in part, by the direct binding of GRAF1 to phosphoinositides (PI(3)P, PI(4)P, and PI(5)P) on autophagosomes. In addition, PINK1-dependent phosphorylation of Parkin promotes Parkin-GRAF1-LC3 complex formation, and PINK1-dependent phosphorylation of GRAF1 (on S668 and S671) facilitates the clustering and clearance of mitochondria. Herein, we developed new phosphor-specific antibodies to these sites and showed that these post-translational modifications are differentially modified in human hypertrophic cardiomyopathy and dilated cardiomyopathy. Furthermore, our metabolic studies using serum collected from isoproterenol-treated WT and GRAF1CKO mice revealed defects in mitophagy-dependent cardiomyocyte fuel flexibility that have widespread impacts on systemic metabolism. In summary, our study reveals that GRAF1 co-regulates actin and membrane dynamics to promote cardiomyocyte mitophagy and that dysregulation of GRAF1 post-translational modifications may underlie cardiac disease pathogenesis.
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Affiliation(s)
- Qiang Zhu
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (Q.Z.); (M.E.C.); (C.P.M.)
| | - Matthew E. Combs
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (Q.Z.); (M.E.C.); (C.P.M.)
| | - Dawn E. Bowles
- Division of Surgical Sciences, Duke University Medical Center, Durham, NC 27710, USA; (D.E.B.); (R.T.G.); (M.M.P.)
| | - Ryan T. Gross
- Division of Surgical Sciences, Duke University Medical Center, Durham, NC 27710, USA; (D.E.B.); (R.T.G.); (M.M.P.)
| | - Michelle Mendiola Pla
- Division of Surgical Sciences, Duke University Medical Center, Durham, NC 27710, USA; (D.E.B.); (R.T.G.); (M.M.P.)
| | - Christopher P. Mack
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (Q.Z.); (M.E.C.); (C.P.M.)
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Joan M. Taylor
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; (Q.Z.); (M.E.C.); (C.P.M.)
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599, USA
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3
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Pareek G, Kundu M. Physiological functions of ULK1/2. J Mol Biol 2024:168472. [PMID: 38311233 DOI: 10.1016/j.jmb.2024.168472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
UNC-51-like kinases 1 and 2 (ULK1/2) are serine/threonine kinases that are best known for their evolutionarily conserved role in the autophagy pathway. Upon sensing the nutrient status of a cell, ULK1/2 integrate signals from upstream cellular energy sensors such as mTOR and AMPK and relay them to the downstream components of the autophagy machinery. ULK1/2 also play indispensable roles in the selective autophagy pathway, removing damaged mitochondria, invading pathogens, and toxic protein aggregates. Additional functions of ULK1/2 have emerged beyond autophagy, including roles in protein trafficking, RNP granule dynamics, and signaling events impacting innate immunity, axon guidance, cellular homeostasis, and cell fate. Therefore, it is no surprise that alterations in ULK1/2 expression and activity have been linked with pathophysiological processes, including cancer, neurological disorders, and cardiovascular diseases. Growing evidence suggests that ULK1/2 function as biological rheostats, tuning cellular functions to intra and extra-cellular cues. Given their broad physiological relevance, ULK1/2 are candidate targets for small molecule activators or inhibitors that may pave the way for the development of therapeutics for the treatment of diseases in humans.
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Affiliation(s)
- Gautam Pareek
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mondira Kundu
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, TN, USA.
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4
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Hanley SE, Willis SD, Doyle SJ, Strich R, Cooper KF. Ksp1 is an autophagic receptor protein for the Snx4-assisted autophagy of Ssn2/Med13. Autophagy 2024; 20:397-415. [PMID: 37733395 PMCID: PMC10813586 DOI: 10.1080/15548627.2023.2259708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023] Open
Abstract
Ksp1 is a casein II-like kinase whose activity prevents aberrant macroautophagy/autophagy induction in nutrient-rich conditions in yeast. Here, we describe a kinase-independent role of Ksp1 as a novel autophagic receptor protein for Ssn2/Med13, a known cargo of Snx4-assisted autophagy of transcription factors. In this pathway, a subset of conserved transcriptional regulators, Ssn2/Med13, Rim15, and Msn2, are selectively targeted for vacuolar proteolysis following nitrogen starvation, assisted by the sorting nexin heterodimer Snx4-Atg20. Here we show that phagophores also engulf Ksp1 alongside its cargo for vacuolar proteolysis. Ksp1 directly associates with Atg8 following nitrogen starvation at the interface of an Atg8-family interacting motif (AIM)/LC3-interacting region (LIR) in Ksp1 and the LIR/AIM docking site (LDS) in Atg8. Mutating the LDS site prevents the autophagic degradation of Ksp1. However, deletion of the C terminal canonical AIM still permitted Ssn2/Med13 proteolysis, suggesting that additional non-canonical AIMs may mediate the Ksp1-Atg8 interaction. Ksp1 is recruited to the perivacuolar phagophore assembly site by Atg29, a member of the trimeric scaffold complex. This interaction is independent of Atg8 and Snx4, suggesting that Ksp1 is recruited early to phagophores, with Snx4 delivering Ssn2/Med13 thereafter. Finally, normal cell survival following prolonged nitrogen starvation requires Ksp1. Together, these studies define a kinase-independent role for Ksp1 as an autophagic receptor protein mediating Ssn2/Med13 degradation. They also suggest that phagophores built by the trimeric scaffold complex are capable of receptor-mediated autophagy. These results demonstrate the dual functionality of Ksp1, whose kinase activity prevents autophagy while it plays a scaffolding role supporting autophagic degradation.Abbreviations: 3-AT: 3-aminotriazole; 17C: Atg17-Atg31-Atg29 trimeric scaffold complex; AIM: Atg8-family interacting motif; ATG: autophagy related; CKM: CDK8 kinase module; Cvt: cytoplasm-to-vacuole targeting; IDR: intrinsically disordered region; LIR: LC3-interacting region; LDS: LIR/AIM docking site; MoRF: molecular recognition feature; NPC: nuclear pore complex; PAS: phagophore assembly site; PKA: protein kinase A; RBP: RNA-binding protein; UPS: ubiquitin-proteasome system. SAA-TF: Snx4-assisted autophagy of transcription factors; Y2H: yeast two-hybrid.
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Affiliation(s)
- Sara E. Hanley
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering & Sciences, Rowan University, Stratford, NJ, USA
| | - Stephen D. Willis
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering & Sciences, Rowan University, Stratford, NJ, USA
| | - Steven J. Doyle
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering & Sciences, Rowan University, Stratford, NJ, USA
- School of Osteopathic Medicine, Rowan University, Stratford, NJ, USA
| | - Randy Strich
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering & Sciences, Rowan University, Stratford, NJ, USA
| | - Katrina F. Cooper
- Department of Molecular Biology, Rowan-Virtua School of Translational Biomedical Engineering & Sciences, Rowan University, Stratford, NJ, USA
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5
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Xiong Y, Cui MY, Li ZL, Fu YQ, Zheng Y, Yu Y, Zhang C, Huang XY, Chen BH. ULK1 confers neuroprotection by regulating microglial/macrophages activation after ischemic stroke. Int Immunopharmacol 2024; 127:111379. [PMID: 38141409 DOI: 10.1016/j.intimp.2023.111379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/28/2023] [Accepted: 12/11/2023] [Indexed: 12/25/2023]
Abstract
Microglial activation and autophagy play a critical role in the progression of ischemic stroke and contribute to the regulation of neuroinflammation. Unc-51-like kinase 1 (ULK1) is the primary autophagy kinase involved in autophagosome formation. However, the impact of ULK1 on neuroprotection and microglial activation after ischemic stroke remains unclear. In this study, we established a photothrombotic stroke model, and administered SBI-0206965 (SBI), an ULK1 inhibitor, and LYN-1604 hydrochloride (LYN), an ULK1 agonist, to modulate ULK1 activity in vivo. We assessed sensorimotor deficits, neuronal apoptosis, and microglial/macrophage activation to evaluate the neurofunctional outcome. Immunofluorescence results revealed ULK1 was primarily localized in the microglia of the infarct area following ischemia. Upregulating ULK1 through LYN treatment significantly reduced infarct volume, improved motor function, promoted the increase of anti-inflammatory microglia. In conclusion, ULK1 facilitated neuronal repair and promoted the formation of anti-inflammatory microglia pathway after ischemic injury.
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Affiliation(s)
- Ye Xiong
- Department of Neurosurgery, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Mai Yin Cui
- Department of Histology and Embryology, Institute of Neuroscience, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China; Department of Rehabilitation and Traditional Chinese Medicine, the Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310051, Zhejiang, China
| | - Zhuo Li Li
- Department of Histology and Embryology, Institute of Neuroscience, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Yan Qiong Fu
- Department of Histology and Embryology, Institute of Neuroscience, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Yu Zheng
- Department of Histology and Embryology, Institute of Neuroscience, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Yi Yu
- Institute of Stomatology, School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Chan Zhang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Xin Yi Huang
- Department of Histology and Embryology, Institute of Neuroscience, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Bai Hui Chen
- Department of Histology and Embryology, Institute of Neuroscience, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China.
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6
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Nguyen A, Faesen AC. The role of the HORMA domain proteins ATG13 and ATG101 in initiating autophagosome biogenesis. FEBS Lett 2024; 598:114-126. [PMID: 37567770 DOI: 10.1002/1873-3468.14717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023]
Abstract
Autophagy is a process of regulated degradation. It eliminates damaged and unnecessary cellular components by engulfing them with a de novo-generated organelle: the double-membrane autophagosome. The past three decades have provided us with a detailed parts list of the autophagy initiation machinery, have developed important insights into how these processes function and have identified regulatory proteins. It is now clear that autophagosome biogenesis requires the timely assembly of a complex machinery. However, it is unclear how a putative stable machine is assembled and disassembled and how the different parts cooperate to perform its overall function. Although they have long been somewhat enigmatic in their precise role, HORMA domain proteins (first identified in Hop1p, Rev7p and MAD2 proteins) autophagy-related protein 13 (ATG13) and ATG101 of the ULK-kinase complex have emerged as important coordinators of the autophagy-initiating subcomplexes. Here, we will particularly focus on ATG13 and ATG101 and the role of their unusual metamorphosis in initiating autophagosome biogenesis. We will also explore how this metamorphosis could potentially be purposefully rate-limiting and speculate on how it could regulate the spontaneous self-assembly of the autophagy-initiating machinery.
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Affiliation(s)
- Anh Nguyen
- Laboratory of Biochemistry of Signal Dynamics, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Alex C Faesen
- Laboratory of Biochemistry of Signal Dynamics, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
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7
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Rogov VV, Nezis IP, Tsapras P, Zhang H, Dagdas Y, Noda NN, Nakatogawa H, Wirth M, Mouilleron S, McEwan DG, Behrends C, Deretic V, Elazar Z, Tooze SA, Dikic I, Lamark T, Johansen T. Atg8 family proteins, LIR/AIM motifs and other interaction modes. AUTOPHAGY REPORTS 2023; 2:27694127.2023.2188523. [PMID: 38214012 PMCID: PMC7615515 DOI: 10.1080/27694127.2023.2188523] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
The Atg8 family of ubiquitin-like proteins play pivotal roles in autophagy and other processes involving vesicle fusion and transport where the lysosome/vacuole is the end station. Nuclear roles of Atg8 proteins are also emerging. Here, we review the structural and functional features of Atg8 family proteins and their protein-protein interaction modes in model organisms such as yeast, Arabidopsis, C. elegans and Drosophila to humans. Although varying in number of homologs, from one in yeast to seven in humans, and more than ten in some plants, there is a strong evolutionary conservation of structural features and interaction modes. The most prominent interaction mode is between the LC3 interacting region (LIR), also called Atg8 interacting motif (AIM), binding to the LIR docking site (LDS) in Atg8 homologs. There are variants of these motifs like "half-LIRs" and helical LIRs. We discuss details of the binding modes and how selectivity is achieved as well as the role of multivalent LIR-LDS interactions in selective autophagy. A number of LIR-LDS interactions are known to be regulated by phosphorylation. New methods to predict LIR motifs in proteins have emerged that will aid in discovery and analyses. There are also other interaction surfaces than the LDS becoming known where we presently lack detailed structural information, like the N-terminal arm region and the UIM-docking site (UDS). More interaction modes are likely to be discovered in future studies.
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Affiliation(s)
- Vladimir V. Rogov
- Institute for Pharmaceutical Chemistry, Department of Biochemistry, Chemistry and Pharmacy, Goethe University, 60438 Frankfurt, am Main, and Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Ioannis P. Nezis
- School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK
| | | | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China and College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yasin Dagdas
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Nobuo N. Noda
- Institute for Genetic Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo 060-0815, Japan
| | - Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Martina Wirth
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Stephane Mouilleron
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | | | - Christian Behrends
- Munich Cluster of Systems Neurology, Ludwig-Maximilians-Universität München, München, Germany
| | - Vojo Deretic
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM and Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Zvulun Elazar
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Sharon A. Tooze
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Ivan Dikic
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt am Main, and Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Trond Lamark
- Autophagy Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Terje Johansen
- Autophagy Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
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8
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Mende H, Khatri A, Lange C, Poveda-Cuevas SA, Tascher G, Covarrubias-Pinto A, Löhr F, Koschade SE, Dikic I, Münch C, Bremm A, Brunetti L, Brandts CH, Uckelmann H, Dötsch V, Rogov VV, Bhaskara RM, Müller S. An atypical GABARAP binding module drives the pro-autophagic potential of the AML-associated NPM1c variant. Cell Rep 2023; 42:113484. [PMID: 37999976 DOI: 10.1016/j.celrep.2023.113484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/22/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
The nucleolar scaffold protein NPM1 is a multifunctional regulator of cellular homeostasis, genome integrity, and stress response. NPM1 mutations, known as NPM1c variants promoting its aberrant cytoplasmic localization, are the most frequent genetic alterations in acute myeloid leukemia (AML). A hallmark of AML cells is their dependency on elevated autophagic flux. Here, we show that NPM1 and NPM1c induce the autophagy-lysosome pathway by activating the master transcription factor TFEB, thereby coordinating the expression of lysosomal proteins and autophagy regulators. Importantly, both NPM1 and NPM1c bind to autophagy modifiers of the GABARAP subfamily through an atypical binding module preserved within its N terminus. The propensity of NPM1c to induce autophagy depends on this module, likely indicating that NPM1c exerts its pro-autophagic activity by direct engagement with GABARAPL1. Our data report a non-canonical binding mode of GABARAP family members that drives the pro-autophagic potential of NPM1c, potentially enabling therapeutic options.
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Affiliation(s)
- Hannah Mende
- Goethe University Frankfurt, Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Anshu Khatri
- Goethe University Frankfurt, Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Max-von-Laue Street 9, 60438 Frankfurt, Germany
| | - Carolin Lange
- Goethe University Frankfurt, Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany; Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences, Max-von-Laue Street 15, 60438 Frankfurt, Germany
| | - Sergio Alejandro Poveda-Cuevas
- Goethe University Frankfurt, Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany; Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences, Max-von-Laue Street 15, 60438 Frankfurt, Germany
| | - Georg Tascher
- Goethe University Frankfurt, Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Adriana Covarrubias-Pinto
- Goethe University Frankfurt, Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Frank Löhr
- Goethe University Frankfurt, Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Max-von-Laue Street 9, 60438 Frankfurt, Germany
| | - Sebastian E Koschade
- Goethe University Frankfurt, Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany; Goethe University Frankfurt, University Hospital, Department of Medicine, Hematology/Oncology, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Ivan Dikic
- Goethe University Frankfurt, Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Christian Münch
- Goethe University Frankfurt, Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Anja Bremm
- Goethe University Frankfurt, Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Lorenzo Brunetti
- Marche Polytechnic University, Department of Clinical and Molecular Sciences, Via Tronto 10, 60020 Ancona, Italy
| | - Christian H Brandts
- Goethe University Frankfurt, University Hospital, Department of Medicine, Hematology/Oncology, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Hannah Uckelmann
- Goethe University Frankfurt, University Hospital, Department of Pediatrics, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Volker Dötsch
- Goethe University Frankfurt, Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Max-von-Laue Street 9, 60438 Frankfurt, Germany
| | - Vladimir V Rogov
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue Street 15, 60438 Frankfurt, Germany; Goethe University Frankfurt, Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Max-von-Laue Street 15, 60438 Frankfurt, Germany
| | - Ramachandra M Bhaskara
- Goethe University Frankfurt, Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany; Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences, Max-von-Laue Street 15, 60438 Frankfurt, Germany.
| | - Stefan Müller
- Goethe University Frankfurt, Institute of Biochemistry II, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany.
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9
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Chatzichristofi A, Sagris V, Pallaris A, Eftychiou M, Kalvari I, Price N, Theodosiou T, Iliopoulos I, Nezis IP, Promponas VJ. LIRcentral: a manually curated online database of experimentally validated functional LIR motifs. Autophagy 2023; 19:3189-3200. [PMID: 37530436 PMCID: PMC10621281 DOI: 10.1080/15548627.2023.2235851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/06/2023] [Indexed: 08/03/2023] Open
Abstract
Several selective macroautophagy receptor and adaptor proteins bind members of the Atg8 (autophagy related 8) family using short linear motifs (SLiMs), most often referred to as Atg8-family interacting motifs (AIMs) or LC3-interacting regions (LIRs). AIM/LIR motifs have been extensively studied during the last fifteen years, since they can uncover the underlying biological mechanisms and possible substrates for this key catabolic process of eukaryotic cells. Prompted by the fact that experimental information regarding LIR motifs can be found scattered across heterogeneous literature resources, we have developed LIRcentral (https://lircentral.eu), a freely available online repository for user-friendly access to comprehensive, high-quality information regarding LIR motifs from manually curated publications. Herein, we describe the development of LIRcentral and showcase currently available data and features, along with our plans for the expansion of this resource. Information incorporated in LIRcentral is useful for accomplishing a variety of research tasks, including: (i) guiding wet biology researchers for the characterization of novel instances of LIR motifs, (ii) giving bioinformaticians/computational biologists access to high-quality LIR motifs for building novel prediction methods for LIR motifs and LIR containing proteins (LIRCPs) and (iii) performing analyses to better understand the biological importance/features of functional LIR motifs. We welcome feedback on the LIRcentral content and functionality by all interested researchers and anticipate this work to spearhead a community effort for sustaining this resource which will further promote progress in studying LIR motifs/LIRCPs.Abbreviations: AIM, Atg8-family interacting motif; Atg8, autophagy related 8; GABARAP, GABA type A receptor-associated protein; LIR, LC3-interacting region; LIRCP, LIR-containing protein; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; PMID, PubMed identifier; PPI, protein-protein interaction; SLiM, short linear motif.
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Affiliation(s)
- Agathangelos Chatzichristofi
- Division of Basic Sciences, School of Medicine, University of Crete, Heraklion, Crete, Greece
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Vasileios Sagris
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Aristos Pallaris
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Marios Eftychiou
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Ioanna Kalvari
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Nicholas Price
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Theodosios Theodosiou
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Ioannis Iliopoulos
- Division of Basic Sciences, School of Medicine, University of Crete, Heraklion, Crete, Greece
| | | | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
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10
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Ye J, Zhang J, Zhu Y, Wang L, Jiang X, Liu B, He G. Targeting autophagy and beyond: Deconvoluting the complexity of Beclin-1 from biological function to cancer therapy. Acta Pharm Sin B 2023; 13:4688-4714. [PMID: 38045051 PMCID: PMC10692397 DOI: 10.1016/j.apsb.2023.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/05/2023] [Accepted: 08/02/2023] [Indexed: 12/05/2023] Open
Abstract
Beclin-1 is the firstly-identified mammalian protein of the autophagy machinery, which functions as a molecular scaffold for the assembly of PI3KC3 (class III phosphatidylinositol 3 kinase) complex, thus controlling autophagy induction and other cellular trafficking events. Notably, there is mounting evidence establishing the implications of Beclin-1 in diverse tumorigenesis processes, including tumor suppression and progression as well as resistance to cancer therapeutics and CSC (cancer stem-like cell) maintenance. More importantly, Beclin-1 has been confirmed as a potential target for the treatment of multiple cancers. In this review, we provide a comprehensive survey of the structure, functions, and regulations of Beclin-1, and we discuss recent advances in understanding the controversial roles of Beclin-1 in oncology. Moreover, we focus on summarizing the targeted Beclin-1-regulating strategies in cancer therapy, providing novel insights into a promising strategy for regulating Beclin-1 to improve cancer therapeutics in the future.
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Affiliation(s)
- Jing Ye
- Department of Dermatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jin Zhang
- Department of Dermatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yanghui Zhu
- Department of Dermatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lian Wang
- Department of Dermatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease Related Molecular Network, Chengdu 610041, China
| | - Xian Jiang
- Department of Dermatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Bo Liu
- Department of Dermatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Gu He
- Department of Dermatology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease Related Molecular Network, Chengdu 610041, China
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11
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Nieto-Torres JL, Zaretski S, Liu T, Adams PD, Hansen M. Post-translational modifications of ATG8 proteins - an emerging mechanism of autophagy control. J Cell Sci 2023; 136:jcs259725. [PMID: 37589340 PMCID: PMC10445744 DOI: 10.1242/jcs.259725] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023] Open
Abstract
Autophagy is a recycling mechanism involved in cellular homeostasis with key implications for health and disease. The conjugation of the ATG8 family proteins, which includes LC3B (also known as MAP1LC3B), to autophagosome membranes, constitutes a hallmark of the canonical autophagy process. After ATG8 proteins are conjugated to the autophagosome membranes via lipidation, they orchestrate a plethora of protein-protein interactions that support key steps of the autophagy process. These include binding to cargo receptors to allow cargo recruitment, association with proteins implicated in autophagosome transport and autophagosome-lysosome fusion. How these diverse and critical protein-protein interactions are regulated is still not well understood. Recent reports have highlighted crucial roles for post-translational modifications of ATG8 proteins in the regulation of ATG8 functions and the autophagy process. This Review summarizes the main post-translational regulatory events discovered to date to influence the autophagy process, mostly described in mammalian cells, including ubiquitylation, acetylation, lipidation and phosphorylation, as well as their known contributions to the autophagy process, physiology and disease.
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Affiliation(s)
- Jose L. Nieto-Torres
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
- Department of Biomedical Sciences, School of Health Sciences and Veterinary, Universidad Cardenal Herrera-CEU, CEU Universities, 46113 Moncada, Spain
| | - Sviatlana Zaretski
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
| | - Tianhui Liu
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
| | - Peter D. Adams
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
| | - Malene Hansen
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
- The Buck Institute for Aging Research, Novato, CA 94945, USA
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12
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Chen J, Zhao H, Liu M, Chen L. A new perspective on the autophagic and non-autophagic functions of the GABARAP protein family: a potential therapeutic target for human diseases. Mol Cell Biochem 2023:10.1007/s11010-023-04800-5. [PMID: 37440122 DOI: 10.1007/s11010-023-04800-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/24/2023] [Indexed: 07/14/2023]
Abstract
Mammalian autophagy-related protein Atg8, including the LC3 subfamily and GABARAP subfamily. Atg8 proteins play a vital role in autophagy initiation, autophagosome formation and transport, and autophagy-lysosome fusion. GABARAP subfamily proteins (GABARAPs) share a high degree of homology with LC3 family proteins, and their unique roles are often overlooked. GABARAPs are as indispensable as LC3 in autophagy. Deletion of GABARAPs fails autophagy flux induction and autophagy lysosomal fusion, which leads to the failure of autophagy. GABARAPs are also involved in the transport of selective autophagy receptors. They are engaged in various particular autophagy processes, including mitochondrial autophagy, endoplasmic reticulum autophagy, Golgi autophagy, centrosome autophagy, and dorphagy. Furthermore, GABARAPs are closely related to the transport and delivery of the inhibitory neurotransmitter γ-GABAA and the angiotensin II AT1 receptor (AT1R), tumor growth, metastasis, and prognosis. GABARAPs also have been confirmed to be involved in various diseases, such as cancer, cardiovascular disease, and neurodegenerative diseases. In order to better understand the role and therapeutic potential of GABARAPs, this article comprehensively reviews the autophagic and non-autophagic functions of GABARAPs, as well as the research progress of the role and mechanism of GABARAPs in cancer, cardiovascular diseases and neurodegenerative diseases. It emphasizes the significance of GABARAPs in the clinical prevention and treatment of diseases, and may provide new therapeutic ideas and targets for human diseases. GABARAP and GABARAPL1 in the serum of cancer patients are positively correlated with the prognosis of patients, which can be used as a clinical biomarker, predictor and potential therapeutic target. GABARAP family proteins: autophagy and non-autophagy related functions in diseases. By Figdraw ( https://www.figdraw.com ).
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Affiliation(s)
- Jiawei Chen
- Central Laboratory of Yan'nan Hospital Affiliated to Kunming, Medical University, Key Laboratory of Cardiovascular Diseases of Yunnan Province, Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, No. 245, Renmin East Road, Kunming, 650000, Yunnan, China
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Hong Zhao
- Central Laboratory of Yan'nan Hospital Affiliated to Kunming, Medical University, Key Laboratory of Cardiovascular Diseases of Yunnan Province, Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, No. 245, Renmin East Road, Kunming, 650000, Yunnan, China
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
- School of Nursing, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Meiqing Liu
- Central Laboratory of Yan'nan Hospital Affiliated to Kunming, Medical University, Key Laboratory of Cardiovascular Diseases of Yunnan Province, Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, No. 245, Renmin East Road, Kunming, 650000, Yunnan, China.
| | - Linxi Chen
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
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13
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Vo MT, Choi CY, Choi YB. The mitophagy receptor NIX induces vIRF-1 oligomerization and interaction with GABARAPL1 for the promotion of HHV-8 reactivation-induced mitophagy. PLoS Pathog 2023; 19:e1011548. [PMID: 37459327 PMCID: PMC10374065 DOI: 10.1371/journal.ppat.1011548] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 07/27/2023] [Accepted: 07/07/2023] [Indexed: 07/28/2023] Open
Abstract
Recently, viruses have been shown to regulate selective autophagy for productive infections. For instance, human herpesvirus 8 (HHV-8), also known as Kaposi's sarcoma-associated herpesvirus (KSHV), activates selective autophagy of mitochondria, termed mitophagy, thereby inhibiting antiviral innate immune responses during lytic infection in host cells. We previously demonstrated that HHV-8 viral interferon regulatory factor 1 (vIRF-1) plays a crucial role in lytic replication-activated mitophagy by interacting with cellular mitophagic proteins, including NIX and TUFM. However, the precise molecular mechanisms by which these interactions lead to mitophagy activation remain to be determined. Here, we show that vIRF-1 binds directly to mammalian autophagy-related gene 8 (ATG8) proteins, preferentially GABARAPL1 in infected cells, in an LC3-interacting region (LIR)-independent manner. Accordingly, we identified key residues in vIRF-1 and GABARAPL1 required for mutual interaction and demonstrated that the interaction is essential for mitophagy activation and HHV-8 productive replication. Interestingly, the mitophagy receptor NIX promotes vIRF-1-GABARAPL1 interaction, and NIX/vIRF-1-induced mitophagy is significantly inhibited in GABARAPL1-deficient cells. Moreover, a vIRF-1 variant defective in GABARAPL1 binding substantially loses the ability to induce vIRF-1/NIX-induced mitophagy. These results suggest that NIX supports vIRF-1 activity as a mitophagy mediator. In addition, we found that NIX promotes vIRF-1 aggregation and stabilizes aggregated vIRF-1. Together, these findings indicate that vIRF-1 plays a role as a viral mitophagy mediator that can be activated by a cellular mitophagy receptor.
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Affiliation(s)
- Mai Tram Vo
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Chang-Yong Choi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Young Bong Choi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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14
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Yang S, Nie T, She H, Tao K, Lu F, Hu Y, Huang L, Zhu L, Feng D, He D, Qi J, Kukar T, Ma L, Mao Z, Yang Q. Regulation of TFEB nuclear localization by HSP90AA1 promotes autophagy and longevity. Autophagy 2023; 19:822-838. [PMID: 35941759 PMCID: PMC9980472 DOI: 10.1080/15548627.2022.2105561] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/02/2022] Open
Abstract
TFEB (transcription factor EB) regulates multiple genes involved in the process of macroautophagy/autophagy and plays a critical role in lifespan determination. However, the detailed mechanisms that regulate TFEB activity are not fully clear. In this study, we identified a role for HSP90AA1 in modulating TFEB. HSP90AA1 was phosphorylated by CDK5 at Ser 595 under basal condition. This phosphorylation inhibited HSP90AA1, disrupted its binding to TFEB, and impeded TFEB's nuclear localization and subsequent autophagy induction. Pro-autophagy signaling attenuated CDK5 activity and enhanced TFEB function in an HSP90AA1-dependent manner. Inhibition of HSP90AA1 function or decrease in its expression significantly attenuated TFEB's nuclear localization and transcriptional function following autophagy induction. HSP90AA1-mediated regulation of a TFEB ortholog was involved in the extended lifespan of Caenorhabditis elegans in the absence of its food source bacteria. Collectively, these findings reveal that this regulatory process plays an important role in modulation of TFEB, autophagy, and longevity.Abbreviations : AL: autolysosome; AP: autophagosome; ATG: autophagy related; BafA1: bafilomycin A1; CDK5: cyclin-dependent kinase 5; CDK5R1: cyclin dependent kinase 5 regulatory subunit 1; CR: calorie restriction; FUDR: 5-fluorodeoxyuridine; HSP90AA1: heat shock protein 90 alpha family class A member 1; MAP1LC3: microtubule associated protein 1 light chain 3; NB: novobiocin sodium; SQSTM1: sequestosome 1; TFEB: transcription factor EB; WT: wild type.
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Affiliation(s)
- Shaosong Yang
- Department of Experimental Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing, China
| | - Tiejian Nie
- Department of Experimental Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Hua She
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Kai Tao
- Department of Experimental Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Fangfang Lu
- Department of Experimental Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Yiman Hu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lu Huang
- Department of Experimental Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Lin Zhu
- Department of Experimental Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Dayun Feng
- Department of Experimental Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Dan He
- Department of Experimental Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Jing Qi
- Department of Experimental Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Thomas Kukar
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Long Ma
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zixu Mao
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Qian Yang
- Department of Experimental Surgery, Tangdu Hospital, the Fourth Military Medical University, Xi’an, Shaanxi, China
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15
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Zhen Y, Stenmark H. Autophagosome Biogenesis. Cells 2023; 12:cells12040668. [PMID: 36831335 PMCID: PMC9954227 DOI: 10.3390/cells12040668] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Autophagy-the lysosomal degradation of cytoplasm-plays a central role in cellular homeostasis and protects cells from potentially harmful agents that may accumulate in the cytoplasm, including pathogens, protein aggregates, and dysfunctional organelles. This process is initiated by the formation of a phagophore membrane, which wraps around a portion of cytoplasm or cargo and closes to form a double-membrane autophagosome. Upon the fusion of the autophagosome with a lysosome, the sequestered material is degraded by lysosomal hydrolases in the resulting autolysosome. Several alternative membrane sources of autophagosomes have been proposed, including the plasma membrane, endosomes, mitochondria, endoplasmic reticulum, lipid droplets, hybrid organelles, and de novo synthesis. Here, we review recent progress in our understanding of how the autophagosome is formed and highlight the proposed role of vesicles that contain the lipid scramblase ATG9 as potential seeds for phagophore biogenesis. We also discuss how the phagophore is sealed by the action of the endosomal sorting complex required for transport (ESCRT) proteins.
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Affiliation(s)
- Yan Zhen
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Montebello, N-0379 Oslo, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, N-0379 Oslo, Norway
- Correspondence: (Y.Z.); (H.S.); Tel.: +47-22781911 (Y.Z.); +47-22781818 (H.S.)
| | - Harald Stenmark
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Montebello, N-0379 Oslo, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, N-0379 Oslo, Norway
- Correspondence: (Y.Z.); (H.S.); Tel.: +47-22781911 (Y.Z.); +47-22781818 (H.S.)
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16
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Schwalm MP, Knapp S, Rogov VV. Toward effective Atg8-based ATTECs: Approaches and perspectives. J Cell Biochem 2023. [PMID: 36780422 DOI: 10.1002/jcb.30380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/15/2023]
Abstract
Induction of Atg8-family protein (LC3/GABARAP proteins in human) interactions with target proteins of interest by proximity-inducing small molecules offers the possibility for novel targeted protein degradation approaches. However, despite intensive screening campaigns during the last 5 years, no potent ligands for LC3/GABARAPs have been developed, rendering this approach largely unexplored and unsuitable for therapeutic exploitation. In this Viewpoint, we analyze the reported attempts identifying LC3/GABARAP inhibitors and provide our own point of view why no potent inhibitors have been found. Additionally, we designate reasonable directions for the identification of potent and probably selective LC3/GABARAP inhibitors for alternative therapeutic applications.
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Affiliation(s)
- Martin P Schwalm
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Stefan Knapp
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Vladimir V Rogov
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
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17
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Waku T, Nakada S, Masuda H, Sumi H, Wada A, Hirose S, Aketa I, Kobayashi A. The CNC-family transcription factor Nrf3 coordinates the melanogenesis cascade through macropinocytosis and autophagy regulation. Cell Rep 2023; 42:111906. [PMID: 36640303 DOI: 10.1016/j.celrep.2022.111906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 10/06/2022] [Accepted: 12/09/2022] [Indexed: 12/31/2022] Open
Abstract
Melanin is a pigment produced from the amino acid L-tyrosine in melanosomes. The CNC-family transcription factor Nrf3 is expressed in the basal layer of the epidermis, where melanocytes reside, but its melanogenic function is unclear. Here, we show that Nrf3 regulates macropinocytosis and autophagy to coordinate melanogenesis cascade. In response to an exogenous inducer of melanin production, forskolin, Nrf3 upregulates the core melanogenic gene circuit, which includes Mitf, Tyr, Tyrp1, Pmel, and Oca2. Furthermore, Nrf3 induces the gene expression of Cln3, an autophagosome-related factor, for melanin precursor uptake by macropinocytosis. Ulk2 and Gabarapl2 are also identified as Nrf3-target autophagosome-related genes for melanosome formation. In parallel, Nrf3 prompts autolysosomal melanosome degradation for melanocyte survival. An endogenous melanogenic inducer αMSH also activates Nrf3-mediated melanin production, whereas it is suppressed by an HIV-1 protease inhibitor, nelfinavir. These findings indicate the significant role of Nrf3 in the melanogenesis and the anti-melanogenic potential of nelfinavir.
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Affiliation(s)
- Tsuyoshi Waku
- Laboratory for Genetic Code, Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, 1-3 Miyakodani, Tatara, Kyotanabe, Kyoto 610-0394, Japan.
| | - Sota Nakada
- Laboratory for Genetic Code, Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, 1-3 Miyakodani, Tatara, Kyotanabe, Kyoto 610-0394, Japan
| | - Haruka Masuda
- Laboratory for Genetic Code, Graduate School of Life and Medical Sciences, Doshisha University, 1-3 Miyakodani, Tatara, Kyotanabe, Kyoto 610-0394, Japan
| | - Haruna Sumi
- Laboratory for Genetic Code, Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, 1-3 Miyakodani, Tatara, Kyotanabe, Kyoto 610-0394, Japan
| | - Ayaka Wada
- Laboratory for Genetic Code, Graduate School of Life and Medical Sciences, Doshisha University, 1-3 Miyakodani, Tatara, Kyotanabe, Kyoto 610-0394, Japan
| | - Shuuhei Hirose
- Laboratory for Genetic Code, Graduate School of Life and Medical Sciences, Doshisha University, 1-3 Miyakodani, Tatara, Kyotanabe, Kyoto 610-0394, Japan
| | - Iori Aketa
- Laboratory for Genetic Code, Graduate School of Life and Medical Sciences, Doshisha University, 1-3 Miyakodani, Tatara, Kyotanabe, Kyoto 610-0394, Japan
| | - Akira Kobayashi
- Laboratory for Genetic Code, Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, 1-3 Miyakodani, Tatara, Kyotanabe, Kyoto 610-0394, Japan; Laboratory for Genetic Code, Graduate School of Life and Medical Sciences, Doshisha University, 1-3 Miyakodani, Tatara, Kyotanabe, Kyoto 610-0394, Japan.
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18
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Abstract
Macroautophagy and microautophagy are highly conserved eukaryotic cellular processes that degrade cytoplasmic material in lysosomes. Both pathways involve characteristic membrane dynamics regulated by autophagy-related proteins and other molecules, some of which are shared between the two pathways. Over the past few years, the application of new technologies, such as cryo-electron microscopy, coevolution-based structural prediction and in vitro reconstitution, has revealed the functions of individual autophagy gene products, especially in autophagy induction, membrane reorganization and cargo recognition. Concomitantly, mutations in autophagy genes have been linked to human disorders, particularly neurodegenerative diseases, emphasizing the potential pathogenic implications of autophagy defects. Accumulating genome data have also illuminated the evolution of autophagy genes within eukaryotes as well as their transition from possible ancestral elements in prokaryotes.
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Affiliation(s)
- Hayashi Yamamoto
- grid.26999.3d0000 0001 2151 536XDepartment of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan ,grid.410821.e0000 0001 2173 8328Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Sidi Zhang
- grid.26999.3d0000 0001 2151 536XDepartment of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noboru Mizushima
- grid.26999.3d0000 0001 2151 536XDepartment of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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19
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Wu Y, Liu G, Li Z, Chen M, Wang Q. ATG13 is involved in immune response of pathogen invasion in blood clam Tegillarca granosa. Front Vet Sci 2023; 10:1141284. [PMID: 36937017 PMCID: PMC10017841 DOI: 10.3389/fvets.2023.1141284] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Mammalian autophagy-related gene 13 (ATG13) is a vital component of the ATG1 autophagy initiation complex which plays an essential role in autophagy. However, the molecular function of ATG13 in pathogen defense in invertebrates is still poorly understood. In this study, the full-length cDNA sequence of blood clam Tegillarca granosa ATG13 (TgATG13) was obtained, which was 1,918 bp in length, including 283 bp 5' UTR, 252 bp 3' UTR and 1,383 bp open reading frame (ORF) encoding 460 amino acids. Phylogenetic analysis revealed that TgATG13 had the closest relationship with that of Crassostrea Virginica. Quantitative real-time PCR results showed that the transcript of TgATG13 was universally expressed in various tissues of blood clam, with the highest expression level in hemocytes. The expression level of TgATG13 was robustly increased after exposure of both Vibrio alginolyticus and LPS. Fluorescence confocal microscopy further showed that TgATG13 promoted the production of autophagosome. In summary, our study demonstrated that TgATG13 was involved in the immune regulation of blood clam during pathogen invasion, deepening our understanding of the innate immune mechanism of blood clam.
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Affiliation(s)
- Yuling Wu
- State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- School of Life Science, Xiamen University, Xiamen, China
| | - Guosheng Liu
- State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
| | - Zengpeng Li
- State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- *Correspondence: Zengpeng Li
| | - Mingliang Chen
- State Key Laboratory Breeding Base of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- Co-innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, China
- School of Marine Biology, Xiamen Ocean Vocational College, Xiamen, China
- Mingliang Chen
| | - Qin Wang
- School of Life Science, Xiamen University, Xiamen, China
- Qin Wang
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20
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Zhou J, Rasmussen NL, Olsvik HL, Akimov V, Hu Z, Evjen G, Kaeser-Pebernard S, Sankar DS, Roubaty C, Verlhac P, van de Beck N, Reggiori F, Abudu YP, Blagoev B, Lamark T, Johansen T, Dengjel J. TBK1 phosphorylation activates LIR-dependent degradation of the inflammation repressor TNIP1. J Cell Biol 2022; 222:213785. [PMID: 36574265 PMCID: PMC9797988 DOI: 10.1083/jcb.202108144] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 06/24/2022] [Accepted: 08/17/2022] [Indexed: 12/28/2022] Open
Abstract
Limitation of excessive inflammation due to selective degradation of pro-inflammatory proteins is one of the cytoprotective functions attributed to autophagy. In the current study, we highlight that selective autophagy also plays a vital role in promoting the establishment of a robust inflammatory response. Under inflammatory conditions, here TLR3-activation by poly(I:C) treatment, the inflammation repressor TNIP1 (TNFAIP3 interacting protein 1) is phosphorylated by Tank-binding kinase 1 (TBK1) activating an LIR motif that leads to the selective autophagy-dependent degradation of TNIP1, supporting the expression of pro-inflammatory genes and proteins. This selective autophagy efficiently reduces TNIP1 protein levels early (0-4 h) upon poly(I:C) treatment to allow efficient initiation of the inflammatory response. At 6 h, TNIP1 levels are restored due to increased transcription avoiding sustained inflammation. Thus, similarly as in cancer, autophagy may play a dual role in controlling inflammation depending on the exact state and timing of the inflammatory response.
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Affiliation(s)
- Jianwen Zhou
- https://ror.org/022fs9h90Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Nikoline Lander Rasmussen
- Autophagy Research Group, Department of Medical Biology, University of Tromsø—The Arctic University of Norway, Tromsø, Norway
| | - Hallvard Lauritz Olsvik
- Autophagy Research Group, Department of Medical Biology, University of Tromsø—The Arctic University of Norway, Tromsø, Norway
| | - Vyacheslav Akimov
- https://ror.org/03yrrjy16Department of Biochemistry and Molecular Biology, Center for Experimental BioInformatics, University of Southern Denmark, Odense, Denmark
| | - Zehan Hu
- https://ror.org/022fs9h90Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Gry Evjen
- Autophagy Research Group, Department of Medical Biology, University of Tromsø—The Arctic University of Norway, Tromsø, Norway
| | | | | | - Carole Roubaty
- https://ror.org/022fs9h90Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Pauline Verlhac
- https://ror.org/03cv38k47Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Nicole van de Beck
- https://ror.org/03cv38k47Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Fulvio Reggiori
- https://ror.org/03cv38k47Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands,https://ror.org/01aj84f44Department of Biomedicine, Aarhus University, Aarhus, Denmark,https://ror.org/01aj84f44Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus, Denmark
| | - Yakubu Princely Abudu
- Autophagy Research Group, Department of Medical Biology, University of Tromsø—The Arctic University of Norway, Tromsø, Norway
| | - Blagoy Blagoev
- https://ror.org/03yrrjy16Department of Biochemistry and Molecular Biology, Center for Experimental BioInformatics, University of Southern Denmark, Odense, Denmark
| | - Trond Lamark
- Autophagy Research Group, Department of Medical Biology, University of Tromsø—The Arctic University of Norway, Tromsø, Norway
| | - Terje Johansen
- Autophagy Research Group, Department of Medical Biology, University of Tromsø—The Arctic University of Norway, Tromsø, Norway,Terje Johansen:
| | - Jörn Dengjel
- https://ror.org/022fs9h90Department of Biology, University of Fribourg, Fribourg, Switzerland,Correspondence to Jörn Dengjel:
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21
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Huang T, Jiang G, Zhang Y, Lei Y, Liu S, Li H, Lu K. The RNA polymerase II subunit Rpb9 activates ATG1 transcription and autophagy. EMBO Rep 2022; 23:e54993. [PMID: 36102592 PMCID: PMC9638876 DOI: 10.15252/embr.202254993] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 08/01/2023] Open
Abstract
Macroautophagy/autophagy is a conserved process in eukaryotic cells that mediates the degradation and recycling of intracellular substrates. Proteins encoded by autophagy-related (ATG) genes are essentially involved in the autophagy process and must be tightly regulated in response to various circumstances, such as nutrient-rich and starvation conditions. However, crucial transcriptional activators of ATG genes have remained obscure. Here, we identify the RNA polymerase II subunit Rpb9 as an essential regulator of autophagy by a high-throughput screen of a Saccharomyces cerevisiae gene knockout library. Rpb9 plays a crucial and specific role in upregulating ATG1 transcription, and its deficiency decreases autophagic activities. Rpb9 promotes ATG1 transcription by binding to its promoter region, which is mediated by Gcn4. Furthermore, the function of Rpb9 in autophagy and its regulation of ATG1/ULK1 transcription are conserved in mammalian cells. Together, our results indicate that Rpb9 specifically activates ATG1 transcription and thus positively regulates the autophagy process.
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Affiliation(s)
- Ting Huang
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Gaoyue Jiang
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Yabin Zhang
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Yuqing Lei
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Shiyan Liu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Huihui Li
- West China Second University HospitalSichuan UniversityChengduChina
| | - Kefeng Lu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
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22
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Lu G, Wang Y, Shi Y, Zhang Z, Huang C, He W, Wang C, Shen HM. Autophagy in health and disease: From molecular mechanisms to therapeutic target. MedComm (Beijing) 2022; 3:e150. [PMID: 35845350 PMCID: PMC9271889 DOI: 10.1002/mco2.150] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 02/05/2023] Open
Abstract
Macroautophagy/autophagy is an evolutionally conserved catabolic process in which cytosolic contents, such as aggregated proteins, dysfunctional organelle, or invading pathogens, are sequestered by the double‐membrane structure termed autophagosome and delivered to lysosome for degradation. Over the past two decades, autophagy has been extensively studied, from the molecular mechanisms, biological functions, implications in various human diseases, to development of autophagy‐related therapeutics. This review will focus on the latest development of autophagy research, covering molecular mechanisms in control of autophagosome biogenesis and autophagosome–lysosome fusion, and the upstream regulatory pathways including the AMPK and MTORC1 pathways. We will also provide a systematic discussion on the implication of autophagy in various human diseases, including cancer, neurodegenerative disorders (Alzheimer disease, Parkinson disease, Huntington's disease, and Amyotrophic lateral sclerosis), metabolic diseases (obesity and diabetes), viral infection especially SARS‐Cov‐2 and COVID‐19, cardiovascular diseases (cardiac ischemia/reperfusion and cardiomyopathy), and aging. Finally, we will also summarize the development of pharmacological agents that have therapeutic potential for clinical applications via targeting the autophagy pathway. It is believed that decades of hard work on autophagy research is eventually to bring real and tangible benefits for improvement of human health and control of human diseases.
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Affiliation(s)
- Guang Lu
- Department of Physiology, Zhongshan School of Medicine Sun Yat-sen University Guangzhou China
| | - Yu Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu China
| | - Yin Shi
- Department of Biochemistry Zhejiang University School of Medicine Hangzhou China
| | - Zhe Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine Sichuan University and Collaborative Innovation Center for Biotherapy Chengdu China
| | - Weifeng He
- State Key Laboratory of Trauma, Burn and Combined Injury, Institute of Burn Research Southwest Hospital Army Medical University Chongqing China
| | - Chuang Wang
- Department of Pharmacology, Provincial Key Laboratory of Pathophysiology Ningbo University School of Medicine Ningbo Zhejiang China
| | - Han-Ming Shen
- Department of Biomedical Sciences, Faculty of Health Sciences, Ministry of Education Frontiers Science Center for Precision Oncology University of Macau Macau China
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23
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Function and regulation of ULK1: From physiology to pathology. Gene 2022; 840:146772. [PMID: 35905845 DOI: 10.1016/j.gene.2022.146772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/03/2022] [Accepted: 07/24/2022] [Indexed: 11/21/2022]
Abstract
The expression of ULK1, a core protein of autophagy, is closely related to autophagic activity. Numerous studies have shown that pathological abnormal expression of ULK1 is associated with various human diseases such as neurological disorders, infections, cardiovascular diseases, liver diseases and cancers. In addition, new advances in the regulation of ULK1 have been identified. Furthermore, targeting ULK1 as a therapeutic strategy for diseases is gaining attention as new corresponding activators or inhibitors are being developed. In this review, we describe the structure and regulation of ULK1 as well as the current targeted activators and inhibitors. Moreover, we highlight the pathological disorders of ULK1 expression and its critical role in human diseases.
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24
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Peng G, Tsukamoto S, Ikutama R, Le Thanh Nguyen H, Umehara Y, Trujillo-Paez JV, Yue H, Takahashi M, Ogawa T, Kishi R, Tominaga M, Takamori K, Kitaura J, Kageyama S, Komatsu M, Okumura K, Ogawa H, Ikeda S, Niyonsaba F. Human-β-defensin-3 attenuates atopic dermatitis-like inflammation through autophagy activation and the aryl hydrocarbon receptor signaling pathway. J Clin Invest 2022; 132:156501. [PMID: 35834333 PMCID: PMC9435650 DOI: 10.1172/jci156501] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 07/12/2022] [Indexed: 01/18/2023] Open
Abstract
Human β-defensin-3 (hBD-3) exhibits antimicrobial and immunomodulatory activities; however, its contribution to autophagy regulation remains unclear, and the role of autophagy in the regulation of the epidermal barrier in atopic dermatitis (AD) is poorly understood. Here, keratinocyte autophagy was restrained in the skin lesions of patients with AD and murine models of AD. Interestingly, hBD-3 alleviated the IL-4– and IL-13–mediated impairment of the tight junction (TJ) barrier through keratinocyte autophagy activation, which involved aryl hydrocarbon receptor (AhR) signaling. While autophagy deficiency impaired the epidermal barrier and exacerbated inflammation, hBD-3 attenuated skin inflammation and enhanced the TJ barrier in AD. Importantly, hBD-3–mediated improvement of the TJ barrier was abolished in autophagy-deficient AD mice and in AhR-suppressed AD mice, suggesting a role for hBD-3–mediated autophagy in the regulation of the epidermal barrier and inflammation in AD. Thus, autophagy contributes to the pathogenesis of AD, and hBD-3 could be used for therapeutic purposes.
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Affiliation(s)
- Ge Peng
- Department of Dermatology and Allergology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Saya Tsukamoto
- Department of Dermatology and Allergology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Risa Ikutama
- Department of Dermatology and Allergology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hai Le Thanh Nguyen
- Department of Dermatology and Allergology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yoshie Umehara
- Atopy (Allergy) Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Juan V Trujillo-Paez
- Atopy (Allergy) Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hainan Yue
- Department of Dermatology and Allergology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Miho Takahashi
- Department of Dermatology and Allergology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Takasuke Ogawa
- Department of Dermatology and Allergology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Ryoma Kishi
- Institute for Environmental and Gender Specific Medicine, Juntendo University Graduate School of Medicine, Chiba, Japan
| | - Mitsutoshi Tominaga
- Institute for Environmental and Gender Specific Medicine, Juntendo University Graduate School of Medicine, Chiba, Japan
| | - Kenji Takamori
- Institute for Environmental and Gender Specific Medicine, Juntendo University Graduate School of Medicine, Chiba, Japan
| | - Jiro Kitaura
- Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shun Kageyama
- Department of Physiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Ko Okumura
- Atopy (Allergy) Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Hideoki Ogawa
- Atopy (Allergy) Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shigaku Ikeda
- Department of Dermatology and Allergology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - François Niyonsaba
- Atopy (Allergy) Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
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25
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Majeed ST, Majeed R, Andrabi KI. Expanding the view of the molecular mechanisms of autophagy pathway. J Cell Physiol 2022; 237:3257-3277. [DOI: 10.1002/jcp.30819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 01/18/2023]
Affiliation(s)
- Sheikh Tahir Majeed
- Department of Biotechnology Central University of Kashmir Ganderbal Jammu and Kashmir India
- Growth Factor Signaling Laboratory, Department of Biotechnology University of Kashmir Srinagar Jammu and Kashmir India
| | - Rabiya Majeed
- Growth Factor Signaling Laboratory, Department of Biotechnology University of Kashmir Srinagar Jammu and Kashmir India
- Department of Biochemistry University of Kashmir Srinagar Jammu and Kashmir India
| | - Khurshid I. Andrabi
- Growth Factor Signaling Laboratory, Department of Biotechnology University of Kashmir Srinagar Jammu and Kashmir India
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26
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Sun S, Feng L, Chung KP, Lee KM, Cheung HHY, Luo M, Ren K, Law KC, Jiang L, Wong KB, Zhuang X. Mechanistic insights into an atypical interaction between ATG8 and SH3P2 in Arabidopsis thaliana. Autophagy 2022; 18:1350-1366. [PMID: 34657568 PMCID: PMC9225624 DOI: 10.1080/15548627.2021.1976965] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In selective macroautophagy/autophagy, cargo receptors are recruited to the forming autophagosome by interacting with Atg8 (autophagy-related 8)-family proteins and facilitate the selective sequestration of specific cargoes for autophagic degradation. In addition, Atg8 interacts with a number of adaptors essential for autophagosome biogenesis, including ATG and non-ATG proteins. The majority of these adaptors and receptors are characterized by an Atg8-family interacting motif (AIM) for binding to Atg8. However, the molecular basis for the interaction mode between ATG8 and regulators or cargo receptors in plants remains largely unclear. In this study, we unveiled an atypical interaction mode for Arabidopsis ATG8f with a plant unique adaptor protein, SH3P2 (SH3 domain-containing protein 2), but not with the other two SH3 proteins. By structure analysis of the unbound form of ATG8f, we identified the unique conformational changes in ATG8f upon binding to the AIM sequence of a plant known autophagic receptor, NBR1. To compare the binding affinity of SH3P2-ATG8f with that of ATG8f-NBR1, we performed a gel filtration assay to show that ubiquitin-associated domain of NBR1 outcompetes the SH3 domain of SH3P2 for ATG8f interaction. Biochemical and cellular analysis revealed that distinct interfaces were employed by ATG8f to interact with NBR1 and SH3P2. Further subcellular analysis showed that the AIM-like motif of SH3P2 is essential for its recruitment to the phagophore membrane but is dispensable for its trafficking in endocytosis. Taken together, our study provides an insightful structural basis for the ATG8 binding specificity toward a plant-specific autophagic adaptor and a conserved autophagic receptor.Abbreviations: ATG, autophagy-related; AIM, Atg8-family interacting motif; BAR, Bin-Amphiphysin-Rvs; BFA, brefeldin A; BTH, benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester; CCV, clathrin-coated-vesicle; CLC2, clathrin light chain 2; Conc A, concanamycin A; ER, endoplasmic reticulum; LDS, LIR docking site; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; LIR, LC3-interacting region; PE, phosphatidylethanolamine; SH3P2, SH3 domain containing protein 2; SH3, Src-Homology-3; UBA, ubiquitin-associated; UIM, ubiquitin-interacting motif.
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Affiliation(s)
- Shuangli Sun
- Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Lanlan Feng
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kin Pan Chung
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China,Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Ka-Ming Lee
- Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Hayley Hei-Yin Cheung
- Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Mengqian Luo
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kaike Ren
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kai Ching Law
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Liwen Jiang
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China,The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Kam-Bo Wong
- Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaohong Zhuang
- Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China,CONTACT Xiaohong Zhuang Centre for Cell and Developmental Biology, State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
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27
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Mameli E, Martello A, Caporali A. Autophagy at the interface of endothelial cell homeostasis and vascular disease. FEBS J 2022; 289:2976-2991. [PMID: 33934518 DOI: 10.1111/febs.15873] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/16/2021] [Accepted: 04/09/2021] [Indexed: 12/19/2022]
Abstract
Autophagy is an essential intracellular process for cellular quality control. It enables cell homeostasis through the selective degradation of harmful protein aggregates and damaged organelles. Autophagy is essential for recycling nutrients, generating energy to maintain cell viability in most tissues and during adverse conditions such as hypoxia/ischaemia. The progressive understanding of the mechanisms modulating autophagy in the vasculature has recently led numerous studies to link intact autophagic responses with endothelial cell (EC) homeostasis and function. Preserved autophagic flux within the ECs has an essential role in maintaining their physiological characteristics, whereas defective autophagy can promote endothelial pro-inflammatory and atherogenic phenotype. However, we still lack a good knowledge of the complete molecular repertoire controlling various aspects of endothelial autophagy and how this is associated with vascular diseases. Here, we provide an overview of the current state of the art of autophagy in ECs. We review the discoveries that have so far defined autophagy as an essential mechanism in vascular biology and analyse how autophagy influences ECs behaviour in vascular disease. Finally, we emphasise opportunities for compounds to regulate autophagy in ECs and discuss the challenges of exploiting them to resolve vascular disease.
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Affiliation(s)
- Eleonora Mameli
- University/BHF Centre for Cardiovascular Science, QMRI, University of Edinburgh, UK
| | | | - Andrea Caporali
- University/BHF Centre for Cardiovascular Science, QMRI, University of Edinburgh, UK
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28
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Morris-Love J, O’Hara BA, Gee GV, Dugan AS, O’Rourke RS, Armstead BE, Assetta B, Haley SA, Atwood WJ. Biogenesis of JC polyomavirus associated extracellular vesicles. JOURNAL OF EXTRACELLULAR BIOLOGY 2022; 1:e43. [PMID: 36688929 PMCID: PMC9854252 DOI: 10.1002/jex2.43] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/13/2022] [Indexed: 01/26/2023]
Abstract
JC polyomavirus (JCPyV) is a small, non-enveloped virus that persists in the kidney in about half the adult population. In severely immune-compromised individuals JCPyV causes the neurodegenerative disease progressive multifocal leukoencephalopathy (PML) in the brain. JCPyV has been shown to infect cells by both direct and indirect mechanisms, the latter involving extracellular vesicle (EV) mediated infection. While direct mechanisms of infection are well studied indirect EV mediated mechanisms are poorly understood. Using a combination of chemical and genetic approaches we show that several overlapping intracellular pathways are responsible for the biogenesis of virus containing EV. Here we show that targeting neutral sphingomyelinase 2 (nSMase2) with the drug cambinol decreased the spread of JCPyV over several viral life cycles. Genetic depletion of nSMase2 by either shRNA or CRISPR/Cas9 reduced EV-mediated infection. Individual knockdown of seven ESCRT-related proteins including HGS, ALIX, TSG101, VPS25, VPS20, CHMP4A, and VPS4A did not significantly reduce JCPyV associated EV (JCPyV(+) EV) infectivity, whereas knockdown of the tetraspanins CD9 and CD81 or trafficking and/or secretory autophagy-related proteins RAB8A, RAB27A, and GRASP65 all significantly reduced the spread of JCPyV and decreased EV-mediated infection. These findings point to a role for exosomes and secretory autophagosomes in the biogenesis of JCPyV associated EVs with specific roles for nSMase2, CD9, CD81, RAB8A, RAB27A, and GRASP65 proteins.
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Affiliation(s)
- Jenna Morris-Love
- Graduate Program in Pathobiology, Brown University, Providence, RI, USA
- Department of Molecular biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Bethany A. O’Hara
- Department of Molecular biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Gretchen V. Gee
- Department of Molecular biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI, USA
- MassBiologics, University of Massachusetts Medical School, Fall River, MA, USA
| | - Aisling S. Dugan
- Department of Biology, Assumption University, Worcester, MA, USA
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Ryan S. O’Rourke
- Graduate Program in Pathobiology, Brown University, Providence, RI, USA
- Department of Molecular biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI, USA
| | | | - Benedetta Assetta
- Department of Molecular biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Sheila A. Haley
- Department of Molecular biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Walter J. Atwood
- Department of Molecular biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI, USA
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29
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Popelka H, Klionsky DJ. The RB1CC1 Claw-binding motif: a new piece in the puzzle of autophagy regulation. Autophagy 2022; 18:237-239. [PMID: 35133947 PMCID: PMC8942483 DOI: 10.1080/15548627.2022.2029234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Indexed: 11/02/2022] Open
Abstract
RB1CC1/FIP200 is a subunit of the ULK1 complex in more complex eukaryotes. This large polypeptide was proposed to be a functional homolog of the Atg17 and Atg11 scaffolding proteins in yeast. Previous studies showed that RB1CC1 can bind to various proteins of the macroautophagy/autophagy machinery, where the RB1CC1 Claw domain directly interacts with a short linear segment of its interactors. A mechanistic insight into how the small globular RB1CC1 Claw domain can interact with such an array of structurally variable proteins has been elusive. The recent study by Zhou et al., discussed here, yields structural data that not only provide a unifying mechanistic explanation of these interactions, but also reveals previously unknown RB1CC1 interactors and opens a new field for exploration of autophagy regulation.Abbreviations: FIR: FIP200-interacting region; LIR: LC3-interacting region; pS/p-S: phosphorylated serine.
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Affiliation(s)
- Hana Popelka
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
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30
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Molecular regulation of autophagosome formation. Biochem Soc Trans 2022; 50:55-69. [PMID: 35076688 PMCID: PMC9022990 DOI: 10.1042/bst20210819] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/21/2021] [Accepted: 01/04/2022] [Indexed: 12/11/2022]
Abstract
Macroautophagy, hereafter autophagy, is a degradative process conserved among eukaryotes, which is essential to maintain cellular homeostasis. Defects in autophagy lead to numerous human diseases, including various types of cancer and neurodegenerative disorders. The hallmark of autophagy is the de novo formation of autophagosomes, which are double-membrane vesicles that sequester and deliver cytoplasmic materials to lysosomes/vacuoles for degradation. The mechanism of autophagosome biogenesis entered a molecular era with the identification of autophagy-related (ATG) proteins. Although there are many unanswered questions and aspects that have raised some controversies, enormous advances have been done in our understanding of the process of autophagy in recent years. In this review, we describe the current knowledge about the molecular regulation of autophagosome formation, with a particular focus on budding yeast and mammalian cells.
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31
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Tsapras P, Petridi S, Chan S, Geborys M, Jacomin AC, Sagona AP, Meier P, Nezis IP. Selective autophagy controls innate immune response through a TAK1/TAB2/SH3PX1 axis. Cell Rep 2022; 38:110286. [PMID: 35081354 DOI: 10.1016/j.celrep.2021.110286] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 12/07/2021] [Accepted: 12/29/2021] [Indexed: 12/20/2022] Open
Abstract
Selective autophagy is a catabolic route that turns over specific cellular material for degradation by lysosomes, and whose role in the regulation of innate immunity is largely unexplored. Here, we show that the apical kinase of the Drosophila immune deficiency (IMD) pathway Tak1, as well as its co-activator Tab2, are both selective autophagy substrates that interact with the autophagy protein Atg8a. We also present a role for the Atg8a-interacting protein Sh3px1 in the downregulation of the IMD pathway, by facilitating targeting of the Tak1/Tab2 complex to the autophagy platform through its interaction with Tab2. Our findings show the Tak1/Tab2/Sh3px1 interactions with Atg8a mediate the removal of the Tak1/Tab2 signaling complex by selective autophagy. This in turn prevents constitutive activation of the IMD pathway in Drosophila. This study provides mechanistic insight on the regulation of innate immune responses by selective autophagy.
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Affiliation(s)
| | - Stavroula Petridi
- School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK
| | - Selina Chan
- School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK
| | - Marta Geborys
- School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK
| | | | - Antonia P Sagona
- School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK
| | - Pascal Meier
- The Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, Fulham Road, London SW3 6JB, UK
| | - Ioannis P Nezis
- School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK.
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Direct Interaction of ATP7B and LC3B Proteins Suggests a Cooperative Role of Copper Transportation and Autophagy. Cells 2021; 10:cells10113118. [PMID: 34831341 PMCID: PMC8625360 DOI: 10.3390/cells10113118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/01/2021] [Accepted: 11/05/2021] [Indexed: 11/17/2022] Open
Abstract
Macroautophagy/autophagy plays an important role in cellular copper clearance. The means by which the copper metabolism and autophagy pathways interact mechanistically is vastly unexplored. Dysfunctional ATP7B, a copper-transporting ATPase, is involved in the development of monogenic Wilson disease, a disorder characterized by disturbed copper transport. Using in silico prediction, we found that ATP7B contains a number of potential binding sites for LC3, a central protein in the autophagy pathway, the so-called LC3 interaction regions (LIRs). The conserved LIR3, located at the C-terminal end of ATP7B, was found to directly interact with LC3B in vitro. Replacing the two conserved hydrophobic residues W1452 and L1455 of LIR3 significantly reduced interaction. Furthermore, autophagy was induced in normal human hepatocellular carcinoma cells (HepG2) leading to enhanced colocalization of ATP7B and LC3B on the autophagosome membranes. By contrast, HepG2 cells deficient of ATP7B (HepG2 ATP7B-/-) showed autophagy deficiency at elevated copper condition. This phenotype was complemented by heterologous ATP7B expression. These findings suggest a cooperative role of ATP7B and LC3B in autophagy-mediated copper clearance.
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33
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Fas BA, Maiani E, Sora V, Kumar M, Mashkoor M, Lambrughi M, Tiberti M, Papaleo E. The conformational and mutational landscape of the ubiquitin-like marker for autophagosome formation in cancer. Autophagy 2021; 17:2818-2841. [PMID: 33302793 PMCID: PMC8525936 DOI: 10.1080/15548627.2020.1847443] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 10/28/2020] [Accepted: 11/03/2020] [Indexed: 02/06/2023] Open
Abstract
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.
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Affiliation(s)
- Burcu Aykac Fas
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Emiliano Maiani
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Valentina Sora
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Mukesh Kumar
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Maliha Mashkoor
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Tiberti
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
- Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark
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34
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Jacquet M, Hervouet E, Baudu T, Herfs M, Parratte C, Feugeas JP, Perez V, Reynders C, Ancion M, Vigneron M, Baguet A, Guittaut M, Fraichard A, Despouy G. GABARAPL1 Inhibits EMT Signaling through SMAD-Tageted Negative Feedback. BIOLOGY 2021; 10:biology10100956. [PMID: 34681055 PMCID: PMC8533302 DOI: 10.3390/biology10100956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/10/2021] [Accepted: 09/14/2021] [Indexed: 12/03/2022]
Abstract
Simple Summary Epithelial–mesenchymal transition (EMT) is involved in metastasis formation, chemoresistance, apoptosis resistance, and acquisition of stem cell properties, making this process an attractive target in cancer. However, direct targeting of EMT remains challenging. Autophagy—an intracellular mechanism—has been noted to be involved in the regulation of EMT—mainly by its involvement in the degradation of EMT actors, explaining why understanding of how autophagy could regulate EMT might be promising in the development of new cancer therapies. Here, we found that GABARAPL1—an autophagy-related gene—was increased in human NSCLC mesenchymal tumors compared to epithelial tumors, and induction of EMT in an A549 lung cancer cell line by TGF-β/TNF-α cytokines also led to an increase in GABARAPL1 expression. This regulation could involve the EMT-related transcription factors of the SMAD family. To understand the role of GABARAPL1 in EMT regulation in lung cancer cells, A549 KO GABARAPL1 were designed and used to investigate whether GABARAPL1 could inhibit EMT via its involvement in SMAD degradation. The results indicate that GABARAPL1-mediated autophagic degradation could intervene as a negative EMT-regulatory loop. Abstract The pathway of selective autophagy, leading to a targeted elimination of specific intracellular components, is mediated by the ATG8 proteins, and has been previously suggested to be involved in the regulation of the Epithelial–mesenchymal transition (EMT) during cancer’s etiology. However, the molecular factors and steps of selective autophagy occurring during EMT remain unclear. We therefore analyzed a cohort of lung adenocarcinoma tumors using transcriptome analysis and immunohistochemistry, and found that the expression of ATG8 genes is correlated with that of EMT-related genes, and that GABARAPL1 protein levels are increased in EMT+ tumors compared to EMT- ones. Similarly, the induction of EMT in the A549 lung adenocarcinoma cell line using TGF-β/TNF-α led to a high increase in GABARAPL1 expression mediated by the EMT-related transcription factors of the SMAD family, whereas the other ATG8 genes were less modified. To determine the role of GABARAPL1 during EMT, we used the CRISPR/Cas9 technology in A549 and ACHN kidney adenocarcinoma cell lines to deplete GABARAPL1. We then observed that GABARAPL1 knockout induced EMT linked to a defect of GABARAPL1-mediated degradation of the SMAD proteins. These findings suggest that, during EMT, GABARAPL1 might intervene in an EMT-regulatory loop. Indeed, induction of EMT led to an increase in GABARAPL1 levels through the activation of the SMAD signaling pathway, and then GABARAPL1 induced the autophagy-selective degradation of SMAD proteins, leading to EMT inhibition.
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Affiliation(s)
- Marine Jacquet
- Université Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; (M.J.); (E.H.); (T.B.); (C.P.); (J.-P.F.); (V.P.); (A.B.); (M.G.); (A.F.)
| | - Eric Hervouet
- Université Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; (M.J.); (E.H.); (T.B.); (C.P.); (J.-P.F.); (V.P.); (A.B.); (M.G.); (A.F.)
- DImaCellplatform, Université Bourgogne Franche-Comté, F-25000 Besançon, France
- EPIGENExp, Université Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Timothée Baudu
- Université Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; (M.J.); (E.H.); (T.B.); (C.P.); (J.-P.F.); (V.P.); (A.B.); (M.G.); (A.F.)
| | - Michaël Herfs
- Laboratory of Experimental Pathology, GIGA-Cancer, University of Liege, 4000 Liege, Belgium; (M.H.); (C.R.); (M.A.)
| | - Chloé Parratte
- Université Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; (M.J.); (E.H.); (T.B.); (C.P.); (J.-P.F.); (V.P.); (A.B.); (M.G.); (A.F.)
| | - Jean-Paul Feugeas
- Université Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; (M.J.); (E.H.); (T.B.); (C.P.); (J.-P.F.); (V.P.); (A.B.); (M.G.); (A.F.)
| | - Valérie Perez
- Université Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; (M.J.); (E.H.); (T.B.); (C.P.); (J.-P.F.); (V.P.); (A.B.); (M.G.); (A.F.)
| | - Célia Reynders
- Laboratory of Experimental Pathology, GIGA-Cancer, University of Liege, 4000 Liege, Belgium; (M.H.); (C.R.); (M.A.)
| | - Marie Ancion
- Laboratory of Experimental Pathology, GIGA-Cancer, University of Liege, 4000 Liege, Belgium; (M.H.); (C.R.); (M.A.)
| | - Marc Vigneron
- Team Replisome Dynamics and Cancer, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie de Strasbourg, CNRS-Université de Strasbourg, F-67412 Illkirch, France;
| | - Aurélie Baguet
- Université Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; (M.J.); (E.H.); (T.B.); (C.P.); (J.-P.F.); (V.P.); (A.B.); (M.G.); (A.F.)
| | - Michaël Guittaut
- Université Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; (M.J.); (E.H.); (T.B.); (C.P.); (J.-P.F.); (V.P.); (A.B.); (M.G.); (A.F.)
- DImaCellplatform, Université Bourgogne Franche-Comté, F-25000 Besançon, France
| | - Annick Fraichard
- Université Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; (M.J.); (E.H.); (T.B.); (C.P.); (J.-P.F.); (V.P.); (A.B.); (M.G.); (A.F.)
| | - Gilles Despouy
- Université Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, F-25000 Besançon, France; (M.J.); (E.H.); (T.B.); (C.P.); (J.-P.F.); (V.P.); (A.B.); (M.G.); (A.F.)
- Correspondence:
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35
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Tu YXI, Sydor AM, Coyaud E, Laurent EMN, Dyer D, Mellouk N, St-Germain J, Vernon RM, Forman-Kay JD, Li T, Hua R, Zhao K, Ridgway ND, Kim PK, Raught B, Brumell JH. Global Proximity Interactome of the Human Macroautophagy Pathway. Autophagy 2021; 18:1174-1186. [PMID: 34524948 PMCID: PMC9196747 DOI: 10.1080/15548627.2021.1965711] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Macroautophagy is a highly conserved eukaryotic cellular pathway involving the engulfment of macromolecules, organelles, and invading microbes by a double-membrane compartment and subsequent lysosomal degradation. The mechanisms that regulate macroautophagy, and the interaction of its components with other cellular pathways, have remained unclear. Here, we performed proximity-dependent biotin identification (BioID) on 39 core human macroautophagy proteins, identifying over 700 unique high confidence proximity interactors with new putative connections between macroautophagic and essential cellular processes. Of note, we identify members of the OSBPL (oxysterol binding protein like) family as Atg8-family protein interactors. We subsequently conducted comprehensive screens of the OSBPL family for LC3B-binding and roles in xenophagy and aggrephagy. OSBPL7 and OSBPL11 emerged as novel lipid transfer proteins required for macroautophagy of selective cargo. Altogether, our proximity interaction map provides a valuable resource for the study of autophagy and highlights the critical role of membrane contact site proteins in the pathway.
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Affiliation(s)
- Yi Xin Iris Tu
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Andrew M Sydor
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Estelle M N Laurent
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Diana Dyer
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Nora Mellouk
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Robert M Vernon
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Julie D Forman-Kay
- Molecular Medicine Program, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Taoyingnan Li
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Rong Hua
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Kexin Zhao
- Departments of Pediatrics and Biochemistry and Molecular Biology, Atlantic Research Centre, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Neale D Ridgway
- Departments of Pediatrics and Biochemistry and Molecular Biology, Atlantic Research Centre, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Peter K Kim
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John H Brumell
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.,SickKids IBD Centre, Hospital for Sick Children, Toronto, Ontario, Canada
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36
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Rana T, Behl T, Sehgal A, Mehta V, Singh S, Bhatia S, Al-Harrasi A, Bungau S. Exploring the Role of Autophagy Dysfunction in Neurodegenerative Disorders. Mol Neurobiol 2021; 58:4886-4905. [PMID: 34212304 DOI: 10.1007/s12035-021-02472-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/21/2021] [Indexed: 12/12/2022]
Abstract
Autophagy is a catabolic pathway by which misfolded proteins or damaged organelles are engulfed by autophagosomes and then transported to lysosomes for degradation. Recently, a great improvement has been done to explain the molecular mechanisms and roles of autophagy in several important cellular metabolic processes. Besides being a vital clearance pathway or a cell survival pathway in response to different stresses, autophagy dysfunction, either upregulated or down-regulated, has been suggested to be linked with numerous neurodegenerative disorders like Alzheimer's disease, Parkinson's disease, Huntington's disease, and Amyotrophic lateral sclerosis. Impairment at different stages of autophagy results in the formation of large protein aggregates and damaged organelles, which leads to the onset and progression of different neurodegenerative disorders. This article elucidates the recent progress about the role of autophagy in neurodegenerative disorders and explains how autophagy dysfunction is linked with the pathogenesis of such disorders as well as the novel potential autophagy-associated therapies for treating them.
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Affiliation(s)
- Tarapati Rana
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
- Government Pharmacy College, Seraj, Mandi, Himachal Pradesh, India
| | - Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab, India.
| | - Aayush Sehgal
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Vineet Mehta
- Government College of Pharmacy, Rohru, Distt. Shimla, Himachal Pradesh, India
| | - Sukhbir Singh
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Saurabh Bhatia
- Amity Institute of Pharmacy, Amity University, Haryana, India
- Natural & Medical Sciences Research Centre, University of Nizwa, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Centre, University of Nizwa, Nizwa, Oman
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
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37
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Deretic V, Kroemer G. Autophagy in metabolism and quality control: opposing, complementary or interlinked functions? Autophagy 2021; 18:283-292. [PMID: 34036900 DOI: 10.1080/15548627.2021.1933742] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The sensu stricto autophagy, macroautophagy, is considered to be both a metabolic process as well as a bona fide quality control process. The question as to how these two aspects of autophagy are coordinated and whether and why they overlap has implications for fundamental aspects, pathophysiological effects, and pharmacological manipulation of autophagy. At the top of the regulatory cascade controlling autophagy are master regulators of cellular metabolism, such as MTOR and AMPK, which render the system responsive to amino acid and glucose starvation. At the other end exists a variety of specific autophagy receptors, engaged in the selective removal of a diverse array of intracellular targets, from protein aggregates/condensates to whole organelles such as mitochondria, ER, peroxisomes, lysosomes and lipid droplets. Are the roles of autophagy in metabolism and quality control mutually exclusive, independent or interlocked? How are priorities established? What are the molecular links between both phenomena? This article will provide a starting point to formulate these questions, the responses to which should be taken into consideration in future autophagy-based interventions.
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Affiliation(s)
- Vojo Deretic
- Autophagy Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.,Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France.,Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.,Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China.,Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden
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38
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Abstract
Selective autophagy is the lysosomal degradation of specific intracellular components sequestered into autophagosomes, late endosomes, or lysosomes through the activity of selective autophagy receptors (SARs). SARs interact with autophagy-related (ATG)8 family proteins via sequence motifs called LC3-interacting region (LIR) motifs in vertebrates and Atg8-interacting motifs (AIMs) in yeast and plants. SARs can be divided into two broad groups: soluble or membrane bound. Cargo or substrate selection may be independent or dependent of ubiquitin labeling of the cargo. In this review, we discuss mechanisms of mammalian selective autophagy with a focus on the unifying principles employed in substrate recognition, interaction with the forming autophagosome via LIR-ATG8 interactions, and the recruitment of core autophagy components for efficient autophagosome formation on the substrate. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Trond Lamark
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, 9037 Tromsø, Norway; ,
| | - Terje Johansen
- Molecular Cancer Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, 9037 Tromsø, Norway; ,
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39
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Lizama BN, Chu CT. Neuronal autophagy and mitophagy in Parkinson's disease. Mol Aspects Med 2021; 82:100972. [PMID: 34130867 DOI: 10.1016/j.mam.2021.100972] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 05/18/2021] [Accepted: 05/29/2021] [Indexed: 12/11/2022]
Abstract
Autophagy is the process by which cells can selectively or non-selectively remove damaged proteins and organelles. As the cell's main means of sequestering damaged mitochondria for removal, mitophagy is central to cellular function and survival. Research on autophagy and mitochondrial quality control has increased exponentially in relation to the pathogenesis of numerous disease conditions, from cancer and immune diseases to chronic neurodegenerative diseases like Parkinson's disease (PD). Understanding how components of the autophagic/mitophagic machinery are affected during disease, as well as the contextual relationship of autophagy with determining neuronal health and function, is essential to the goal of designing therapies for human disease. In this review, we will summarize key signaling molecules that consign damaged mitochondria for autophagic degradation, describe the relationship of genes linked to PD to autophagy/mitophagy dysfunction, and discuss additional roles of both mitochondrial and cytosolic pools of PTEN-induced kinase 1 (PINK1) in mitochondrial homeostasis, dendritic morphogenesis and inflammation.
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Affiliation(s)
- Britney N Lizama
- Dept of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Charleen T Chu
- Dept of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA; Pittsburgh Institute for Neurodegenerative Diseases, McGowan Institute for Regenerative Medicine, Center for Protein Conformational Diseases and Center for Neuroscience at the University of Pittsburgh, Pittsburgh, PA, 15261, USA.
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40
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Wirth M, Mouilleron S, Zhang W, Sjøttem E, Princely Abudu Y, Jain A, Lauritz Olsvik H, Bruun JA, Razi M, Jefferies HB, Lee R, Joshi D, O'Reilly N, Johansen T, Tooze SA. Phosphorylation of the LIR Domain of SCOC Modulates ATG8 Binding Affinity and Specificity. J Mol Biol 2021; 433:166987. [DOI: https:/doi.org/10.1016/j.jmb.2021.166987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
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41
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Model-based analysis uncovers mutations altering autophagy selectivity in human cancer. Nat Commun 2021; 12:3258. [PMID: 34059679 PMCID: PMC8166871 DOI: 10.1038/s41467-021-23539-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 04/28/2021] [Indexed: 02/07/2023] Open
Abstract
Autophagy can selectively target protein aggregates, pathogens, and dysfunctional organelles for the lysosomal degradation. Aberrant regulation of autophagy promotes tumorigenesis, while it is far less clear whether and how tumor-specific alterations result in autophagic aberrance. To form a link between aberrant autophagy selectivity and human cancer, we establish a computational pipeline and prioritize 222 potential LIR (LC3-interacting region) motif-associated mutations (LAMs) in 148 proteins. We validate LAMs in multiple proteins including ATG4B, STBD1, EHMT2 and BRAF that impair their interactions with LC3 and autophagy activities. Using a combination of transcriptomic, metabolomic and additional experimental assays, we show that STBD1, a poorly-characterized protein, inhibits tumor growth via modulating glycogen autophagy, while a patient-derived W203C mutation on LIR abolishes its cancer inhibitory function. This work suggests that altered autophagy selectivity is a frequently-used mechanism by cancer cells to survive during various stresses, and provides a framework to discover additional autophagy-related pathways that influence carcinogenesis. Although autophagy has been linked to tumourigenesis, it is unclear how genomic alterations affect autophagy selectivity in tumours. Here, the authors establish a pipeline that integrates computational and experimental approaches to show that altered autophagy selectivity is frequent in cancer cells and link glycogen autophagy with tumourigenesis.
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42
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Barz S, Kriegenburg F, Sánchez-Martín P, Kraft C. Small but mighty: Atg8s and Rabs in membrane dynamics during autophagy. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119064. [PMID: 34048862 PMCID: PMC8261831 DOI: 10.1016/j.bbamcr.2021.119064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/04/2021] [Accepted: 05/21/2021] [Indexed: 11/17/2022]
Abstract
Autophagy is a degradative pathway during which autophagosomes are formed that enwrap cytosolic material destined for turnover within the lytic compartment. Autophagosome biogenesis requires controlled lipid and membrane rearrangements to allow the formation of an autophagosomal seed and its subsequent elongation into a fully closed and fusion-competent double membrane vesicle. Different membrane remodeling events are required, which are orchestrated by the distinct autophagy machinery. An important player among these autophagy proteins is the small lipid-modifier Atg8. Atg8 proteins facilitate various aspects of autophagosome formation and serve as a binding platform for autophagy factors. Also Rab GTPases have been implicated in autophagosome biogenesis. As Atg8 proteins interact with several Rab GTPase regulators, they provide a possible link between autophagy progression and Rab GTPase activity. Here, we review central aspects in membrane dynamics during autophagosome biogenesis with a focus on Atg8 proteins and selected Rab GTPases.
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Affiliation(s)
- Saskia Barz
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
| | - Franziska Kriegenburg
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Pablo Sánchez-Martín
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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43
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Gatica D, Chiong M, Lavandero S, Klionsky DJ. The role of autophagy in cardiovascular pathology. Cardiovasc Res 2021; 118:934-950. [PMID: 33956077 DOI: 10.1093/cvr/cvab158] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/30/2021] [Indexed: 12/11/2022] Open
Abstract
Macroautophagy/autophagy is a conserved catabolic recycling pathway in which cytoplasmic components are sequestered, degraded, and recycled to survive various stress conditions. Autophagy dysregulation has been observed and linked with the development and progression of several pathologies, including cardiovascular diseases, the leading cause of death in the developed world. In this review, we aim to provide a broad understanding of the different molecular factors that govern autophagy regulation and how these mechanisms are involved in the development of specific cardiovascular pathologies, including ischemic and reperfusion injury, myocardial infarction, cardiac hypertrophy, cardiac remodeling, and heart failure.
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Affiliation(s)
- Damián Gatica
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Mario Chiong
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas & Facultad de Medicina, Universidad de Chile, Santiago 8380492, Chile
| | - Sergio Lavandero
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas & Facultad de Medicina, Universidad de Chile, Santiago 8380492, Chile.,Corporación Centro de Estudios Científicos de las Enfermedades Crónicas (CECEC), Santiago 7860201, Chile.,Department of Internal Medicine (Cardiology Division), University of Texas Southwestern Medical Center, Dallas, TX 75390-8573, USA
| | - Daniel J Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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44
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Carinci M, Testa B, Bordi M, Milletti G, Bonora M, Antonucci L, Ferraina C, Carro M, Kumar M, Ceglie D, Eck F, Nardacci R, le Guerroué F, Petrini S, Soriano ME, Caruana I, Doria V, Manifava M, Peron C, Lambrughi M, Tiranti V, Behrends C, Papaleo E, Pinton P, Giorgi C, Ktistakis NT, Locatelli F, Nazio F, Cecconi F. TFG binds LC3C to regulate ULK1 localization and autophagosome formation. EMBO J 2021; 40:e103563. [PMID: 33932238 PMCID: PMC8126910 DOI: 10.15252/embj.2019103563] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/17/2021] [Accepted: 03/01/2021] [Indexed: 12/14/2022] Open
Abstract
The early secretory pathway and autophagy are two essential and evolutionarily conserved endomembrane processes that are finely interlinked. Although growing evidence suggests that intracellular trafficking is important for autophagosome biogenesis, the molecular regulatory network involved is still not fully defined. In this study, we demonstrate a crucial effect of the COPII vesicle-related protein TFG (Trk-fused gene) on ULK1 puncta number and localization during autophagy induction. This, in turn, affects formation of the isolation membrane, as well as the correct dynamics of association between LC3B and early ATG proteins, leading to the proper formation of both omegasomes and autophagosomes. Consistently, fibroblasts derived from a hereditary spastic paraparesis (HSP) patient carrying mutated TFG (R106C) show defects in both autophagy and ULK1 puncta accumulation. In addition, we demonstrate that TFG activity in autophagy depends on its interaction with the ATG8 protein LC3C through a canonical LIR motif, thereby favouring LC3C-ULK1 binding. Altogether, our results uncover a link between TFG and autophagy and identify TFG as a molecular scaffold linking the early secretion pathway to autophagy.
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Affiliation(s)
- Marianna Carinci
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Rome, Italy.,Department of Medical Sciences, University of Ferrara, Laboratory of Technologies for Advanced Therapy (LTTA), Technopole of Ferrara, Ferrara, Italy
| | - Beatrice Testa
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Matteo Bordi
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Rome, Italy.,Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Giacomo Milletti
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Rome, Italy.,Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Massimo Bonora
- Department of Medical Sciences, University of Ferrara, Laboratory of Technologies for Advanced Therapy (LTTA), Technopole of Ferrara, Ferrara, Italy
| | - Laura Antonucci
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Caterina Ferraina
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Marta Carro
- Department of Biology, University of Padua, Padua, Italy
| | - Mukesh Kumar
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Donatella Ceglie
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Franziska Eck
- Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität (LMU), München, Germany
| | - Roberta Nardacci
- Department of Epidemiology and Preclinical Research, National Institute for Infectious Diseases IRCCS "L. Spallanzani", Rome, Italy
| | - Francois le Guerroué
- Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität (LMU), München, Germany
| | - Stefania Petrini
- Confocal Microscopy Core Facility, Research Laboratories, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | | | - Ignazio Caruana
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Valentina Doria
- Confocal Microscopy Core Facility, Research Laboratories, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | | | - Camille Peron
- UO Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico C. Besta, Milan, Italy
| | - Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Valeria Tiranti
- UO Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico C. Besta, Milan, Italy
| | - Christian Behrends
- Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität (LMU), München, Germany
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark.,Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark
| | - Paolo Pinton
- Department of Medical Sciences, University of Ferrara, Laboratory of Technologies for Advanced Therapy (LTTA), Technopole of Ferrara, Ferrara, Italy
| | - Carlotta Giorgi
- Department of Medical Sciences, University of Ferrara, Laboratory of Technologies for Advanced Therapy (LTTA), Technopole of Ferrara, Ferrara, Italy
| | | | - Franco Locatelli
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Rome, Italy.,Department of Gynecology/Obstetrics and Pediatrics, Sapienza University, Rome, Italy
| | - Francesca Nazio
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Francesco Cecconi
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Rome, Italy.,Department of Biology, University of Rome Tor Vergata, Rome, Italy.,Unit of Cell Stress and Survival, Danish Cancer Society Research Center, Copenhagen, Denmark
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45
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Cabrera-Rodríguez R, Pérez-Yanes S, Estévez-Herrera J, Márquez-Arce D, Cabrera C, Espert L, Blanco J, Valenzuela-Fernández A. The Interplay of HIV and Autophagy in Early Infection. Front Microbiol 2021; 12:661446. [PMID: 33995324 PMCID: PMC8113651 DOI: 10.3389/fmicb.2021.661446] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/31/2021] [Indexed: 12/11/2022] Open
Abstract
HIV/AIDS is still a global threat despite the notable efforts made by the scientific and health communities to understand viral infection, to design new drugs or to improve existing ones, as well as to develop advanced therapies and vaccine designs for functional cure and viral eradication. The identification and analysis of HIV-1 positive individuals that naturally control viral replication in the absence of antiretroviral treatment has provided clues about cellular processes that could interact with viral proteins and RNA and define subsequent viral replication and clinical progression. This is the case of autophagy, a degradative process that not only maintains cell homeostasis by recycling misfolded/old cellular elements to obtain nutrients, but is also relevant in the innate and adaptive immunity against viruses, such as HIV-1. Several studies suggest that early steps of HIV-1 infection, such as virus binding to CD4 or membrane fusion, allow the virus to modulate autophagy pathways preparing cells to be permissive for viral infection. Confirming this interplay, strategies based on autophagy modulation are able to inhibit early steps of HIV-1 infection. Moreover, autophagy dysregulation in late steps of the HIV-1 replication cycle may promote autophagic cell-death of CD4+ T cells or control of HIV-1 latency, likely contributing to disease progression and HIV persistence in infected individuals. In this scenario, understanding the molecular mechanisms underlying HIV/autophagy interplay may contribute to the development of new strategies to control HIV-1 replication. Therefore, the aim of this review is to summarize the knowledge of the interplay between autophagy and the early events of HIV-1 infection, and how autophagy modulation could impair or benefit HIV-1 infection and persistence, impacting viral pathogenesis, immune control of viral replication, and clinical progression of HIV-1 infected patients.
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Affiliation(s)
- Romina Cabrera-Rodríguez
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, e IUETSPC de la Universidad de La Laguna, Campus de Ofra s/n, Tenerife, Spain
| | - Silvia Pérez-Yanes
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, e IUETSPC de la Universidad de La Laguna, Campus de Ofra s/n, Tenerife, Spain
| | - Judith Estévez-Herrera
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, e IUETSPC de la Universidad de La Laguna, Campus de Ofra s/n, Tenerife, Spain
| | - Daniel Márquez-Arce
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, e IUETSPC de la Universidad de La Laguna, Campus de Ofra s/n, Tenerife, Spain
| | - Cecilia Cabrera
- AIDS Research Institute IrsiCaixa, Institut de Recerca en Ciències de la Salut Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Lucile Espert
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS, Montpellier, France
| | - Julià Blanco
- AIDS Research Institute IrsiCaixa, Institut de Recerca en Ciències de la Salut Germans Trias i Pujol (IGTP), Barcelona, Spain.,Universitat de Vic-Central de Catalunya (UVIC-UCC), Catalonia, Spain
| | - Agustín Valenzuela-Fernández
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, e IUETSPC de la Universidad de La Laguna, Campus de Ofra s/n, Tenerife, Spain
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46
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Phosphorylation of the LIR Domain of SCOC Modulates ATG8 Binding Affinity and Specificity. J Mol Biol 2021; 433:166987. [PMID: 33845085 PMCID: PMC8202330 DOI: 10.1016/j.jmb.2021.166987] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/27/2021] [Accepted: 04/04/2021] [Indexed: 12/15/2022]
Abstract
Autophagy is a highly conserved degradative pathway, essential for cellular homeostasis and implicated in diseases including cancer and neurodegeneration. Autophagy-related 8 (ATG8) proteins play a central role in autophagosome formation and selective delivery of cytoplasmic cargo to lysosomes by recruiting autophagy adaptors and receptors. The LC3-interacting region (LIR) docking site (LDS) of ATG8 proteins binds to LIR motifs present in autophagy adaptors and receptors. LIR-ATG8 interactions can be highly selective for specific mammalian ATG8 family members (LC3A-C, GABARAP, and GABARAPL1-2) and how this specificity is generated and regulated is incompletely understood. We have identified a LIR motif in the Golgi protein SCOC (short coiled-coil protein) exhibiting strong binding to GABARAP, GABARAPL1, LC3A and LC3C. The residues within and surrounding the core LIR motif of the SCOC LIR domain were phosphorylated by autophagy-related kinases (ULK1-3, TBK1) increasing specifically LC3 family binding. More distant flanking residues also contributed to ATG8 binding. Loss of these residues was compensated by phosphorylation of serine residues immediately adjacent to the core LIR motif, indicating that the interactions of the flanking LIR regions with the LDS are important and highly dynamic. Our comprehensive structural, biophysical and biochemical analyses support and provide novel mechanistic insights into how phosphorylation of LIR domain residues regulates the affinity and binding specificity of ATG8 proteins towards autophagy adaptors and receptors.
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47
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Chang C, Shi X, Jensen LE, Yokom AL, Fracchiolla D, Martens S, Hurley JH. Reconstitution of cargo-induced LC3 lipidation in mammalian selective autophagy. SCIENCE ADVANCES 2021; 7:7/17/eabg4922. [PMID: 33893090 PMCID: PMC8064641 DOI: 10.1126/sciadv.abg4922] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/05/2021] [Indexed: 05/14/2023]
Abstract
Selective autophagy of damaged mitochondria, protein aggregates, and other cargoes is essential for health. Cargo initiates phagophore biogenesis, which entails the conjugation of LC3 to phosphatidylethanolamine. Current models suggest that clustered ubiquitin chains on a cargo trigger a cascade from autophagic cargo receptors through the core complexes ULK1 and class III phosphatidylinositol 3-kinase complex I, WIPI2, and the ATG7, ATG3, and ATG12ATG5-ATG16L1 machinery of LC3 lipidation. This was tested using giant unilamellar vesicles (GUVs), GST-Ub4 as a model cargo, the cargo receptors NDP52, TAX1BP1, and OPTN, and the autophagy core complexes. All three cargo receptors potently stimulated LC3 lipidation on GUVs. NDP52- and TAX1BP1-induced LC3 lipidation required all components, but not ULK1 kinase activity. However, OPTN bypassed the ULK1 requirement. Thus, cargo-dependent stimulation of LC3 lipidation is common to multiple autophagic cargo receptors, yet the details of core complex engagement vary between the different receptors.
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Affiliation(s)
- Chunmei Chang
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Xiaoshan Shi
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Liv E Jensen
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Adam L Yokom
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
| | - Dorotea Fracchiolla
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Sascha Martens
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - James H Hurley
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD 20185, USA
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48
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Hartmann M, Huber J, Kramer JS, Heering J, Pietsch L, Stark H, Odadzic D, Bischoff I, Fürst R, Schröder M, Akutsu M, Chaikuad A, Dötsch V, Knapp S, Biondi RM, Rogov VV, Proschak E. Demonstrating Ligandability of the LC3A and LC3B Adapter Interface. J Med Chem 2021; 64:3720-3746. [PMID: 33769048 DOI: 10.1021/acs.jmedchem.0c01564] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Autophagy is the common name for a number of lysosome-based degradation pathways of cytosolic cargos. The key components of autophagy are members of Atg8 family proteins involved in almost all steps of the process, from autophagosome formation to their selective fusion with lysosomes. In this study, we show that the homologous members of the human Atg8 family proteins, LC3A and LC3B, are druggable by a small molecule inhibitor novobiocin. Structure-activity relationship (SAR) studies of the 4-hydroxy coumarin core scaffold were performed, supported by a crystal structure of the LC3A dihydronovobiocin complex. The study reports the first nonpeptide inhibitors for these protein interaction targets and will lay the foundation for the development of more potent chemical probes for the Atg8 protein family which may also find applications for the development of autophagy-mediated degraders (AUTACs).
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Affiliation(s)
- Markus Hartmann
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Jessica Huber
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Jan S Kramer
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Jan Heering
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt, Germany
| | - Larissa Pietsch
- Department of Internal Medicine I, Goethe University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt, Germany
| | - Holger Stark
- German translational cancer network (DKTK), site Frankfurt/Mainz, 60438 Frankfurt, Germany.,Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Dalibor Odadzic
- German translational cancer network (DKTK), site Frankfurt/Mainz, 60438 Frankfurt, Germany
| | - Iris Bischoff
- Institute of Pharmaceutical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Robert Fürst
- Institute of Pharmaceutical Biology, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Martin Schröder
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Masato Akutsu
- Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany.,German translational cancer network (DKTK), site Frankfurt/Mainz, 60438 Frankfurt, Germany
| | - Ricardo M Biondi
- Department of Internal Medicine I, Goethe University Hospital Frankfurt, Theodor-Stern-Kai 7, 60596 Frankfurt, Germany
| | - Vladimir V Rogov
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany.,Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt, Germany.,German translational cancer network (DKTK), site Frankfurt/Mainz, 60438 Frankfurt, Germany
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49
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Melia TJ, Lystad AH, Simonsen A. Autophagosome biogenesis: From membrane growth to closure. J Cell Biol 2021; 219:151729. [PMID: 32357219 PMCID: PMC7265318 DOI: 10.1083/jcb.202002085] [Citation(s) in RCA: 155] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/04/2020] [Accepted: 04/06/2020] [Indexed: 12/14/2022] Open
Abstract
Autophagosome biogenesis involves de novo formation of a membrane that elongates to sequester cytoplasmic cargo and closes to form a double-membrane vesicle (an autophagosome). This process has remained enigmatic since its initial discovery >50 yr ago, but our understanding of the mechanisms involved in autophagosome biogenesis has increased substantially during the last 20 yr. Several key questions do remain open, however, including, What determines the site of autophagosome nucleation? What is the origin and lipid composition of the autophagosome membrane? How is cargo sequestration regulated under nonselective and selective types of autophagy? This review provides key insight into the core molecular mechanisms underlying autophagosome biogenesis, with a specific emphasis on membrane modeling events, and highlights recent conceptual advances in the field.
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Affiliation(s)
- Thomas J Melia
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT
| | - Alf H Lystad
- Department of Molecular Medicine, Institute of Basic Medical Sciences and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences and Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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50
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Pavel M, Park SJ, Frake RA, Son SM, Manni MM, Bento CF, Renna M, Ricketts T, Menzies FM, Tanasa R, Rubinsztein DC. α-Catenin levels determine direction of YAP/TAZ response to autophagy perturbation. Nat Commun 2021; 12:1703. [PMID: 33731717 PMCID: PMC7969950 DOI: 10.1038/s41467-021-21882-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 02/18/2021] [Indexed: 12/14/2022] Open
Abstract
The factors regulating cellular identity are critical for understanding the transition from health to disease and responses to therapies. Recent literature suggests that autophagy compromise may cause opposite effects in different contexts by either activating or inhibiting YAP/TAZ co-transcriptional regulators of the Hippo pathway via unrelated mechanisms. Here, we confirm that autophagy perturbation in different cell types can cause opposite responses in growth-promoting oncogenic YAP/TAZ transcriptional signalling. These apparently contradictory responses can be resolved by a feedback loop where autophagy negatively regulates the levels of α-catenins, LC3-interacting proteins that inhibit YAP/TAZ, which, in turn, positively regulate autophagy. High basal levels of α-catenins enable autophagy induction to positively regulate YAP/TAZ, while low α-catenins cause YAP/TAZ activation upon autophagy inhibition. These data reveal how feedback loops enable post-transcriptional determination of cell identity and how levels of a single intermediary protein can dictate the direction of response to external or internal perturbations.
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Affiliation(s)
- Mariana Pavel
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
- Department of Immunology, Grigore T. Popa University of Medicine and Pharmacy of Iasi, Iasi, Romania
| | - So Jung Park
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
- UK Dementia Research Institute, Cambridge Biomedical Campus, Cambridge, UK
| | - Rebecca A Frake
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
| | - Sung Min Son
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
- UK Dementia Research Institute, Cambridge Biomedical Campus, Cambridge, UK
| | - Marco M Manni
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
- UK Dementia Research Institute, Cambridge Biomedical Campus, Cambridge, UK
| | - Carla F Bento
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
| | - Maurizio Renna
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
| | - Thomas Ricketts
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
| | - Fiona M Menzies
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK
| | - Radu Tanasa
- Department of Physics, Alexandru Ioan Cuza University of Iasi, Iasi, Romania
| | - David C Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge, UK.
- UK Dementia Research Institute, Cambridge Biomedical Campus, Cambridge, UK.
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